#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	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_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
ABCA13	154664	hgsc.bcm.edu	37	7	48428801	48428801	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:48428801G>A	ENST00000435803.1	+	37	11662	c.11638G>A	c.(11638-11640)Ggg>Agg	p.G3880R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3880	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAACGGTGCCGGGAAAACCAC	0.483																																																	0			7											45.0	47.0	46.0					7																	48428801		1873	4120	5993	48399347	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11638G>A	7.37:g.48428801G>A	ENSP00000411096:p.Gly3880Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48399347	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.473386	0.63737	.	.	ENSG00000179869	ENST00000435803	D	0.99878	-7.42	4.59	4.59	0.56863	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.43747	D	0.000537	D	0.99928	0.9967	H	0.99830	4.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95889	0.8905	10	0.87932	D	0	.	14.4612	0.67450	0.0:0.0:1.0:0.0	.	1582;3880	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	R	3880	ENSP00000411096:G3880R	ENSP00000411096:G3880R	G	+	1	0	ABCA13	48399347	1.000000	0.71417	0.918000	0.36340	0.464000	0.32679	8.057000	0.89457	2.254000	0.74563	0.655000	0.94253	GGG		ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
C7orf72	100130988	hgsc.bcm.edu	37	7	50191071	50191071	+	Missense_Mutation	SNP	G	G	A	rs139200555	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:50191071G>A	ENST00000297001.6	+	8	1161	c.1111G>A	c.(1111-1113)Ggc>Agc	p.G371S		NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	371										NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						AGGATATACCGGCAAGGTTCA	0.398													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17304	0.0		0.0	False		,,,				2504	0.0																0			7											211.0	172.0	184.0					7																	50191071		692	1591	2283	50161617	SO:0001583	missense	0				CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.1111G>A	7.37:g.50191071G>A	ENSP00000297001:p.Gly371Ser	Somatic		Capture	Illumina HiSeq	Phase_I	50161617	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	37	CCDS47585.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	17.23	3.337423	0.60963	.	.	ENSG00000164500	ENST00000297001	.	.	.	5.29	4.41	0.53225	.	0.178277	0.39759	N	0.001277	T	0.36138	0.0956	L	0.36672	1.1	0.36857	D	0.888183	P	0.44690	0.841	B	0.40199	0.322	T	0.54450	-0.8292	9	0.59425	D	0.04	.	14.3589	0.66757	0.072:0.0:0.928:0.0	.	371	A4D263	CG072_HUMAN	S	371	.	ENSP00000297001:G371S	G	+	1	0	C7orf72	50161617	1.000000	0.71417	0.968000	0.41197	0.977000	0.68977	3.645000	0.54389	1.356000	0.45884	0.650000	0.86243	GGC		C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
CASD1	64921	hgsc.bcm.edu	37	7	94168340	94168340	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:94168340T>C	ENST00000297273.4	+	10	1615	c.1328T>C	c.(1327-1329)tTg>tCg	p.L443S		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	443						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CTTGTGATTTTGATTTATCAC	0.318																																																	0			7											119.0	115.0	117.0					7																	94168340		2203	4298	6501	94006276	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1328T>C	7.37:g.94168340T>C	ENSP00000297273:p.Leu443Ser	Somatic		Capture	Illumina HiSeq	Phase_I	94006276	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.330568	0.81690	.	.	ENSG00000127995	ENST00000297273	T	0.63255	-0.03	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000001	T	0.81819	0.4903	M	0.88775	2.98	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	D	0.85886	0.1425	10	0.87932	D	0	.	14.6718	0.68951	0.0:0.0:0.0:1.0	.	443;443	Q8WZ77;Q96PB1	.;CASD1_HUMAN	S	443	ENSP00000297273:L443S	ENSP00000297273:L443S	L	+	2	0	CASD1	94006276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.928000	0.87587	1.938000	0.56188	0.482000	0.46254	TTG		CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900	
CYP3A43	64816	hgsc.bcm.edu	37	7	99434084	99434084	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:99434084C>G	ENST00000354829.2	+	2	183	c.80C>G	c.(79-81)aCc>aGc	p.T27S	CYP3A43_ENST00000222382.5_Missense_Mutation_p.T27S|CYP3A43_ENST00000421837.2_Missense_Mutation_p.T27S|CYP3A43_ENST00000417625.1_Missense_Mutation_p.T27S|CYP3A43_ENST00000312017.5_Missense_Mutation_p.T27S|CYP3A43_ENST00000415413.1_Missense_Mutation_p.T27S|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000342499.4_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	27			T -> A (in dbSNP:rs45558032).|YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	AGTTATGGGACCCATTCACAT	0.388																																																	0			7											80.0	80.0	80.0					7																	99434084		2203	4300	6503	99272020	SO:0001583	missense	64816			AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.80C>G	7.37:g.99434084C>G	ENSP00000346887:p.Thr27Ser	Somatic		Capture	Illumina HiSeq	Phase_I	99272020	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.515296	0.27123	.	.	ENSG00000021461	ENST00000354829;ENST00000421837;ENST00000417625;ENST00000415413;ENST00000312017;ENST00000222382;ENST00000379654	T;T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0;3.0	2.44	2.44	0.29823	.	0.404335	0.24859	N	0.035040	T	0.21718	0.0523	M	0.61703	1.905	0.37616	D	0.92111	P;B;B;B	0.52170	0.951;0.007;0.004;0.02	P;B;B;B	0.60012	0.867;0.005;0.002;0.005	T	0.03887	-1.0995	10	0.42905	T	0.14	.	8.4505	0.32869	0.0:1.0:0.0:0.0	.	27;27;27;27	Q495Y1;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;CP343_HUMAN	S	27	ENSP00000346887:T27S;ENSP00000397332:T27S;ENSP00000416581:T27S;ENSP00000401521:T27S;ENSP00000312110:T27S;ENSP00000222382:T27S	ENSP00000222382:T27S	T	+	2	0	CYP3A43	99272020	0.554000	0.26522	0.252000	0.24328	0.474000	0.32979	1.065000	0.30592	1.658000	0.50742	0.205000	0.17691	ACC		CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
RELN	5649	hgsc.bcm.edu	37	7	103276881	103276881	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:103276881T>C	ENST00000428762.1	-	18	2263	c.2104A>G	c.(2104-2106)Atg>Gtg	p.M702V	RELN_ENST00000424685.2_Missense_Mutation_p.M702V|RELN_ENST00000343529.5_Missense_Mutation_p.M702V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	702					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TGGGATGCCATCTCACAAGCT	0.428																																					NSCLC(146;835 1944 15585 22231 52158)												0			7											43.0	47.0	46.0					7																	103276881		2203	4300	6503	103064117	SO:0001583	missense	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2104A>G	7.37:g.103276881T>C	ENSP00000392423:p.Met702Val	Somatic		Capture	Illumina HiSeq	Phase_I	103064117	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	7.599	0.672404	0.14776	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.06849	3.25;3.25;3.25	5.76	5.76	0.90799	.	0.102069	0.64402	D	0.000001	T	0.05410	0.0143	N	0.14661	0.345	0.35253	D	0.778912	B;B	0.13594	0.008;0.004	B;B	0.18263	0.021;0.007	T	0.11372	-1.0590	10	0.02654	T	1	.	16.0711	0.80936	0.0:0.0:0.0:1.0	.	702;702	P78509-2;P78509	.;RELN_HUMAN	V	702	ENSP00000392423:M702V;ENSP00000345694:M702V;ENSP00000388446:M702V	ENSP00000345694:M702V	M	-	1	0	RELN	103064117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.912000	0.63335	2.197000	0.70478	0.482000	0.46254	ATG		RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
TRIM24	8805	hgsc.bcm.edu	37	7	138262232	138262232	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:138262232C>T	ENST00000343526.4	+	14	2370	c.2155C>T	c.(2155-2157)Cca>Tca	p.P719S	TRIM24_ENST00000415680.2_Missense_Mutation_p.P685S			O15164	TIF1A_HUMAN	tripartite motif containing 24	719					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						CATGCTGGAGCCAATTCGAAT	0.423																																					Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)												0			7											85.0	84.0	84.0					7																	138262232		2203	4300	6503	137912772	SO:0001583	missense	8805			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	11812	protein-coding gene	gene with protein product		603406	"""transcriptional intermediary factor 1"", ""tripartite motif-containing 24"""	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.2155C>T	7.37:g.138262232C>T	ENSP00000340507:p.Pro719Ser	Somatic		Capture	Illumina HiSeq	Phase_I	137912772	A4D1R7|A4D1R8|O95854	Missense_Mutation	SNP	ENST00000343526.4	37	CCDS5847.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163749	0.57476	.	.	ENSG00000122779	ENST00000343526;ENST00000536822;ENST00000415680	T;T	0.75704	-0.95;-0.96	5.67	5.67	0.87782	.	0.104158	0.64402	D	0.000002	T	0.62036	0.2395	L	0.29908	0.895	0.58432	D	0.999997	P;B	0.38420	0.63;0.383	B;B	0.32928	0.113;0.155	T	0.60627	-0.7226	10	0.12766	T	0.61	-14.7886	19.3578	0.94422	0.0:1.0:0.0:0.0	.	719;685	O15164;O15164-2	TIF1A_HUMAN;.	S	719;630;685	ENSP00000340507:P719S;ENSP00000390829:P685S	ENSP00000340507:P719S	P	+	1	0	TRIM24	137912772	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.266000	0.65525	2.661000	0.90470	0.460000	0.39030	CCA		TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905	
WEE2	494551	hgsc.bcm.edu	37	7	141423048	141423048	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:141423048A>G	ENST00000397541.2	+	6	1401	c.995A>G	c.(994-996)aAc>aGc	p.N332S	WEE2-AS1_ENST00000486906.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000462383.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	332	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> K (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					TACATCCACAACTCTAGCATG	0.408																																																	0			7											283.0	265.0	271.0					7																	141423048		1917	4131	6048	141069517	SO:0001583	missense	494551			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.995A>G	7.37:g.141423048A>G	ENSP00000380675:p.Asn332Ser	Somatic		Capture	Illumina HiSeq	Phase_I	141069517		Missense_Mutation	SNP	ENST00000397541.2	37	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	A	2.325	-0.354835	0.05138	.	.	ENSG00000214102	ENST00000397541;ENST00000493845	T;T	0.61980	1.31;0.06	5.65	-2.26	0.06867	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.409615	0.25427	N	0.030743	T	0.18002	0.0432	N	0.00358	-1.6	0.23896	N	0.996531	B	0.06786	0.001	B	0.08055	0.003	T	0.41106	-0.9527	10	0.02654	T	1	.	9.2863	0.37760	0.3638:0.1243:0.5119:0.0	.	332	P0C1S8	WEE2_HUMAN	S	332;107	ENSP00000380675:N332S;ENSP00000420388:N107S	ENSP00000380675:N332S	N	+	2	0	WEE2	141069517	0.833000	0.29383	0.436000	0.26797	0.871000	0.50021	0.121000	0.15667	-0.674000	0.05253	0.528000	0.53228	AAC		WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558	
PTPRN2	5799	hgsc.bcm.edu	37	7	157874041	157874041	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:157874041C>T	ENST00000389418.4	-	11	1681	c.1672G>A	c.(1672-1674)Gtg>Atg	p.V558M	PTPRN2_ENST00000409483.1_Missense_Mutation_p.V520M|PTPRN2_ENST00000389413.3_Missense_Mutation_p.V529M|PTPRN2_ENST00000389416.4_Missense_Mutation_p.V541M|PTPRN2_ENST00000404321.2_Missense_Mutation_p.V581M	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	558					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V558M(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TTGGCGCTCACTTTGAAGGTC	0.502																																																	1	Substitution - Missense(1)	ovary(1)	7											301.0	212.0	242.0					7																	157874041		2203	4300	6503	157566802	SO:0001583	missense	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1672G>A	7.37:g.157874041C>T	ENSP00000374069:p.Val558Met	Somatic		Capture	Illumina HiSeq	Phase_I	157566802	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132425	0.37630	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.05786	3.42;3.67;3.4;3.42;3.39	5.06	4.17	0.49024	.	0.464362	0.14485	U	0.316708	T	0.20292	0.0488	L	0.52573	1.65	0.32210	N	0.576637	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.80764	0.99;0.994;0.99;0.986;0.994	T	0.08700	-1.0709	10	0.87932	D	0	.	14.3595	0.66761	0.0:0.851:0.149:0.0	.	581;520;529;541;558	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	M	520;529;541;558;581	ENSP00000387114:V520M;ENSP00000374064:V529M;ENSP00000374067:V541M;ENSP00000374069:V558M;ENSP00000385464:V581M	ENSP00000374064:V529M	V	-	1	0	PTPRN2	157566802	1.000000	0.71417	0.319000	0.25293	0.044000	0.14063	1.771000	0.38542	1.131000	0.42111	0.650000	0.86243	GTG		PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
MYH7B	57644	hgsc.bcm.edu	37	20	33568496	33568496	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:33568496T>C	ENST00000262873.7	+	6	676	c.584T>C	c.(583-585)aTa>aCa	p.I195T	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	153	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CCGCCCCATATATATGCGGTG	0.612																																																	0			20											70.0	79.0	76.0					20																	33568496		2115	4242	6357	33032157	SO:0001583	missense	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.584T>C	20.37:g.33568496T>C	ENSP00000262873:p.Ile195Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33032157	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102722	0.56183	.	.	ENSG00000078814	ENST00000262873	D	0.90620	-2.7	4.46	4.46	0.54185	Myosin head, motor domain (2);	0.000000	0.41823	D	0.000806	D	0.97284	0.9112	H	0.98951	4.38	0.58432	D	0.999996	D	0.65815	0.995	D	0.91635	0.999	D	0.98595	1.0656	10	0.87932	D	0	.	14.1848	0.65598	0.0:0.0:0.0:1.0	.	153	A7E2Y1	MYH7B_HUMAN	T	195	ENSP00000262873:I195T	ENSP00000262873:I195T	I	+	2	0	MYH7B	33032157	1.000000	0.71417	0.738000	0.30950	0.022000	0.10575	7.868000	0.87116	2.001000	0.58596	0.533000	0.62120	ATA		MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872956	51872956	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:51872956G>A	ENST00000371497.5	+	2	3846	c.2959G>A	c.(2959-2961)Gaa>Aaa	p.E987K	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.E984K|TSHZ2_ENST00000603338.2_Missense_Mutation_p.E984K	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	987					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			AATAGCTGCCGAAGAGGACAC	0.502																																																	0			20											84.0	68.0	73.0					20																	51872956		2203	4300	6503	51306363	SO:0001583	missense	128553			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2959G>A	20.37:g.51872956G>A	ENSP00000360552:p.Glu987Lys	Somatic		Capture	Illumina HiSeq	Phase_I	51306363	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.972459	0.92919	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.20598	2.07;2.06	5.69	5.69	0.88448	.	0.103320	0.64402	D	0.000002	T	0.44159	0.1280	M	0.78223	2.4	0.80722	D	1	D	0.61080	0.989	P	0.54270	0.747	T	0.43393	-0.9394	10	0.87932	D	0	-3.8792	19.8075	0.96536	0.0:0.0:1.0:0.0	.	987	Q9NRE2	TSH2_HUMAN	K	987;984;513	ENSP00000360552:E987K;ENSP00000333114:E984K	ENSP00000333114:E984K	E	+	1	0	TSHZ2	51306363	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.470000	0.97683	2.681000	0.91329	0.637000	0.83480	GAA		TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
MC3R	4159	hgsc.bcm.edu	37	20	54824096	54824096	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:54824096A>G	ENST00000243911.2	+	1	309	c.197A>G	c.(196-198)aAc>aGc	p.N66S		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	66					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			GTGGTCAGGAACGGCAACCTG	0.567																																																	0			20											91.0	73.0	79.0					20																	54824096		2203	4300	6503	54257503	SO:0001583	missense	4159				CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"""GPCR / Class A : Melanocortin receptors"""	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.197A>G	20.37:g.54824096A>G	ENSP00000243911:p.Asn66Ser	Somatic		Capture	Illumina HiSeq	Phase_I	54257503	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	37	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	A	19.84	3.901786	0.72754	.	.	ENSG00000124089	ENST00000243911	T	0.03772	3.81	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.17323	0.0416	L	0.55990	1.75	0.50313	D	0.999861	D	0.76494	0.999	D	0.83275	0.996	T	0.00276	-1.1855	10	0.87932	D	0	.	14.4027	0.67060	1.0:0.0:0.0:0.0	.	103	P41968	MC3R_HUMAN	S	66	ENSP00000243911:N66S	ENSP00000243911:N66S	N	+	2	0	MC3R	54257503	1.000000	0.71417	0.033000	0.17914	0.896000	0.52359	9.103000	0.94232	1.878000	0.54408	0.528000	0.53228	AAC		MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2		
RTEL1	51750	hgsc.bcm.edu	37	20	62324588	62324588	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr20:62324588C>G	ENST00000360203.5	+	30	3269	c.2944C>G	c.(2944-2946)Cac>Gac	p.H982D	RTEL1_ENST00000370003.1_Missense_Mutation_p.H227D|RTEL1_ENST00000370018.3_Missense_Mutation_p.H982D|RTEL1_ENST00000318100.4_Missense_Mutation_p.H982D|RTEL1_ENST00000508582.2_Missense_Mutation_p.H1006D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.H982D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			TCGGCCTGAGCACAGCATTCC	0.617																																																	0			20											90.0	93.0	92.0					20																	62324588		2198	4289	6487	61795032	SO:0001583	missense	51750			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2944C>G	20.37:g.62324588C>G	ENSP00000353332:p.His982Asp	Somatic		Capture	Illumina HiSeq	Phase_I	61795032		Missense_Mutation	SNP	ENST00000360203.5	37		.	.	.	.	.	.	.	.	.	.	C	15.94	2.981294	0.53827	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94	4.52	2.42	0.29668	.	0.549660	0.19745	N	0.107026	T	0.19005	0.0456	L	0.58101	1.795	0.27457	N	0.953256	P;P;P;D	0.55385	0.716;0.672;0.594;0.971	P;B;B;P	0.51999	0.49;0.268;0.215;0.687	T	0.03641	-1.1017	10	0.62326	D	0.03	-6.1252	11.5019	0.50444	0.3378:0.6622:0.0:0.0	.	1006;227;982;982	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	982;982;1006;982;227	ENSP00000359035:H982D;ENSP00000322287:H982D;ENSP00000424307:H1006D;ENSP00000353332:H982D;ENSP00000359020:H227D	ENSP00000353332:H982D	H	+	1	0	AL353715.1	61795032	0.998000	0.40836	0.001000	0.08648	0.020000	0.10135	2.364000	0.44187	0.270000	0.21984	0.289000	0.19496	CAC		RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
ISX	91464	hgsc.bcm.edu	37	22	35481587	35481587	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr22:35481587T>C	ENST00000308700.6	+	4	1591	c.639T>C	c.(637-639)ccT>ccC	p.P213P	ISX_ENST00000404699.2_Silent_p.P213P	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	213					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						AAACACAGCCTGTCCCAGGTC	0.572																																																	0			22											222.0	151.0	175.0					22																	35481587		2203	4300	6503	33811587	SO:0001819	synonymous_variant	91464			AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.639T>C	22.37:g.35481587T>C		Somatic		Capture	Illumina HiSeq	Phase_I	33811587	Q68DJ5	Silent	SNP	ENST00000308700.6	37	CCDS33640.1																																																																																				ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
NAGA	4668	hgsc.bcm.edu	37	22	42456978	42456978	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr22:42456978A>G	ENST00000396398.3	-	8	1583	c.1051T>C	c.(1051-1053)Tac>Cac	p.Y351H	NAGA_ENST00000403363.1_Missense_Mutation_p.Y351H|NAGA_ENST00000402937.1_Missense_Mutation_p.Y351H	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	351					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GAGGAGTGGTAGCGATAAGGC	0.557																																																	0			22											121.0	105.0	110.0					22																	42456978		2203	4300	6503	40786924	SO:0001583	missense	4668				CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.1051T>C	22.37:g.42456978A>G	ENSP00000379680:p.Tyr351His	Somatic		Capture	Illumina HiSeq	Phase_I	40786924		Missense_Mutation	SNP	ENST00000396398.3	37	CCDS14030.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.732489	0.89482	.	.	ENSG00000198951	ENST00000396398;ENST00000403363;ENST00000402937	D;D;D	0.88741	-2.42;-2.42;-2.42	5.68	5.68	0.88126	Glycosyl hydrolase, family 13, all-beta (1);	0.113006	0.64402	D	0.000007	D	0.89441	0.6716	M	0.76328	2.33	0.58432	D	0.999999	B	0.21688	0.059	B	0.29267	0.1	D	0.87182	0.2228	10	0.56958	D	0.05	-22.3075	14.5003	0.67716	1.0:0.0:0.0:0.0	.	351	P17050	NAGAB_HUMAN	H	351	ENSP00000379680:Y351H;ENSP00000385283:Y351H;ENSP00000384603:Y351H	ENSP00000379680:Y351H	Y	-	1	0	NAGA	40786924	1.000000	0.71417	0.591000	0.28745	0.393000	0.30537	7.948000	0.87774	2.163000	0.67991	0.496000	0.49642	TAC		NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1		
OR4K5	79317	hgsc.bcm.edu	37	14	20389325	20389325	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:20389325T>G	ENST00000315915.4	+	1	585	c.560T>G	c.(559-561)cTt>cGt	p.L187R		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GTCACCAAACTTGCCTGCCTG	0.408																																																	0			14											248.0	262.0	257.0					14																	20389325		2203	4300	6503	19459165	SO:0001583	missense	79317			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.560T>G	14.37:g.20389325T>G	ENSP00000319511:p.Leu187Arg	Somatic		Capture	Illumina HiSeq	Phase_I	19459165	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	11.89	1.773765	0.31411	.	.	ENSG00000176281	ENST00000315915	T	0.00411	7.53	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000430	T	0.02418	0.0074	H	0.99675	4.695	0.22266	N	0.999246	D	0.89917	1.0	D	0.97110	1.0	T	0.40572	-0.9556	10	0.87932	D	0	.	6.648	0.22947	0.0:0.106:0.0:0.894	.	187	Q8NGD3	OR4K5_HUMAN	R	187	ENSP00000319511:L187R	ENSP00000319511:L187R	L	+	2	0	OR4K5	19459165	0.429000	0.25530	0.919000	0.36401	0.073000	0.16967	4.076000	0.57591	1.886000	0.54624	0.533000	0.62120	CTT		OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483	
OR4K1	79544	hgsc.bcm.edu	37	14	20404428	20404428	+	Silent	SNP	G	G	A	rs149331677	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:20404428G>A	ENST00000285600.4	+	1	662	c.603G>A	c.(601-603)acG>acA	p.T201T		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		TGACCCTAACGAACAGTGGCC	0.448													G|||	5	0.000998403	0.0	0.0029	5008	,	,		28853	0.0		0.003	False		,,,				2504	0.0																0			14						G		2,4404		0,2,2201	153.0	154.0	154.0		603	-7.7	0.1	14	dbSNP_134	154	28,8572		0,28,4272	no	coding-synonymous	OR4K1	NM_001004063.2		0,30,6473	AA,AG,GG		0.3256,0.0454,0.2307		201/312	20404428	30,12976	2203	4300	6503	19474268	SO:0001819	synonymous_variant	79544				CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"""GPCR / Class A : Olfactory receptors"""	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.603G>A	14.37:g.20404428G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19474268	B9EKV9|Q8NGD6|Q96R73	Silent	SNP	ENST00000285600.4	37	CCDS32025.1																																																																																				OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1		
KLHL33	123103	hgsc.bcm.edu	37	14	20897326	20897326	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:20897326C>A	ENST00000344581.4	-	4	1506	c.1284G>T	c.(1282-1284)gaG>gaT	p.E428D		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	428												all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		GGTCCTCAGTCTCACCCAGCC	0.597																																																	0			14											144.0	152.0	150.0					14																	20897326		692	1591	2283	19967166	SO:0001583	missense	123103				CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.1284G>T	14.37:g.20897326C>A	ENSP00000341549:p.Glu428Asp	Somatic		Capture	Illumina HiSeq	Phase_I	19967166		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	.	.	.	.	.	.	.	.	.	.	C	7.927	0.739874	0.15642	.	.	ENSG00000185271	ENST00000344581	T	0.64991	-0.13	5.44	1.3	0.21679	Kelch-type beta propeller (1);	0.387872	0.28036	N	0.016846	T	0.31451	0.0797	N	0.04705	-0.18	0.23640	N	0.997227	B	0.02656	0.0	B	0.06405	0.002	T	0.26643	-1.0097	10	0.02654	T	1	.	9.6245	0.39741	0.0:0.5046:0.4179:0.0775	.	428	A6NCF5	KLH33_HUMAN	D	428	ENSP00000341549:E428D	ENSP00000341549:E428D	E	-	3	2	KLHL33	19967166	0.002000	0.14202	0.995000	0.50966	0.990000	0.78478	0.425000	0.21346	0.387000	0.25024	0.655000	0.94253	GAG		KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
OR6S1	341799	hgsc.bcm.edu	37	14	21109839	21109839	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:21109839A>T	ENST00000320704.3	-	1	11	c.12T>A	c.(10-12)gaT>gaA	p.D4E		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TGTGGTTCCCATCAGGACTCA	0.438																																																	0			14											98.0	104.0	102.0					14																	21109839		2202	4300	6502	20179679	SO:0001583	missense	341799			AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.12T>A	14.37:g.21109839A>T	ENSP00000313110:p.Asp4Glu	Somatic		Capture	Illumina HiSeq	Phase_I	20179679	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	A	7.681	0.688936	0.14973	.	.	ENSG00000181803	ENST00000320704	T	0.00000	9.95	5.31	-10.6	0.00265	.	1.090690	0.07137	N	0.846613	T	0.00039	0.0001	N	0.04132	-0.27	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.40098	-0.9581	10	0.02654	T	1	0.0949	7.4898	0.27456	0.1439:0.2078:0.5458:0.1025	.	4	Q8NH40	OR6S1_HUMAN	E	4	ENSP00000313110:D4E	ENSP00000313110:D4E	D	-	3	2	OR6S1	20179679	0.000000	0.05858	0.000000	0.03702	0.832000	0.47134	-2.869000	0.00721	-2.264000	0.00689	0.533000	0.62120	GAT		OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
CHD8	57680	hgsc.bcm.edu	37	14	21876941	21876941	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:21876941T>C	ENST00000557364.1	-	12	2671	c.2408A>G	c.(2407-2409)cAt>cGt	p.H803R	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Missense_Mutation_p.H524R|CHD8_ENST00000399982.2_Missense_Mutation_p.H803R			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	803					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.H803R(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TTTATATTCATGTGATAGCTC	0.388																																																	1	Substitution - Missense(1)	ovary(1)	14											89.0	76.0	80.0					14																	21876941		1810	4080	5890	20946781	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2408A>G	14.37:g.21876941T>C	ENSP00000451601:p.His803Arg	Somatic		Capture	Illumina HiSeq	Phase_I	20946781	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	T	3.139	-0.176663	0.06380	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.93189	-3.18;-3.18;-3.18	5.31	5.31	0.75309	.	0.061993	0.64402	D	0.000007	T	0.71350	0.3329	N	0.00254	-1.765	0.34308	D	0.685128	B	0.02656	0.0	B	0.01281	0.0	T	0.73199	-0.4058	10	0.02654	T	1	-21.6595	8.9353	0.35695	0.0:0.0833:0.0:0.9167	.	524	Q9HCK8-2	.	R	524;803;523;803	ENSP00000406288:H524R;ENSP00000382863:H803R;ENSP00000451601:H803R	ENSP00000262707:H523R	H	-	2	0	CHD8	20946781	0.992000	0.36948	1.000000	0.80357	0.993000	0.82548	1.457000	0.35212	2.219000	0.72066	0.528000	0.53228	CAT		CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
KCNH5	27133	hgsc.bcm.edu	37	14	63174536	63174536	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:63174536T>C	ENST00000322893.7	-	11	2925	c.2657A>G	c.(2656-2658)gAg>gGg	p.E886G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	886					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGGACTGTGCTCTAGCGGACT	0.502																																																	0			14											128.0	115.0	119.0					14																	63174536		2203	4300	6503	62244289	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2657A>G	14.37:g.63174536T>C	ENSP00000321427:p.Glu886Gly	Somatic		Capture	Illumina HiSeq	Phase_I	62244289	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.522810	0.27211	.	.	ENSG00000140015	ENST00000322893	D	0.99060	-5.38	5.44	5.44	0.79542	.	0.278712	0.35772	N	0.002984	D	0.96275	0.8785	N	0.14661	0.345	0.80722	D	1	B	0.22683	0.073	B	0.24701	0.055	D	0.94546	0.7749	10	0.30854	T	0.27	.	15.6661	0.77230	0.0:0.0:0.0:1.0	.	886	Q8NCM2	KCNH5_HUMAN	G	886	ENSP00000321427:E886G	ENSP00000321427:E886G	E	-	2	0	KCNH5	62244289	1.000000	0.71417	0.998000	0.56505	0.529000	0.34654	4.510000	0.60455	2.285000	0.76669	0.533000	0.62120	GAG		KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72200383	72200383	+	Splice_Site	SNP	G	G	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:72200383G>C	ENST00000555818.1	+	19	5273	c.4925G>C	c.(4924-4926)gGa>gCa	p.G1642A	SIPA1L1_ENST00000358550.2_Splice_Site_p.G1621A|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_Splice_Site_p.G1621A|SIPA1L1_ENST00000537413.1_Splice_Site_p.G1096A	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1642					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.G1642A(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CTTCCCGCAGGAGAGTTCTCA	0.557																																																	1	Substitution - Missense(1)	lung(1)	14											85.0	87.0	86.0					14																	72200383		2203	4300	6503	71270136	SO:0001630	splice_region_variant	26037			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4925-1G>C	14.37:g.72200383G>C		Somatic		Capture	Illumina HiSeq	Phase_I	71270136	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.412373	0.25465	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.09	5.09	0.68999	.	0.048793	0.85682	D	0.000000	T	0.29945	0.0749	L	0.36672	1.1	0.80722	D	1	P;P;B;P;B	0.45531	0.86;0.816;0.118;0.577;0.09	B;B;B;B;B	0.42422	0.359;0.387;0.129;0.269;0.114	T	0.02251	-1.1188	9	.	.	.	.	18.8772	0.92343	0.0:0.0:1.0:0.0	.	1096;1642;1096;1621;1642	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	A	1621;1642;1621;1096	ENSP00000370630:G1621A;ENSP00000450832:G1642A;ENSP00000351352:G1621A;ENSP00000440682:G1096A	.	G	+	2	0	SIPA1L1	71270136	1.000000	0.71417	0.998000	0.56505	0.084000	0.17831	5.629000	0.67798	2.526000	0.85167	0.561000	0.74099	GGA		SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	Missense_Mutation
RBM25	58517	hgsc.bcm.edu	37	14	73576088	73576088	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:73576088A>G	ENST00000261973.7	+	14	1865	c.1580A>G	c.(1579-1581)aAg>aGg	p.K527R	RBM25_ENST00000527432.1_Missense_Mutation_p.K527R|RBM25_ENST00000532483.1_3'UTR	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	527	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K527R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		GATAGAGAAAAGGAAATGGAA	0.438																																																	1	Substitution - Missense(1)	ovary(1)	14											120.0	124.0	123.0					14																	73576088		2203	4300	6503	72645841	SO:0001583	missense	58517			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1580A>G	14.37:g.73576088A>G	ENSP00000261973:p.Lys527Arg	Somatic		Capture	Illumina HiSeq	Phase_I	72645841	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449694	0.63290	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.10860	2.83;2.83	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.15349	0.0370	N	0.17379	0.485	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.16837	-1.0389	10	0.08599	T	0.76	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	527	P49756	RBM25_HUMAN	R	527	ENSP00000261973:K527R;ENSP00000431150:K527R	ENSP00000261973:K527R	K	+	2	0	RBM25	72645841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.141000	0.94612	2.288000	0.76882	0.533000	0.62120	AAG		RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330	
AREL1	9870	hgsc.bcm.edu	37	14	75150178	75150178	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:75150178T>C	ENST00000356357.4	-	5	817	c.302A>G	c.(301-303)cAc>cGc	p.H101R	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	101					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										ATGAGAGATGTGAACTCTTAG	0.512																																																	0			14											109.0	102.0	104.0					14																	75150178		1942	4140	6082	74219931	SO:0001583	missense	9870			AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"""KIAA0317"""	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.302A>G	14.37:g.75150178T>C	ENSP00000348714:p.His101Arg	Somatic		Capture	Illumina HiSeq	Phase_I	74219931	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	37	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.600712	0.46423	.	.	ENSG00000119682	ENST00000356357;ENST00000555249	T;T	0.49720	0.77;0.77	5.68	5.68	0.88126	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.090386	0.85682	D	0.000000	T	0.28034	0.0691	N	0.08118	0	0.45852	D	0.998713	B;B	0.10296	0.003;0.001	B;B	0.10450	0.005;0.003	T	0.09487	-1.0672	10	0.45353	T	0.12	.	10.2988	0.43639	0.0:0.0733:0.0:0.9267	.	101;101	O15033-2;O15033	.;K0317_HUMAN	R	101	ENSP00000348714:H101R;ENSP00000450458:H101R	ENSP00000348714:H101R	H	-	2	0	KIAA0317	74219931	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.938000	0.70170	2.158000	0.67659	0.533000	0.62120	CAC		AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821	
PSMC1	5700	hgsc.bcm.edu	37	14	90734705	90734705	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:90734705C>T	ENST00000261303.8	+	8	932	c.829C>T	c.(829-831)Cat>Tat	p.H277Y	PSMC1_ENST00000543772.2_Missense_Mutation_p.H204Y	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	277					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		TGCTGAAGAACATGCACCGTC	0.448																																																	0			14											103.0	97.0	99.0					14																	90734705		2203	4297	6500	89804458	SO:0001583	missense	5700			L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.829C>T	14.37:g.90734705C>T	ENSP00000261303:p.His277Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	89804458	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	Missense_Mutation	SNP	ENST00000261303.8	37	CCDS32139.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998544	0.54147	.	.	ENSG00000100764	ENST00000261303;ENST00000543772	D;D	0.92911	-3.13;-3.13	5.04	5.04	0.67666	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.86703	0.5996	N	0.16368	0.405	0.80722	D	1	B	0.11235	0.004	B	0.12156	0.007	T	0.81865	-0.0736	10	0.48119	T	0.1	-14.4757	18.7511	0.91816	0.0:1.0:0.0:0.0	.	277	P62191	PRS4_HUMAN	Y	277;204	ENSP00000261303:H277Y;ENSP00000445147:H204Y	ENSP00000261303:H277Y	H	+	1	0	PSMC1	89804458	1.000000	0.71417	0.959000	0.39883	0.995000	0.86356	7.818000	0.86416	2.502000	0.84385	0.563000	0.77884	CAT		PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802	
TRIP11	9321	hgsc.bcm.edu	37	14	92465662	92465662	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:92465662C>G	ENST00000267622.4	-	13	5187	c.4814G>C	c.(4813-4815)aGa>aCa	p.R1605T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1605					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TTTAGCCTCTCTATCTTCTGC	0.358			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)			Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0			14											113.0	104.0	107.0					14																	92465662		2203	4300	6503	91535415	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4814G>C	14.37:g.92465662C>G	ENSP00000267622:p.Arg1605Thr	Somatic		Capture	Illumina HiSeq	Phase_I	91535415	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.106400|4.106400	0.77096|0.77096	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.06528|.	3.29|.	5.38|5.38	4.5|4.5	0.54988|0.54988	.|.	0.046152|.	0.85682|.	D|.	0.000000|.	T|.	0.73450|.	0.3588|.	M|M	0.76574|0.76574	2.34|2.34	0.45867|0.45867	D|D	0.998721|0.998721	D;D|.	0.89917|.	0.992;1.0|.	P;D|.	0.74348|.	0.891;0.983|.	T|.	0.74275|.	-0.3718|.	10|.	0.51188|.	T|.	0.08|.	.|.	14.0449|14.0449	0.64700|0.64700	0.0:0.9275:0.0:0.0725|0.0:0.9275:0.0:0.0725	.|.	1341;1605|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	T|Y	1605;1341|1320	ENSP00000267622:R1605T|.	ENSP00000267622:R1605T|.	R|X	-|-	2|3	0|2	TRIP11|TRIP11	91535415|91535415	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.415000|5.415000	0.66411|0.66411	1.290000|1.290000	0.44636|0.44636	0.655000|0.655000	0.94253|0.94253	AGA|TAG		TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105408336	105408336	+	Silent	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr14:105408336G>A	ENST00000333244.5	-	7	13571	c.13452C>T	c.(13450-13452)gtC>gtT	p.V4484V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4484						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CATCCACCGAGACCTCGATGG	0.562																																																	0			14											186.0	193.0	191.0					14																	105408336		2036	4179	6215	104479381	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13452C>T	14.37:g.105408336G>A		Somatic		Capture	Illumina HiSeq	Phase_I	104479381	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
KDM4B	23030	hgsc.bcm.edu	37	19	5131093	5131093	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:5131093G>A	ENST00000159111.4	+	12	1540	c.1322G>A	c.(1321-1323)gGg>gAg	p.G441E	KDM4B_ENST00000536461.1_Missense_Mutation_p.G475E	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	441					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						ACAGAGGACGGGAGGGGCAAG	0.657																																																	0			19											16.0	21.0	19.0					19																	5131093		2174	4284	6458	5082093	SO:0001583	missense	23030			AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1322G>A	19.37:g.5131093G>A	ENSP00000159111:p.Gly441Glu	Somatic		Capture	Illumina HiSeq	Phase_I	5082093	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	37	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.129239	0.37533	.	.	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.18502	2.21;2.28	4.09	4.09	0.47781	.	1.406310	0.04489	N	0.379144	T	0.13543	0.0328	N	0.25286	0.73	0.09310	N	1	P;P	0.44429	0.835;0.745	B;B	0.40066	0.318;0.169	T	0.04976	-1.0914	10	0.02654	T	1	-24.7636	14.6691	0.68932	0.0:0.0:1.0:0.0	.	475;441	F5GX28;O94953	.;KDM4B_HUMAN	E	441;475	ENSP00000159111:G441E;ENSP00000440495:G475E	ENSP00000159111:G441E	G	+	2	0	KDM4B	5082093	0.953000	0.32496	0.322000	0.25334	0.647000	0.38526	5.860000	0.69546	2.114000	0.64651	0.561000	0.74099	GGG		KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
PNPLA6	10908	hgsc.bcm.edu	37	19	7623912	7623912	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:7623912C>T	ENST00000221249.6	+	31	3891	c.3460C>T	c.(3460-3462)Cgc>Tgc	p.R1154C	PNPLA6_ENST00000600737.1_Missense_Mutation_p.R1192C|PNPLA6_ENST00000545201.2_Missense_Mutation_p.R1127C|PNPLA6_ENST00000450331.3_Missense_Mutation_p.R1154C|PNPLA6_ENST00000414982.3_Missense_Mutation_p.R1202C	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	1193					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						AATCCAGTCCCGCCTGGCCTA	0.607																																																	0			19											84.0	64.0	71.0					19																	7623912		2203	4300	6503	7529912	SO:0001583	missense	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.3460C>T	19.37:g.7623912C>T	ENSP00000221249:p.Arg1154Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7529912	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.550757	0.86127	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	4.78	4.78	0.61160	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.058982	0.64402	N	0.000001	T	0.65954	0.2741	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.76494	0.976;0.986;0.986;0.999	P;P;P;D	0.64776	0.624;0.616;0.792;0.929	T	0.75717	-0.3220	10	0.87932	D	0	-26.932	15.3194	0.74109	0.0:1.0:0.0:0.0	.	1193;1127;1192;1154	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	C	1154;1127;1202;1154	ENSP00000221249:R1154C;ENSP00000443323:R1127C;ENSP00000407509:R1202C;ENSP00000394348:R1154C	ENSP00000221249:R1154C	R	+	1	0	PNPLA6	7529912	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.858000	0.62947	2.209000	0.71365	0.561000	0.74099	CGC		PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
OR7A5	26659	hgsc.bcm.edu	37	19	14938830	14938830	+	Missense_Mutation	SNP	G	G	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:14938830G>C	ENST00000322301.3	-	2	311	c.224C>G	c.(223-225)tCc>tGc	p.S75C	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Missense_Mutation_p.S75C			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	75					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						AATGGTGGTGGAAGTAACACA	0.458																																																	0			19											189.0	168.0	175.0					19																	14938830		2203	4300	6503	14799830	SO:0001583	missense	26659			X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.224C>G	19.37:g.14938830G>C	ENSP00000316955:p.Ser75Cys	Somatic		Capture	Illumina HiSeq	Phase_I	14799830	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	37	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	g	11.39	1.623268	0.28889	.	.	ENSG00000188269	ENST00000322301	T	0.12039	2.72	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31507	U	0.007530	T	0.31009	0.0783	M	0.90145	3.09	0.09310	N	1	P	0.52842	0.956	P	0.49829	0.623	T	0.31052	-0.9957	10	0.87932	D	0	.	12.25	0.54593	0.0:0.0:1.0:0.0	.	75	Q15622	OR7A5_HUMAN	C	75	ENSP00000316955:S75C	ENSP00000316955:S75C	S	-	2	0	OR7A5	14799830	0.025000	0.19082	0.347000	0.25668	0.452000	0.32318	2.004000	0.40854	1.807000	0.52817	0.134000	0.15878	TCC		OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
OR7C2	26658	hgsc.bcm.edu	37	19	15052697	15052697	+	Missense_Mutation	SNP	A	A	G	rs202241920		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:15052697A>G	ENST00000248072.3	+	1	397	c.397A>G	c.(397-399)Acg>Gcg	p.T133A		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					CCTGCACTACACGGTCATCAT	0.517																																																	0			19											128.0	121.0	123.0					19																	15052697		2203	4300	6503	14913697	SO:0001583	missense	26658			U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"""GPCR / Class A : Olfactory receptors"""	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.397A>G	19.37:g.15052697A>G	ENSP00000248072:p.Thr133Ala	Somatic		Capture	Illumina HiSeq	Phase_I	14913697	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	37	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	a	9.120	1.008835	0.19199	.	.	ENSG00000127529	ENST00000248072	T	0.19250	2.16	4.19	-4.43	0.03568	GPCR, rhodopsin-like superfamily (1);	1.912540	0.03002	U	0.148334	T	0.18341	0.0440	L	0.48877	1.53	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.32402	-0.9908	10	0.51188	T	0.08	.	6.5883	0.22632	0.3482:0.2509:0.4009:0.0	.	133	O60412	OR7C2_HUMAN	A	133	ENSP00000248072:T133A	ENSP00000248072:T133A	T	+	1	0	OR7C2	14913697	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.478000	0.00457	-0.947000	0.03673	-1.955000	0.00483	ACG		OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1		
ILVBL	10994	hgsc.bcm.edu	37	19	15234379	15234379	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:15234379C>G	ENST00000263383.3	-	3	283	c.144G>C	c.(142-144)aaG>aaC	p.K48N	ILVBL_ENST00000534378.1_5'UTR|ILVBL_ENST00000531635.1_5'UTR|AC003956.1_ENST00000598450.1_RNA	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	48						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						GGACGCTTGCCTTGTCCACCT	0.642																																																	0			19											52.0	47.0	49.0					19																	15234379		2203	4300	6503	15095379	SO:0001583	missense	10994			U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.144G>C	19.37:g.15234379C>G	ENSP00000263383:p.Lys48Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15095379	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	37	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	C	2.003	-0.429003	0.04701	.	.	ENSG00000105135	ENST00000263383;ENST00000269733;ENST00000527093;ENST00000533747	T	0.30981	1.51	4.19	2.88	0.33553	.	0.809573	0.11365	N	0.571476	T	0.25082	0.0609	L	0.50333	1.59	0.09310	N	1	B	0.25772	0.134	B	0.24155	0.051	T	0.12477	-1.0546	10	0.36615	T	0.2	-4.269	5.2754	0.15647	0.2057:0.6668:0.0:0.1275	.	48	A1L0T0	ILVBL_HUMAN	N	48	ENSP00000263383:K48N	ENSP00000263383:K48N	K	-	3	2	ILVBL	15095379	0.000000	0.05858	0.362000	0.25862	0.084000	0.17831	-0.783000	0.04638	1.890000	0.54733	0.462000	0.41574	AAG		ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
HIPK4	147746	hgsc.bcm.edu	37	19	40886845	40886845	+	Silent	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:40886845C>T	ENST00000291823.2	-	3	1337	c.1053G>A	c.(1051-1053)caG>caA	p.Q351Q		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	351					histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			CACTGCGCAGCTGCTGCATGG	0.657																																																	0			19											70.0	69.0	69.0					19																	40886845		2203	4300	6503	45578685	SO:0001819	synonymous_variant	147746			BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.1053G>A	19.37:g.40886845C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45578685	A8K863|Q96M54	Silent	SNP	ENST00000291823.2	37	CCDS12555.1																																																																																				HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49378015	49378015	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:49378015G>A	ENST00000200453.5	+	2	1794	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	509	4 X 34 AA approximate repeats.|Interaction with KMT2A/MLL1.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CCCCTTCCGAGTGGCCATCTA	0.627																																																	0			19											59.0	56.0	57.0					19																	49378015		2203	4300	6503	54069827	SO:0001583	missense	23645			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1525G>A	19.37:g.49378015G>A	ENSP00000200453:p.Val509Met	Somatic		Capture	Illumina HiSeq	Phase_I	54069827	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248583	0.80024	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.11169	2.8	4.43	4.43	0.53597	.	0.224693	0.29145	N	0.013007	T	0.27419	0.0673	L	0.54323	1.7	0.44006	D	0.996719	D	0.89917	1.0	D	0.87578	0.998	T	0.00684	-1.1611	10	0.72032	D	0.01	-19.8211	13.3017	0.60328	0.0:0.0:1.0:0.0	.	509	O75807	PR15A_HUMAN	M	509;349;467	ENSP00000200453:V509M	ENSP00000200453:V509M	V	+	1	0	PPP1R15A	54069827	0.990000	0.36364	0.974000	0.42286	0.983000	0.72400	2.314000	0.43743	2.414000	0.81942	0.650000	0.86243	GTG		PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
CEACAM18	729767	hgsc.bcm.edu	37	19	51983772	51983772	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:51983772A>G	ENST00000396477.4	+	2	259	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	CEACAM18_ENST00000451626.1_Missense_Mutation_p.S141G	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	80										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAAACCGCCCAGTGCCCAGCA	0.552																																																	0			19											56.0	58.0	58.0					19																	51983772		2022	4178	6200	56675584	SO:0001583	missense	729767					19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.238A>G	19.37:g.51983772A>G	ENSP00000379738:p.Ser80Gly	Somatic		Capture	Illumina HiSeq	Phase_I	56675584	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		.	.	.	.	.	.	.	.	.	.	.	4.038	0.004689	0.07866	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.01474	4.85	2.79	-4.06	0.03986	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01523	0.0049	L	0.35854	1.095	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.44050	-0.9353	9	0.31617	T	0.26	0.3836	5.4071	0.16328	0.3578:0.1778:0.4643:0.0	.	141	A8MTB9	CEA18_HUMAN	G	141;80;80	ENSP00000402203:S141G	ENSP00000379738:S80G	S	+	1	0	CEACAM18	56675584	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.347000	0.02632	-1.116000	0.02969	0.529000	0.55759	AGT		CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
ZNF534	147658	hgsc.bcm.edu	37	19	52941770	52941770	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:52941770C>A	ENST00000332323.6	+	4	1157	c.1096C>A	c.(1096-1098)Cca>Aca	p.P366T	ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.P353T	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						TGGAGAGAGACCATACAAATG	0.418																																																	0			19											103.0	99.0	100.0					19																	52941770		692	1591	2283	57633582	SO:0001583	missense	147658			AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"""Zinc fingers, C2H2-type"", ""-"""	26337	protein-coding gene	gene with protein product			"""KRAB domain only 3"""	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.1096C>A	19.37:g.52941770C>A	ENSP00000327538:p.Pro366Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57633582	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	37	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.190978	0.38707	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.28895	1.59;1.59	1.82	1.82	0.25136	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49729	0.1574	M	0.66560	2.04	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.87578	0.864;0.998	T	0.52866	-0.8518	9	0.87932	D	0	.	10.6089	0.45410	0.0:1.0:0.0:0.0	.	353;366	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	T	366;353;365	ENSP00000327538:P366T;ENSP00000391358:P353T	ENSP00000327538:P366T	P	+	1	0	ZNF534	57633582	0.001000	0.12720	0.029000	0.17559	0.004000	0.04260	1.477000	0.35431	0.983000	0.38602	0.467000	0.42956	CCA		ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512	
NLRP11	204801	hgsc.bcm.edu	37	19	56303710	56303710	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:56303710T>C	ENST00000589093.1	-	7	2563	c.2470A>G	c.(2470-2472)Acg>Gcg	p.T824A	NLRP11_ENST00000360133.3_Missense_Mutation_p.T770A|NLRP11_ENST00000443188.1_Missense_Mutation_p.T824A|NLRP11_ENST00000592953.1_Missense_Mutation_p.T725A|NLRP11_ENST00000589824.2_Missense_Mutation_p.T770A			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	824							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AAGGGAAACGTCACATGCAAC	0.483																																																	0			19											201.0	176.0	185.0					19																	56303710		2203	4300	6503	60995522	SO:0001583	missense	204801			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2470A>G	19.37:g.56303710T>C	ENSP00000466285:p.Thr824Ala	Somatic		Capture	Illumina HiSeq	Phase_I	60995522	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	T	6.420	0.445561	0.12164	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.48836	0.8;0.8	2.18	-4.36	0.03645	.	.	.	.	.	T	0.26955	0.0660	N	0.14661	0.345	0.09310	N	1	B;P	0.36378	0.09;0.55	B;B	0.41691	0.046;0.364	T	0.22487	-1.0215	9	0.66056	D	0.02	.	1.0411	0.01559	0.4876:0.1279:0.1643:0.2202	.	824;770	P59045;P59045-2	NAL11_HUMAN;.	A	824;770	ENSP00000409898:T824A;ENSP00000353251:T770A	ENSP00000353251:T770A	T	-	1	0	NLRP11	60995522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.012000	0.03649	-2.085000	0.00864	-1.221000	0.01599	ACG		NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58564801	58564801	+	Silent	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:58564801C>A	ENST00000282326.1	+	6	856	c.609C>A	c.(607-609)tcC>tcA	p.S203S		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	203					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CCACAGGGTCCCGGGCCCGCT	0.652																																																	0			19											44.0	47.0	46.0					19																	58564801		2203	4296	6499	63256613	SO:0001819	synonymous_variant	284312			AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.609C>A	19.37:g.58564801C>A		Somatic		Capture	Illumina HiSeq	Phase_I	63256613	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	37	CCDS12969.1																																																																																				ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
DUSP26	78986	hgsc.bcm.edu	37	8	33451072	33451072	+	Missense_Mutation	SNP	G	G	A	rs376826832		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:33451072G>A	ENST00000256261.4	-	3	932	c.415C>T	c.(415-417)Cgg>Tgg	p.R139W	DUSP26_ENST00000523956.1_Missense_Mutation_p.R139W	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	139	Tyrosine-protein phosphatase.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		CTCAGCGCCCGGTGGATGAAG	0.607																																																	0			8											47.0	43.0	44.0					8																	33451072		2203	4300	6503	33570614	SO:0001583	missense	285193			AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.415C>T	8.37:g.33451072G>A	ENSP00000256261:p.Arg139Trp	Somatic		Capture	Illumina HiSeq	Phase_I	33570614	D3DSV8|Q9BTW0	Missense_Mutation	SNP	ENST00000256261.4	37	CCDS6092.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365295	0.41902	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	D;D;D	0.86097	-2.07;-2.07;-2.07	4.77	3.86	0.44501	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.326541	0.29473	N	0.012052	D	0.86936	0.6053	M	0.88570	2.965	0.39036	D	0.960046	B	0.22146	0.065	B	0.23419	0.046	D	0.86329	0.1697	10	0.87932	D	0	-13.375	11.8524	0.52419	0.0:0.0:0.5538:0.4462	.	139	Q9BV47	DUS26_HUMAN	W	139	ENSP00000256261:R139W;ENSP00000429176:R139W;ENSP00000430922:R139W	ENSP00000256261:R139W	R	-	1	2	DUSP26	33570614	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.712000	0.47186	1.073000	0.40885	0.563000	0.77884	CGG		DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025	
LETM2	137994	hgsc.bcm.edu	37	8	38250441	38250441	+	Silent	SNP	C	C	T	rs369104625		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:38250441C>T	ENST00000379957.4	+	3	556	c.429C>T	c.(427-429)gaC>gaT	p.D143D	LETM2_ENST00000523983.2_Silent_p.D96D|LETM2_ENST00000524874.1_Silent_p.D143D|LETM2_ENST00000519476.2_Silent_p.D143D|LETM2_ENST00000297720.5_Silent_p.D96D	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	143	LETM1.					integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			TTTGGATTGACGCCAAAGTTG	0.393																																																	0			8						C	,,	0,4406		0,0,2203	61.0	62.0	62.0		288,,288	3.9	1.0	8		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-5,coding-synonymous	LETM2	NM_001199659.1,NM_001199660.1,NM_144652.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	96/445,,96/397	38250441	1,13005	2203	4300	6503	38369598	SO:0001819	synonymous_variant	137994			AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"""EF-hand domain containing"""	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.429C>T	8.37:g.38250441C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38369598	A6NMG3|Q8NCR2|Q96LL1	Silent	SNP	ENST00000379957.4	37																																																																																					LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652	
RP1	6101	hgsc.bcm.edu	37	8	55534038	55534038	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:55534038T>G	ENST00000220676.1	+	2	660	c.512T>G	c.(511-513)cTt>cGt	p.L171R		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	171	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CGTGCGGTTCTTCTGAGCAGG	0.652																																					Colon(91;1014 1389 7634 14542 40420)												0			8											101.0	102.0	102.0					8																	55534038		2203	4300	6503	55696591	SO:0001583	missense	10982			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.512T>G	8.37:g.55534038T>G	ENSP00000220676:p.Leu171Arg	Somatic		Capture	Illumina HiSeq	Phase_I	55696591		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.401866	0.42613	.	.	ENSG00000104237	ENST00000220676	D	0.93076	-3.16	5.14	3.97	0.46021	Doublecortin domain (5);	0.836191	0.10222	N	0.700757	D	0.94251	0.8154	L	0.46157	1.445	0.09310	N	1	D	0.54397	0.966	P	0.58331	0.837	D	0.85918	0.1444	10	0.87932	D	0	0.0111	10.9459	0.47299	0.0:0.0742:0.0:0.9258	.	171	P56715	RP1_HUMAN	R	171	ENSP00000220676:L171R	ENSP00000220676:L171R	L	+	2	0	RP1	55696591	0.811000	0.29063	0.001000	0.08648	0.154000	0.21943	5.012000	0.64017	0.790000	0.33803	0.528000	0.53228	CTT		RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
TRAM1	23471	hgsc.bcm.edu	37	8	71487172	71487172	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:71487172A>G	ENST00000262213.2	-	11	1289	c.1120T>C	c.(1120-1122)Tca>Cca	p.S374P	TRAM1_ENST00000536748.1_Missense_Mutation_p.S343P|TRAM1_ENST00000521425.1_Missense_Mutation_p.S288P	NM_014294.5	NP_055109.1	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	374					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	17			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			ATTCATTATGAAGATTTCTCT	0.313																																					Ovarian(85;984 1334 5116 12432 40638)												0			8											44.0	44.0	44.0					8																	71487172		2201	4290	6491	71649726	SO:0001583	missense	23471			X63679	CCDS6207.1	8q13.1	2004-01-22			ENSG00000067167	ENSG00000067167			20568	protein-coding gene	gene with protein product		605190				1315422	Standard	NM_014294		Approved	TRAM, TRAMP	uc003xyo.2	Q15629	OTTHUMG00000164428	ENST00000262213.2:c.1120T>C	8.37:g.71487172A>G	ENSP00000262213:p.Ser374Pro	Somatic		Capture	Illumina HiSeq	Phase_I	71649726	B4E0K2	Missense_Mutation	SNP	ENST00000262213.2	37	CCDS6207.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554624	0.65425	.	.	ENSG00000067167	ENST00000521425;ENST00000262213;ENST00000536748	T;T;T	0.54479	0.57;1.19;1.19	5.94	5.94	0.96194	.	0.065801	0.64402	D	0.000005	T	0.60625	0.2283	L	0.39566	1.225	0.58432	D	0.999997	D	0.63046	0.992	D	0.63488	0.915	T	0.53844	-0.8381	10	0.13470	T	0.59	.	16.3998	0.83635	1.0:0.0:0.0:0.0	.	374	Q15629	TRAM1_HUMAN	P	288;374;343	ENSP00000428052:S288P;ENSP00000262213:S374P;ENSP00000439359:S343P	ENSP00000262213:S374P	S	-	1	0	TRAM1	71649726	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.404000	0.73268	2.275000	0.75901	0.528000	0.53228	TCA		TRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378738.1	NM_014294	
PI15	51050	hgsc.bcm.edu	37	8	75756320	75756320	+	Silent	SNP	T	T	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:75756320T>A	ENST00000260113.2	+	3	557	c.378T>A	c.(376-378)tcT>tcA	p.S126S	RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000522914.1_RNA|PI15_ENST00000523773.1_Silent_p.S126S|RP11-758M4.4_ENST00000518128.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	126	SCP.					extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			AAAATCTATCTGTACGCACTG	0.418																																																	0			8											167.0	164.0	165.0					8																	75756320		2203	4300	6503	75918875	SO:0001819	synonymous_variant	51050			D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"""protease inhibitor 15"""			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.378T>A	8.37:g.75756320T>A		Somatic		Capture	Illumina HiSeq	Phase_I	75918875	Q68CY1	Silent	SNP	ENST00000260113.2	37	CCDS6218.1																																																																																				PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886	
ZFHX4	79776	hgsc.bcm.edu	37	8	77765695	77765695	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:77765695A>G	ENST00000521891.2	+	10	6986	c.6538A>G	c.(6538-6540)Acg>Gcg	p.T2180A	ZFHX4_ENST00000050961.6_Missense_Mutation_p.T2135A|ZFHX4_ENST00000455469.2_Missense_Mutation_p.T2135A|ZFHX4_ENST00000518282.1_Missense_Mutation_p.T2154A	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTTTAGAAATACGCTTTTTAA	0.368										HNSCC(33;0.089)																																							0			8											112.0	109.0	110.0					8																	77765695		1835	4088	5923	77928250	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6538A>G	8.37:g.77765695A>G	ENSP00000430497:p.Thr2180Ala	Somatic		Capture	Illumina HiSeq	Phase_I	77928250	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779563	0.49891	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.95949	-3.86;-3.86;-3.86;-3.86	3.92	3.92	0.45320	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.45867	U	0.000339	D	0.95404	0.8508	L	0.34521	1.04	0.80722	D	1	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.80764	0.994;0.99;0.99	D	0.94233	0.7478	10	0.33141	T	0.24	.	13.2107	0.59822	1.0:0.0:0.0:0.0	.	2135;2135;2180	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	A	2180;2164;2135;2135;2154	ENSP00000430497:T2180A;ENSP00000399605:T2135A;ENSP00000050961:T2135A;ENSP00000430848:T2154A	ENSP00000050961:T2135A	T	+	1	0	ZFHX4	77928250	1.000000	0.71417	0.787000	0.31911	0.733000	0.41908	9.013000	0.93629	1.784000	0.52394	0.374000	0.22700	ACG		ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
VPS13B	157680	hgsc.bcm.edu	37	8	100711856	100711856	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:100711856T>C	ENST00000358544.2	+	36	6336	c.6225T>C	c.(6223-6225)agT>agC	p.S2075S	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Silent_p.S2050S	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2075					protein transport (GO:0015031)					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)			ATGCACACAGTTTGGCACATA	0.373																																					Colon(161;2205 2542 7338 31318)												0			8											79.0	81.0	80.0					8																	100711856		2203	4300	6503	100781032	SO:0001819	synonymous_variant	157680			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.6225T>C	8.37:g.100711856T>C		Somatic		Capture	Illumina HiSeq	Phase_I	100781032	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																				VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
RIMS2	9699	hgsc.bcm.edu	37	8	104943609	104943609	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:104943609T>C	ENST00000436393.2	+	10	1938	c.1697T>C	c.(1696-1698)cTt>cCt	p.L566P	RIMS2_ENST00000262231.10_Missense_Mutation_p.L627P|RIMS2_ENST00000406091.3_Missense_Mutation_p.L788P|RIMS2_ENST00000507740.1_Missense_Mutation_p.L580P			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	850					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.L580P(1)|p.L566P(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			ATTTACTTTCTTCCAGACAGA	0.333										HNSCC(12;0.0054)																																							2	Substitution - Missense(2)	ovary(2)	8											50.0	49.0	50.0					8																	104943609		1800	4058	5858	105012785	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1697T>C	8.37:g.104943609T>C	ENSP00000390665:p.Leu566Pro	Somatic		Capture	Illumina HiSeq	Phase_I	105012785	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	T	23.2	4.391061	0.82902	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	6.07	6.07	0.98685	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	D	0.93187	0.7830	H	0.96460	3.825	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.998;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;0.999;1.0	D	0.95085	0.8217	9	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	850;850;566;627;580;788	Q9UQ26;Q9UQ26-2;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.;.	P	788;803;788;850;580;627;580;580;566	ENSP00000427018:L788P;ENSP00000384892:L788P;ENSP00000425205:L580P;ENSP00000262231:L627P;ENSP00000423559:L580P;ENSP00000386228:L580P;ENSP00000390665:L566P	ENSP00000262231:L627P	L	+	2	0	RIMS2	105012785	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.991000	0.88244	2.326000	0.78906	0.533000	0.62120	CTT		RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
ANGPT1	284	hgsc.bcm.edu	37	8	108315592	108315592	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:108315592A>G	ENST00000520734.1	-	4	497	c.212T>C	c.(211-213)tTa>tCa	p.L71S	ANGPT1_ENST00000520052.1_Missense_Mutation_p.L70S|ANGPT1_ENST00000518386.1_Intron			Q15389	ANGP1_HUMAN	angiopoietin 1	271					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TCCCTTTAGTAAAACTGCAAA	0.323																																																	0			8											67.0	78.0	74.0					8																	108315592		2201	4300	6501	108384768	SO:0001583	missense	284			D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"""Fibrinogen C domain containing"""	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.212T>C	8.37:g.108315592A>G	ENSP00000430750:p.Leu71Ser	Somatic		Capture	Illumina HiSeq	Phase_I	108384768	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	37		.	.	.	.	.	.	.	.	.	.	A	3.169	-0.170398	0.06461	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000395820;ENST00000520734;ENST00000520052	T;T;T;T	0.53857	0.99;0.92;0.6;0.6	4.45	4.45	0.53987	.	0.564434	0.18578	N	0.137133	T	0.36303	0.0962	L	0.36672	1.1	0.39285	D	0.964633	B;B;B	0.09022	0.0;0.002;0.002	B;B;B	0.09377	0.0;0.004;0.004	T	0.15464	-1.0436	10	0.07325	T	0.83	.	8.5917	0.33690	0.914:0.0:0.086:0.0	.	70;271;271	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	S	271;270;83;71;70	ENSP00000428340:L271S;ENSP00000297450:L270S;ENSP00000430750:L71S;ENSP00000429349:L70S	ENSP00000297450:L270S	L	-	2	0	ANGPT1	108384768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.623000	0.61247	1.862000	0.54008	0.528000	0.53228	TTA		ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290	
CSMD3	114788	hgsc.bcm.edu	37	8	113266531	113266531	+	Missense_Mutation	SNP	T	T	C	rs376050476		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:113266531T>C	ENST00000297405.5	-	63	10305	c.10061A>G	c.(10060-10062)aAc>aGc	p.N3354S	CSMD3_ENST00000455883.2_Missense_Mutation_p.N3185S|CSMD3_ENST00000343508.3_Missense_Mutation_p.N3314S|CSMD3_ENST00000352409.3_Missense_Mutation_p.N3284S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3354	Sushi 27. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N3354T(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CACACCTGGGTTTTCACAAGA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							1	Substitution - Missense(1)	ovary(1)	8											189.0	189.0	189.0					8																	113266531		2203	4300	6503	113335707	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10061A>G	8.37:g.113266531T>C	ENSP00000297405:p.Asn3354Ser	Somatic		Capture	Illumina HiSeq	Phase_I	113335707	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.214579	0.58452	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	5.22	5.22	0.72569	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	L	0.35723	1.085	0.49582	D	0.999805	D;D;B	0.76494	0.996;0.999;0.178	D;D;B	0.83275	0.957;0.996;0.108	T	0.62300	-0.6883	10	0.11794	T	0.64	.	15.284	0.73814	0.0:0.0:0.0:1.0	.	3185;3354;3314	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	3314;3354;2624;3185;3284	ENSP00000345799:N3314S;ENSP00000297405:N3354S;ENSP00000341558:N2624S;ENSP00000412263:N3185S;ENSP00000343124:N3284S	ENSP00000297405:N3354S	N	-	2	0	CSMD3	113335707	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	5.683000	0.68189	2.201000	0.70794	0.533000	0.62120	AAC		CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CSMD3	114788	hgsc.bcm.edu	37	8	113871405	113871405	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:113871405A>G	ENST00000297405.5	-	11	1968	c.1724T>C	c.(1723-1725)gTc>gCc	p.V575A	CSMD3_ENST00000455883.2_Missense_Mutation_p.V471A|CSMD3_ENST00000343508.3_Missense_Mutation_p.V535A|CSMD3_ENST00000352409.3_Missense_Mutation_p.V575A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	575	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GATGACCCAGACACATTGTGC	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							0			8											148.0	133.0	138.0					8																	113871405		2203	4299	6502	113940581	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1724T>C	8.37:g.113871405A>G	ENSP00000297405:p.Val575Ala	Somatic		Capture	Illumina HiSeq	Phase_I	113940581	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322555	0.81580	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.67	5.67	0.87782	CUB (5);	0.000000	0.64402	D	0.000007	T	0.50360	0.1611	M	0.70595	2.14	0.42474	D	0.992835	D;D;P	0.69078	0.997;0.996;0.814	D;D;P	0.85130	0.967;0.997;0.9	T	0.51694	-0.8673	10	0.05620	T	0.96	.	15.9132	0.79488	1.0:0.0:0.0:0.0	.	471;575;535	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	535;575;471;575	ENSP00000345799:V535A;ENSP00000297405:V575A;ENSP00000412263:V471A;ENSP00000343124:V575A	ENSP00000297405:V575A	V	-	2	0	CSMD3	113940581	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	9.251000	0.95483	2.154000	0.67381	0.482000	0.46254	GTC		CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
JRK	8629	hgsc.bcm.edu	37	8	143747023	143747023	+	RNA	SNP	C	C	A	rs201592742	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr8:143747023C>A	ENST00000507178.2	-	0	787							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ctgcttttcactggatgcatc	0.572																																																	0			8											40.0	46.0	44.0					8																	143747023		1759	3576	5335	143744025			8629			AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143747023C>A		Somatic		Capture	Illumina HiSeq	Phase_I	143744025	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																					JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
CROCC	9696	hgsc.bcm.edu	37	1	17263152	17263152	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:17263152G>T	ENST00000375541.5	+	9	1046	c.977G>T	c.(976-978)gGg>gTg	p.G326V	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCTGGGAGGGGAGCTGGCC	0.652																																																	0			1											7.0	8.0	8.0					1																	17263152		2058	4053	6111	17135739	SO:0001583	missense	9696			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.977G>T	1.37:g.17263152G>T	ENSP00000364691:p.Gly326Val	Somatic		Capture	Illumina HiSeq	Phase_I	17135739		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.892579	0.33442	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09630	2.96	3.91	2.91	0.33838	.	.	.	.	.	T	0.11452	0.0279	L	0.41236	1.265	0.48901	D	0.999728	B;B;P	0.50819	0.291;0.291;0.939	B;B;P	0.51101	0.091;0.204;0.659	T	0.09618	-1.0666	9	0.33141	T	0.24	.	2.999	0.06008	0.2044:0.0:0.5628:0.2329	.	189;189;326	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	V	326;207	ENSP00000364691:G326V	ENSP00000364691:G326V	G	+	2	0	CROCC	17135739	0.605000	0.26941	1.000000	0.80357	0.708000	0.40852	0.395000	0.20850	2.188000	0.69820	0.462000	0.41574	GGG		CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SPOCD1	90853	hgsc.bcm.edu	37	1	32262199	32262199	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:32262199C>T	ENST00000360482.2	-	10	2392	c.2263G>A	c.(2263-2265)Gat>Aat	p.D755N	SPOCD1_ENST00000257100.3_Missense_Mutation_p.D248N|SPOCD1_ENST00000533231.1_Missense_Mutation_p.D755N|SPOCD1_ENST00000373648.2_3'UTR	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	755					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		accaccaGATCCTCCAGGGTC	0.607																																																	0			1											161.0	126.0	138.0					1																	32262199		2203	4300	6503	32034786	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2263G>A	1.37:g.32262199C>T	ENSP00000353670:p.Asp755Asn	Somatic		Capture	Illumina HiSeq	Phase_I	32034786	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432521	0.43224	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231	T;T;T;T	0.47869	0.83;1.84;0.88;1.84	4.34	3.34	0.38264	.	.	.	.	.	T	0.57607	0.2065	L	0.58101	1.795	0.80722	D	1	D;P;P;P	0.64830	0.994;0.811;0.713;0.713	D;B;B;B	0.63703	0.917;0.284;0.209;0.224	T	0.54357	-0.8306	9	0.35671	T	0.21	-10.6938	9.6546	0.39919	0.0:0.787:0.213:0.0	.	99;755;192;755	Q6ZMY3-4;Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;.;SPOC1_HUMAN	N	248;755;153;192;755	ENSP00000257100:D248N;ENSP00000353670:D755N;ENSP00000399778:D192N;ENSP00000435851:D755N	ENSP00000257100:D248N	D	-	1	0	SPOCD1	32034786	1.000000	0.71417	0.998000	0.56505	0.463000	0.32649	1.556000	0.36288	2.140000	0.66376	0.462000	0.41574	GAT		SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
GJB4	127534	hgsc.bcm.edu	37	1	35227018	35227018	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:35227018A>T	ENST00000339480.1	+	2	533	c.163A>T	c.(163-165)Acc>Tcc	p.T55S	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	55					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGTCTGCAACACCAAGCAGCC	0.612																																																	0			1											227.0	155.0	179.0					1																	35227018		2203	4300	6503	34999605	SO:0001583	missense	127534				CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.163A>T	1.37:g.35227018A>T	ENSP00000345868:p.Thr55Ser	Somatic		Capture	Illumina HiSeq	Phase_I	34999605	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.972821	0.92919	.	.	ENSG00000189433	ENST00000339480	D	0.99338	-5.76	5.56	4.42	0.53409	Connexin, conserved site (1);Connexin, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.99263	0.9743	M	0.90082	3.085	0.36543	D	0.871404	D	0.53745	0.962	P	0.55545	0.778	D	0.99919	1.1240	10	0.66056	D	0.02	.	12.4477	0.55659	0.8597:0.1403:0.0:0.0	.	55	Q9NTQ9	CXB4_HUMAN	S	55	ENSP00000345868:T55S	ENSP00000345868:T55S	T	+	1	0	GJB4	34999605	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.281000	0.95811	0.930000	0.37217	0.533000	0.62120	ACC		GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
PIK3R3	8503	hgsc.bcm.edu	37	1	46509456	46509456	+	Silent	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:46509456C>T	ENST00000262741.5	-	10	1964	c.1275G>A	c.(1273-1275)ctG>ctA	p.L425L	PIK3R3_ENST00000540385.1_Silent_p.L471L|PIK3R3_ENST00000420542.1_Silent_p.L425L|PIK3R3_ENST00000372006.1_Silent_p.L425L|PIK3R3_ENST00000423209.1_Silent_p.L366L|PIK3R3_ENST00000354242.4_Silent_p.L366L|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000340332.6_Silent_p.L330L	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	425	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CTAGCTCCTTCAGAGAGCTGT	0.547																																																	0			1											146.0	123.0	131.0					1																	46509456		2203	4300	6503	46282043	SO:0001819	synonymous_variant	8503			BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"""SH2 domain containing"""	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.1275G>A	1.37:g.46509456C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46282043	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Silent	SNP	ENST00000262741.5	37	CCDS529.1																																																																																				PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	
CACHD1	57685	hgsc.bcm.edu	37	1	65130218	65130218	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:65130218T>C	ENST00000371073.2	+	15	2132	c.2132T>C	c.(2131-2133)gTc>gCc	p.V711A	CACHD1_ENST00000290039.5_Missense_Mutation_p.V660A|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	711					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ACCAGCCACGTCACAGATGAA	0.443																																																	0			1											128.0	113.0	118.0					1																	65130218		2203	4300	6503	64902806	SO:0001583	missense	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2132T>C	1.37:g.65130218T>C	ENSP00000360113:p.Val711Ala	Somatic		Capture	Illumina HiSeq	Phase_I	64902806	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	T	15.45	2.836663	0.50951	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.24151	1.87;1.88	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.07999	0.0200	N	0.16478	0.41	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.18085	-1.0348	10	0.25106	T	0.35	-33.1974	13.7672	0.63002	0.0:0.0:0.1275:0.8725	.	711	Q5VU97	CAHD1_HUMAN	A	711;660	ENSP00000360113:V711A;ENSP00000290039:V660A	ENSP00000290039:V660A	V	+	2	0	CACHD1	64902806	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.001000	0.70685	2.371000	0.80710	0.533000	0.62120	GTC		CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
IL12RB2	3595	hgsc.bcm.edu	37	1	67787504	67787504	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:67787504T>C	ENST00000262345.1	+	3	936	c.296T>C	c.(295-297)tTt>tCt	p.F99S	IL12RB2_ENST00000541374.1_Missense_Mutation_p.F99S|IL12RB2_ENST00000544434.1_Missense_Mutation_p.F99S|IL12RB2_ENST00000371000.1_Missense_Mutation_p.F99S	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	99					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.F99C(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ACAACCTTGTTTGTCTGCAAA	0.393																																																	1	Substitution - Missense(1)	ovary(1)	1											168.0	161.0	163.0					1																	67787504		2203	4300	6503	67560092	SO:0001583	missense	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.296T>C	1.37:g.67787504T>C	ENSP00000262345:p.Phe99Ser	Somatic		Capture	Illumina HiSeq	Phase_I	67560092	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.699980	0.48307	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.95	5.95	0.96441	Immunoglobulin C2-set-like, ligand-binding (1);	0.144837	0.64402	D	0.000005	T	0.77765	0.4179	L	0.36672	1.1	0.45139	D	0.998156	B;D;D;D	0.89917	0.163;1.0;0.993;0.997	B;D;P;D	0.74674	0.076;0.984;0.854;0.955	T	0.80975	-0.1142	10	0.56958	D	0.05	-28.3087	12.8126	0.57647	0.0:0.0:0.0:1.0	.	99;99;99;99	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	S	99	ENSP00000262345:F99S;ENSP00000360039:F99S;ENSP00000445276:F99S;ENSP00000442443:F99S	ENSP00000262345:F99S	F	+	2	0	IL12RB2	67560092	0.996000	0.38824	0.961000	0.40146	0.005000	0.04900	3.848000	0.55903	2.274000	0.75844	0.528000	0.53228	TTT		IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
VCAM1	7412	hgsc.bcm.edu	37	1	101198073	101198073	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:101198073C>T	ENST00000294728.2	+	7	1726	c.1625C>T	c.(1624-1626)cCg>cTg	p.P542L	VCAM1_ENST00000347652.2_Missense_Mutation_p.P450L|VCAM1_ENST00000370115.1_Missense_Mutation_p.P343L|VCAM1_ENST00000370119.4_Missense_Mutation_p.P480L	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	542	Ig-like C2-type 6.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTTCCTGCTCCGAAAATCCTG	0.512																																																	0			1											51.0	54.0	53.0					1																	101198073		2203	4300	6503	100970661	SO:0001583	missense	7412			M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1625C>T	1.37:g.101198073C>T	ENSP00000294728:p.Pro542Leu	Somatic		Capture	Illumina HiSeq	Phase_I	100970661	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.956312	0.53293	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.57	5.57	0.84162	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.386787	0.30446	N	0.009613	T	0.64821	0.2633	M	0.92077	3.27	0.44188	D	0.997003	D;P;D	0.56287	0.968;0.956;0.975	P;P;P	0.58820	0.846;0.633;0.771	T	0.72766	-0.4194	10	0.66056	D	0.02	-13.211	17.0763	0.86587	0.0:1.0:0.0:0.0	.	480;450;542	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	L	480;450;542;343	ENSP00000359137:P480L;ENSP00000304611:P450L;ENSP00000294728:P542L;ENSP00000359133:P343L	ENSP00000294728:P542L	P	+	2	0	VCAM1	100970661	0.108000	0.22018	0.631000	0.29282	0.319000	0.28217	2.897000	0.48664	2.785000	0.95823	0.655000	0.94253	CCG		VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078	
OLFM3	118427	hgsc.bcm.edu	37	1	102270066	102270066	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:102270066A>G	ENST00000338858.5	-	6	1164	c.1165T>C	c.(1165-1167)Tac>Cac	p.Y389H	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.Y369H|OLFM3_ENST00000536598.1_3'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	389	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CTCTTGGGGTAGCCAGTGCTC	0.478																																																	0			1											127.0	107.0	114.0					1																	102270066		2203	4300	6503	102042654	SO:0001583	missense	118427			AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"""optimedin"""	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.1165T>C	1.37:g.102270066A>G	ENSP00000345192:p.Tyr389His	Somatic		Capture	Illumina HiSeq	Phase_I	102042654	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	37		.	.	.	.	.	.	.	.	.	.	A	17.35	3.367022	0.61513	.	.	ENSG00000118733	ENST00000370103;ENST00000338858	D;D	0.89196	-2.48;-2.48	5.67	5.67	0.87782	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.89399	0.6704	L	0.33245	0.995	0.80722	D	1	B;D	0.76494	0.118;0.999	B;D	0.85130	0.12;0.997	D	0.90279	0.4313	10	0.46703	T	0.11	.	15.8913	0.79299	1.0:0.0:0.0:0.0	.	369;389	Q5T3V6;Q96PB7	.;NOE3_HUMAN	H	369;389	ENSP00000359121:Y369H;ENSP00000345192:Y389H	ENSP00000345192:Y389H	Y	-	1	0	OLFM3	102042654	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.339000	0.96797	2.157000	0.67596	0.528000	0.53228	TAC		OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1		
COL11A1	1301	hgsc.bcm.edu	37	1	103540200	103540200	+	Missense_Mutation	SNP	T	T	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:103540200T>A	ENST00000370096.3	-	4	937	c.625A>T	c.(625-627)Agg>Tgg	p.R209W	COL11A1_ENST00000512756.1_Missense_Mutation_p.R209W|COL11A1_ENST00000358392.2_Missense_Mutation_p.R209W|COL11A1_ENST00000353414.4_Missense_Mutation_p.R209W	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	209	Laminin G-like.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCCAAAATCCTTGTTCCAAAA	0.343																																																	0			1											135.0	124.0	128.0					1																	103540200		2202	4300	6502	103312788	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.625A>T	1.37:g.103540200T>A	ENSP00000359114:p.Arg209Trp	Somatic		Capture	Illumina HiSeq	Phase_I	103312788	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.996035	0.54147	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.73	4.6	0.57074	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.87289	0.6140	M	0.92649	3.33	0.58432	D	0.999998	D;D;D;D	0.71674	0.995;0.997;0.998;0.997	D;D;D;D	0.67900	0.954;0.924;0.924;0.954	D	0.90034	0.4137	10	0.87932	D	0	.	13.0354	0.58867	0.0:0.0:0.1347:0.8653	.	209;209;209;209	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	W	209;209;209;209;209;136	ENSP00000359114:R209W;ENSP00000351163:R209W;ENSP00000302551:R209W;ENSP00000426533:R209W;ENSP00000408640:R209W;ENSP00000410177:R136W	ENSP00000302551:R209W	R	-	1	2	COL11A1	103312788	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.091000	0.57700	0.975000	0.38392	0.528000	0.53228	AGG		COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
PI4KB	5298	hgsc.bcm.edu	37	1	151274711	151274711	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:151274711A>G	ENST00000368873.1	-	7	1752	c.1584T>C	c.(1582-1584)ccT>ccC	p.P528P	PI4KB_ENST00000271657.5_Silent_p.P540P|PI4KB_ENST00000368872.1_Silent_p.P513P|PI4KB_ENST00000529142.1_Silent_p.P196P|PI4KB_ENST00000368874.4_Silent_p.P513P|PI4KB_ENST00000368875.2_Silent_p.P540P|RN7SL444P_ENST00000578948.1_RNA			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	528					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAACTGCAGAAGGATCTTCTG	0.537																																					Colon(154;765 1838 9854 28443 37492)												0			1											149.0	145.0	146.0					1																	151274711		2203	4300	6503	149541335	SO:0001819	synonymous_variant	5298			AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368873.1:c.1584T>C	1.37:g.151274711A>G		Somatic		Capture	Illumina HiSeq	Phase_I	149541335	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Silent	SNP	ENST00000368873.1	37																																																																																					PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651	
TCHH	7062	hgsc.bcm.edu	37	1	152085111	152085111	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:152085111C>G	ENST00000368804.1	-	2	581	c.582G>C	c.(580-582)caG>caC	p.Q194H		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	194					keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTTGCAACTCTGCAGCTGCT	0.607																																																	0			1											91.0	98.0	96.0					1																	152085111		2060	4188	6248	150351735	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.582G>C	1.37:g.152085111C>G	ENSP00000357794:p.Gln194His	Somatic		Capture	Illumina HiSeq	Phase_I	150351735	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	8.948	0.967395	0.18659	.	.	ENSG00000159450	ENST00000368804	T	0.05649	3.41	4.51	-0.047	0.13845	.	.	.	.	.	T	0.02047	0.0064	N	0.08118	0	0.09310	N	1	D	0.61080	0.989	P	0.55965	0.788	T	0.42766	-0.9432	9	0.48119	T	0.1	-1.4809	5.2514	0.15524	0.0:0.5292:0.1628:0.308	.	194	Q07283	TRHY_HUMAN	H	194	ENSP00000357794:Q194H	ENSP00000357794:Q194H	Q	-	3	2	TCHH	150351735	0.000000	0.05858	0.000000	0.03702	0.192000	0.23643	-1.143000	0.03200	0.127000	0.18452	0.502000	0.49764	CAG		TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
DENND4B	9909	hgsc.bcm.edu	37	1	153910230	153910230	+	Missense_Mutation	SNP	G	G	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:153910230G>C	ENST00000361217.4	-	14	2493	c.2075C>G	c.(2074-2076)cCa>cGa	p.P692R		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	692					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACTGCCCTCTGGTAAGGCAGG	0.567																																																	0			1											155.0	155.0	155.0					1																	153910230		1985	4176	6161	152176854	SO:0001583	missense	9909			AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2075C>G	1.37:g.153910230G>C	ENSP00000354597:p.Pro692Arg	Somatic		Capture	Illumina HiSeq	Phase_I	152176854	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629272	0.28978	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.08008	3.14;3.14	5.18	4.25	0.50352	.	0.499546	0.21946	N	0.066801	T	0.03695	0.0105	L	0.58810	1.83	0.09310	N	1	B	0.14438	0.01	B	0.22386	0.039	T	0.33445	-0.9868	10	0.25106	T	0.35	-0.1149	11.8729	0.52531	0.0869:0.0:0.9131:0.0	.	692	O75064	DEN4B_HUMAN	R	692;703	ENSP00000354597:P692R;ENSP00000357635:P703R	ENSP00000354597:P692R	P	-	2	0	DENND4B	152176854	1.000000	0.71417	0.067000	0.19924	0.670000	0.39368	7.473000	0.81007	1.374000	0.46228	0.655000	0.94253	CCA		DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
TNFSF4	7292	hgsc.bcm.edu	37	1	173155919	173155919	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:173155919G>T	ENST00000281834.3	-	3	424	c.288C>A	c.(286-288)aaC>aaA	p.N96K	TNFSF4_ENST00000488053.1_5'Flank|TNFSF4_ENST00000367718.1_Missense_Mutation_p.N46K	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	96					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						ACCCATCACAGTTGATGATGA	0.453																																																	0			1											115.0	118.0	117.0					1																	173155919		2203	4300	6503	171422542	SO:0001583	missense	7292			D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11934	protein-coding gene	gene with protein product		603594	"""tax-transcriptionally activated glycoprotein 1, 34kD"""	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.288C>A	1.37:g.173155919G>T	ENSP00000281834:p.Asn96Lys	Somatic		Capture	Illumina HiSeq	Phase_I	171422542	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	G	5.729	0.318930	0.10845	.	.	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94417	-3.42;-3.42	5.76	-8.17	0.01057	Tumour necrosis factor (2);Tumour necrosis factor-like (1);Tumour necrosis factor, conserved site (1);	1.693150	0.02418	N	0.082257	T	0.76162	0.3949	L	0.43152	1.355	0.09310	N	0.999996	B;B	0.22800	0.075;0.026	B;B	0.14578	0.011;0.011	T	0.73116	-0.4084	10	0.02654	T	1	0.119	7.7885	0.29106	0.0708:0.5744:0.1566:0.1982	.	96;46	P23510;Q8IV74	TNFL4_HUMAN;.	K	46;96;46	ENSP00000356691:N46K;ENSP00000281834:N96K	ENSP00000281834:N96K	N	-	3	2	TNFSF4	171422542	0.018000	0.18449	0.004000	0.12327	0.455000	0.32408	-0.146000	0.10250	-0.875000	0.04022	0.655000	0.94253	AAC		TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1		
PAPPA2	60676	hgsc.bcm.edu	37	1	176564652	176564652	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:176564652G>A	ENST00000367662.3	+	3	3076	c.1912G>A	c.(1912-1914)Gac>Aac	p.D638N	PAPPA2_ENST00000367661.3_Missense_Mutation_p.D638N	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	638	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CATGCTGAACGACTTTGACGA	0.602																																																	0			1											70.0	76.0	74.0					1																	176564652		2168	4268	6436	174831275	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1912G>A	1.37:g.176564652G>A	ENSP00000356634:p.Asp638Asn	Somatic		Capture	Illumina HiSeq	Phase_I	174831275	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.017218	0.54576	.	.	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.30182	4.78;1.54	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.26593	0.0650	L	0.28400	0.85	0.43195	D	0.99503	B;D	0.56968	0.354;0.978	B;P	0.46479	0.044;0.518	T	0.01476	-1.1345	10	0.21014	T	0.42	-25.7887	13.1942	0.59728	0.0769:0.0:0.9231:0.0	.	638;638	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	N	638	ENSP00000356634:D638N;ENSP00000356633:D638N	ENSP00000356633:D638N	D	+	1	0	PAPPA2	174831275	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	3.863000	0.56016	2.542000	0.85734	0.650000	0.86243	GAC		PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
USH2A	7399	hgsc.bcm.edu	37	1	216256829	216256829	+	Missense_Mutation	SNP	A	A	G	rs368520422		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:216256829A>G	ENST00000307340.3	-	26	5653	c.5267T>C	c.(5266-5268)gTt>gCt	p.V1756A	USH2A_ENST00000366943.2_Missense_Mutation_p.V1756A|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1756	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTTGTTATAAACGAAAAGAAG	0.303										HNSCC(13;0.011)																																							0			1						A	ALA/VAL	0,4404		0,0,2202	96.0	100.0	98.0		5267	3.2	0.7	1		98	1,8597	1.2+/-3.3	0,1,4298	no	missense	USH2A	NM_206933.2	64	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	benign	1756/5203	216256829	1,13001	2202	4299	6501	214323452	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5267T>C	1.37:g.216256829A>G	ENSP00000305941:p.Val1756Ala	Somatic		Capture	Illumina HiSeq	Phase_I	214323452	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	10.38	1.333660	0.24167	0.0	1.16E-4	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.76839	-1.05;-1.05	4.38	3.25	0.37280	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.783880	0.10646	N	0.650406	T	0.62998	0.2474	L	0.27053	0.805	0.20074	N	0.999939	B	0.20459	0.045	B	0.21360	0.034	T	0.43081	-0.9413	10	0.08179	T	0.78	.	9.8214	0.40885	0.9176:0.0:0.0824:0.0	.	1756	O75445	USH2A_HUMAN	A	1756	ENSP00000305941:V1756A;ENSP00000355910:V1756A	ENSP00000305941:V1756A	V	-	2	0	USH2A	214323452	0.879000	0.30193	0.685000	0.30070	0.941000	0.58515	3.282000	0.51693	0.656000	0.30886	0.533000	0.62120	GTT		USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
OR2C3	81472	hgsc.bcm.edu	37	1	247695310	247695310	+	Silent	SNP	C	C	T	rs544163828		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:247695310C>T	ENST00000366487.3	-	2	865	c.504G>A	c.(502-504)ccG>ccA	p.P168P	GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000527541.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			TCCCACACAGCGGTAGGAGCA	0.547													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22838	0.0		0.0	False		,,,				2504	0.0																0			1											67.0	61.0	63.0					1																	247695310		2203	4300	6503	245761933	SO:0001819	synonymous_variant	81472			BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.504G>A	1.37:g.247695310C>T		Somatic		Capture	Illumina HiSeq	Phase_I	245761933	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	37	CCDS1634.2																																																																																				OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
RRP8	23378	hgsc.bcm.edu	37	11	6622505	6622505	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:6622505C>T	ENST00000254605.6	-	3	908	c.791G>A	c.(790-792)aGt>aAt	p.S264N	ILK_ENST00000396751.2_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000299421.4_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000528995.1_5'Flank|RRP8_ENST00000534343.1_Intron	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	264					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						CTGTGCAGCACTGCTGGGCCC	0.607																																																	0			11											30.0	29.0	29.0					11																	6622505		2201	4296	6497	6579081	SO:0001583	missense	23378			AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"""KIAA0409"""	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.791G>A	11.37:g.6622505C>T	ENSP00000254605:p.Ser264Asn	Somatic		Capture	Illumina HiSeq	Phase_I	6579081	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927745	0.52759	.	.	ENSG00000132275	ENST00000254605;ENST00000533907	T;T	0.46819	0.86;0.86	5.85	4.88	0.63580	.	0.268520	0.43579	D	0.000557	T	0.35480	0.0933	N	0.21282	0.65	0.80722	D	1	B	0.13594	0.008	B	0.16289	0.015	T	0.09422	-1.0675	10	0.38643	T	0.18	-16.0634	15.2066	0.73183	0.0:0.8588:0.1412:0.0	.	264	O43159	RRP8_HUMAN	N	264	ENSP00000254605:S264N;ENSP00000436246:S264N	ENSP00000254605:S264N	S	-	2	0	RRP8	6579081	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.505000	0.45424	2.773000	0.95371	0.650000	0.86243	AGT		RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324	
SYT9	143425	hgsc.bcm.edu	37	11	7441835	7441835	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:7441835A>G	ENST00000318881.6	+	6	1673	c.1436A>G	c.(1435-1437)aAg>aGg	p.K479R		NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	479					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TATCCTCGGAAGCCCATTGCA	0.498																																																	0			11											166.0	135.0	146.0					11																	7441835		2201	4296	6497	7398411	SO:0001583	missense	143425			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"""Synaptotagmins"""	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1436A>G	11.37:g.7441835A>G	ENSP00000324419:p.Lys479Arg	Somatic		Capture	Illumina HiSeq	Phase_I	7398411		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.821745	0.71028	.	.	ENSG00000170743	ENST00000318881	T	0.72282	-0.64	5.64	5.64	0.86602	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000012	T	0.76198	0.3954	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70963	-0.4729	10	0.10636	T	0.68	.	13.8014	0.63202	1.0:0.0:0.0:0.0	.	479	Q86SS6	SYT9_HUMAN	R	479	ENSP00000324419:K479R	ENSP00000324419:K479R	K	+	2	0	SYT9	7398411	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.148000	0.66965	0.533000	0.62120	AAG		SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733	
RAG1	5896	hgsc.bcm.edu	37	11	36596672	36596672	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:36596672A>G	ENST00000299440.5	+	2	1930	c.1818A>G	c.(1816-1818)ggA>ggG	p.G606G		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	606					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G606G(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				ATGGAATGGGAGACGTGAGTG	0.473									Familial Hemophagocytic Lymphohistiocytosis																												Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)												1	Substitution - coding silent(1)	kidney(1)	11											108.0	90.0	96.0					11																	36596672		2202	4298	6500	36553248	SO:0001819	synonymous_variant	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1818A>G	11.37:g.36596672A>G		Somatic		Capture	Illumina HiSeq	Phase_I	36553248	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	37	CCDS7902.1																																																																																				RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
CARNS1	57571	hgsc.bcm.edu	37	11	67191083	67191083	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:67191083C>T	ENST00000307823.3	+	9	1947	c.1495C>T	c.(1495-1497)Cgc>Tgc	p.R499C	CARNS1_ENST00000423745.2_Missense_Mutation_p.R499C|CARNS1_ENST00000524740.1_3'UTR|CARNS1_ENST00000531040.1_Missense_Mutation_p.R596C|CARNS1_ENST00000445895.2_Missense_Mutation_p.R622C	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	499					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						AGCTGCCATGCGCCTGGCTAA	0.647																																																	0			11											25.0	31.0	29.0					11																	67191083		2163	4248	6411	66947659	SO:0001583	missense	0				CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1495C>T	11.37:g.67191083C>T	ENSP00000308268:p.Arg499Cys	Somatic		Capture	Illumina HiSeq	Phase_I	66947659	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	C	9.869	1.198358	0.22037	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.37	-1.85	0.07784	.	0.817364	0.10808	N	0.631986	T	0.15652	0.0377	N	0.14661	0.345	0.40671	D	0.982218	B;B	0.13145	0.004;0.007	B;B	0.12156	0.003;0.007	T	0.07770	-1.0755	10	0.44086	T	0.13	-8.0023	6.8584	0.24054	0.2303:0.5722:0.0:0.1974	.	499;638	A5YM72;A5YM72-3	CRNS1_HUMAN;.	C	596;499;596;499;622	ENSP00000431670:R596C;ENSP00000308268:R499C;ENSP00000401519:R499C;ENSP00000389009:R622C	ENSP00000308268:R499C	R	+	1	0	CARNS1	66947659	1.000000	0.71417	0.996000	0.52242	0.581000	0.36288	0.973000	0.29422	-0.149000	0.11215	0.549000	0.68633	CGC		CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
ATM	472	hgsc.bcm.edu	37	11	108188129	108188129	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108188129T>C	ENST00000452508.2	+	44	6417	c.6228T>C	c.(6226-6228)atT>atC	p.I2076I	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.I2076I			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2076	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TCTGCCATATTCTTTCCGTCT	0.358			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	0			11	GRCh37	CD000915	ATM	D							86.0	87.0	87.0					11																	108188129		2201	4298	6499	107693339	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.6228T>C	11.37:g.108188129T>C		Somatic		Capture	Illumina HiSeq	Phase_I	107693339	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
ATM	472	hgsc.bcm.edu	37	11	108199781	108199781	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108199781A>G	ENST00000452508.2	+	50	7312	c.7123A>G	c.(7123-7125)Agt>Ggt	p.S2375G	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.S2375G			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2375	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGATGGAGAAAGTAGTGATGA	0.313			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	0			11											65.0	69.0	68.0					11																	108199781		2201	4298	6499	107704991	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7123A>G	11.37:g.108199781A>G	ENSP00000388058:p.Ser2375Gly	Somatic		Capture	Illumina HiSeq	Phase_I	107704991	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131768	0.37630	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.68624	-0.34;-0.34	5.7	3.3	0.37823	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.464389	0.28268	N	0.015971	T	0.55497	0.1924	L	0.46157	1.445	0.80722	D	1	B	0.22276	0.067	B	0.27380	0.079	T	0.48758	-0.9007	10	0.30078	T	0.28	.	6.6774	0.23102	0.7925:0.0:0.0725:0.135	.	2375	Q13315	ATM_HUMAN	G	2375	ENSP00000278616:S2375G;ENSP00000388058:S2375G	ENSP00000278616:S2375G	S	+	1	0	ATM	107704991	0.999000	0.42202	0.967000	0.41034	0.832000	0.47134	2.544000	0.45761	0.993000	0.38866	-0.256000	0.11100	AGT		ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
EXPH5	23086	hgsc.bcm.edu	37	11	108381959	108381959	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:108381959A>G	ENST00000265843.4	-	6	4385	c.4275T>C	c.(4273-4275)tcT>tcC	p.S1425S	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Silent_p.S1349S|EXPH5_ENST00000525344.1_Silent_p.S1418S|EXPH5_ENST00000443411.1_Silent_p.S1237S	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1425					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTGGAAGACTAGAGGGACCAC	0.378																																																	0			11											107.0	107.0	107.0					11																	108381959		2201	4298	6499	107887169	SO:0001819	synonymous_variant	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4275T>C	11.37:g.108381959A>G		Somatic		Capture	Illumina HiSeq	Phase_I	107887169	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																				EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ANKK1	255239	hgsc.bcm.edu	37	11	113269881	113269881	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:113269881C>A	ENST00000303941.3	+	8	1284	c.1190C>A	c.(1189-1191)aCg>aAg	p.T397K		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	397							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TCTGGATACACGCCCCTCCTG	0.652																																																	0			11											31.0	34.0	33.0					11																	113269881		2095	4200	6295	112775091	SO:0001583	missense	255239			AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1190C>A	11.37:g.113269881C>A	ENSP00000306678:p.Thr397Lys	Somatic		Capture	Illumina HiSeq	Phase_I	112775091		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.614236	0.28712	.	.	ENSG00000170209	ENST00000303941	T	0.30182	1.54	4.69	1.71	0.24356	Ankyrin repeat-containing domain (4);	0.213462	0.31747	N	0.007128	T	0.57917	0.2086	M	0.91140	3.18	0.41295	D	0.987002	D	0.89917	1.0	D	0.80764	0.994	T	0.60224	-0.7305	10	0.87932	D	0	-6.4367	8.4287	0.32744	0.0:0.7306:0.0:0.2694	.	397	Q8NFD2	ANKK1_HUMAN	K	397	ENSP00000306678:T397K	ENSP00000306678:T397K	T	+	2	0	ANKK1	112775091	0.978000	0.34361	0.129000	0.21949	0.023000	0.10783	2.518000	0.45537	0.178000	0.19917	-0.384000	0.06662	ACG		ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
USP28	57646	hgsc.bcm.edu	37	11	113704982	113704982	+	Missense_Mutation	SNP	G	G	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:113704982G>C	ENST00000003302.4	-	6	678	c.610C>G	c.(610-612)Cga>Gga	p.R204G	USP28_ENST00000542033.1_5'UTR|USP28_ENST00000537706.1_Missense_Mutation_p.R204G|USP28_ENST00000545540.1_Missense_Mutation_p.R79G|USP28_ENST00000260188.5_Missense_Mutation_p.R204G	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	204	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		GTATGACTTCGACAATTTTCA	0.373																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)												0			11											135.0	120.0	125.0					11																	113704982		2201	4296	6497	113210192	SO:0001583	missense	57646			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.610C>G	11.37:g.113704982G>C	ENSP00000003302:p.Arg204Gly	Somatic		Capture	Illumina HiSeq	Phase_I	113210192	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307198	0.40795	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000545540;ENST00000537706	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.08	4.17	0.49024	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.191511	0.45867	D	0.000325	T	0.40448	0.1117	L	0.56199	1.76	0.35679	D	0.813928	B;B;B;P	0.34699	0.142;0.42;0.09;0.464	B;B;B;P	0.46796	0.111;0.18;0.152;0.527	T	0.51834	-0.8655	10	0.41790	T	0.15	-0.2028	12.5263	0.56087	0.0808:0.0:0.9192:0.0	.	204;79;204;204	B4E2Q2;B4E3L3;Q6NZX9;Q96RU2	.;.;.;UBP28_HUMAN	G	204;204;79;204	ENSP00000003302:R204G;ENSP00000260188:R204G;ENSP00000444991:R79G;ENSP00000445743:R204G	ENSP00000003302:R204G	R	-	1	2	USP28	113210192	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	3.845000	0.55880	1.139000	0.42245	0.460000	0.39030	CGA		USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		
HSPA8	3312	hgsc.bcm.edu	37	11	122931831	122931831	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:122931831A>T	ENST00000532636.1	-	2	321	c.202T>A	c.(202-204)Ttt>Att	p.F68I	HSPA8_ENST00000526110.1_Missense_Mutation_p.F68I|HSPA8_ENST00000534319.1_5'Flank|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534624.1_Missense_Mutation_p.F68I|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Missense_Mutation_p.F68I|SNORD14C_ENST00000365382.1_RNA|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.F68I|HSPA8_ENST00000533540.1_Missense_Mutation_p.F68I			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	68					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AACTCACCAAAAACTGTGTTG	0.408																																					Colon(21;486 594 5900 6733 14272)												0			11											51.0	47.0	48.0					11																	122931831		2202	4299	6501	122437041	SO:0001583	missense	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.202T>A	11.37:g.122931831A>T	ENSP00000437125:p.Phe68Ile	Somatic		Capture	Illumina HiSeq	Phase_I	122437041	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	32	5.119719	0.94385	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000528292;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.03889	3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77;3.77	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.30823	0.0777	H	0.95365	3.66	0.80722	D	1	P;D;D;D;D	0.76494	0.869;0.999;0.995;0.994;0.986	B;D;D;D;D	0.72982	0.397;0.979;0.971;0.951;0.979	T	0.48536	-0.9027	10	0.87932	D	0	.	13.9807	0.64304	1.0:0.0:0.0:0.0	.	68;68;68;68;68	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	I	68;68;68;68;68;68;8;68;68;68;68;68;68;68	ENSP00000437125:F68I;ENSP00000437189:F68I;ENSP00000432083:F68I;ENSP00000404372:F68I;ENSP00000227378:F68I;ENSP00000433584:F68I;ENSP00000432884:F8I;ENSP00000436762:F68I;ENSP00000435154:F68I;ENSP00000431641:F68I;ENSP00000436183:F68I;ENSP00000434415:F68I;ENSP00000434565:F68I;ENSP00000434851:F68I	ENSP00000227378:F68I	F	-	1	0	HSPA8	122437041	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.337000	0.96545	1.748000	0.51833	0.397000	0.26171	TTT		HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
ERVFRD-1	405754	hgsc.bcm.edu	37	6	11105007	11105007	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:11105007A>G	ENST00000472091.1	-	2	912	c.537T>C	c.(535-537)acT>acC	p.T179T	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Silent_p.T179T	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	179					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						CCTGAGGAAAAGTAATATTTG	0.448																																																	0			6											138.0	152.0	147.0					6																	11105007		2203	4299	6502	11212993	SO:0001819	synonymous_variant	0			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.537T>C	6.37:g.11105007A>G		Somatic		Capture	Illumina HiSeq	Phase_I	11212993		Silent	SNP	ENST00000472091.1	37	CCDS4519.1																																																																																				ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582	
UBR2	23304	hgsc.bcm.edu	37	6	42612253	42612253	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:42612253T>C	ENST00000372899.1	+	20	2521	c.2263T>C	c.(2263-2265)Tac>Cac	p.Y755H	UBR2_ENST00000372883.3_Missense_Mutation_p.Y259H|UBR2_ENST00000372901.1_Missense_Mutation_p.Y755H	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	755					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AGAAATGCTATACCTCATTAT	0.313																																																	0			6											96.0	97.0	97.0					6																	42612253		2203	4299	6502	42720231	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2263T>C	6.37:g.42612253T>C	ENSP00000361990:p.Tyr755His	Somatic		Capture	Illumina HiSeq	Phase_I	42720231	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.637932	0.29157	.	.	ENSG00000024048	ENST00000372899;ENST00000372901;ENST00000372883	T;T;T	0.48201	0.82;0.82;0.82	5.86	5.86	0.93980	.	0.055638	0.85682	D	0.000000	T	0.06462	0.0166	N	0.00599	-1.345	0.49582	D	0.999801	B;B	0.12630	0.006;0.0	B;B	0.13407	0.009;0.001	T	0.33574	-0.9863	10	0.13108	T	0.6	0.0073	10.8408	0.46715	0.0:0.0702:0.0:0.9298	.	755;755	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	H	755;755;259	ENSP00000361990:Y755H;ENSP00000361992:Y755H;ENSP00000361974:Y259H	ENSP00000361974:Y259H	Y	+	1	0	UBR2	42720231	1.000000	0.71417	0.979000	0.43373	0.974000	0.67602	3.792000	0.55476	2.367000	0.80283	0.528000	0.53228	TAC		UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
CDC5L	988	hgsc.bcm.edu	37	6	44387290	44387290	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:44387290A>G	ENST00000371477.3	+	9	1496	c.1197A>G	c.(1195-1197)cgA>cgG	p.R399R		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	399	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCCACAGCGACAAGTTGTAC	0.428																																																	0			6											160.0	142.0	148.0					6																	44387290		2203	4300	6503	44495268	SO:0001819	synonymous_variant	988			D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"""CDC5 (cell division cycle 5, S. pombe, homolog)-like"", ""CDC5 cell division cycle 5-like (S. pombe)"""			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1197A>G	6.37:g.44387290A>G		Somatic		Capture	Illumina HiSeq	Phase_I	44495268	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																				CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
PKHD1	5314	hgsc.bcm.edu	37	6	51889913	51889913	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:51889913A>G	ENST00000371117.3	-	32	4970	c.4695T>C	c.(4693-4695)gtT>gtC	p.V1565V	PKHD1_ENST00000340994.4_Silent_p.V1565V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1565	IPT/TIG 10.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGTGTCTGGAAACATTACCAG	0.453																																																	0			6											66.0	66.0	66.0					6																	51889913		2203	4300	6503	51997872	SO:0001819	synonymous_variant	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.4695T>C	6.37:g.51889913A>G		Somatic		Capture	Illumina HiSeq	Phase_I	51997872	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																				PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DOPEY1	23033	hgsc.bcm.edu	37	6	83843971	83843971	+	Silent	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:83843971A>T	ENST00000349129.2	+	19	3095	c.2835A>T	c.(2833-2835)atA>atT	p.I945I	DOPEY1_ENST00000369739.3_Silent_p.I936I|DOPEY1_ENST00000237163.5_Silent_p.I926I	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	945					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		ATCTCCATATAAATAAATCTT	0.343																																																	0			6											121.0	117.0	119.0					6																	83843971		2203	4300	6503	83900690	SO:0001819	synonymous_variant	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2835A>T	6.37:g.83843971A>T		Somatic		Capture	Illumina HiSeq	Phase_I	83900690	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																				DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
SNX14	57231	hgsc.bcm.edu	37	6	86223808	86223808	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:86223808G>T	ENST00000314673.3	-	25	2713	c.2537C>A	c.(2536-2538)tCa>tAa	p.S846*	SNX14_ENST00000505648.1_Nonsense_Mutation_p.S794*|SNX14_ENST00000346348.3_Nonsense_Mutation_p.S793*|SNX14_ENST00000513865.1_Nonsense_Mutation_p.S565*|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000369627.2_Nonsense_Mutation_p.S837*	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	846					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TGTTATGAGTGAGACCAAACG	0.338																																																	0			6											102.0	106.0	104.0					6																	86223808		2203	4300	6503	86280527	SO:0001587	stop_gained	57231			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.2537C>A	6.37:g.86223808G>T	ENSP00000313121:p.Ser846*	Somatic		Capture	Illumina HiSeq	Phase_I	86280527	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Nonsense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	42|42	9.721242|9.721242	0.99247|0.99247	.|.	.|.	ENSG00000135317|ENSG00000135317	ENST00000508658|ENST00000346348;ENST00000314673;ENST00000513865;ENST00000505648;ENST00000369627;ENST00000515216	.|.	.|.	.|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.47783|.	0.1464|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.45731|.	-0.9241|.	3|.	.|0.08179	.|T	.|0.78	-11.9075|-11.9075	20.221|20.221	0.98325|0.98325	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	N|X	85|793;846;565;794;837;764	.|.	.|ENSP00000313121:S846X	H|S	-|-	1|2	0|0	SNX14|SNX14	86280527|86280527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.476000|9.476000	0.97823|0.97823	2.792000|2.792000	0.96026|0.96026	0.555000|0.555000	0.69702|0.69702	CAC|TCA		SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
GPR63	81491	hgsc.bcm.edu	37	6	97246935	97246935	+	Nonsense_Mutation	SNP	G	G	A	rs146501968		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:97246935G>A	ENST00000229955.3	-	2	1018	c.673C>T	c.(673-675)Cga>Tga	p.R225*	GPR63_ENST00000417980.1_Nonsense_Mutation_p.R225*	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TGGGGAGCTCGGGAAGGTATC	0.458																																																	0			6						G	stop/ARG,stop/ARG	0,4406		0,0,2203	73.0	77.0	76.0		673,673	1.8	1.0	6	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	GPR63	NM_001143957.1,NM_030784.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	225/420,225/420	97246935	1,13005	2203	4300	6503	97353656	SO:0001587	stop_gained	81491			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"""GPCR / Class A : Orphans"""	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.673C>T	6.37:g.97246935G>A	ENSP00000229955:p.Arg225*	Somatic		Capture	Illumina HiSeq	Phase_I	97353656	Q9UJH3	Nonsense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	G	40	8.086701	0.98646	0.0	1.16E-4	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	.	.	.	5.2	1.76	0.24704	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2961	13.2464	0.60026	0.0:0.0:0.2866:0.7134	.	.	.	.	X	249;225;225;225	.	ENSP00000229955:R225X	R	-	1	2	GPR63	97353656	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.371000	0.44248	0.638000	0.30545	0.650000	0.86243	CGA		GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2		
ROS1	6098	hgsc.bcm.edu	37	6	117645542	117645542	+	Missense_Mutation	SNP	G	G	A	rs373534757		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:117645542G>A	ENST00000368508.3	-	34	5792	c.5594C>T	c.(5593-5595)aCt>aTt	p.T1865I	ROS1_ENST00000368507.3_Missense_Mutation_p.T1859I|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1865					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AACTATAATAGTAAGTATGAA	0.284			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																			Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	0			6											45.0	48.0	47.0					6																	117645542		2201	4289	6490	117752235	SO:0001583	missense	6098			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.5594C>T	6.37:g.117645542G>A	ENSP00000357494:p.Thr1865Ile	Somatic		Capture	Illumina HiSeq	Phase_I	117752235	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	6.522	0.464621	0.12402	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70516	-0.49;-0.49	5.41	0.353	0.16058	.	0.877075	0.09899	N	0.741325	T	0.29093	0.0723	N	0.19112	0.55	0.09310	N	1	B	0.20887	0.049	B	0.19148	0.024	T	0.19353	-1.0308	10	0.32370	T	0.25	.	6.1554	0.20334	0.3365:0.131:0.5326:0.0	.	1865	P08922	ROS1_HUMAN	I	1865;1859	ENSP00000357494:T1865I;ENSP00000357493:T1859I	ENSP00000357493:T1859I	T	-	2	0	ROS1	117752235	0.003000	0.15002	0.043000	0.18650	0.564000	0.35744	-0.080000	0.11339	-0.150000	0.11195	-0.810000	0.03169	ACT		ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
LAMA2	3908	hgsc.bcm.edu	37	6	129712777	129712777	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:129712777A>G	ENST00000421865.2	+	36	5262	c.5213A>G	c.(5212-5214)gAa>gGa	p.E1738G		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1738	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACACAAAAGGAAATTGCTGAA	0.348																																																	0			6											111.0	124.0	120.0					6																	129712777		2203	4300	6503	129754470	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5213A>G	6.37:g.129712777A>G	ENSP00000400365:p.Glu1738Gly	Somatic		Capture	Illumina HiSeq	Phase_I	129754470	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533615	0.27387	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.21031	2.03	6.06	6.06	0.98353	Laminin I (1);	0.238690	0.44688	D	0.000428	T	0.08758	0.0217	L	0.29908	0.895	0.29874	N	0.826613	P;P	0.39576	0.679;0.485	B;B	0.40066	0.318;0.248	T	0.10268	-1.0637	10	0.42905	T	0.14	.	12.4313	0.55575	0.9333:0.0:0.0667:0.0	.	1738;1738	A6NF00;P24043	.;LAMA2_HUMAN	G	1738	ENSP00000400365:E1738G	ENSP00000346769:E1738G	E	+	2	0	LAMA2	129754470	1.000000	0.71417	1.000000	0.80357	0.175000	0.22909	3.080000	0.50112	2.323000	0.78572	0.528000	0.53228	GAA		LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
TNFAIP3	7128	hgsc.bcm.edu	37	6	138199578	138199578	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:138199578A>G	ENST00000237289.4	+	7	1062	c.996A>G	c.(994-996)gaA>gaG	p.E332E	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	332	2 X approximate repeats.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.?(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GGTTGGATGAAGCTAACTTAC	0.358			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																GBM(130;153 1739 22295 28918 47987)			Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	26	Whole gene deletion(25)|Unknown(1)	haematopoietic_and_lymphoid_tissue(26)	6											37.0	38.0	37.0					6																	138199578		2203	4300	6503	138241271	SO:0001819	synonymous_variant	7128			M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.996A>G	6.37:g.138199578A>G		Somatic		Capture	Illumina HiSeq	Phase_I	138241271	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																				TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
ZNF594	84622	hgsc.bcm.edu	37	17	5085266	5085266	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:5085266C>A	ENST00000399604.4	-	1	2426	c.2286G>T	c.(2284-2286)tgG>tgT	p.W762C	ZNF594_ENST00000575779.1_Missense_Mutation_p.W762C			Q96JF6	ZN594_HUMAN	zinc finger protein 594	762					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ACTGATTACACCAATAAACTT	0.418																																																	0			17											208.0	210.0	209.0					17																	5085266		1984	4167	6151	5025990	SO:0001583	missense	84622			AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2286G>T	17.37:g.5085266C>A	ENSP00000382513:p.Trp762Cys	Somatic		Capture	Illumina HiSeq	Phase_I	5025990	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	2.538	-0.307054	0.05458	.	.	ENSG00000180626	ENST00000399604	T	0.14766	2.48	1.04	-0.0977	0.13631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06600	0.0169	N	0.11201	0.11	0.20975	N	0.999816	B	0.02656	0.0	B	0.01281	0.0	T	0.34304	-0.9834	9	0.72032	D	0.01	.	4.8952	0.13746	0.0:0.7309:0.0:0.2691	.	762	Q96JF6	ZN594_HUMAN	C	762	ENSP00000382513:W762C	ENSP00000382513:W762C	W	-	3	0	ZNF594	5025990	.	.	0.012000	0.15200	0.113000	0.19764	.	.	0.496000	0.27904	0.298000	0.19748	TGG		ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
TP53	7157	hgsc.bcm.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	17	GRCh37	CM062017|CM951224	TP53	M	rs28934578						50.0	50.0	50.0					17																	7578406		2203	4300	6503	7519131	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His	Somatic		Capture	Illumina HiSeq	Phase_I	7519131	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MYH13	8735	hgsc.bcm.edu	37	17	10219218	10219218	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:10219218T>G	ENST00000418404.3	-	27	4026	c.3863A>C	c.(3862-3864)aAt>aCt	p.N1288T	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.N1288T			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1288					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						ATTCTCACCATTTTGGGTCTG	0.527																																																	0			17											226.0	223.0	224.0					17																	10219218		1992	4155	6147	10159943	SO:0001583	missense	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3863A>C	17.37:g.10219218T>G	ENSP00000404570:p.Asn1288Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10159943	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	T	9.042	0.989839	0.18966	.	.	ENSG00000006788	ENST00000252172	T	0.80738	-1.41	4.39	4.39	0.52855	Myosin tail (1);	.	.	.	.	T	0.79375	0.4435	M	0.68317	2.08	0.34672	D	0.723824	B	0.02656	0.0	B	0.17979	0.02	T	0.82319	-0.0516	9	0.54805	T	0.06	.	13.8848	0.63702	0.0:0.0:0.0:1.0	.	1288	Q9UKX3	MYH13_HUMAN	T	1288	ENSP00000252172:N1288T	ENSP00000252172:N1288T	N	-	2	0	MYH13	10159943	0.189000	0.23263	1.000000	0.80357	0.157000	0.22087	1.372000	0.34261	1.734000	0.51633	0.450000	0.29827	AAT		MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
TNS4	84951	hgsc.bcm.edu	37	17	38633853	38633853	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:38633853G>T	ENST00000254051.6	-	13	2293	c.2135C>A	c.(2134-2136)gCa>gAa	p.A712E		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	712	Phosphatase tensin-type.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CATCCTTTCTGCGTCCTGCAG	0.607																																																	0			17											116.0	94.0	101.0					17																	38633853		2203	4300	6503	35887379	SO:0001583	missense	84951			AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.2135C>A	17.37:g.38633853G>T	ENSP00000254051:p.Ala712Glu	Somatic		Capture	Illumina HiSeq	Phase_I	35887379	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	37	CCDS11368.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978985	0.34942	.	.	ENSG00000131746	ENST00000377816;ENST00000394072;ENST00000254051	T	0.17691	2.26	5.27	2.19	0.27852	.	1.178600	0.06142	N	0.672496	T	0.14013	0.0339	L	0.34521	1.04	0.19945	N	0.999948	B;P	0.39576	0.183;0.679	B;B	0.36030	0.131;0.216	T	0.27806	-1.0063	10	0.72032	D	0.01	2.3817	7.2818	0.26316	0.2598:0.0:0.7402:0.0	.	712;125	Q8IZW8;F2Z318	TENS4_HUMAN;.	E	712;125;712	ENSP00000254051:A712E	ENSP00000254051:A712E	A	-	2	0	TNS4	35887379	0.216000	0.23585	0.862000	0.33874	0.367000	0.29736	2.498000	0.45363	1.250000	0.43966	-0.219000	0.12488	GCA		TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
TEX14	56155	hgsc.bcm.edu	37	17	56676529	56676529	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:56676529A>T	ENST00000240361.8	-	14	2280	c.2195T>A	c.(2194-2196)cTc>cAc	p.L732H	TEX14_ENST00000389934.3_Missense_Mutation_p.L726H|TEX14_ENST00000349033.5_Missense_Mutation_p.L726H			Q8IWB6	TEX14_HUMAN	testis expressed 14	732					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTACTGATGAGATACTCCTC	0.443																																																	0			17											282.0	267.0	272.0					17																	56676529		2203	4300	6503	54031528	SO:0001583	missense	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2195T>A	17.37:g.56676529A>T	ENSP00000240361:p.Leu732His	Somatic		Capture	Illumina HiSeq	Phase_I	54031528	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	A	6.273	0.418536	0.11870	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78481	-1.18;-1.18;-1.14	0.235	-0.47	0.12131	.	.	.	.	.	T	0.45776	0.1359	N	0.08118	0	0.20307	N	0.999917	B;B;B	0.34264	0.318;0.446;0.446	B;B;B	0.22753	0.019;0.041;0.041	T	0.34502	-0.9826	8	0.12430	T	0.62	.	.	.	.	.	732;726;726	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	H	732;726;726	ENSP00000240361:L732H;ENSP00000374584:L726H;ENSP00000268910:L726H	ENSP00000240361:L732H	L	-	2	0	TEX14	54031528	0.996000	0.38824	0.947000	0.38551	0.438000	0.31896	-0.499000	0.06413	-0.931000	0.03746	-0.991000	0.02546	CTC		TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
ABCA6	23460	hgsc.bcm.edu	37	17	67133464	67133464	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:67133464T>C	ENST00000284425.2	-	3	448	c.274A>G	c.(274-276)Aaa>Gaa	p.K92E	ABCA6_ENST00000590645.1_Missense_Mutation_p.K92E	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	92					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AGTGCTGTTTTATTCATTATC	0.343																																																	0			17											110.0	115.0	113.0					17																	67133464		2203	4300	6503	64645059	SO:0001583	missense	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.274A>G	17.37:g.67133464T>C	ENSP00000284425:p.Lys92Glu	Somatic		Capture	Illumina HiSeq	Phase_I	64645059	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	t	15.77	2.931129	0.52866	.	.	ENSG00000154262	ENST00000284425	D	0.86865	-2.18	4.79	2.41	0.29592	.	0.398453	0.21064	N	0.080766	D	0.90570	0.7044	M	0.69358	2.11	0.23501	N	0.997541	D;P	0.89917	1.0;0.795	D;P	0.87578	0.998;0.649	T	0.81269	-0.1009	10	0.32370	T	0.25	.	8.7968	0.34885	0.0:0.0:0.375:0.625	.	92;92	Q8N139-3;Q8N139	.;ABCA6_HUMAN	E	92	ENSP00000284425:K92E	ENSP00000284425:K92E	K	-	1	0	ABCA6	64645059	0.605000	0.26941	0.996000	0.52242	0.675000	0.39556	0.495000	0.22483	0.360000	0.24265	0.524000	0.50904	AAA		ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
FASN	2194	hgsc.bcm.edu	37	17	80039654	80039654	+	Missense_Mutation	SNP	C	C	T	rs141935205	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:80039654C>T	ENST00000306749.2	-	37	6447	c.6229G>A	c.(6229-6231)Gac>Aac	p.D2077N	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2077	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	ACGATCGTGTCGTTGGTGCTC	0.667													.|||	3	0.000599042	0.0015	0.0	5008	,	,		13005	0.0		0.001	False		,,,				2504	0.0				Colon(59;314 1043 11189 28578 32273)												0			17						C	ASN/ASP	3,4401	6.2+/-15.9	0,3,2199	65.0	54.0	58.0		6229	3.7	0.1	17	dbSNP_134	58	0,8596		0,0,4298	yes	missense	FASN	NM_004104.4	23	0,3,6497	TT,TC,CC		0.0,0.0681,0.0231	benign	2077/2512	80039654	3,12997	2202	4298	6500	77632943	SO:0001583	missense	2194			U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6229G>A	17.37:g.80039654C>T	ENSP00000304592:p.Asp2077Asn	Somatic		Capture	Illumina HiSeq	Phase_I	77632943	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	8.242	0.806964	0.16467	6.81E-4	0.0	ENSG00000169710	ENST00000306749	T	0.28069	1.63	4.68	3.71	0.42584	NAD(P)-binding domain (1);	0.236860	0.40728	N	0.001031	T	0.33990	0.0882	M	0.73962	2.25	0.45216	D	0.998224	B	0.11235	0.004	B	0.09377	0.004	T	0.13764	-1.0497	10	0.33940	T	0.23	-34.348	13.0177	0.58768	0.0:0.9201:0.0:0.0799	.	2077	P49327	FAS_HUMAN	N	2077	ENSP00000304592:D2077N	ENSP00000304592:D2077N	D	-	1	0	FASN	77632943	1.000000	0.71417	0.060000	0.19600	0.001000	0.01503	4.340000	0.59328	0.946000	0.37632	-0.671000	0.03813	GAC		FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
WDR45B	56270	hgsc.bcm.edu	37	17	80579568	80579568	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:80579568C>A	ENST00000392325.4	-	6	729	c.535G>T	c.(535-537)Gtg>Ttg	p.V179L	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	179																	GGAATGTCCACGGGTGGCTTC	0.567																																																	0			17											102.0	78.0	86.0					17																	80579568		2203	4300	6503	78172857	SO:0001583	missense	56270			AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.535G>T	17.37:g.80579568C>A	ENSP00000376139:p.Val179Leu	Somatic		Capture	Illumina HiSeq	Phase_I	78172857	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	C	3.430	-0.116287	0.06881	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.76968	-1.06	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.54062	0.1835	N	0.01779	-0.725	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.54070	-0.8348	10	0.11485	T	0.65	-14.3782	18.2586	0.90026	0.0:1.0:0.0:0.0	.	179	Q5MNZ6	WIPI3_HUMAN	L	179;151	ENSP00000376139:V179L	ENSP00000376139:V179L	V	-	1	0	WDR45L	78172857	1.000000	0.71417	0.941000	0.38009	0.150000	0.21749	5.604000	0.67626	2.389000	0.81357	0.563000	0.77884	GTG		WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19725329	19725329	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:19725329A>G	ENST00000284885.3	-	10	1095	c.1062T>C	c.(1060-1062)tgT>tgC	p.C354C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	354	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GGACCCAGAAACAAAAGCCAT	0.333																																																	0			21											80.0	85.0	83.0					21																	19725329		2203	4300	6503	18647200	SO:0001819	synonymous_variant	0				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1062T>C	21.37:g.19725329A>G		Somatic		Capture	Illumina HiSeq	Phase_I	18647200	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																				TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
TTC3	7267	hgsc.bcm.edu	37	21	38525452	38525452	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:38525452A>T	ENST00000399017.2	+	27	5362	c.2615A>T	c.(2614-2616)tAt>tTt	p.Y872F	TTC3_ENST00000354749.2_Missense_Mutation_p.Y872F|TTC3_ENST00000355666.1_Missense_Mutation_p.Y872F|TTC3_ENST00000540756.1_Missense_Mutation_p.Y562F|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	872					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCAGTGGACTATGTTATTCGC	0.373																																					Ovarian(38;194 1649 35661)												0			21											91.0	99.0	97.0					21																	38525452		2203	4299	6502	37447322	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2615A>T	21.37:g.38525452A>T	ENSP00000381981:p.Tyr872Phe	Somatic		Capture	Illumina HiSeq	Phase_I	37447322	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.95|12.95	2.091181|2.091181	0.36855|0.36855	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000414818;ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	.|T;T;T;T;T;T	.|0.43294	.|2.75;2.75;3.09;0.95;3.09;3.09	5.31|5.31	0.825|0.825	0.18824|0.18824	.|.	.|0.743599	.|0.12354	.|N	.|0.476242	T|T	0.34337|0.34337	0.0894|0.0894	L|L	0.57536|0.57536	1.79|1.79	0.25122|0.25122	N|N	0.990631|0.990631	.|B;B	.|0.16166	.|0.0;0.016	.|B;B	.|0.14023	.|0.001;0.01	T|T	0.32877|0.32877	-0.9890|-0.9890	5|10	.|0.52906	.|T	.|0.07	-4.6424|-4.6424	4.3559|4.3559	0.11178|0.11178	0.6612:0.0:0.1601:0.1787|0.6612:0.0:0.1601:0.1787	.|.	.|562;872	.|B4DSZ9;P53804	.|.;TTC3_HUMAN	L|F	236;10|872;854;872;562;872;872	.|ENSP00000403943:Y872F;ENSP00000391891:Y854F;ENSP00000347889:Y872F;ENSP00000442875:Y562F;ENSP00000381981:Y872F;ENSP00000346791:Y872F	.|ENSP00000346791:Y872F	M|Y	+|+	1|2	0|0	TTC3|TTC3	37447322|37447322	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.986000|0.986000	0.74619|0.74619	2.417000|2.417000	0.44653|0.44653	0.338000|0.338000	0.23692|0.23692	0.528000|0.528000	0.53228|0.53228	ATG|TAT		TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959553	45959553	+	Missense_Mutation	SNP	A	A	C	rs9980010		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:45959553A>C	ENST00000400375.1	-	1	525	c.481T>G	c.(481-483)Tct>Gct	p.S161A	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	161	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						CAGCATGAAGAGGAATCCTCA	0.617																																																	0			21											105.0	111.0	109.0					21																	45959553		2203	4300	6503	44783981	SO:0001583	missense	386677			AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"""Keratin associated proteins"""	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.481T>G	21.37:g.45959553A>C	ENSP00000383226:p.Ser161Ala	Somatic		Capture	Illumina HiSeq	Phase_I	44783981	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	.	.	.	.	.	.	.	.	.	.	a	0.029	-1.345627	0.01266	.	.	ENSG00000215455	ENST00000400375;ENST00000545982	T	0.01106	5.33	2.39	-0.157	0.13387	.	.	.	.	.	T	0.01695	0.0054	M	0.78049	2.395	0.09310	N	1	B	0.29253	0.239	B	0.29524	0.103	T	0.42649	-0.9439	9	0.33940	T	0.23	.	2.0673	0.03605	0.4619:0.0:0.2957:0.2423	.	161	P60331	KR101_HUMAN	A	161	ENSP00000383226:S161A	ENSP00000383226:S161A	S	-	1	0	KRTAP10-1	44783981	0.012000	0.17670	0.008000	0.14137	0.022000	0.10575	1.191000	0.32138	-0.040000	0.13580	0.358000	0.22013	TCT		KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
IFT140	9742	hgsc.bcm.edu	37	16	1636257	1636257	+	Silent	SNP	G	G	A	rs556379159		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:1636257G>A	ENST00000426508.2	-	10	1392	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	343					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.T343T(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				GCCCTCTGTCGGTACCAGCGG	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		17974	0.0		0.0	False		,,,				2504	0.001																1	Substitution - coding silent(1)	endometrium(1)	16											82.0	76.0	78.0					16																	1636257		2199	4300	6499	1576258	SO:0001819	synonymous_variant	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1029C>T	16.37:g.1636257G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1576258	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
DNAH3	55567	hgsc.bcm.edu	37	16	20975977	20975977	+	Missense_Mutation	SNP	G	G	A	rs372316224		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:20975977G>A	ENST00000261383.3	-	53	9228	c.9229C>T	c.(9229-9231)Cgc>Tgc	p.R3077C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3077	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R3077C(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AAGGCCCAGCGTCTGGAATTG	0.483																																																	2	Substitution - Missense(2)	large_intestine(2)	16						G	CYS/ARG	0,4402		0,0,2201	80.0	74.0	76.0		9229	4.9	1.0	16		76	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH3	NM_017539.1	180	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3077/4117	20975977	1,13001	2201	4300	6501	20883478	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.9229C>T	16.37:g.20975977G>A	ENSP00000261383:p.Arg3077Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20883478	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.112425	0.56398	0.0	1.16E-4	ENSG00000158486	ENST00000261383	T	0.34072	1.38	5.88	4.88	0.63580	.	0.062427	0.64402	D	0.000010	T	0.76343	0.3974	H	0.99525	4.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85743	0.1338	10	0.87932	D	0	.	14.1248	0.65213	0.0:0.0:0.7441:0.2559	.	3077	Q8TD57	DYH3_HUMAN	C	3077	ENSP00000261383:R3077C	ENSP00000261383:R3077C	R	-	1	0	DNAH3	20883478	1.000000	0.71417	0.983000	0.44433	0.939000	0.58152	3.322000	0.52007	2.797000	0.96272	0.561000	0.74099	CGC		DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ARMC5	79798	hgsc.bcm.edu	37	16	31477995	31477995	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:31477995G>A	ENST00000563544.1	+	7	3139	c.2593G>A	c.(2593-2595)Ggc>Agc	p.G865S	ARMC5_ENST00000408912.3_Missense_Mutation_p.G960S|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000412665.2_Missense_Mutation_p.G509S|ARMC5_ENST00000538189.1_Missense_Mutation_p.G897S|ARMC5_ENST00000268314.4_Missense_Mutation_p.G865S			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	865										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						ACCCCAGGGTGGCCCGGAGTC	0.716																																																	0			16											18.0	28.0	24.0					16																	31477995		2166	4263	6429	31385496	SO:0001583	missense	79798			AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2593G>A	16.37:g.31477995G>A	ENSP00000456877:p.Gly865Ser	Somatic		Capture	Illumina HiSeq	Phase_I	31385496	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	G	7.329	0.618629	0.14129	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.40756	2.3;2.33;2.34;1.02	5.07	-0.357	0.12579	.	0.877779	0.09945	N	0.735429	T	0.18383	0.0441	N	0.08118	0	0.09310	N	1	B;B;B;B	0.14805	0.0;0.0;0.011;0.0	B;B;B;B	0.14023	0.005;0.005;0.01;0.005	T	0.21827	-1.0234	10	0.59425	D	0.04	-16.304	0.5668	0.00688	0.2925:0.193:0.3411:0.1735	.	897;897;960;865	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	S	960;897;865;509	ENSP00000386125:G960S;ENSP00000443995:G897S;ENSP00000268314:G865S;ENSP00000400183:G509S	ENSP00000268314:G865S	G	+	1	0	ARMC5	31385496	0.008000	0.16893	0.098000	0.21074	0.740000	0.42216	0.475000	0.22164	0.095000	0.17434	0.448000	0.29417	GGC		ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
CYLD	1540	hgsc.bcm.edu	37	16	50810186	50810186	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:50810186C>T	ENST00000427738.3	+	6	1224	c.1019C>T	c.(1018-1020)aCa>aTa	p.T340I	CYLD_ENST00000564326.1_Missense_Mutation_p.T337I|CYLD_ENST00000398568.2_Missense_Mutation_p.T337I|CYLD_ENST00000568704.2_Missense_Mutation_p.T337I|CYLD_ENST00000540145.1_Missense_Mutation_p.T340I|CYLD_ENST00000311559.9_Missense_Mutation_p.T340I|CYLD_ENST00000569418.1_Missense_Mutation_p.T337I|CYLD_ENST00000566206.1_Missense_Mutation_p.T337I			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	340	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CCAAAGGCTACAGGTATGGAT	0.383			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																														yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											83.0	83.0	83.0					16																	50810186		1862	4092	5954	49367687	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1019C>T	16.37:g.50810186C>T	ENSP00000392025:p.Thr340Ile	Somatic		Capture	Illumina HiSeq	Phase_I	49367687	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.019298	0.54576	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D	0.93712	-3.27;-3.27;-3.27	6.17	6.17	0.99709	.	0.095441	0.64402	D	0.000001	D	0.88001	0.6320	N	0.24115	0.695	0.41967	D	0.990738	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.08055	0.001;0.003;0.003;0.001	T	0.82204	-0.0573	10	0.27785	T	0.31	-16.9065	14.9696	0.71223	0.0:0.9306:0.0:0.0694	.	337;340;337;340	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	I	340;340;337;337	ENSP00000445447:T340I;ENSP00000308928:T340I;ENSP00000381574:T337I	ENSP00000308928:T340I	T	+	2	0	CYLD	49367687	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.879000	0.39618	2.941000	0.99782	0.655000	0.94253	ACA		CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
NAE1	8883	hgsc.bcm.edu	37	16	66842914	66842914	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:66842914A>G	ENST00000290810.3	-	16	1312	c.1215T>C	c.(1213-1215)gaT>gaC	p.D405D	NAE1_ENST00000379463.2_Silent_p.D399D|NAE1_ENST00000394074.2_Silent_p.D316D|NAE1_ENST00000359087.4_Silent_p.D408D			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1	405					mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	TGTTAATTGTATCCAAACCAT	0.308																																																	0			16											89.0	84.0	86.0					16																	66842914		2200	4300	6500	65400415	SO:0001819	synonymous_variant	8883			U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"""Ubiquitin-like modifier activating enzymes"""	621	protein-coding gene	gene with protein product		603385	"""amyloid beta precursor protein binding protein 1, 59kDa"""	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.1215T>C	16.37:g.66842914A>G		Somatic		Capture	Illumina HiSeq	Phase_I	65400415	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Silent	SNP	ENST00000290810.3	37	CCDS10820.1																																																																																				NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905	
HYDIN	54768	hgsc.bcm.edu	37	16	70867911	70867911	+	Missense_Mutation	SNP	C	C	T	rs200437208		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:70867911C>T	ENST00000393567.2	-	79	13708	c.13558G>A	c.(13558-13560)Ggc>Agc	p.G4520S		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4520			G -> S (in dbSNP:rs2292127).		cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGCAGCAGCCGCTAAGGAGG	0.567																																																	0			16											7.0	7.0	7.0					16																	70867911		1591	3556	5147	69425412	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13558G>A	16.37:g.70867911C>T	ENSP00000377197:p.Gly4520Ser	Somatic		Capture	Illumina HiSeq	Phase_I	69425412	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443704	0.83993	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.03860	3.78	4.87	4.87	0.63330	.	0.000000	0.33631	U	0.004719	T	0.24967	0.0606	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02214	-1.1194	10	0.54805	T	0.06	.	17.6354	0.88120	0.0:1.0:0.0:0.0	rs2292127	4519	F8WD23	.	S	4520;4519	ENSP00000377197:G4520S	ENSP00000313052:G4519S	G	-	1	0	HYDIN	69425412	1.000000	0.71417	0.945000	0.38365	0.470000	0.32858	7.043000	0.76572	2.257000	0.74773	0.511000	0.50034	GGC		HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	hgsc.bcm.edu	37	16	70917831	70917831	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:70917831C>G	ENST00000393567.2	-	59	10121	c.9971G>C	c.(9970-9972)tGt>tCt	p.C3324S		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3324					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ACCTGGTAGACAGGCTTCAGC	0.532																																																	0			16											44.0	48.0	47.0					16																	70917831		1915	4142	6057	69475332	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.9971G>C	16.37:g.70917831C>G	ENSP00000377197:p.Cys3324Ser	Somatic		Capture	Illumina HiSeq	Phase_I	69475332	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724868	0.48833	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01139	5.28	5.01	5.01	0.66863	.	0.000000	0.36134	U	0.002768	T	0.02727	0.0082	M	0.72118	2.19	0.80722	D	1	B	0.31680	0.335	B	0.34722	0.188	T	0.57130	-0.7864	10	0.32370	T	0.25	.	17.9159	0.88950	0.0:1.0:0.0:0.0	.	3323	F8WD23	.	S	3324;3323	ENSP00000377197:C3324S	ENSP00000313052:C3323S	C	-	2	0	HYDIN	69475332	1.000000	0.71417	0.979000	0.43373	0.573000	0.36030	5.337000	0.65941	2.325000	0.78763	0.511000	0.50034	TGT		HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
LAMA1	284217	hgsc.bcm.edu	37	18	6983192	6983192	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr18:6983192C>A	ENST00000389658.3	-	40	5795	c.5702G>T	c.(5701-5703)aGt>aTt	p.S1901I		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1901	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATAGGCTGCACTGGTGGCATT	0.448																																																	0			18											114.0	100.0	105.0					18																	6983192		2203	4300	6503	6973192	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5702G>T	18.37:g.6983192C>A	ENSP00000374309:p.Ser1901Ile	Somatic		Capture	Illumina HiSeq	Phase_I	6973192		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613846	0.28712	.	.	ENSG00000101680	ENST00000389658	T	0.18502	2.21	5.87	4.0	0.46444	.	0.491230	0.22779	N	0.055742	T	0.12817	0.0311	L	0.46157	1.445	0.25284	N	0.989412	B	0.12630	0.006	B	0.13407	0.009	T	0.09796	-1.0658	10	0.42905	T	0.14	.	3.0858	0.06277	0.1347:0.4535:0.2758:0.136	.	1901	P25391	LAMA1_HUMAN	I	1901	ENSP00000374309:S1901I	ENSP00000374309:S1901I	S	-	2	0	LAMA1	6973192	0.050000	0.20438	0.964000	0.40570	0.722000	0.41435	-0.012000	0.12699	2.774000	0.95407	0.650000	0.86243	AGT		LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
LAMA1	284217	hgsc.bcm.edu	37	18	7013845	7013845	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr18:7013845C>G	ENST00000389658.3	-	23	3425	c.3332G>C	c.(3331-3333)tGt>tCt	p.C1111S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1111	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCCTCCACACAGCCGCAGAG	0.577																																																	0			18											61.0	61.0	61.0					18																	7013845		2203	4300	6503	7003845	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3332G>C	18.37:g.7013845C>G	ENSP00000374309:p.Cys1111Ser	Somatic		Capture	Illumina HiSeq	Phase_I	7003845		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452256	0.63290	.	.	ENSG00000101680	ENST00000389658	T	0.23552	1.9	5.36	5.36	0.76844	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	T	0.58708	0.2141	M	0.87381	2.88	0.52501	D	0.999953	D	0.89917	1.0	D	0.79784	0.993	T	0.62905	-0.6755	10	0.51188	T	0.08	.	19.4486	0.94859	0.0:1.0:0.0:0.0	.	1111	P25391	LAMA1_HUMAN	S	1111	ENSP00000374309:C1111S	ENSP00000374309:C1111S	C	-	2	0	LAMA1	7003845	1.000000	0.71417	0.996000	0.52242	0.565000	0.35776	5.343000	0.65976	2.668000	0.90789	0.637000	0.83480	TGT		LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TGFBR2	7048	hgsc.bcm.edu	37	3	30729947	30729947	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:30729947A>G	ENST00000295754.5	+	6	1850	c.1468A>G	c.(1468-1470)Aac>Gac	p.N490D	TGFBR2_ENST00000359013.4_Missense_Mutation_p.N515D	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	490	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> S (in a gastric adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CATGAAGGACAACGTGTTGAG	0.488																																																	0			3											127.0	118.0	121.0					3																	30729947		2203	4300	6503	30704951	SO:0001583	missense	7048				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1468A>G	3.37:g.30729947A>G	ENSP00000295754:p.Asn490Asp	Somatic		Capture	Illumina HiSeq	Phase_I	30704951	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047392	0.75846	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	T;T	0.65178	-0.14;-0.14	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.239102	0.48767	D	0.000176	T	0.47967	0.1474	N	0.16201	0.385	0.58432	D	0.999997	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.45220	-0.9276	10	0.62326	D	0.03	.	15.6821	0.77376	1.0:0.0:0.0:0.0	.	490;515	P37173;D2JYI1	TGFR2_HUMAN;.	D	490;515;320	ENSP00000295754:N490D;ENSP00000351905:N515D	ENSP00000295754:N490D	N	+	1	0	TGFBR2	30704951	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	9.065000	0.93941	2.165000	0.68154	0.482000	0.46254	AAC		TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
USP4	7375	hgsc.bcm.edu	37	3	49337909	49337909	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:49337909T>C	ENST00000265560.4	-	11	1549	c.1503A>G	c.(1501-1503)agA>agG	p.R501R	USP4_ENST00000488520.1_5'Flank|USP4_ENST00000351842.4_Silent_p.R454R	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	501	USP.|Ubiquitin-like 2.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		CCTGAGTAGGTCTGCAGTGAG	0.532																																																	0			3											116.0	114.0	114.0					3																	49337909		2203	4300	6503	49312913	SO:0001819	synonymous_variant	7375			U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1503A>G	3.37:g.49337909T>C		Somatic		Capture	Illumina HiSeq	Phase_I	49312913	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.280966	0.23392	.	.	ENSG00000114316	ENST00000431357	.	.	.	5.83	0.917	0.19380	.	.	.	.	.	T	0.55800	0.1943	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47394	-0.9121	4	.	.	.	-18.5278	8.833	0.35096	0.0:0.2953:0.0:0.7047	.	.	.	.	A	240	.	.	T	-	1	0	USP4	49312913	0.996000	0.38824	0.997000	0.53966	0.991000	0.79684	0.344000	0.19962	0.141000	0.18875	0.459000	0.35465	ACC		USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
NEK4	6787	hgsc.bcm.edu	37	3	52800367	52800367	+	Missense_Mutation	SNP	G	G	T	rs141525620		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:52800367G>T	ENST00000233027.5	-	3	587	c.385C>A	c.(385-387)Cat>Aat	p.H129N	NEK4_ENST00000383721.4_Missense_Mutation_p.H129N|NEK4_ENST00000535191.1_Missense_Mutation_p.H40N	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	129	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		AGATCTCGATGAAGGATGTGT	0.328																																																	0			3											171.0	152.0	158.0					3																	52800367		2203	4300	6503	52775407	SO:0001583	missense	6787			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.385C>A	3.37:g.52800367G>T	ENSP00000233027:p.His129Asn	Somatic		Capture	Illumina HiSeq	Phase_I	52775407	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	G	31	5.071423	0.93950	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.66099	-0.19;-0.07;-0.19;-0.07	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89822	0.6826	H	0.99719	4.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93794	0.7095	10	0.87932	D	0	.	20.3697	0.98890	0.0:0.0:1.0:0.0	.	40;129;129	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	N	129;40;129;40	ENSP00000233027:H129N;ENSP00000437703:H40N;ENSP00000373227:H129N;ENSP00000419666:H40N	ENSP00000233027:H129N	H	-	1	0	NEK4	52775407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.811000	0.96726	0.655000	0.94253	CAT		NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
ACOX2	8309	hgsc.bcm.edu	37	3	58519219	58519219	+	Missense_Mutation	SNP	A	A	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:58519219A>T	ENST00000302819.5	-	5	827	c.536T>A	c.(535-537)gTg>gAg	p.V179E	ACOX2_ENST00000459701.2_Missense_Mutation_p.V179E	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	179					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GCTGTGTATCACAAACTCCTG	0.532											OREG0015638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			3											171.0	170.0	170.0					3																	58519219		2203	4300	6503	58494259	SO:0001583	missense	8309			X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.536T>A	3.37:g.58519219A>T	ENSP00000307697:p.Val179Glu	Somatic	1031	Capture	Illumina HiSeq	Phase_I	58494259	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	37	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133429	0.77662	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	D;D	0.96232	-3.95;-3.95	4.85	3.66	0.41972	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.210963	0.31859	N	0.006947	D	0.96433	0.8836	L	0.55743	1.74	0.48762	D	0.999708	D	0.61697	0.99	P	0.60286	0.872	D	0.95496	0.8573	10	0.59425	D	0.04	-0.2733	10.7347	0.46117	0.857:0.0:0.0:0.143	.	179	Q99424	ACOX2_HUMAN	E	179	ENSP00000418562:V179E;ENSP00000307697:V179E	ENSP00000307697:V179E	V	-	2	0	ACOX2	58494259	0.999000	0.42202	0.947000	0.38551	0.991000	0.79684	4.219000	0.58561	0.782000	0.33613	0.459000	0.35465	GTG		ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
MAGI1	9223	hgsc.bcm.edu	37	3	65607705	65607705	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:65607705A>G	ENST00000497477.2	-	2	371	c.372T>C	c.(370-372)tcT>tcC	p.S124S	MAGI1_ENST00000483466.1_Silent_p.S124S|MAGI1_ENST00000330909.8_Silent_p.S124S|MAGI1_ENST00000402939.2_Silent_p.S124S|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	124	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.			S -> F (in Ref. 1; BAA32002 and 2; AAK94064/AAK94065/AAK94066/AAC51326). {ECO:0000305}.	cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CATGATCAGGAGACCCCTTCT	0.478																																																	0			3											152.0	133.0	139.0					3																	65607705		2203	4300	6503	65582745	SO:0001819	synonymous_variant	154043			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.372T>C	3.37:g.65607705A>G		Somatic		Capture	Illumina HiSeq	Phase_I	65582745	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37																																																																																					MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
EPHA3	2042	hgsc.bcm.edu	37	3	89391111	89391111	+	Missense_Mutation	SNP	A	A	G	rs533112669		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:89391111A>G	ENST00000336596.2	+	5	1402	c.1177A>G	c.(1177-1179)Acg>Gcg	p.T393A	EPHA3_ENST00000494014.1_Missense_Mutation_p.T393A|EPHA3_ENST00000452448.2_Missense_Mutation_p.T393A	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	393	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CACCAACACCACGGTGACAGT	0.483										TSP Lung(6;0.00050)																																							0			3											104.0	89.0	94.0					3																	89391111		2203	4300	6503	89473801	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1177A>G	3.37:g.89391111A>G	ENSP00000337451:p.Thr393Ala	Somatic		Capture	Illumina HiSeq	Phase_I	89473801	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.840910	0.32513	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.58506	0.33;0.33;0.33	5.66	5.66	0.87406	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	L	0.36672	1.1	0.58432	D	0.999999	B;B	0.30211	0.273;0.059	B;B	0.34590	0.186;0.06	T	0.43956	-0.9359	9	.	.	.	.	12.4245	0.55538	0.8745:0.0:0.0:0.1255	.	393;393	P29320;P29320-2	EPHA3_HUMAN;.	A	393	ENSP00000337451:T393A;ENSP00000399926:T393A;ENSP00000419190:T393A	.	T	+	1	0	EPHA3	89473801	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	6.082000	0.71318	2.285000	0.76669	0.533000	0.62120	ACG		EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
EPHA6	285220	hgsc.bcm.edu	37	3	96963114	96963114	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:96963114T>G	ENST00000389672.5	+	5	1627	c.1589T>G	c.(1588-1590)gTg>gGg	p.V530G	EPHA6_ENST00000470610.2_Missense_Mutation_p.V530G	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	436	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						GCTATTACAGTGACCACGGAT	0.393																																																	0			3											105.0	99.0	101.0					3																	96963114		1881	4121	6002	98445804	SO:0001583	missense	285220			AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.1589T>G	3.37:g.96963114T>G	ENSP00000374323:p.Val530Gly	Somatic		Capture	Illumina HiSeq	Phase_I	98445804	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006414	0.74932	.	.	ENSG00000080224	ENST00000470610;ENST00000389672	T;T	0.57107	4.45;0.42	5.49	5.49	0.81192	.	.	.	.	.	T	0.72407	0.3456	M	0.83774	2.66	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61477	0.889;0.889	T	0.77854	-0.2433	9	0.87932	D	0	.	15.6046	0.76652	0.0:0.0:0.0:1.0	.	530;530	B3KS12;E7EU71	.;.	G	530	ENSP00000420598:V530G;ENSP00000374323:V530G	ENSP00000374323:V530G	V	+	2	0	EPHA6	98445804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.685000	0.84117	2.089000	0.63090	0.528000	0.53228	GTG		EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826045	125826045	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:125826045T>C	ENST00000393434.2	-	21	2741	c.2392A>G	c.(2392-2394)Atg>Gtg	p.M798V	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.M798V|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.M697V|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.M808V	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	798	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	GCTATGAACATGTGGTCTTCC	0.532																																																	0			3											181.0	155.0	164.0					3																	125826045		2203	4300	6503	127308735	SO:0001583	missense	10840			AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2392A>G	3.37:g.125826045T>C	ENSP00000377083:p.Met798Val	Somatic		Capture	Illumina HiSeq	Phase_I	127308735	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209220	0.58343	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	3.98	3.98	0.46160	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.88640	0.6491	H	0.94542	3.55	0.80722	D	1	D;D;D	0.60160	0.987;0.984;0.975	P;P;P	0.59221	0.822;0.854;0.73	D	0.90851	0.4731	10	0.87932	D	0	.	10.8723	0.46891	0.0:0.0:0.0:1.0	.	697;333;798	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	808;798;697;798	ENSP00000273450:M808V;ENSP00000420293:M798V;ENSP00000395881:M697V;ENSP00000377083:M798V	ENSP00000273450:M808V	M	-	1	0	ALDH1L1	127308735	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	7.527000	0.81931	1.677000	0.50941	0.260000	0.18958	ATG		ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
COL6A6	131873	hgsc.bcm.edu	37	3	130287019	130287019	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:130287019C>T	ENST00000358511.6	+	5	2003	c.1972C>T	c.(1972-1974)Cgg>Tgg	p.R658W	COL6A6_ENST00000453409.2_Missense_Mutation_p.R658W	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	658	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGGACCAGATCGGGTGCAAAT	0.418																																																	0			3											166.0	160.0	162.0					3																	130287019		1887	4109	5996	131769709	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1972C>T	3.37:g.130287019C>T	ENSP00000351310:p.Arg658Trp	Somatic		Capture	Illumina HiSeq	Phase_I	131769709	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	3.726	-0.056643	0.07362	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79141	-1.24;-1.24	5.53	0.305	0.15801	von Willebrand factor, type A (3);	0.395727	0.21379	N	0.075504	T	0.74596	0.3737	M	0.82517	2.595	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.66842	-0.5821	10	0.72032	D	0.01	.	6.5339	0.22341	0.5293:0.3035:0.1039:0.0634	.	658	A6NMZ7	CO6A6_HUMAN	W	658	ENSP00000351310:R658W;ENSP00000399236:R658W	ENSP00000351310:R658W	R	+	1	2	COL6A6	131769709	0.000000	0.05858	0.018000	0.16275	0.030000	0.12068	-0.547000	0.06055	-0.237000	0.09739	-0.182000	0.12963	CGG		COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
NEK11	79858	hgsc.bcm.edu	37	3	130947448	130947448	+	Missense_Mutation	SNP	G	G	T	rs145914506		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:130947448G>T	ENST00000510769.1	+	11	1414	c.1161G>T	c.(1159-1161)gaG>gaT	p.E387D	NEK11_ENST00000412440.2_Missense_Mutation_p.E308D|NEK11_ENST00000508196.1_Missense_Mutation_p.E492D|NEK11_ENST00000510688.1_Missense_Mutation_p.E492D|NEK11_ENST00000383366.4_Missense_Mutation_p.E492D|NEK11_ENST00000429253.2_Missense_Mutation_p.E492D					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						AGAGTGATGAGGAGGAAGAAG	0.433																																																	0			3						G	ASP/GLU,ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	130.0	120.0	124.0		1476,1476	0.3	1.0	3	dbSNP_134	124	0,8600		0,0,4300	no	missense,missense	NEK11	NM_001146003.1,NM_024800.4	45,45	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	benign,benign	492/600,492/646	130947448	1,13005	2203	4300	6503	132430138	SO:0001583	missense	79858			AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1161G>T	3.37:g.130947448G>T	ENSP00000421549:p.Glu387Asp	Somatic		Capture	Illumina HiSeq	Phase_I	132430138		Missense_Mutation	SNP	ENST00000510769.1	37		.	.	.	.	.	.	.	.	.	.	G	8.229	0.804269	0.16467	2.27E-4	0.0	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000510688;ENST00000383366;ENST00000412440;ENST00000508196	T;T;T;T;T;T	0.73469	-0.7;-0.52;-0.65;-0.52;-0.75;-0.52	5.53	0.33	0.15929	.	0.502608	0.16645	N	0.205469	T	0.46405	0.1391	N	0.12746	0.255	0.27115	N	0.962279	B;B;B;B	0.13145	0.004;0.004;0.003;0.007	B;B;B;B	0.14578	0.011;0.005;0.011;0.007	T	0.18023	-1.0350	10	0.15499	T	0.54	.	2.1536	0.03806	0.1468:0.1211:0.3602:0.3719	.	387;308;492;492	E9PHI8;B4DDN2;Q8NG66-4;Q8NG66	.;.;.;NEK11_HUMAN	D	387;492;492;492;308;492	ENSP00000421549:E387D;ENSP00000397180:E492D;ENSP00000423458:E492D;ENSP00000372857:E492D;ENSP00000411888:E308D;ENSP00000421851:E492D	ENSP00000372857:E492D	E	+	3	2	NEK11	132430138	0.777000	0.28628	0.990000	0.47175	0.449000	0.32228	-0.157000	0.10085	-0.002000	0.14469	0.561000	0.74099	GAG		NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
XRN1	54464	hgsc.bcm.edu	37	3	142102234	142102234	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:142102234G>A	ENST00000264951.4	-	22	2641	c.2524C>T	c.(2524-2526)Cgt>Tgt	p.R842C	XRN1_ENST00000392981.2_Missense_Mutation_p.R842C	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	842					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R842S(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TTGGAGAAACGGGAGTCGAAA	0.353																																																	1	Substitution - Missense(1)	large_intestine(1)	3											72.0	71.0	71.0					3																	142102234		2203	4300	6503	143584924	SO:0001583	missense	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.2524C>T	3.37:g.142102234G>A	ENSP00000264951:p.Arg842Cys	Somatic		Capture	Illumina HiSeq	Phase_I	143584924	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499535	0.85176	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.37058	1.22;1.23	5.97	5.97	0.96955	.	0.169118	0.56097	D	0.000032	T	0.54240	0.1846	M	0.73430	2.235	0.80722	D	1	P;D;D	0.69078	0.877;0.997;0.995	B;P;P	0.54924	0.093;0.764;0.586	T	0.57470	-0.7806	10	0.87932	D	0	-16.1482	15.8636	0.79043	0.0:0.1348:0.8652:0.0	.	703;842;842	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	C	842	ENSP00000264951:R842C;ENSP00000376707:R842C	ENSP00000264951:R842C	R	-	1	0	XRN1	143584924	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.659000	0.61504	2.833000	0.97629	0.585000	0.79938	CGT		XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
PLSCR1	5359	hgsc.bcm.edu	37	3	146239397	146239397	+	Silent	SNP	T	T	C	rs201312426		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:146239397T>C	ENST00000342435.4	-	7	1082	c.672A>G	c.(670-672)agA>agG	p.R224R	PLSCR1_ENST00000448787.2_Silent_p.R143R|PLSCR1_ENST00000448205.1_Intron|PLSCR1_ENST00000487389.1_Silent_p.R217R	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	224					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						GTACATCCTCTCTTTTCTCAT	0.368																																																	0			3											194.0	186.0	189.0					3																	146239397		2203	4300	6503	147722087	SO:0001819	synonymous_variant	5359			AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.672A>G	3.37:g.146239397T>C		Somatic		Capture	Illumina HiSeq	Phase_I	147722087	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	37	CCDS3135.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	8.294	0.818427	0.16607	.	.	ENSG00000188313	ENST00000483300	.	.	.	5.17	2.46	0.29980	.	.	.	.	.	T	0.27313	0.0670	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.18999	-1.0319	4	.	.	.	.	5.6164	0.17434	0.1324:0.1702:0.0:0.6974	.	.	.	.	G	91	.	.	E	-	2	0	PLSCR1	147722087	0.000000	0.05858	0.894000	0.35097	0.934000	0.57294	0.005000	0.13129	0.828000	0.34709	0.528000	0.53228	GAG		PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105	
ZIC1	7545	hgsc.bcm.edu	37	3	147130434	147130434	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:147130434A>G	ENST00000282928.4	+	2	1841	c.1112A>G	c.(1111-1113)tAc>tGc	p.Y371C		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	371					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GACAAGTCCTACACGCATCCC	0.597																																																	0			3											155.0	120.0	132.0					3																	147130434		2203	4300	6503	148613124	SO:0001583	missense	7545			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"""Zinc fingers, C2H2-type"""	12872	protein-coding gene	gene with protein product		600470	"""Zic family member 1 (odd-paired Drosophila homolog)"", ""Zic family member 1 (odd-paired homolog, Drosophila)"""			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.1112A>G	3.37:g.147130434A>G	ENSP00000282928:p.Tyr371Cys	Somatic		Capture	Illumina HiSeq	Phase_I	148613124	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.288029|4.288029	0.80803|0.80803	.|.	.|.	ENSG00000152977|ENSG00000152977	ENST00000488404|ENST00000282928	.|T	.|0.53423	.|0.62	4.12|4.12	4.12|4.12	0.48240|0.48240	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.64402	.|U	.|0.000001	T|T	0.59891|0.59891	0.2227|0.2227	L|L	0.42686|0.42686	1.345|1.345	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.63633|0.63633	-0.6593|-0.6593	5|10	.|0.87932	.|D	.|0	.|.	13.1397|13.1397	0.59428|0.59428	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|371	.|Q15915	.|ZIC1_HUMAN	A|C	60|371	.|ENSP00000282928:Y371C	.|ENSP00000282928:Y371C	T|Y	+|+	1|2	0|0	ZIC1|ZIC1	148613124|148613124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	8.833000|8.833000	0.92089|0.92089	1.506000|1.506000	0.48736|0.48736	0.379000|0.379000	0.24179|0.24179	ACA|TAC		ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412	
AADAC	13	hgsc.bcm.edu	37	3	151545933	151545933	+	Nonsense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:151545933T>G	ENST00000232892.7	+	5	1299	c.1173T>G	c.(1171-1173)taT>taG	p.Y391*	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	391					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TAAATCAGTATATTGAGTGGC	0.323																																					Ovarian(30;839 841 2699 32801 46334)												0			3											35.0	38.0	37.0					3																	151545933		2185	4293	6478	153028623	SO:0001587	stop_gained	13			L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"""arylacetamide deacetylase (esterase)"""			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.1173T>G	3.37:g.151545933T>G	ENSP00000232892:p.Tyr391*	Somatic		Capture	Illumina HiSeq	Phase_I	153028623	A8K3L3|D3DNJ6|Q8N1A9	Nonsense_Mutation	SNP	ENST00000232892.7	37	CCDS33877.1	.	.	.	.	.	.	.	.	.	.	T	33	5.220925	0.95139	.	.	ENSG00000114771	ENST00000232892	.	.	.	4.79	2.43	0.29744	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.3419	6.3466	0.21353	0.0:0.6027:0.0:0.3973	.	.	.	.	X	391	.	ENSP00000232892:Y391X	Y	+	3	2	AADAC	153028623	0.017000	0.18338	0.306000	0.25113	0.451000	0.32288	-0.171000	0.09883	0.677000	0.31305	0.482000	0.46254	TAT		AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086	
ZMAT3	64393	hgsc.bcm.edu	37	3	178742984	178742984	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178742984T>A	ENST00000311417.2	-	6	1432	c.691A>T	c.(691-693)Aga>Tga	p.R231*	ZMAT3_ENST00000432729.1_Nonsense_Mutation_p.R230*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			CGTGGAATTCTCTGCCGAGAG	0.423																																																	0			3											68.0	61.0	63.0					3																	178742984		2203	4300	6503	180225678	SO:0001587	stop_gained	64393			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"""Zinc fingers, matrin-type"""	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.691A>T	3.37:g.178742984T>A	ENSP00000311221:p.Arg231*	Somatic		Capture	Illumina HiSeq	Phase_I	180225678		Nonsense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	T	43	10.207832	0.99359	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	.	.	.	5.6	3.14	0.36123	.	0.048656	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-13.1297	8.6177	0.33842	0.1165:0.0:0.1938:0.6896	.	.	.	.	X	231;230	.	ENSP00000311221:R231X	R	-	1	2	ZMAT3	180225678	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.689000	0.54706	2.123000	0.65237	0.528000	0.53228	AGA		ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240	
PIK3CA	5290	hgsc.bcm.edu	37	3	178916663	178916663	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178916663C>T	ENST00000263967.3	+	2	207	c.50C>T	c.(49-51)cCc>cTc	p.P17L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	17	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.I13_R19del(1)|p.L15_V22>PM(1)|p.P17del(1)|p.E9_R19del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CACTTGATGCCCCCAAGAATC	0.383		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	4	Deletion - In frame(3)|Complex - deletion inframe(1)	endometrium(2)|central_nervous_system(2)	3											56.0	56.0	56.0					3																	178916663		1854	4093	5947	180399357	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.50C>T	3.37:g.178916663C>T	ENSP00000263967:p.Pro17Leu	Somatic		Capture	Illumina HiSeq	Phase_I	180399357	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569902	0.86542	.	.	ENSG00000121879	ENST00000477735;ENST00000263967;ENST00000468036	T;T	0.73047	-0.67;-0.71	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.82259	0.4998	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.83082	-0.0137	10	0.54805	T	0.06	-23.0055	18.8096	0.92053	0.0:1.0:0.0:0.0	.	17	P42336	PK3CA_HUMAN	L	17	ENSP00000263967:P17L;ENSP00000417479:P17L	ENSP00000263967:P17L	P	+	2	0	PIK3CA	180399357	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.394000	0.79862	2.506000	0.84524	0.650000	0.86243	CCC		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178927975	178927975	+	Splice_Site	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178927975A>G	ENST00000263967.3	+	8	1410	c.1253A>G	c.(1252-1254)gAa>gGa	p.E418G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	418	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTTTTTAAGGAACACTGTCCA	0.323		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											77.0	73.0	74.0					3																	178927975		1816	4075	5891	180410669	SO:0001630	splice_region_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1252-1A>G	3.37:g.178927975A>G		Somatic		Capture	Illumina HiSeq	Phase_I	180410669	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.005342	0.54254	.	.	ENSG00000121879	ENST00000263967	T	0.76578	-1.03	5.29	5.29	0.74685	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.057452	0.64402	D	0.000002	T	0.74329	0.3702	L	0.45698	1.435	0.80722	D	1	P	0.39737	0.685	B	0.41412	0.356	T	0.73691	-0.3903	10	0.33940	T	0.23	-10.6747	15.2222	0.73320	1.0:0.0:0.0:0.0	.	418	P42336	PK3CA_HUMAN	G	418	ENSP00000263967:E418G	ENSP00000263967:E418G	E	+	2	0	PIK3CA	180410669	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.962000	0.93254	2.012000	0.59069	0.460000	0.39030	GAA		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		Missense_Mutation
PIK3CA	5290	hgsc.bcm.edu	37	3	178952076	178952076	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:178952076A>G	ENST00000263967.3	+	21	3288	c.3131A>G	c.(3130-3132)aAt>aGt	p.N1044S	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1044	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N1044S(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAACAAATGAATGATGCACAT	0.373		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	3											99.0	89.0	92.0					3																	178952076		1910	4124	6034	180434770	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3131A>G	3.37:g.178952076A>G	ENSP00000263967:p.Asn1044Ser	Somatic		Capture	Illumina HiSeq	Phase_I	180434770	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813104	0.50527	.	.	ENSG00000121879	ENST00000263967	T	0.81078	-1.45	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.39566	1.225	0.80722	D	1	P	0.45078	0.85	B	0.39339	0.297	T	0.71708	-0.4511	10	0.19590	T	0.45	-24.648	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1044	P42336	PK3CA_HUMAN	S	1044	ENSP00000263967:N1044S	ENSP00000263967:N1044S	N	+	2	0	PIK3CA	180434770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	AAT		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
APOD	347	hgsc.bcm.edu	37	3	195295922	195295922	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr3:195295922A>G	ENST00000343267.3	-	5	780	c.419T>C	c.(418-420)cTt>cCt	p.L140P		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	140					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CACGTGAAAAAGTTGGATGAT	0.448																																																	0			3											151.0	152.0	151.0					3																	195295922		2203	4300	6503	196777211	SO:0001583	missense	347				CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"""Lipocalins"", ""Apolipoproteins"""	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.419T>C	3.37:g.195295922A>G	ENSP00000345179:p.Leu140Pro	Somatic		Capture	Illumina HiSeq	Phase_I	196777211	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.933118	0.52866	.	.	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.29397	1.57;1.57;1.96	6.06	6.06	0.98353	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.33381	0.0861	L	0.59436	1.845	0.80722	D	1	B	0.29552	0.248	B	0.31245	0.126	T	0.11179	-1.0598	10	0.54805	T	0.06	-19.8325	13.0011	0.58676	1.0:0.0:0.0:0.0	.	140	P05090	APOD_HUMAN	P	140;168;140	ENSP00000345179:L140P;ENSP00000415235:L168P;ENSP00000393076:L140P	ENSP00000345179:L140P	L	-	2	0	APOD	196777211	1.000000	0.71417	0.982000	0.44146	0.009000	0.06853	8.321000	0.89997	2.324000	0.78689	0.533000	0.62120	CTT		APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647	
KDM5A	5927	hgsc.bcm.edu	37	12	406230	406230	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:406230G>T	ENST00000399788.2	-	25	4573	c.4211C>A	c.(4210-4212)tCt>tAt	p.S1404Y	KDM5A_ENST00000382815.4_Missense_Mutation_p.S1404Y	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1404					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CTTAGAAGCAGAAGAATAAGC	0.398			T	NUP98	AML																																			Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	0			12											58.0	57.0	57.0					12																	406230		1863	4106	5969	276491	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4211C>A	12.37:g.406230G>T	ENSP00000382688:p.Ser1404Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	276491	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933069	0.34096	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.86956	-2.19;-2.01	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.88760	0.6524	N	0.22421	0.69	0.58432	D	0.999999	D;D	0.69078	0.995;0.997	D;D	0.80764	0.986;0.994	D	0.85178	0.1002	10	0.16896	T	0.51	-14.8326	19.7243	0.96157	0.0:0.0:1.0:0.0	.	1404;1404	P29375;P29375-2	KDM5A_HUMAN;.	Y	1404	ENSP00000382688:S1404Y;ENSP00000372265:S1404Y	ENSP00000372265:S1404Y	S	-	2	0	KDM5A	276491	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.836000	0.99456	2.647000	0.89833	0.655000	0.94253	TCT		KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
VWF	7450	hgsc.bcm.edu	37	12	6219731	6219731	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:6219731G>A	ENST00000261405.5	-	5	595	c.341C>T	c.(340-342)gCc>gTc	p.A114V	VWF_ENST00000572068.1_Missense_Mutation_p.A151V	NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	114	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCTTTGGAGGCATAGGGCAT	0.532																																																	0			12											77.0	81.0	80.0					12																	6219731		2203	4300	6503	6089992	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.341C>T	12.37:g.6219731G>A	ENSP00000261405:p.Ala114Val	Somatic		Capture	Illumina HiSeq	Phase_I	6089992	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	24.2	4.509418	0.85282	.	.	ENSG00000110799	ENST00000261405	T	0.59083	0.29	5.9	5.9	0.94986	von Willebrand factor, type D domain (3);	0.000000	0.42821	D	0.000648	T	0.73202	0.3557	L	0.48986	1.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.994	T	0.73436	-0.3983	10	0.72032	D	0.01	.	19.2581	0.93955	0.0:0.0:1.0:0.0	.	114;151;114	B4DNX0;Q8TCE8;P04275	.;.;VWF_HUMAN	V	114	ENSP00000261405:A114V	ENSP00000261405:A114V	A	-	2	0	VWF	6089992	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.269000	0.72558	2.804000	0.96469	0.655000	0.94253	GCC		VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
CD163	9332	hgsc.bcm.edu	37	12	7640085	7640085	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:7640085T>C	ENST00000359156.4	-	8	2122	c.1920A>G	c.(1918-1920)aaA>aaG	p.K640K	CD163_ENST00000396620.3_Silent_p.K673K|CD163_ENST00000541972.1_Silent_p.K628K|CD163_ENST00000432237.2_Silent_p.K640K|CD163_ENST00000539632.1_5'Flank	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	640	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GACCATTTCCTTTTCCAAAAC	0.478																																																	0			12											154.0	140.0	145.0					12																	7640085		2203	4300	6503	7531352	SO:0001819	synonymous_variant	9332			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1920A>G	12.37:g.7640085T>C		Somatic		Capture	Illumina HiSeq	Phase_I	7531352	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																				CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
STK38L	23012	hgsc.bcm.edu	37	12	27461382	27461382	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:27461382A>G	ENST00000389032.3	+	4	466	c.297A>G	c.(295-297)ggA>ggG	p.G99G	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TAGGAAGAGGAGCTTTTGGAG	0.383																																																	0			12											107.0	112.0	110.0					12																	27461382		2203	4300	6503	27352649	SO:0001819	synonymous_variant	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.297A>G	12.37:g.27461382A>G		Somatic		Capture	Illumina HiSeq	Phase_I	27352649		Silent	SNP	ENST00000389032.3	37	CCDS31761.1																																																																																				STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	
LRRK2	120892	hgsc.bcm.edu	37	12	40692172	40692172	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:40692172T>G	ENST00000298910.7	+	24	3282	c.3224T>G	c.(3223-3225)gTt>gGt	p.V1075G	LRRK2_ENST00000343742.2_Missense_Mutation_p.V1075G	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1075					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CCCTCAGTGGTTTTAGATCCT	0.363																																																	0			12											143.0	135.0	138.0					12																	40692172		2203	4300	6503	38978439	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.3224T>G	12.37:g.40692172T>G	ENSP00000298910:p.Val1075Gly	Somatic		Capture	Illumina HiSeq	Phase_I	38978439	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	9.683	1.149822	0.21288	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.71934	2.23;-0.61	5.85	0.629	0.17687	.	0.418063	0.26112	N	0.026269	T	0.48572	0.1507	N	0.22421	0.69	0.19300	N	0.999979	B;B	0.20887	0.049;0.014	B;B	0.16722	0.016;0.013	T	0.22906	-1.0203	10	0.23891	T	0.37	.	5.8643	0.18767	0.1339:0.4187:0.0:0.4474	.	1075;1075	E9PC85;Q5S007	.;LRRK2_HUMAN	G	1075	ENSP00000341930:V1075G;ENSP00000298910:V1075G	ENSP00000298910:V1075G	V	+	2	0	LRRK2	38978439	0.014000	0.17966	0.003000	0.11579	0.974000	0.67602	0.391000	0.20784	0.072000	0.16694	-0.250000	0.11733	GTT		LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
SENP1	29843	hgsc.bcm.edu	37	12	48457593	48457593	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:48457593C>T	ENST00000004980.5	-	13	1785	c.1307G>A	c.(1306-1308)cGt>cAt	p.R436H	SENP1_ENST00000549518.1_Missense_Mutation_p.R436H|SENP1_ENST00000549595.1_Missense_Mutation_p.R436H|SENP1_ENST00000551330.1_Missense_Mutation_p.R436H|SENP1_ENST00000448372.1_Missense_Mutation_p.R436H|SENP1_ENST00000339976.6_3'UTR			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	436					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				ATTCCCATTACGAAATACATT	0.383																																																	0			12											122.0	113.0	116.0					12																	48457593		1868	4109	5977	46743860	SO:0001583	missense	29843			AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.1307G>A	12.37:g.48457593C>T	ENSP00000004980:p.Arg436His	Somatic		Capture	Illumina HiSeq	Phase_I	46743860	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	37	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	C	15.56	2.871056	0.51695	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.42900	0.96;1.53;0.96;1.53;0.96	5.24	5.24	0.73138	.	0.222255	0.41605	D	0.000860	T	0.24624	0.0597	L	0.28054	0.825	0.80722	D	1	P;P	0.37423	0.594;0.59	B;B	0.25614	0.016;0.062	T	0.07809	-1.0753	10	0.15066	T	0.55	-11.017	13.7327	0.62799	0.154:0.846:0.0:0.0	.	436;436	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	H	436	ENSP00000004980:R436H;ENSP00000394791:R436H;ENSP00000446681:R436H;ENSP00000450076:R436H;ENSP00000447328:R436H	ENSP00000004980:R436H	R	-	2	0	SENP1	46743860	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.912000	0.48782	2.615000	0.88500	0.655000	0.94253	CGT		SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
DDX23	9416	hgsc.bcm.edu	37	12	49230468	49230468	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:49230468G>A	ENST00000308025.3	-	10	1199	c.1120C>T	c.(1120-1122)Cgt>Tgt	p.R374C	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	374					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.R374C(1)		NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TAGTCCTCACGGAAGATCCGC	0.522																																																	1	Substitution - Missense(1)	kidney(1)	12											159.0	139.0	146.0					12																	49230468		2203	4300	6503	47516735	SO:0001583	missense	9416			AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"""DEAD-boxes"""	17347	protein-coding gene	gene with protein product		612172	"""PRP28 homolog, yeast"""			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1120C>T	12.37:g.49230468G>A	ENSP00000310723:p.Arg374Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47516735	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905236	0.52333	.	.	ENSG00000174243	ENST00000308025	T	0.25414	1.8	5.82	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	H	0.95645	3.7	0.80722	D	1	P	0.47191	0.891	B	0.32677	0.15	T	0.60182	-0.7313	10	0.87932	D	0	-1.5578	13.0504	0.58952	0.0:0.0:0.7076:0.2924	.	374	Q9BUQ8	DDX23_HUMAN	C	374	ENSP00000310723:R374C	ENSP00000310723:R374C	R	-	1	0	DDX23	47516735	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.381000	0.52455	1.450000	0.47717	0.561000	0.74099	CGT		DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818	
ERBB3	2065	hgsc.bcm.edu	37	12	56477659	56477659	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:56477659A>G	ENST00000267101.3	+	2	647	c.207A>G	c.(205-207)ggA>ggG	p.G69G	ERBB3_ENST00000411731.2_Silent_p.G69G|ERBB3_ENST00000415288.2_Silent_p.G10G|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	69					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TGCTCACGGGACACAATGCCG	0.542																																																	0			12											277.0	221.0	240.0					12																	56477659		2203	4300	6503	54763926	SO:0001819	synonymous_variant	2065			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.207A>G	12.37:g.56477659A>G		Somatic		Capture	Illumina HiSeq	Phase_I	54763926	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																				ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
KIF5A	3798	hgsc.bcm.edu	37	12	57970146	57970146	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:57970146T>C	ENST00000455537.2	+	19	2457	c.2183T>C	c.(2182-2184)aTt>aCt	p.I728T	KIF5A_ENST00000286452.5_Missense_Mutation_p.I639T	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	728					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAGAAGACCATTGATGAGCTC	0.592																																																	0			12											37.0	43.0	41.0					12																	57970146		2203	4300	6503	56256413	SO:0001583	missense	3798			U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"""Kinesins"""	6323	protein-coding gene	gene with protein product		602821	"""spastic paraplegia 10 (autosomal dominant)"""	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2183T>C	12.37:g.57970146T>C	ENSP00000408979:p.Ile728Thr	Somatic		Capture	Illumina HiSeq	Phase_I	56256413	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699072	0.68501	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.74737	-0.87;-0.87	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.85710	2.77	0.58432	D	0.999991	P;P	0.50443	0.935;0.914	P;P	0.54590	0.756;0.71	D	0.85496	0.1188	10	0.52906	T	0.07	.	13.0026	0.58685	0.0:0.0:0.0:1.0	.	639;728	B7Z2M7;Q12840	.;KIF5A_HUMAN	T	728;639	ENSP00000408979:I728T;ENSP00000286452:I639T	ENSP00000286452:I639T	I	+	2	0	KIF5A	56256413	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.640000	0.83355	2.082000	0.62665	0.459000	0.35465	ATT		KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984	
PTPRR	5801	hgsc.bcm.edu	37	12	71029607	71029607	+	IGR	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:71029607C>T	ENST00000283228.2	-	0	3529				PTPRB_ENST00000550358.1_Missense_Mutation_p.E99K|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.E99K|PTPRB_ENST00000551525.1_Missense_Mutation_p.E98K|PTPRR_ENST00000537619.2_5'Flank	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AGGAAGCCTTCCTGATCATAG	0.557																																																	0			12											51.0	50.0	50.0					12																	71029607		1926	4131	6057	69315874	SO:0001628	intergenic_variant	5787			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502		12.37:g.71029607C>T		Somatic		Capture	Illumina HiSeq	Phase_I	69315874	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652964	0.47362	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.05258	4.01;3.97;3.47	6.04	2.12	0.27331	.	.	.	.	.	T	0.04907	0.0132	L	0.27053	0.805	0.09310	N	0.999994	B;B;B;B	0.26195	0.144;0.006;0.006;0.006	B;B;B;B	0.15870	0.014;0.007;0.003;0.003	T	0.37220	-0.9715	9	0.87932	D	0	.	7.4804	0.27402	0.0:0.6049:0.2566:0.1384	.	99;98;99;99	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	K	99;99;99;98	ENSP00000334928:E99K;ENSP00000448058:E99K;ENSP00000448349:E98K	ENSP00000334928:E99K	E	-	1	0	PTPRB	69315874	0.999000	0.42202	0.004000	0.12327	0.841000	0.47740	1.967000	0.40491	0.122000	0.18314	0.563000	0.77884	GAA		PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
PAH	5053	hgsc.bcm.edu	37	12	103288665	103288665	+	Missense_Mutation	SNP	G	G	C	rs199475570		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:103288665G>C	ENST00000553106.1	-	3	672	c.200C>G	c.(199-201)tCt>tGt	p.S67C	PAH_ENST00000551988.1_5'UTR|PAH_ENST00000307000.2_Missense_Mutation_p.S62C	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	67	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.		S -> P (in PKU; haplotype 4).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	AGAAGGTCTAGATTCAATGTG	0.438																																																	0			12											127.0	119.0	122.0					12																	103288665		2203	4300	6503	101812795	SO:0001583	missense	5053			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.200C>G	12.37:g.103288665G>C	ENSP00000448059:p.Ser67Cys	Somatic		Capture	Illumina HiSeq	Phase_I	101812795	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994030	0.93167	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337;ENST00000546844	D;D;D;D	0.99207	-5.56;-5.56;-5.56;-5.56	6.17	6.17	0.99709	Amino acid-binding ACT (1);	0.000000	0.85682	D	0.000000	D	0.99771	0.9906	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97122	0.9812	10	0.87932	D	0	-29.0654	20.8794	0.99867	0.0:0.0:1.0:0.0	.	67;67	B4DPN2;P00439	.;PH4H_HUMAN	C	67;62;67;67	ENSP00000448059:S67C;ENSP00000303500:S62C;ENSP00000447620:S67C;ENSP00000446658:S67C	ENSP00000303500:S62C	S	-	2	0	PAH	101812795	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.877000	0.92386	2.941000	0.99782	0.655000	0.94253	TCT		PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
PTPN11	5781	hgsc.bcm.edu	37	12	112926888	112926888	+	Missense_Mutation	SNP	G	G	T	rs397507546		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:112926888G>T	ENST00000351677.2	+	13	1706	c.1508G>T	c.(1507-1509)gGg>gTg	p.G503V		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	507	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.G503A(12)|p.G503V(8)|p.G503E(2)|p.G503L(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						CAGAGGTCAGGGATGGTCCAG	0.468			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																															Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	23	Substitution - Missense(23)	haematopoietic_and_lymphoid_tissue(21)|lung(2)	12	GRCh37	CM086897	PTPN11	M							181.0	169.0	173.0					12																	112926888		2203	4300	6503	111411271	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1508G>T	12.37:g.112926888G>T	ENSP00000340944:p.Gly503Val	Somatic		Capture	Illumina HiSeq	Phase_I	111411271	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172790	0.94807	.	.	ENSG00000179295	ENST00000351677	D	0.99399	-5.83	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97291	0.9924	10	0.66056	D	0.02	.	18.9358	0.92584	0.0:0.0:1.0:0.0	.	503	Q06124-2	.	V	503	ENSP00000340944:G503V	ENSP00000340944:G503V	G	+	2	0	PTPN11	111411271	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.420000	0.97426	2.553000	0.86117	0.650000	0.86243	GGG		PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
P2RX7	5027	hgsc.bcm.edu	37	12	121570848	121570848	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:121570848T>C	ENST00000546057.1	+	1	218	c.75T>C	c.(73-75)aaT>aaC	p.N25N	P2RX7_ENST00000328963.5_5'UTR|P2RX7_ENST00000377162.2_Silent_p.N25N|P2RX7_ENST00000535250.1_5'UTR|P2RX7_ENST00000541446.1_5'UTR|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	25			N -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AGAGCATGAATTATGGCACCA	0.537																																																	0			12											196.0	156.0	170.0					12																	121570848		2203	4300	6503	120055231	SO:0001819	synonymous_variant	5027			Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.75T>C	12.37:g.121570848T>C		Somatic		Capture	Illumina HiSeq	Phase_I	120055231	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Silent	SNP	ENST00000546057.1	37	CCDS9213.1																																																																																				P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32908529	32908529	+	Silent	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:32908529C>T	ENST00000361627.3	+	1	839	c.117C>T	c.(115-117)gcC>gcT	p.A39A	ARHGAP11A_ENST00000567348.1_Silent_p.A39A|ARHGAP11A_ENST00000543522.1_Intron|ARHGAP11A_ENST00000563864.1_Silent_p.A39A|ARHGAP11A_ENST00000565905.1_Intron|RP11-1000B6.5_ENST00000500941.2_lincRNA|AC123768.4_ENST00000576873.1_lincRNA	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	39					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AAACAGCAGCCACGGAAATAG	0.483																																					Colon(45;757 1134 30003 36652)												0			15											50.0	47.0	48.0					15																	32908529		2201	4292	6493	30695821	SO:0001819	synonymous_variant	9824			D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.117C>T	15.37:g.32908529C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30695821	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																				ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42438057	42438057	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:42438057C>T	ENST00000382396.4	-	15	1665	c.1579G>A	c.(1579-1581)Ggg>Agg	p.G527R	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.G529R			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	527	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACATAAGCCCCGTACTTGGGG	0.592																																																	0			15																																								40225349	SO:0001583	missense	255189				CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1579G>A	15.37:g.42438057C>T	ENSP00000371833:p.Gly527Arg	Somatic		Capture	Illumina HiSeq	Phase_I	40225349	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731369	0.69189	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.05717	3.4;3.4	5.52	5.52	0.82312	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.211792	0.33938	N	0.004401	T	0.29882	0.0747	M	0.81614	2.55	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.01925	-1.1246	10	0.87932	D	0	-35.3945	19.4533	0.94876	0.0:1.0:0.0:0.0	.	314;527	A2RRC4;Q68DD2	.;PA24F_HUMAN	R	523;529;527;527	ENSP00000380442:G529R;ENSP00000371833:G527R	ENSP00000290497:G523R	G	-	1	0	PLA2G4F	40225349	1.000000	0.71417	0.898000	0.35279	0.111000	0.19643	6.096000	0.71446	2.604000	0.88044	0.555000	0.69702	GGG		PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
SMAD3	4088	hgsc.bcm.edu	37	15	67473777	67473777	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:67473777C>G	ENST00000327367.4	+	6	1167	c.857C>G	c.(856-858)aCa>aGa	p.T286R	SMAD3_ENST00000439724.3_Missense_Mutation_p.T242R|SMAD3_ENST00000540846.2_Missense_Mutation_p.T181R|SMAD3_ENST00000537194.2_Missense_Mutation_p.T91R	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	286	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.|Sufficient for interaction with XPO4.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GTGGAGCTGACACGGAGACAC	0.627																																																	0			15											54.0	51.0	52.0					15																	67473777		2201	4299	6500	65260831	SO:0001583	missense	4088			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.857C>G	15.37:g.67473777C>G	ENSP00000332973:p.Thr286Arg	Somatic		Capture	Illumina HiSeq	Phase_I	65260831	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429109	0.62844	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47	5.1	5.1	0.69264	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.99690	1.1001	10	0.87932	D	0	.	18.8753	0.92332	0.0:1.0:0.0:0.0	.	242;286	B7Z4Z5;P84022	.;SMAD3_HUMAN	R	286;286;181;242;91	ENSP00000332973:T286R;ENSP00000437757:T181R;ENSP00000401133:T242R;ENSP00000445348:T91R	ENSP00000332973:T286R	T	+	2	0	SMAD3	65260831	1.000000	0.71417	0.648000	0.29521	0.202000	0.24057	7.675000	0.84002	2.515000	0.84797	0.555000	0.69702	ACA		SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	
FEM1B	10116	hgsc.bcm.edu	37	15	68583063	68583063	+	Missense_Mutation	SNP	A	A	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:68583063A>C	ENST00000306917.4	+	2	1982	c.1367A>C	c.(1366-1368)aAa>aCa	p.K456T		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	456					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						ATCTCTACCAAAACACAGTGC	0.388																																																	0			15											128.0	118.0	122.0					15																	68583063		2200	4298	6498	66370117	SO:0001583	missense	10116				CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"""Ankyrin repeat domain containing"""	3649	protein-coding gene	gene with protein product		613539	"""FEM-1 (C. elegans) homolog b"""			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1367A>C	15.37:g.68583063A>C	ENSP00000307298:p.Lys456Thr	Somatic		Capture	Illumina HiSeq	Phase_I	66370117	O43146	Missense_Mutation	SNP	ENST00000306917.4	37	CCDS10228.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670629	0.29693	.	.	ENSG00000169018	ENST00000306917	T	0.47869	0.83	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.61426	0.2346	M	0.64404	1.975	0.80722	D	1	D	0.67145	0.996	P	0.58970	0.849	T	0.58842	-0.7565	10	0.32370	T	0.25	2.3198	15.5864	0.76485	1.0:0.0:0.0:0.0	.	456	Q9UK73	FEM1B_HUMAN	T	456	ENSP00000307298:K456T	ENSP00000307298:K456T	K	+	2	0	FEM1B	66370117	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.268000	0.95675	2.279000	0.76181	0.402000	0.26972	AAA		FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1		
HCN4	10021	hgsc.bcm.edu	37	15	73617474	73617474	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:73617474G>T	ENST00000261917.3	-	6	2793	c.1800C>A	c.(1798-1800)gaC>gaA	p.D600E		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	600					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		CGAAGTTGGGGTCCGCATTGG	0.562																																																	0			15											141.0	124.0	129.0					15																	73617474		2198	4297	6495	71404527	SO:0001583	missense	10021			AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1800C>A	15.37:g.73617474G>T	ENSP00000261917:p.Asp600Glu	Somatic		Capture	Illumina HiSeq	Phase_I	71404527	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534257	0.45073	.	.	ENSG00000138622	ENST00000261917	D	0.96940	-4.18	3.65	0.593	0.17478	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	.	.	.	.	D	0.96741	0.8936	M	0.77486	2.375	0.49798	D	0.999825	D	0.57571	0.98	P	0.60236	0.871	D	0.93983	0.7260	9	0.33940	T	0.23	.	9.1471	0.36939	0.3284:0.0:0.6716:0.0	.	600	Q9Y3Q4	HCN4_HUMAN	E	600	ENSP00000261917:D600E	ENSP00000261917:D600E	D	-	3	2	HCN4	71404527	0.998000	0.40836	0.992000	0.48379	0.954000	0.61252	0.419000	0.21247	-0.055000	0.13244	0.561000	0.74099	GAC		HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
ARNT2	9915	hgsc.bcm.edu	37	15	80762677	80762677	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:80762677A>G	ENST00000303329.4	+	4	478	c.313A>G	c.(313-315)Atc>Gtc	p.I105V	ARNT2_ENST00000533983.1_Missense_Mutation_p.I94V|ARNT2_ENST00000531595.3_3'UTR|ARNT2_ENST00000527771.1_Missense_Mutation_p.I94V	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	105	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.I105V(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			CAAGCTCACCATCCTCCGCAT	0.587																																																	1	Substitution - Missense(1)	central_nervous_system(1)	15											98.0	75.0	83.0					15																	80762677		2203	4300	6503	78549732	SO:0001583	missense	9915			AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.313A>G	15.37:g.80762677A>G	ENSP00000307479:p.Ile105Val	Somatic		Capture	Illumina HiSeq	Phase_I	78549732	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492889	0.84962	.	.	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	D	0.98958	-5.27	5.0	5.0	0.66597	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.96445	0.8840	N	0.10782	0.045	0.80722	D	1	P;P	0.41546	0.677;0.754	P;P	0.51415	0.584;0.669	D	0.95502	0.8578	10	0.12103	T	0.63	.	14.8575	0.70351	1.0:0.0:0.0:0.0	.	105;105	Q9HBZ2;Q86TN1	ARNT2_HUMAN;.	V	94;105;105	ENSP00000307479:I105V	ENSP00000307479:I105V	I	+	1	0	ARNT2	78549732	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.697000	0.91307	2.099000	0.63709	0.528000	0.53228	ATC		ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
SLC28A1	9154	hgsc.bcm.edu	37	15	85431000	85431000	+	Missense_Mutation	SNP	C	C	G	rs8187737	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:85431000C>G	ENST00000286749.3	+	2	99	c.9C>G	c.(7-9)aaC>aaG	p.N3K	SLC28A1_ENST00000338602.2_Missense_Mutation_p.N3K|SLC28A1_ENST00000537216.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000537624.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000538177.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000394573.1_Missense_Mutation_p.N3K|SLC28A1_ENST00000537703.1_5'UTR			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	3					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	ACATGGAGAACGACCCCTCGA	0.592																																																	0			15											137.0	115.0	123.0					15																	85431000		2203	4299	6502	83232004	SO:0001583	missense	9154			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.9C>G	15.37:g.85431000C>G	ENSP00000286749:p.Asn3Lys	Somatic		Capture	Illumina HiSeq	Phase_I	83232004	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358397	0.24598	.	.	ENSG00000156222	ENST00000338602;ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T;T;T	0.12361	2.69;4.56;4.31;4.74;4.75;4.75	4.21	-1.74	0.08056	.	1.284090	0.05783	N	0.609075	T	0.05823	0.0152	N	0.22421	0.69	0.21878	N	0.999492	B;B;B;B;P	0.38978	0.057;0.002;0.11;0.033;0.652	B;B;B;B;B	0.29353	0.019;0.004;0.032;0.019;0.101	T	0.29058	-1.0024	10	0.22109	T	0.4	-10.9961	0.632	0.00796	0.3904:0.2592:0.1411:0.2093	.	3;3;3;3;3	B7Z533;F5H560;B7Z3L6;O00337;O00337-2	.;.;.;S28A1_HUMAN;.	K	3	ENSP00000341629:N3K;ENSP00000440546:N3K;ENSP00000443752:N3K;ENSP00000444700:N3K;ENSP00000286749:N3K;ENSP00000378074:N3K	ENSP00000286749:N3K	N	+	3	2	SLC28A1	83232004	0.002000	0.14202	0.029000	0.17559	0.079000	0.17450	-0.482000	0.06544	-0.127000	0.11661	0.563000	0.77884	AAC		SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
ACAN	176	hgsc.bcm.edu	37	15	89381985	89381985	+	Silent	SNP	C	C	T	rs377037099	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr15:89381985C>T	ENST00000561243.1	+	2	162	c.162C>T	c.(160-162)atC>atT	p.I54I	ACAN_ENST00000352105.7_Silent_p.I54I|ACAN_ENST00000439576.2_Silent_p.I54I|ACAN_ENST00000558207.1_Silent_p.I54I|ACAN_ENST00000559004.1_Silent_p.I54I			P16112	PGCA_HUMAN	aggrecan	54	G1-A.|Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCTATTTCATCGACCCCATGC	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		17737	0.002		0.0	False		,,,				2504	0.0																0			15						C	,	1,4013		0,1,2006	100.0	111.0	108.0		162,162	2.2	1.0	15		108	0,8312		0,0,4156	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	0,1,6162	TT,TC,CC		0.0,0.0249,0.0081	,	54/2432,54/2531	89381985	1,12325	2007	4156	6163	87182989	SO:0001819	synonymous_variant	176			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.162C>T	15.37:g.89381985C>T		Somatic		Capture	Illumina HiSeq	Phase_I	87182989	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																				ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
ZNF645	158506	hgsc.bcm.edu	37	X	22292291	22292291	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:22292291C>T	ENST00000323684.1	+	1	1227	c.1183C>T	c.(1183-1185)Cga>Tga	p.R395*		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	395					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						TGCATGGAAACGACTGTCACC	0.463																																																	0			X											138.0	103.0	115.0					X																	22292291		2203	4300	6503	22202212	SO:0001587	stop_gained	158506			AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.1183C>T	X.37:g.22292291C>T	ENSP00000323348:p.Arg395*	Somatic		Capture	Illumina HiSeq	Phase_I	22202212	A0AV29|A0AV31|E3SBK4|Q6DJY9	Nonsense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.632824	0.47049	.	.	ENSG00000175809	ENST00000323684	.	.	.	3.05	-0.943	0.10395	.	0.275715	0.34531	U	0.003885	.	.	.	.	.	.	0.47476	D	0.999431	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	1.4962	0.02467	0.22:0.1614:0.4528:0.1658	.	.	.	.	X	395	.	ENSP00000323348:R395X	R	+	1	2	ZNF645	22202212	0.998000	0.40836	0.000000	0.03702	0.000000	0.00434	1.600000	0.36762	-0.392000	0.07751	-0.866000	0.03004	CGA		ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
POLA1	5422	hgsc.bcm.edu	37	X	24732734	24732734	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:24732734C>T	ENST00000379059.3	+	5	407	c.392C>T	c.(391-393)cCg>cTg	p.P131L	POLA1_ENST00000379068.3_Missense_Mutation_p.P137L	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	131					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.P131L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GTGACAAAACCGAACAACATT	0.358																																																	1	Substitution - Missense(1)	ovary(1)	X											104.0	93.0	97.0					X																	24732734		2202	4298	6500	24642655	SO:0001583	missense	5422				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.392C>T	X.37:g.24732734C>T	ENSP00000368349:p.Pro131Leu	Somatic		Capture	Illumina HiSeq	Phase_I	24642655	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.391039	0.62066	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.18174	2.23;2.23	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.45115	0.1326	M	0.78637	2.42	0.80722	D	1	P;D	0.89917	0.617;1.0	B;D	0.74023	0.14;0.982	T	0.20240	-1.0281	10	0.34782	T	0.22	-7.8106	19.2516	0.93926	0.0:1.0:0.0:0.0	.	137;131	A6NMQ1;P09884	.;DPOLA_HUMAN	L	137;131	ENSP00000368358:P137L;ENSP00000368349:P131L	ENSP00000368349:P131L	P	+	2	0	POLA1	24642655	1.000000	0.71417	0.997000	0.53966	0.634000	0.38068	6.872000	0.75536	2.498000	0.84270	0.600000	0.82982	CCG		POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
KDM6A	7403	hgsc.bcm.edu	37	X	44929213	44929213	+	Silent	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:44929213T>C	ENST00000377967.4	+	17	2354	c.2313T>C	c.(2311-2313)ggT>ggC	p.G771G	KDM6A_ENST00000382899.4_Silent_p.G778G|KDM6A_ENST00000543216.1_Silent_p.G692G|KDM6A_ENST00000536777.1_Silent_p.G726G	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	771	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AGTCACCAGGTTTACTAAGTT	0.468			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																Colon(129;1273 1667 15230 27352 52914)			Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	X											136.0	101.0	113.0					X																	44929213		2203	4300	6503	44814157	SO:0001819	synonymous_variant	7403			AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.2313T>C	X.37:g.44929213T>C		Somatic		Capture	Illumina HiSeq	Phase_I	44814157	Q52LL9|Q5JVQ7	Silent	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	T	6.037	0.375209	0.11409	.	.	ENSG00000147050	ENST00000414389;ENST00000433797	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	T	0.70360	0.3215	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70008	-0.4990	4	.	.	.	-0.1176	14.2214	0.65830	0.0:0.0:0.0:1.0	.	.	.	.	L	369;414	.	.	F	+	1	0	KDM6A	44814157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.549000	0.60726	1.805000	0.52779	0.486000	0.48141	TTT		KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
CCNB3	85417	hgsc.bcm.edu	37	X	50053208	50053208	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:50053208T>C	ENST00000376042.1	+	6	2337	c.2039T>C	c.(2038-2040)gTt>gCt	p.V680A	CCNB3_ENST00000276014.7_Missense_Mutation_p.V680A|CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron			Q8WWL7	CCNB3_HUMAN	cyclin B3	680					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TCATTGCATGTTAAGCATACC	0.468																																																	0			X											35.0	29.0	31.0					X																	50053208		2203	4300	6503	50069948	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2039T>C	X.37:g.50053208T>C	ENSP00000365210:p.Val680Ala	Somatic		Capture	Illumina HiSeq	Phase_I	50069948	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953633	0.34471	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.37058	1.22;1.22	4.19	-1.46	0.08800	.	.	.	.	.	T	0.16514	0.0397	N	0.16478	0.41	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.24225	-1.0166	8	.	.	.	.	2.7077	0.05166	0.4249:0.2538:0.0:0.3213	.	680	Q8WWL7	CCNB3_HUMAN	A	680	ENSP00000365210:V680A;ENSP00000276014:V680A	.	V	+	2	0	CCNB3	50069948	0.000000	0.05858	0.000000	0.03702	0.545000	0.35147	-0.905000	0.04075	-0.374000	0.07967	0.486000	0.48141	GTT		CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
OPHN1	4983	hgsc.bcm.edu	37	X	67283810	67283810	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:67283810T>C	ENST00000355520.5	-	21	2685	c.2044A>G	c.(2044-2046)Acc>Gcc	p.T682A	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Intron	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	682	Pro-rich.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						GTGATCTTGGTCCCTCCATCC	0.612																																																	0			X											78.0	59.0	66.0					X																	67283810		2203	4300	6503	67200535	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"""Rho GTPase activating proteins"""	8148	protein-coding gene	gene with protein product		300127	"""mental retardation, X-linked 60"""	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.2044A>G	X.37:g.67283810T>C	ENSP00000347710:p.Thr682Ala	Somatic		Capture	Illumina HiSeq	Phase_I	67200535	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	T	1.656	-0.512610	0.04200	.	.	ENSG00000079482	ENST00000355520	T	0.43294	0.95	4.9	2.48	0.30137	.	0.909070	0.09418	N	0.804851	T	0.18964	0.0455	N	0.08118	0	0.54753	D	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	10	0.12766	T	0.61	.	3.8876	0.09105	0.0:0.1187:0.2398:0.6415	.	682	O60890	OPHN1_HUMAN	A	682	ENSP00000347710:T682A	ENSP00000347710:T682A	T	-	1	0	OPHN1	67200535	0.994000	0.37717	0.856000	0.33681	0.348000	0.29142	0.755000	0.26405	0.705000	0.31890	-0.472000	0.04984	ACC		OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547	
ZDHHC15	158866	hgsc.bcm.edu	37	X	74698819	74698819	+	Splice_Site	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chrX:74698819A>G	ENST00000373367.3	-	3	395	c.165T>C	c.(163-165)gtT>gtC	p.V55V	ZDHHC15_ENST00000541184.1_Splice_Site_p.V46V|ZDHHC15_ENST00000373361.3_Splice_Site_p.V55V	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	55					establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						TGAGGTAAATAACTGAAATAA	0.323																																																	0			X											49.0	42.0	44.0					X																	74698819		2203	4300	6503	74615544	SO:0001630	splice_region_variant	158866			AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383		"""Zinc fingers, DHHC-type"""	20342	protein-coding gene	gene with protein product		300576					Standard	NM_144969		Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.164-1T>C	X.37:g.74698819A>G		Somatic		Capture	Illumina HiSeq	Phase_I	74615544	B3KVG7|Q3SY30|Q6UWH3	Silent	SNP	ENST00000373367.3	37	CCDS14430.1																																																																																				ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057283.1	NM_144969	Silent
EVC2	132884	hgsc.bcm.edu	37	4	5664855	5664855	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:5664855C>G	ENST00000344408.5	-	9	1177	c.1124G>C	c.(1123-1125)aGc>aCc	p.S375T	EVC2_ENST00000344938.1_Missense_Mutation_p.S375T|EVC2_ENST00000310917.2_Missense_Mutation_p.S295T	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	375					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TTGAAGCATGCTCCCAGGGTC	0.448																																																	0			4											117.0	110.0	113.0					4																	5664855		2203	4300	6503	5715756	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1124G>C	4.37:g.5664855C>G	ENSP00000342144:p.Ser375Thr	Somatic		Capture	Illumina HiSeq	Phase_I	5715756	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	14.51	2.555583	0.45487	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.77877	-1.13;-1.13;-1.13	5.07	3.31	0.37934	.	0.276138	0.30890	N	0.008670	T	0.80502	0.4635	M	0.65975	2.015	0.25250	N	0.989681	D	0.57571	0.98	P	0.55713	0.782	T	0.71427	-0.4596	10	0.59425	D	0.04	-8.5276	7.0728	0.25187	0.0:0.7964:0.0:0.2035	.	375	Q86UK5	LBN_HUMAN	T	375;295;375	ENSP00000339954:S375T;ENSP00000311683:S295T;ENSP00000342144:S375T	ENSP00000311683:S295T	S	-	2	0	EVC2	5715756	0.570000	0.26651	0.997000	0.53966	0.367000	0.29736	0.414000	0.21164	1.247000	0.43917	0.655000	0.94253	AGC		EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
PROM1	8842	hgsc.bcm.edu	37	4	15985929	15985929	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:15985929G>T	ENST00000510224.1	-	23	2578	c.2330C>A	c.(2329-2331)aCt>aAt	p.T777N	PROM1_ENST00000447510.2_Missense_Mutation_p.T777N|PROM1_ENST00000540805.1_Missense_Mutation_p.T777N|PROM1_ENST00000539194.1_Missense_Mutation_p.T777N|PROM1_ENST00000543373.1_Missense_Mutation_p.T768N|PROM1_ENST00000508167.1_Missense_Mutation_p.T768N|PROM1_ENST00000505450.1_Missense_Mutation_p.T768N			O43490	PROM1_HUMAN	prominin 1	777					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ATCAACAGCAGTATCTAGAGC	0.438																																																	0			4											82.0	81.0	81.0					4																	15985929		1938	4138	6076	15595027	SO:0001583	missense	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.2330C>A	4.37:g.15985929G>T	ENSP00000426809:p.Thr777Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15595027	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.326084|4.326084	0.81580|0.81580	.|.	.|.	ENSG00000007062|ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373|ENST00000513946	T;T;T;T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.156381|.	0.53938|.	D|.	0.000058|.	T|.	0.54334|.	0.1852|.	N|N	0.17474|0.17474	0.49|0.49	0.41425|0.41425	D|D	0.987821|0.987821	D;D;D;D;P;P|.	0.54964|.	0.969;0.969;0.969;0.969;0.628;0.949|.	P;P;P;P;B;P|.	0.58780|.	0.845;0.845;0.813;0.845;0.184;0.845|.	T|.	0.47736|.	-0.9094|.	9|.	.|.	.|.	.|.	-2.4275|-2.4275	20.2985|20.2985	0.98592|0.98592	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	768;777;768;777;768;777|.	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490|.	.;.;.;.;.;PROM1_HUMAN|.	N|X	777;777;777;768;768;777;768|27	ENSP00000415481:T777N;ENSP00000438045:T777N;ENSP00000443620:T777N;ENSP00000426090:T768N;ENSP00000427346:T768N;ENSP00000426809:T777N;ENSP00000445526:T768N|.	.|.	T|Y	-|-	2|3	0|2	PROM1|PROM1	15595027|15595027	1.000000|1.000000	0.71417|0.71417	0.137000|0.137000	0.22149|0.22149	0.045000|0.045000	0.14185|0.14185	6.141000|6.141000	0.71744|0.71744	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	ACT|TAC		PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
KIT	3815	hgsc.bcm.edu	37	4	55592166	55592166	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:55592166T>C	ENST00000288135.5	+	9	1587	c.1490T>C	c.(1489-1491)gTg>gCg	p.V497A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	497	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E490_F504>DHIVVSLTF(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACAACGATGTGGGCAAGACT	0.398		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	1	Complex - deletion inframe(1)	soft_tissue(1)	4											132.0	118.0	123.0					4																	55592166		2203	4300	6503	55286923	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1490T>C	4.37:g.55592166T>C	ENSP00000288135:p.Val497Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55286923	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	12.42	1.931574	0.34096	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	T;T	0.76839	-1.05;2.5	6.02	4.81	0.61882	Immunoglobulin-like fold (1);	0.111084	0.39759	N	0.001269	T	0.75583	0.3869	M	0.77406	2.37	0.44603	D	0.997579	B;B	0.10296	0.002;0.003	B;B	0.14023	0.01;0.007	T	0.71603	-0.4543	10	0.51188	T	0.08	.	7.909	0.29778	0.0:0.0728:0.1468:0.7804	.	497;497	P10721-2;P10721	.;KIT_HUMAN	A	497	ENSP00000288135:V497A;ENSP00000390987:V497A	ENSP00000288135:V497A	V	+	2	0	KIT	55286923	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.073000	0.50057	1.069000	0.40788	0.533000	0.62120	GTG		KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
KIT	3815	hgsc.bcm.edu	37	4	55593994	55593994	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:55593994A>G	ENST00000288135.5	+	12	1877	c.1780A>G	c.(1780-1782)Acc>Gcc	p.T594A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACAGGGAAAACCCTGGGTGC	0.458		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	0			4											68.0	61.0	64.0					4																	55593994		2203	4300	6503	55288751	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1780A>G	4.37:g.55593994A>G	ENSP00000288135:p.Thr594Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55288751	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610837	0.66558	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.89196	-2.48;-2.48	6.04	4.85	0.62838	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000007	D	0.87458	0.6182	N	0.25201	0.72	0.58432	D	0.999999	B;D;D	0.55800	0.246;0.973;0.961	B;P;P	0.54499	0.27;0.754;0.658	D	0.88026	0.2772	10	0.59425	D	0.04	.	13.5393	0.61664	0.8699:0.1301:0.0:0.0	.	101;590;594	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	A	594;590	ENSP00000288135:T594A;ENSP00000390987:T590A	ENSP00000288135:T594A	T	+	1	0	KIT	55288751	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	9.248000	0.95456	1.092000	0.41356	0.460000	0.39030	ACC		KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
BMP2K	55589	hgsc.bcm.edu	37	4	79786721	79786721	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:79786721A>G	ENST00000335016.5	+	10	1244	c.1078A>G	c.(1078-1080)Acc>Gcc	p.T360A	BMP2K_ENST00000502871.1_Missense_Mutation_p.T360A	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	360					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AATAACAGATACCATTGGACC	0.368																																																	0			4											98.0	91.0	93.0					4																	79786721		2203	4300	6503	80005745	SO:0001583	missense	55589			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1078A>G	4.37:g.79786721A>G	ENSP00000334836:p.Thr360Ala	Somatic		Capture	Illumina HiSeq	Phase_I	80005745	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.41|11.41	1.630669|1.630669	0.28978|0.28978	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502871;ENST00000335016;ENST00000264889|ENST00000502613	T;T|.	0.71698|.	1.92;-0.59|.	5.26|5.26	2.76|2.76	0.32466|0.32466	Protein kinase-like domain (1);|.	0.378699|.	0.27437|.	N|.	0.019370|.	T|T	0.31949|0.31949	0.0813|0.0813	L|L	0.44542|0.44542	1.39|1.39	0.30104|0.30104	N|N	0.807177|0.807177	B;B|.	0.28998|.	0.112;0.23|.	B;B|.	0.27076|.	0.076;0.05|.	T|T	0.33954|0.33954	-0.9848|-0.9848	10|5	0.51188|.	T|.	0.08|.	-12.5546|-12.5546	0.3559|0.3559	0.00356|0.00356	0.4006:0.1333:0.2091:0.2569|0.4006:0.1333:0.2091:0.2569	.|.	360;360|.	Q9NSY1;Q4W5H2|.	BMP2K_HUMAN;.|.	A|C	360;360;374|52	ENSP00000421768:T360A;ENSP00000334836:T360A|.	ENSP00000264889:T374A|.	T|Y	+|+	1|2	0|0	BMP2K|BMP2K	80005745|80005745	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	0.468000|0.468000	0.22051|0.22051	0.378000|0.378000	0.24764|0.24764	-0.290000|-0.290000	0.09829|0.09829	ACC|TAC		BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
HERC3	8916	hgsc.bcm.edu	37	4	89591099	89591099	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:89591099A>G	ENST00000402738.1	+	15	1961	c.1722A>G	c.(1720-1722)agA>agG	p.R574R	HERC3_ENST00000543130.1_Silent_p.R18R|HERC3_ENST00000264345.3_Silent_p.R574R	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	574					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TGAGGGGAAGAAAGACATTCT	0.403																																																	0			4											115.0	116.0	116.0					4																	89591099		2203	4300	6503	89810122	SO:0001819	synonymous_variant	8916			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1722A>G	4.37:g.89591099A>G		Somatic		Capture	Illumina HiSeq	Phase_I	89810122	A8K1S5|Q8IXX3	Silent	SNP	ENST00000402738.1	37	CCDS34028.1																																																																																				HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
MTTP	4547	hgsc.bcm.edu	37	4	100543934	100543934	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:100543934C>A	ENST00000265517.5	+	18	2817	c.2614C>A	c.(2614-2616)Caa>Aaa	p.Q872K	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000511045.1_Missense_Mutation_p.Q899K|MTTP_ENST00000457717.1_Missense_Mutation_p.Q872K			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	872					cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	CCCGCTCCATCAAGAGAACTC	0.433																																																	0			4											161.0	159.0	160.0					4																	100543934		2203	4300	6503	100762957	SO:0001583	missense	4571				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.2614C>A	4.37:g.100543934C>A	ENSP00000265517:p.Gln872Lys	Somatic		Capture	Illumina HiSeq	Phase_I	100762957	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222799	0.95139	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.65364	-0.15;-0.13;-0.13	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.79868	0.4520	M	0.71581	2.175	0.80722	D	1	D;D	0.69078	0.995;0.997	P;D	0.73380	0.777;0.98	T	0.78414	-0.2213	10	0.56958	D	0.05	-19.5906	20.4702	0.99162	0.0:1.0:0.0:0.0	.	899;872	E9PBP6;P55157	.;MTP_HUMAN	K	899;872;872	ENSP00000427679:Q899K;ENSP00000400821:Q872K;ENSP00000265517:Q872K	ENSP00000265517:Q872K	Q	+	1	0	MTTP	100762957	1.000000	0.71417	0.999000	0.59377	0.856000	0.48823	7.142000	0.77339	2.937000	0.99478	0.650000	0.86243	CAA		MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
ELOVL6	79071	hgsc.bcm.edu	37	4	110980783	110980783	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:110980783C>G	ENST00000394607.3	-	4	512	c.349G>C	c.(349-351)Gtg>Ctg	p.V117L	ELOVL6_ENST00000506461.1_5'Flank|ELOVL6_ENST00000302274.3_Missense_Mutation_p.V117L			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	117					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		TTGCTTAGCACAAATGCATAA	0.408																																																	0			4											92.0	80.0	84.0					4																	110980783		2203	4300	6503	111200232	SO:0001583	missense	79071			AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"""ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"""			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.349G>C	4.37:g.110980783C>G	ENSP00000378105:p.Val117Leu	Somatic		Capture	Illumina HiSeq	Phase_I	111200232	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	37	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519622	0.85495	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625	T;T;T	0.22945	1.93;1.93;1.93	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	L	0.28400	0.85	0.80722	D	1	B	0.20988	0.05	B	0.28011	0.085	T	0.04128	-1.0975	10	0.23302	T	0.38	-5.5054	19.8016	0.96509	0.0:1.0:0.0:0.0	.	117	Q9H5J4	ELOV6_HUMAN	L	117	ENSP00000378105:V117L;ENSP00000304736:V117L;ENSP00000425488:V117L	ENSP00000304736:V117L	V	-	1	0	ELOVL6	111200232	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.718000	0.84743	2.770000	0.95276	0.655000	0.94253	GTG		ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090	
TDO2	6999	hgsc.bcm.edu	37	4	156831349	156831349	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:156831349C>A	ENST00000536354.2	+	6	668	c.604C>A	c.(604-606)Ctg>Atg	p.L202M		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		AAAGACACTTCTGGAATTAGT	0.308																																					Colon(57;928 1036 2595 6946 26094)												0			4											55.0	59.0	57.0					4																	156831349		2202	4299	6501	157050799	SO:0001583	missense	6999				CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.604C>A	4.37:g.156831349C>A	ENSP00000444788:p.Leu202Met	Somatic		Capture	Illumina HiSeq	Phase_I	157050799		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.528840	0.44969	.	.	ENSG00000151790	ENST00000536354	.	.	.	4.92	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.74230	0.3689	M	0.85710	2.77	0.80722	D	1	P	0.44006	0.824	P	0.51866	0.682	T	0.76537	-0.2923	9	0.46703	T	0.11	-14.8693	12.6982	0.57016	0.0:0.9177:0.0:0.0823	.	202	P48775	T23O_HUMAN	M	202	.	ENSP00000281525:L202M	L	+	1	2	TDO2	157050799	0.984000	0.35163	0.799000	0.32177	0.126000	0.20510	2.684000	0.46951	1.175000	0.42826	0.644000	0.83932	CTG		TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656131	167656131	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:167656131C>T	ENST00000357154.3	-	12	1389	c.1252G>A	c.(1252-1254)Gat>Aat	p.D418N	SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000506886.1_Missense_Mutation_p.D418N|SPOCK3_ENST00000510741.1_Missense_Mutation_p.D375N|SPOCK3_ENST00000502330.1_Missense_Mutation_p.D418N|SPOCK3_ENST00000541637.1_Missense_Mutation_p.D320N|SPOCK3_ENST00000534949.1_Missense_Mutation_p.D322N|SPOCK3_ENST00000511269.1_Missense_Mutation_p.D415N|SPOCK3_ENST00000421836.2_Missense_Mutation_p.D367N|SPOCK3_ENST00000535728.1_Missense_Mutation_p.D286N|SPOCK3_ENST00000504953.1_Missense_Mutation_p.D415N|SPOCK3_ENST00000512681.1_Missense_Mutation_p.D320N|SPOCK3_ENST00000511531.1_Missense_Mutation_p.D418N|SPOCK3_ENST00000357545.4_Missense_Mutation_p.D415N|SPOCK3_ENST00000541354.1_Missense_Mutation_p.D298N	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	418	Asp-rich.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		tcttcatcatcatcttcaatt	0.348																																																	0			4											180.0	172.0	174.0					4																	167656131		2203	4299	6502	167892706	SO:0001583	missense	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1252G>A	4.37:g.167656131C>T	ENSP00000349677:p.Asp418Asn	Somatic		Capture	Illumina HiSeq	Phase_I	167892706	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	C	7.525	0.657401	0.14645	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.14	5.14	0.70334	.	0.141330	0.44902	U	0.000408	D	0.82926	0.5143	L	0.32530	0.975	0.52501	D	0.999954	D;D;D;D;D;D;D	0.89917	0.993;0.996;1.0;1.0;1.0;0.996;0.993	D;D;D;D;D;D;D	0.80764	0.984;0.993;0.994;0.994;0.994;0.993;0.984	T	0.83062	-0.0147	10	0.45353	T	0.12	-22.9046	18.5789	0.91164	0.0:1.0:0.0:0.0	.	320;322;367;427;375;415;418	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	N	418;415;415;418;418;418;375;298;320;415;286;367;320;322	ENSP00000349677:D418N;ENSP00000350153:D415N;ENSP00000425570:D415N;ENSP00000420920:D418N;ENSP00000423421:D418N;ENSP00000423606:D418N;ENSP00000426716:D375N;ENSP00000444789:D298N;ENSP00000426318:D320N;ENSP00000425502:D415N;ENSP00000441396:D286N;ENSP00000411344:D367N;ENSP00000445430:D320N;ENSP00000438142:D322N	ENSP00000349677:D418N	D	-	1	0	SPOCK3	167892706	1.000000	0.71417	0.990000	0.47175	0.063000	0.16089	5.206000	0.65192	2.552000	0.86080	0.637000	0.83480	GAT		SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		
ALLC	55821	hgsc.bcm.edu	37	2	3750040	3750040	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:3750040G>A	ENST00000252505.3	+	12	1225	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N	AC010907.5_ENST00000441632.1_RNA	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	374					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		CATCGTCCCCGACGGGGGAGT	0.592										HNSCC(21;0.051)																																							0			2											30.0	33.0	32.0					2																	3750040		1922	4120	6042	3727915	SO:0001583	missense	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.1063G>A	2.37:g.3750040G>A	ENSP00000252505:p.Asp355Asn	Somatic		Capture	Illumina HiSeq	Phase_I	3727915	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162708	0.78226	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.04	5.04	0.67666	Allantoicase domain (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.87233	0.6126	H	0.96015	3.755	0.50039	D	0.999845	D	0.89917	1.0	D	0.74348	0.983	D	0.91263	0.5038	9	0.87932	D	0	-6.7836	16.2404	0.82405	0.0:0.0:1.0:0.0	.	374	Q8N6M5	ALLC_HUMAN	N	355	.	ENSP00000252505:D355N	D	+	1	0	ALLC	3727915	1.000000	0.71417	0.373000	0.26003	0.561000	0.35649	6.194000	0.72082	2.494000	0.84150	0.591000	0.81541	GAC		ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
NBAS	51594	hgsc.bcm.edu	37	2	15608582	15608582	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:15608582C>G	ENST00000281513.5	-	17	1826	c.1801G>C	c.(1801-1803)Gaa>Caa	p.E601Q	NBAS_ENST00000441750.1_Missense_Mutation_p.E601Q	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	601					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TGAAGCAGTTCTTTTGCAGCA	0.418																																																	0			2											133.0	131.0	131.0					2																	15608582		2203	4300	6503	15526033	SO:0001583	missense	51594			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1801G>C	2.37:g.15608582C>G	ENSP00000281513:p.Glu601Gln	Somatic		Capture	Illumina HiSeq	Phase_I	15526033	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.338150	0.60963	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.12465	2.68;2.83	5.93	5.05	0.67936	.	0.050150	0.85682	D	0.000000	T	0.25269	0.0614	M	0.70275	2.135	0.27979	N	0.936114	D	0.59767	0.986	P	0.50659	0.647	T	0.15009	-1.0452	10	0.87932	D	0	.	11.6926	0.51525	0.0:0.8482:0.0:0.1518	.	601	A2RRP1	NBAS_HUMAN	Q	601	ENSP00000413201:E601Q;ENSP00000281513:E601Q	ENSP00000281513:E601Q	E	-	1	0	NBAS	15526033	1.000000	0.71417	0.898000	0.35279	0.986000	0.74619	4.989000	0.63870	1.515000	0.48885	0.650000	0.86243	GAA		NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863099	30863099	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:30863099C>T	ENST00000309052.4	+	7	1068	c.859C>T	c.(859-861)Cgg>Tgg	p.R287W	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000540623.1_Missense_Mutation_p.R249W|LCLAT1_ENST00000379509.3_Missense_Mutation_p.R249W	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	287					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R287W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCACGTCCACCGGTATCCAAT	0.507																																																	1	Substitution - Missense(1)	ovary(1)	2											96.0	92.0	93.0					2																	30863099		2203	4300	6503	30716603	SO:0001583	missense	253558			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.859C>T	2.37:g.30863099C>T	ENSP00000310551:p.Arg287Trp	Somatic		Capture	Illumina HiSeq	Phase_I	30716603	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192263	0.38707	.	.	ENSG00000172954	ENST00000379509;ENST00000444270;ENST00000309052;ENST00000540623	T;T;T	0.41758	0.99;0.99;0.99	5.77	2.63	0.31362	.	0.098864	0.64402	D	0.000002	T	0.68430	0.3000	M	0.88241	2.94	0.53688	D	0.999974	D	0.89917	1.0	D	0.85130	0.997	T	0.76187	-0.3051	10	0.72032	D	0.01	-18.7519	14.6333	0.68671	0.5279:0.4721:0.0:0.0	.	287	Q6UWP7	LCLT1_HUMAN	W	249;249;287;249	ENSP00000368823:R249W;ENSP00000310551:R287W;ENSP00000442857:R249W	ENSP00000310551:R287W	R	+	1	2	LCLAT1	30716603	0.803000	0.28956	0.233000	0.24025	0.059000	0.15707	1.579000	0.36536	0.750000	0.32877	0.557000	0.71058	CGG		LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	
ANTXR1	84168	hgsc.bcm.edu	37	2	69297841	69297841	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:69297841T>C	ENST00000303714.4	+	4	681	c.359T>C	c.(358-360)aTg>aCg	p.M120T	ANTXR1_ENST00000409829.3_Missense_Mutation_p.M120T|ANTXR1_ENST00000409349.3_Missense_Mutation_p.M120T	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	120	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						GACACTTACATGCATGAAGGA	0.373									Familial Infantile Hemangioma																																								0			2											78.0	78.0	78.0					2																	69297841		2203	4300	6503	69151345	SO:0001583	missense	84168	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"""anthrax toxin receptor"", ""tumor endothelial marker 8 precursor"""	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.359T>C	2.37:g.69297841T>C	ENSP00000301945:p.Met120Thr	Somatic		Capture	Illumina HiSeq	Phase_I	69151345	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Missense_Mutation	SNP	ENST00000303714.4	37	CCDS1892.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.168585	0.57584	.	.	ENSG00000169604	ENST00000303714;ENST00000409829;ENST00000409349	T;T;T	0.78816	-1.21;-1.21;-1.21	6.03	4.86	0.63082	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.83575	0.5284	L	0.51853	1.615	0.49687	D	0.999813	D;P;P;D	0.89917	1.0;0.931;0.953;1.0	D;P;P;D	0.87578	0.99;0.743;0.831;0.998	T	0.82561	-0.0396	10	0.44086	T	0.13	-25.7359	11.7363	0.51767	0.0:0.0:0.1477:0.8523	.	120;120;120;120	Q9H6X2;Q9H6X2-2;Q9H6X2-4;Q9H6X2-3	ANTR1_HUMAN;.;.;.	T	120	ENSP00000301945:M120T;ENSP00000387058:M120T;ENSP00000386494:M120T	ENSP00000301945:M120T	M	+	2	0	ANTXR1	69151345	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.719000	0.74718	1.081000	0.41110	0.533000	0.62120	ATG		ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208	
TMEM131	23505	hgsc.bcm.edu	37	2	98409024	98409024	+	Silent	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:98409024G>A	ENST00000186436.5	-	31	4197	c.3969C>T	c.(3967-3969)ccC>ccT	p.P1323P		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1323	Pro-rich.					integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CGAGGGGGGCGGGAGACAGCC	0.662																																																	0			2											23.0	26.0	25.0					2																	98409024		2090	4210	6300	97775456	SO:0001819	synonymous_variant	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.3969C>T	2.37:g.98409024G>A		Somatic		Capture	Illumina HiSeq	Phase_I	97775456		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																				TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
UXS1	80146	hgsc.bcm.edu	37	2	106713247	106713247	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:106713247T>C	ENST00000409501.3	-	14	1115	c.1058A>G	c.(1057-1059)gAa>gGa	p.E353G	UXS1_ENST00000283148.7_Missense_Mutation_p.E358G|UXS1_ENST00000540130.1_Missense_Mutation_p.E296G|UXS1_ENST00000409032.1_Missense_Mutation_p.E185G			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	353					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						ATCCTGGGCTTCGGAGAGAAA	0.463																																																	0			2											107.0	96.0	100.0					2																	106713247		1866	4109	5975	106079679	SO:0001583	missense	80146			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	17729	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 6E, member 12"""	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.1058A>G	2.37:g.106713247T>C	ENSP00000387019:p.Glu353Gly	Somatic		Capture	Illumina HiSeq	Phase_I	106079679	Q8NBX3|Q9H5C2	Missense_Mutation	SNP	ENST00000409501.3	37	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976254	0.53720	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.46444	0.1393	L	0.42632	1.34	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.32613	-0.9900	10	0.27785	T	0.31	-9.4366	15.8945	0.79325	0.0:0.0:0.0:1.0	.	358;353;358	Q8NBZ7-2;Q8NBZ7;A8K3Q3	.;UXS1_HUMAN;.	G	358;296;353;185	ENSP00000283148:E358G;ENSP00000438265:E296G;ENSP00000387019:E353G;ENSP00000387096:E185G	ENSP00000283148:E358G	E	-	2	0	UXS1	106079679	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.632000	0.83247	2.152000	0.67230	0.455000	0.32223	GAA		UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3	
LCT	3938	hgsc.bcm.edu	37	2	136564712	136564712	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:136564712A>G	ENST00000264162.2	-	9	4169	c.4159T>C	c.(4159-4161)Tct>Cct	p.S1387P		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1387	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TATGCAGCAGAAGCTGCACTC	0.572																																																	0			2											128.0	102.0	111.0					2																	136564712		2203	4300	6503	136281182	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4159T>C	2.37:g.136564712A>G	ENSP00000264162:p.Ser1387Pro	Somatic		Capture	Illumina HiSeq	Phase_I	136281182	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.384799	0.61956	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.35605	1.3	5.87	-1.37	0.09056	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.345527	0.33346	N	0.005004	T	0.61223	0.2330	M	0.91612	3.225	0.23076	N	0.998335	D	0.56035	0.974	P	0.61874	0.895	T	0.62186	-0.6907	10	0.62326	D	0.03	-17.9564	14.3548	0.66730	0.3265:0.0:0.0:0.6735	.	1387	P09848	LPH_HUMAN	P	1387;819	ENSP00000264162:S1387P	ENSP00000264162:S1387P	S	-	1	0	LCT	136281182	0.079000	0.21365	0.114000	0.21550	0.965000	0.64279	0.372000	0.20467	-0.470000	0.06901	0.533000	0.62120	TCT		LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
ACVR1	90	hgsc.bcm.edu	37	2	158594089	158594089	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:158594089A>G	ENST00000263640.3	-	11	1913	c.1484T>C	c.(1483-1485)tTg>tCg	p.L495S	ACVR1_ENST00000409283.2_Missense_Mutation_p.L495S|ACVR1_ENST00000410057.2_Missense_Mutation_p.L495S|ACVR1_ENST00000434821.1_Missense_Mutation_p.L495S|AC019186.1_ENST00000447019.1_lincRNA	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	495	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AATTTTGGTCAAAGTCTTTTT	0.403																																																	0			2											141.0	128.0	133.0					2																	158594089		2203	4300	6503	158302335	SO:0001583	missense	90				CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.1484T>C	2.37:g.158594089A>G	ENSP00000263640:p.Leu495Ser	Somatic		Capture	Illumina HiSeq	Phase_I	158302335		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.852255	0.71719	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	6.16	6.16	0.99307	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.060701	0.64402	D	0.000002	D	0.98112	0.9377	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99153	1.0859	10	0.87932	D	0	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	495	Q04771	ACVR1_HUMAN	S	495	ENSP00000263640:L495S;ENSP00000387273:L495S;ENSP00000405004:L495S;ENSP00000387127:L495S	ENSP00000263640:L495S	L	-	2	0	ACVR1	158302335	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TTG		ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
TTN	7273	hgsc.bcm.edu	37	2	179410403	179410403	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:179410403C>T	ENST00000591111.1	-	294	90735	c.90511G>A	c.(90511-90513)Ggc>Agc	p.G30171S	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G22747S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G22872S|TTN_ENST00000589042.1_Missense_Mutation_p.G31812S|TTN_ENST00000342992.6_Missense_Mutation_p.G29244S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G22939S|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30171	Fibronectin type-III 120. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGGTATGCCGGGTGGTGAT	0.418																																																	0			2											156.0	148.0	151.0					2																	179410403		1920	4139	6059	179118649	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.90511G>A	2.37:g.179410403C>T	ENSP00000465570:p.Gly30171Ser	Somatic		Capture	Illumina HiSeq	Phase_I	179118649	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.280670	0.80692	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.82	5.82	0.92795	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.66877	0.2834	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67945	-0.5539	9	0.87932	D	0	.	20.1086	0.97902	0.0:1.0:0.0:0.0	.	22747;22872;22939;30171	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	29244;22747;22939;22872;22744	ENSP00000343764:G29244S;ENSP00000434586:G22747S;ENSP00000340554:G22939S;ENSP00000352154:G22872S	ENSP00000340554:G22939S	G	-	1	0	TTN	179118649	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.818000	0.86416	2.756000	0.94617	0.563000	0.77884	GGC		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179591845	179591845	+	Silent	SNP	T	T	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:179591845T>A	ENST00000591111.1	-	67	19520	c.19296A>T	c.(19294-19296)acA>acT	p.T6432T	TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Silent_p.T6749T|TTN_ENST00000342992.6_Silent_p.T5505T|RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	13199	Ig-like 45.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACTGCAGCTTGTGCTGCCAG	0.423																																																	0			2											120.0	117.0	118.0					2																	179591845		1902	4119	6021	179300090	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19296A>T	2.37:g.179591845T>A		Somatic		Capture	Illumina HiSeq	Phase_I	179300090	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MSTN	2660	hgsc.bcm.edu	37	2	190927004	190927004	+	Missense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:190927004C>G	ENST00000260950.4	-	1	451	c.319G>C	c.(319-321)Gaa>Caa	p.E107Q	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	107					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			TCGTCATCTTCCAAAGAGCCA	0.428																																																	0			2											145.0	131.0	136.0					2																	190927004		2203	4300	6503	190635249	SO:0001583	missense	2660			AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"""growth differentiation factor 8"""	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.319G>C	2.37:g.190927004C>G	ENSP00000260950:p.Glu107Gln	Somatic		Capture	Illumina HiSeq	Phase_I	190635249	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	37	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424863	0.83667	.	.	ENSG00000138379	ENST00000260950	T	0.64991	-0.13	5.35	5.35	0.76521	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79522	0.4460	M	0.75085	2.285	0.80722	D	1	D	0.63880	0.993	D	0.68621	0.959	T	0.80867	-0.1190	10	0.72032	D	0.01	-21.5226	19.2576	0.93952	0.0:1.0:0.0:0.0	.	107	O14793	GDF8_HUMAN	Q	107	ENSP00000260950:E107Q	ENSP00000260950:E107Q	E	-	1	0	MSTN	190635249	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.932000	0.70121	2.789000	0.95967	0.655000	0.94253	GAA		MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259	
ALS2CR11	151254	hgsc.bcm.edu	37	2	202483686	202483686	+	Missense_Mutation	SNP	G	G	C	rs142023452	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:202483686G>C	ENST00000286195.3	-	1	212	c.168C>G	c.(166-168)aaC>aaG	p.N56K	ALS2CR11_ENST00000450242.1_Missense_Mutation_p.N56K|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.N56K|ALS2CR11_ENST00000439140.1_Missense_Mutation_p.N56K	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	56										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TCGTGCCCTGGTTCAGGGCGT	0.637																																																	0			2											60.0	59.0	59.0					2																	202483686		2203	4300	6503	202191931	SO:0001583	missense	151254			AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.168C>G	2.37:g.202483686G>C	ENSP00000286195:p.Asn56Lys	Somatic		Capture	Illumina HiSeq	Phase_I	202191931	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	G	0.526	-0.860182	0.02610	.	.	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.44881	0.92;0.92;0.91;0.91	3.26	-1.04	0.10068	.	4.384240	0.00738	N	0.000993	T	0.18551	0.0445	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.13255	-1.0516	10	0.06365	T	0.9	.	2.3281	0.04228	0.1423:0.4475:0.2619:0.1483	.	56;56;56	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	K	56	ENSP00000286195:N56K;ENSP00000400672:N56K;ENSP00000409937:N56K;ENSP00000399016:N56K	ENSP00000286195:N56K	N	-	3	2	ALS2CR11	202191931	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.057000	0.03486	-0.225000	0.09913	0.557000	0.71058	AAC		ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
TRPM8	79054	hgsc.bcm.edu	37	2	234873393	234873393	+	Missense_Mutation	SNP	G	G	A	rs201008719		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:234873393G>A	ENST00000324695.4	+	14	1911	c.1871G>A	c.(1870-1872)cGg>cAg	p.R624Q	TRPM8_ENST00000433712.2_Missense_Mutation_p.R312Q	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	624					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TACGAGACCCGGGCTGTTGGT	0.582																																																	0			2											79.0	62.0	68.0					2																	234873393		2203	4300	6503	234538132	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1871G>A	2.37:g.234873393G>A	ENSP00000323926:p.Arg624Gln	Somatic		Capture	Illumina HiSeq	Phase_I	234538132	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419346	0.25552	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.62788	-0.0;-0.0	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000004	T	0.54287	0.1849	L	0.58428	1.81	0.33618	D	0.604483	P;B	0.38800	0.648;0.123	B;B	0.23852	0.049;0.008	T	0.66980	-0.5786	10	0.29301	T	0.29	-17.911	17.9113	0.88934	0.0:0.0:1.0:0.0	.	312;624	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	Q	624;312	ENSP00000323926:R624Q;ENSP00000404423:R312Q	ENSP00000323926:R624Q	R	+	2	0	TRPM8	234538132	0.730000	0.28100	0.607000	0.28956	0.039000	0.13416	3.958000	0.56737	2.563000	0.86464	0.655000	0.94253	CGG		TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
IFNK	56832	hgsc.bcm.edu	37	9	27524677	27524677	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:27524677C>A	ENST00000276943.2	+	1	366	c.343C>A	c.(343-345)Caa>Aaa	p.Q115K	MOB3B_ENST00000262244.5_Intron	NM_020124.2	NP_064509.2	Q9P0W0	IFNK_HUMAN	interferon, kappa	115					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of cell proliferation (GO:0008285)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of transcription, DNA-templated (GO:0006355)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(1)	1		all_neural(11;7.9e-11)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.000158)		CAAACAAATCCAAATAGGACT	0.403																																																	0			9											139.0	146.0	143.0					9																	27524677		2203	4300	6503	27514677	SO:0001583	missense	56832			AF384048	CCDS6521.1	9p21.2	2008-02-05			ENSG00000147896	ENSG00000147896		"""Interferons"""	21714	protein-coding gene	gene with protein product		615326				12391192, 11514542	Standard	NM_020124		Approved		uc003zqp.3	Q9P0W0	OTTHUMG00000019715	ENST00000276943.2:c.343C>A	9.37:g.27524677C>A	ENSP00000276943:p.Gln115Lys	Somatic		Capture	Illumina HiSeq	Phase_I	27514677	Q5T166	Missense_Mutation	SNP	ENST00000276943.2	37	CCDS6521.1	.	.	.	.	.	.	.	.	.	.	C	1.305	-0.603909	0.03717	.	.	ENSG00000147896	ENST00000276943	T	0.17054	2.3	6.16	4.24	0.50183	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.503507	0.18947	N	0.126783	T	0.20536	0.0494	M	0.70595	2.14	0.09310	N	1	B	0.30068	0.267	B	0.35039	0.194	T	0.17961	-1.0352	10	0.30078	T	0.28	-16.7209	7.3012	0.26422	0.2098:0.705:0.0:0.0851	.	115	Q9P0W0	IFNK_HUMAN	K	115	ENSP00000276943:Q115K	ENSP00000276943:Q115K	Q	+	1	0	IFNK	27514677	0.011000	0.17503	0.002000	0.10522	0.001000	0.01503	0.464000	0.21988	0.802000	0.34089	-0.142000	0.14014	CAA		IFNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051968.1	NM_020124	
PTCH1	5727	hgsc.bcm.edu	37	9	98212180	98212180	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:98212180A>G	ENST00000331920.6	-	21	3791	c.3492T>C	c.(3490-3492)gtT>gtC	p.V1164V	PTCH1_ENST00000429896.2_Silent_p.V1013V|PTCH1_ENST00000437951.1_Silent_p.V1098V|PTCH1_ENST00000418258.1_Silent_p.V1013V|PTCH1_ENST00000430669.2_Silent_p.V1098V|PTCH1_ENST00000375274.2_Silent_p.V1163V|PTCH1_ENST00000421141.1_Silent_p.V1013V	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1164					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GCCCATTGAGAACGCCGAGGA	0.557																																																	0			9											125.0	107.0	113.0					9																	98212180		2203	4300	6503	97252001	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.3492T>C	9.37:g.98212180A>G		Somatic		Capture	Illumina HiSeq	Phase_I	97252001	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
INVS	27130	hgsc.bcm.edu	37	9	103015295	103015295	+	Silent	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:103015295C>T	ENST00000262457.2	+	10	1526	c.1341C>T	c.(1339-1341)atC>atT	p.I447I	INVS_ENST00000541287.1_Silent_p.I351I|INVS_ENST00000262456.2_Silent_p.I447I	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	447					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.I447M(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				AAAATAAGATCAATCCAAATG	0.428																																																	1	Substitution - Missense(1)	ovary(1)	9											100.0	100.0	100.0					9																	103015295		2203	4300	6503	102055116	SO:0001819	synonymous_variant	27130			AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"""Ankyrin repeat domain containing"""	17870	protein-coding gene	gene with protein product	"""nephrocystin 2"""	243305	"""nephronophthisis 2 (infantile)"""	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.1341C>T	9.37:g.103015295C>T		Somatic		Capture	Illumina HiSeq	Phase_I	102055116	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Silent	SNP	ENST00000262457.2	37	CCDS6746.1																																																																																				INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425	
SPTAN1	6709	hgsc.bcm.edu	37	9	131370209	131370209	+	Missense_Mutation	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:131370209G>A	ENST00000372731.4	+	33	4335	c.4225G>A	c.(4225-4227)Gga>Aga	p.G1409R	SPTAN1_ENST00000372739.3_Missense_Mutation_p.G1409R|SPTAN1_ENST00000358161.5_Missense_Mutation_p.G1409R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1409					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.G1409R(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GTTGGCTCACGGACACTATGC	0.547																																					NSCLC(120;833 1744 2558 35612 37579)												1	Substitution - Missense(1)	large_intestine(1)	9											78.0	74.0	75.0					9																	131370209		2203	4300	6503	130410030	SO:0001583	missense	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4225G>A	9.37:g.131370209G>A	ENSP00000361816:p.Gly1409Arg	Somatic		Capture	Illumina HiSeq	Phase_I	130410030	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145205	0.57044	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.54675	0.56;0.56;0.56	5.54	4.65	0.58169	.	0.048617	0.85682	N	0.000000	T	0.68348	0.2991	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	B;D;D	0.75484	0.411;0.976;0.986	T	0.71702	-0.4513	10	0.66056	D	0.02	.	14.7251	0.69339	0.0699:0.0:0.9301:0.0	.	1389;1409;1409	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	R	1409;1409;1409;1389	ENSP00000350882:G1409R;ENSP00000361816:G1409R;ENSP00000361824:G1409R	ENSP00000350882:G1409R	G	+	1	0	SPTAN1	130410030	1.000000	0.71417	0.996000	0.52242	0.938000	0.57974	6.594000	0.74104	1.488000	0.48433	0.591000	0.81541	GGA		SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
COL5A1	1289	hgsc.bcm.edu	37	9	137591756	137591756	+	Splice_Site	SNP	G	G	A	rs145090868		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:137591756G>A	ENST00000371817.3	+	3	693	c.279G>A	c.(277-279)gcG>gcA	p.A93A	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	93	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CTGTTCCAGCGTCTGCATTTC	0.587													g|||	1	0.000199681	0.0	0.0	5008	,	,		16872	0.001		0.0	False		,,,				2504	0.0																0			9						A		0,4406		0,0,2203	81.0	76.0	78.0		279	-9.6	0.0	9	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		93/1839	137591756	1,13005	2203	4300	6503	136731577	SO:0001630	splice_region_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.278-1G>A	9.37:g.137591756G>A		Somatic		Capture	Illumina HiSeq	Phase_I	136731577	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent
COL5A1	1289	hgsc.bcm.edu	37	9	137727033	137727033	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr9:137727033C>A	ENST00000371817.3	+	65	5767	c.5353C>A	c.(5353-5355)Ctg>Atg	p.L1785M		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1785	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CATCCGCGCCCTGGTGGACGG	0.667																																																	0			9											71.0	61.0	64.0					9																	137727033		2203	4300	6503	136866854	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5353C>A	9.37:g.137727033C>A	ENSP00000360882:p.Leu1785Met	Somatic		Capture	Illumina HiSeq	Phase_I	136866854	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.78|14.78	2.638097|2.638097	0.47153|0.47153	.|.	.|.	ENSG00000130635|ENSG00000130635	ENST00000371817;ENST00000355306|ENST00000371820	T|.	0.75589|.	-0.95|.	5.03|5.03	4.07|4.07	0.47477|0.47477	Fibrillar collagen, C-terminal (4);|.	0.521506|.	0.15238|.	U|.	0.273058|.	T|T	0.65647|0.65647	0.2711|0.2711	M|M	0.89715|0.89715	3.055|3.055	0.28690|0.28690	N|N	0.904647|0.904647	P|.	0.42518|.	0.782|.	P|.	0.51742|.	0.678|.	T|T	0.64262|0.64262	-0.6449|-0.6449	10|5	0.66056|.	D|.	0.02|.	.|.	8.3524|8.3524	0.32310|0.32310	0.1353:0.5862:0.2784:0.0|0.1353:0.5862:0.2784:0.0	.|.	1785|.	P20908|.	CO5A1_HUMAN|.	M|H	1785;322|204	ENSP00000360882:L1785M|.	ENSP00000347458:L322M|.	L|P	+|+	1|2	2|0	COL5A1|COL5A1	136866854|136866854	0.678000|0.678000	0.27586|0.27586	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	0.784000|0.784000	0.26816|0.26816	2.340000|2.340000	0.79590|0.79590	0.561000|0.561000	0.74099|0.74099	CTG|CCT		COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
DCLK1	9201	hgsc.bcm.edu	37	13	36700001	36700001	+	Missense_Mutation	SNP	T	T	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:36700001T>G	ENST00000360631.3	-	2	485	c.274A>C	c.(274-276)Acc>Ccc	p.T92P	DCLK1_ENST00000379892.4_Missense_Mutation_p.T92P|DCLK1_ENST00000255448.4_Missense_Mutation_p.T92P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	92	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		AGAGTTCGGGTCAAATCAGCC	0.498																																																	0			13											105.0	96.0	99.0					13																	36700001		2203	4300	6503	35598001	SO:0001583	missense	9201			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.274A>C	13.37:g.36700001T>G	ENSP00000353846:p.Thr92Pro	Somatic		Capture	Illumina HiSeq	Phase_I	35598001	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	T	26.4	4.732617	0.89482	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	D;D;D	0.96427	-4.01;-4.01;-4.01	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.98611	0.9535	M	0.94021	3.485	0.80722	D	1	D	0.71674	0.998	D	0.85130	0.997	D	0.99727	1.1011	10	0.87932	D	0	.	16.1875	0.81962	0.0:0.0:0.0:1.0	.	92	O15075-2	.	P	92	ENSP00000255448:T92P;ENSP00000353846:T92P;ENSP00000369222:T92P	ENSP00000255448:T92P	T	-	1	0	DCLK1	35598001	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.860000	0.86993	2.225000	0.72522	0.533000	0.62120	ACC		DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
FREM2	341640	hgsc.bcm.edu	37	13	39425853	39425853	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:39425853T>C	ENST00000280481.7	+	11	6989	c.6773T>C	c.(6772-6774)tTt>tCt	p.F2258S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2258	Calx-beta 5.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAAACCAAATTTAGTGTCACT	0.383																																																	0			13											48.0	49.0	49.0					13																	39425853		2203	4300	6503	38323853	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6773T>C	13.37:g.39425853T>C	ENSP00000280481:p.Phe2258Ser	Somatic		Capture	Illumina HiSeq	Phase_I	38323853	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.646110	0.67358	.	.	ENSG00000150893	ENST00000280481	T	0.30981	1.51	5.62	5.62	0.85841	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.48696	0.1514	M	0.67700	2.07	0.50171	D	0.999855	D;D	0.60160	0.987;0.978	P;D	0.63033	0.854;0.91	T	0.51474	-0.8701	10	0.72032	D	0.01	.	9.7721	0.40595	0.2657:0.0:0.0:0.7343	.	2258;2258	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	S	2258	ENSP00000280481:F2258S	ENSP00000280481:F2258S	F	+	2	0	FREM2	38323853	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	1.487000	0.35540	2.141000	0.66446	0.528000	0.53228	TTT		FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
NHLRC3	387921	hgsc.bcm.edu	37	13	39613309	39613309	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:39613309A>G	ENST00000379600.3	+	2	443	c.121A>G	c.(121-123)Act>Gct	p.T41A	PROSER1_ENST00000350125.3_5'Flank|PROSER1_ENST00000352251.3_5'Flank|NHLRC3_ENST00000379599.2_Missense_Mutation_p.T41A|NHLRC3_ENST00000470258.1_5'UTR	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	41						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		TTCCTGGAGAACTGAGAAAAT	0.403																																																	0			13											79.0	84.0	82.0					13																	39613309		2203	4300	6503	38511309	SO:0001583	missense	387921				CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.121A>G	13.37:g.39613309A>G	ENSP00000368920:p.Thr41Ala	Somatic		Capture	Illumina HiSeq	Phase_I	38511309	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	37	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.891193	0.33442	.	.	ENSG00000188811	ENST00000379600;ENST00000379599;ENST00000537150	T;D	0.89939	0.98;-2.59	5.11	-9.17	0.00691	.	0.627020	0.15128	N	0.278998	T	0.67468	0.2896	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.59747	-0.7396	9	.	.	.	0.0547	0.3746	0.00385	0.2325:0.2202:0.2658:0.2815	.	41;41;41;41	B4DTL0;Q5JS37;B4DRC8;F5GZB5	.;NHLC3_HUMAN;.;.	A	41	ENSP00000368920:T41A;ENSP00000368919:T41A	.	T	+	1	0	NHLRC3	38511309	0.000000	0.05858	0.000000	0.03702	0.718000	0.41266	0.267000	0.18552	-2.193000	0.00754	-0.609000	0.04063	ACT		NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754	
DCT	1638	hgsc.bcm.edu	37	13	95121161	95121161	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr13:95121161A>G	ENST00000377028.5	-	2	847	c.434T>C	c.(433-435)tTa>tCa	p.L145S	DCT_ENST00000490854.1_5'Flank|DCT_ENST00000446125.1_Missense_Mutation_p.L145S	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	145					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CGCGAGATCTAAGGCGCCCAA	0.572																																																	0			13											224.0	223.0	223.0					13																	95121161		2203	4300	6503	93919162	SO:0001583	missense	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"""dopachrome delta-isomerase"""	191275	"""tyrosine-related protein 2"""	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.434T>C	13.37:g.95121161A>G	ENSP00000366227:p.Leu145Ser	Somatic		Capture	Illumina HiSeq	Phase_I	93919162	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240173	0.58995	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.99167	-5.51;-5.51	5.79	5.79	0.91817	Uncharacterised domain, di-copper centre (2);	0.067025	0.64402	D	0.000011	D	0.99444	0.9803	H	0.95402	3.665	0.80722	D	1	D;D	0.65815	0.995;0.985	P;P	0.61800	0.894;0.691	D	0.98364	1.0550	9	.	.	.	-7.3318	16.1354	0.81481	1.0:0.0:0.0:0.0	.	145;145	Q09GT4;P40126	.;TYRP2_HUMAN	S	145	ENSP00000366227:L145S;ENSP00000392762:L145S	.	L	-	2	0	DCT	93919162	1.000000	0.71417	0.611000	0.29010	0.029000	0.11900	8.962000	0.93254	2.207000	0.71202	0.533000	0.62120	TTA		DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3		
ST8SIA6	338596	hgsc.bcm.edu	37	10	17363274	17363274	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:17363274A>G	ENST00000377602.4	-	8	874	c.800T>C	c.(799-801)cTt>cCt	p.L267P		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	267					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)	p.L267R(1)		endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TGCTGGCAGAAGAAAAAATGC	0.368																																																	1	Substitution - Missense(1)	ovary(1)	10											73.0	81.0	78.0					10																	17363274		2203	4300	6503	17403280	SO:0001583	missense	338596				CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"""Sialyltransferases"""	23317	protein-coding gene	gene with protein product	"""ST8Sia VI"""	610139	"""sialyltransferase 8F (alpha-2, 8-sialyltransferase)"""	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.800T>C	10.37:g.17363274A>G	ENSP00000366827:p.Leu267Pro	Somatic		Capture	Illumina HiSeq	Phase_I	17403280	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.237079	0.79800	.	.	ENSG00000148488	ENST00000377610;ENST00000377602	T	0.33865	1.39	5.18	5.18	0.71444	.	0.061476	0.64402	D	0.000005	T	0.65873	0.2733	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.72316	-0.4330	10	0.56958	D	0.05	-5.111	15.4962	0.75653	1.0:0.0:0.0:0.0	.	267	P61647	SIA8F_HUMAN	P	97;267	ENSP00000366827:L267P	ENSP00000366827:L267P	L	-	2	0	ST8SIA6	17403280	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	6.974000	0.76122	2.307000	0.77673	0.528000	0.53228	CTT		ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470	
STAM	8027	hgsc.bcm.edu	37	10	17730082	17730082	+	Silent	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:17730082A>G	ENST00000377524.3	+	5	569	c.354A>G	c.(352-354)gaA>gaG	p.E118E	STAM_ENST00000540523.1_Silent_p.E7E	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	118	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						GGACAGATGAATTTAAGAATG	0.363																																																	0			10											131.0	134.0	133.0					10																	17730082		2203	4300	6503	17770088	SO:0001819	synonymous_variant	8027			U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.354A>G	10.37:g.17730082A>G		Somatic		Capture	Illumina HiSeq	Phase_I	17770088	B0YJ99|D3DRU5|Q8N6D9	Silent	SNP	ENST00000377524.3	37	CCDS7122.1																																																																																				STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473	
ZNF22	7570	hgsc.bcm.edu	37	10	45498857	45498857	+	Nonsense_Mutation	SNP	C	C	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:45498857C>G	ENST00000298299.3	+	2	634	c.41C>G	c.(40-42)tCa>tGa	p.S14*	C10orf25_ENST00000298298.1_5'Flank|CEP164P1_ENST00000456938.2_RNA	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	14					odontogenesis (GO:0042476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				TCTCGGAGCTCAAGCCAAGGA	0.458																																																	0			10											60.0	64.0	63.0					10																	45498857		2203	4300	6503	44818863	SO:0001587	stop_gained	7570			BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"""Zinc fingers, C2H2-type"""	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.41C>G	10.37:g.45498857C>G	ENSP00000298299:p.Ser14*	Somatic		Capture	Illumina HiSeq	Phase_I	44818863	Q5T741|Q96FM4	Nonsense_Mutation	SNP	ENST00000298299.3	37	CCDS7211.1	.	.	.	.	.	.	.	.	.	.	C	40	8.453381	0.98817	.	.	ENSG00000165512	ENST00000298299	.	.	.	4.94	4.94	0.65067	.	0.385029	0.19198	N	0.120243	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-1.3829	16.0476	0.80731	0.0:1.0:0.0:0.0	.	.	.	.	X	14	.	ENSP00000298299:S14X	S	+	2	0	ZNF22	44818863	0.000000	0.05858	1.000000	0.80357	0.961000	0.63080	0.503000	0.22610	2.706000	0.92434	0.655000	0.94253	TCA		ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963	
ZFAND4	93550	hgsc.bcm.edu	37	10	46148454	46148454	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:46148454C>A	ENST00000344646.5	-	3	453	c.238G>T	c.(238-240)Gat>Tat	p.D80Y	ZFAND4_ENST00000374366.3_Missense_Mutation_p.D6Y|ZFAND4_ENST00000374371.2_Missense_Mutation_p.D80Y|ZFAND4_ENST00000335258.7_Missense_Mutation_p.D80Y	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	80	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.						zinc ion binding (GO:0008270)										AAGCAATAATCATTTTCAAGT	0.303																																																	0			10											170.0	136.0	148.0					10																	46148454		2202	4299	6501	45468460	SO:0001583	missense	93550			AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"""Zinc fingers, AN1-type domain containing"""	23504	protein-coding gene	gene with protein product			"""AN1, ubiquitin-like, homolog (Xenopus laevis)"""	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.238G>T	10.37:g.46148454C>A	ENSP00000339484:p.Asp80Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	45468460	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827608	0.71143	.	.	ENSG00000172671	ENST00000344646;ENST00000374371;ENST00000374366;ENST00000374376;ENST00000335258	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	6.07	4.25	0.50352	Ubiquitin supergroup (1);Ubiquitin (2);	0.189606	0.46758	D	0.000279	T	0.57621	0.2066	M	0.80982	2.52	0.47621	D	0.999475	D;D;D	0.65815	0.981;0.983;0.995	P;P;D	0.64237	0.882;0.905;0.923	T	0.61667	-0.7016	10	0.87932	D	0	-5.3188	10.952	0.47334	0.0:0.8491:0.0:0.1509	.	80;80;80	Q5VVY2;Q5VVY4;Q86XD8	.;.;ANUB1_HUMAN	Y	80;80;6;80;80	ENSP00000339484:D80Y;ENSP00000363491:D80Y;ENSP00000363486:D6Y;ENSP00000335586:D80Y	ENSP00000335586:D80Y	D	-	1	0	ANUBL1	45468460	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.946000	0.75953	0.914000	0.36822	-0.136000	0.14681	GAT		ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890	
JMJD1C	221037	hgsc.bcm.edu	37	10	64936164	64936164	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:64936164T>C	ENST00000399262.2	-	24	7512	c.7294A>G	c.(7294-7296)Aac>Gac	p.N2432D	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.N2250D|JMJD1C_ENST00000402544.1_Missense_Mutation_p.N2195D	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2432	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGCTTTTTGTTCACATACCAA	0.398																																																	0			10											127.0	117.0	120.0					10																	64936164		1866	4086	5952	64606170	SO:0001583	missense	221037			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7294A>G	10.37:g.64936164T>C	ENSP00000382204:p.Asn2432Asp	Somatic		Capture	Illumina HiSeq	Phase_I	64606170	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827337	0.32329	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.71341	-0.56;-0.56;-0.56	5.75	5.75	0.90469	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.046736	0.85682	D	0.000000	T	0.43656	0.1257	N	0.01817	-0.705	0.80722	D	1	P;B	0.40360	0.714;0.025	B;B	0.40134	0.32;0.021	T	0.57213	-0.7850	10	0.02654	T	1	-15.2545	15.7237	0.77736	0.0:0.0:0.0:1.0	.	2432;2250	Q15652;A0T124	JHD2C_HUMAN;.	D	2432;2195;2250	ENSP00000382204:N2432D;ENSP00000384990:N2195D;ENSP00000444682:N2250D	ENSP00000382204:N2432D	N	-	1	0	JMJD1C	64606170	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.204000	0.58460	2.195000	0.70347	0.533000	0.62120	AAC		JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
KAT6B	23522	hgsc.bcm.edu	37	10	76737194	76737194	+	Splice_Site	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:76737194A>G	ENST00000287239.4	+	9	2603	c.2114A>G	c.(2113-2115)gAg>gGg	p.E705G	KAT6B_ENST00000372714.1_Splice_Site_p.E413G|KAT6B_ENST00000372724.1_Splice_Site_p.E413G|KAT6B_ENST00000372725.1_Splice_Site_p.E413G|KAT6B_ENST00000372711.1_Splice_Site_p.E522G|KAT6B_ENST00000490365.1_3'UTR	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	705	Negatively regulates HAT activity.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTTTCTTGGGAGGTAAGGCGA	0.378																																																	0			10											207.0	188.0	194.0					10																	76737194		2203	4300	6503	76407200	SO:0001630	splice_region_variant	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2115+1A>G	10.37:g.76737194A>G		Somatic		Capture	Illumina HiSeq	Phase_I	76407200	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.642470	0.67244	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	5.63	5.63	0.86233	.	0.000000	0.46145	D	0.000317	T	0.81640	0.4865	L	0.41415	1.275	0.47994	D	0.99956	D;P;D	0.63880	0.983;0.939;0.993	P;P;P	0.60886	0.85;0.586;0.88	D	0.83554	0.0103	10	0.72032	D	0.01	-13.1071	14.386	0.66945	1.0:0.0:0.0:0.0	.	522;413;705	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	G	413;413;705;413;522	ENSP00000361810:E413G;ENSP00000361809:E413G;ENSP00000287239:E705G;ENSP00000361799:E413G;ENSP00000361796:E522G	ENSP00000287239:E705G	E	+	2	0	KAT6B	76407200	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.201000	0.72124	2.151000	0.67156	0.477000	0.44152	GAG		KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	Missense_Mutation
HPSE2	60495	hgsc.bcm.edu	37	10	100242479	100242479	+	Missense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:100242479C>A	ENST00000370552.3	-	11	1586	c.1527G>T	c.(1525-1527)aaG>aaT	p.K509N	HPSE2_ENST00000370546.1_Missense_Mutation_p.K509N|HPSE2_ENST00000404542.1_Missense_Mutation_p.K397N|HPSE2_ENST00000370549.1_Missense_Mutation_p.K451N	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	509					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		GCTTGATTTTCTTTCTTGATC	0.478																																																	0			10											139.0	123.0	129.0					10																	100242479		2203	4300	6503	100232469	SO:0001583	missense	60495			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1527G>T	10.37:g.100242479C>A	ENSP00000359583:p.Lys509Asn	Somatic		Capture	Illumina HiSeq	Phase_I	100232469	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.207196	0.79127	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.49139	0.79;0.81;1.42;0.82	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.59742	0.2216	L	0.52126	1.63	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.998	D;D;D;D	0.83275	0.994;0.982;0.996;0.987	T	0.51803	-0.8659	10	0.22109	T	0.4	-9.9925	12.7436	0.57268	0.0:0.925:0.0:0.075	.	397;509;451;509	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	N	509;451;509;397	ENSP00000359583:K509N;ENSP00000359580:K451N;ENSP00000359577:K509N;ENSP00000384384:K397N	ENSP00000359577:K509N	K	-	3	2	HPSE2	100232469	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.677000	0.91161	0.655000	0.94253	AAG		HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
FGF8	2253	hgsc.bcm.edu	37	10	103534937	103534937	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:103534937G>T	ENST00000344255.3	-	3	105	c.106C>A	c.(106-108)Ctc>Atc	p.L36I	FGF8_ENST00000485728.1_Intron|FGF8_ENST00000347978.2_Intron|FGF8_ENST00000346714.3_Intron|FGF8_ENST00000320185.2_Missense_Mutation_p.L36I			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	36					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		AGGGAAGCGAGCTCCCTGCCC	0.667																																																	0			10											5.0	7.0	6.0					10																	103534937		1973	3917	5890	103524927	SO:0001583	missense	2253			D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"""Endogenous ligands"""	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.106C>A	10.37:g.103534937G>T	ENSP00000340039:p.Leu36Ile	Somatic		Capture	Illumina HiSeq	Phase_I	103524927	A1A514|Q14915|Q15766	Missense_Mutation	SNP	ENST00000344255.3	37	CCDS7517.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779244	0.31502	.	.	ENSG00000107831	ENST00000344255;ENST00000320185	T;T	0.81415	-1.49;-1.33	2.84	1.94	0.25998	.	1.124660	0.07297	U	0.873380	T	0.63224	0.2493	N	0.22421	0.69	0.49687	D	0.999816	P;B	0.36354	0.549;0.198	B;B	0.25140	0.058;0.026	T	0.52837	-0.8522	10	0.21014	T	0.42	.	7.8466	0.29428	0.1254:0.0:0.8746:0.0	.	36;36	P55075-4;P55075	.;FGF8_HUMAN	I	36	ENSP00000340039:L36I;ENSP00000321797:L36I	ENSP00000321797:L36I	L	-	1	0	FGF8	103524927	0.034000	0.19679	0.119000	0.21687	0.924000	0.55760	0.669000	0.25142	0.791000	0.33826	-0.381000	0.06696	CTC		FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165	
CNNM2	54805	hgsc.bcm.edu	37	10	104679546	104679546	+	Missense_Mutation	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:104679546G>T	ENST00000369878.4	+	1	1497	c.1309G>T	c.(1309-1311)Ggg>Tgg	p.G437W	CNNM2_ENST00000369875.3_Missense_Mutation_p.G437W|CNNM2_ENST00000433628.2_Missense_Mutation_p.G437W	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	437					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CATCATCCAAGGGGCGCTGGA	0.577																																																	0			10											69.0	66.0	67.0					10																	104679546		2203	4300	6503	104669536	SO:0001583	missense	54805			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1309G>T	10.37:g.104679546G>T	ENSP00000358894:p.Gly437Trp	Somatic		Capture	Illumina HiSeq	Phase_I	104669536	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640439	0.67244	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	T;T;T	0.76968	-1.06;-1.06;-1.06	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	D	0.92922	0.7748	H	0.98333	4.205	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.96052	0.9032	10	0.87932	D	0	.	17.2856	0.87140	0.0:0.0:1.0:0.0	.	437;437;437	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	W	437	ENSP00000392875:G437W;ENSP00000358891:G437W;ENSP00000358894:G437W	ENSP00000286899:G437W	G	+	1	0	CNNM2	104669536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.852000	0.99516	2.043000	0.60533	0.555000	0.69702	GGG		CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
PDCD4	27250	hgsc.bcm.edu	37	10	112653929	112653929	+	Silent	SNP	T	T	G	rs185605824	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:112653929T>G	ENST00000280154.7	+	9	1345	c.1071T>G	c.(1069-1071)ccT>ccG	p.P357P	PDCD4_ENST00000481353.1_3'UTR|PDCD4_ENST00000393104.2_Silent_p.P346P	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	357	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.P357P(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		TGGAAGTACCTCATTTTCACC	0.333													T|||	2	0.000399361	0.0	0.0	5008	,	,		19438	0.002		0.0	False		,,,				2504	0.0				Ovarian(115;1498 1603 9363 40056 40885)												1	Substitution - coding silent(1)	lung(1)	10											130.0	136.0	134.0					10																	112653929		2203	4298	6501	112643919	SO:0001819	synonymous_variant	27250			U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1071T>G	10.37:g.112653929T>G		Somatic		Capture	Illumina HiSeq	Phase_I	112643919	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																				PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118220538	118220538	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:118220538C>A	ENST00000369230.3	+	6	772	c.626C>A	c.(625-627)tCg>tAg	p.S209*		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	209					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CTAGACCCCTCGGATGCCAAC	0.448																																																	0			10											130.0	116.0	121.0					10																	118220538		2203	4300	6503	118210528	SO:0001587	stop_gained	119548			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.626C>A	10.37:g.118220538C>A	ENSP00000358232:p.Ser209*	Somatic		Capture	Illumina HiSeq	Phase_I	118210528		Nonsense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	C	35	5.516483	0.96402	.	.	ENSG00000203837	ENST00000369230	.	.	.	4.78	0.443	0.16587	.	0.299402	0.23400	N	0.048589	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2145	0.54398	0.1167:0.5483:0.335:0.0	.	.	.	.	X	209	.	ENSP00000358232:S209X	S	+	2	0	PNLIPRP3	118210528	0.012000	0.17670	0.271000	0.24616	0.530000	0.34684	1.098000	0.31000	0.559000	0.29153	0.591000	0.81541	TCG		PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
C10orf90	118611	hgsc.bcm.edu	37	10	128193073	128193073	+	Silent	SNP	G	G	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr10:128193073G>T	ENST00000284694.7	-	3	816	c.696C>A	c.(694-696)acC>acA	p.T232T	C10orf90_ENST00000392694.1_Silent_p.T185T|C10orf90_ENST00000454341.1_Silent_p.T232T|C10orf90_ENST00000544758.1_Silent_p.T329T|C10orf90_ENST00000356858.3_Silent_p.T185T|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	232					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GAGAAAAACTGGTCTCTTTGT	0.552											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			10											72.0	77.0	75.0					10																	128193073		2203	4300	6503	128183063	SO:0001819	synonymous_variant	118611			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.696C>A	10.37:g.128193073G>T		Somatic	1563	Capture	Illumina HiSeq	Phase_I	128183063	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																				C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
CDH9	1007	hgsc.bcm.edu	37	5	26885951	26885951	+	Missense_Mutation	SNP	G	G	A	rs370038496		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:26885951G>A	ENST00000231021.4	-	11	1826	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCATCTTTCCGAGTCATGATT	0.343																																					Melanoma(8;187 585 15745 40864 52829)												0			5											59.0	60.0	60.0					5																	26885951		2203	4300	6503	26921708	SO:0001583	missense	1007			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1654C>T	5.37:g.26885951G>A	ENSP00000231021:p.Arg552Trp	Somatic		Capture	Illumina HiSeq	Phase_I	26921708	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791338	0.70452	.	.	ENSG00000113100	ENST00000231021	T	0.20332	2.08	5.79	4.9	0.64082	Cadherin (4);Cadherin-like (1);	0.056327	0.64402	D	0.000002	T	0.54515	0.1863	M	0.92077	3.27	0.41099	D	0.985659	D;D	0.89917	0.999;1.0	D;D	0.83275	0.978;0.996	T	0.64558	-0.6379	9	.	.	.	.	12.9437	0.58362	0.0:0.0:0.6774:0.3226	.	145;552	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	552	ENSP00000231021:R552W	.	R	-	1	2	CDH9	26921708	0.862000	0.29867	1.000000	0.80357	0.978000	0.69477	1.654000	0.37334	2.740000	0.93945	0.563000	0.77884	CGG		CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
AGXT2	64902	hgsc.bcm.edu	37	5	35047957	35047957	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:35047957A>G	ENST00000231420.6	-	1	241	c.41T>C	c.(40-42)cTg>cCg	p.L14P		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	14					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	GGAAGTGACCAGGCACAAGGG	0.547																																																	0			5											72.0	64.0	67.0					5																	35047957		2203	4300	6503	35083714	SO:0001583	missense	64902			AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.41T>C	5.37:g.35047957A>G	ENSP00000231420:p.Leu14Pro	Somatic		Capture	Illumina HiSeq	Phase_I	35083714	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.952327	0.34471	.	.	ENSG00000113492	ENST00000231420	D	0.83914	-1.78	3.42	0.846	0.18955	.	21.161200	0.00166	N	0.000000	T	0.80834	0.4699	L	0.51422	1.61	0.09310	N	0.999991	D;P	0.56968	0.978;0.61	P;B	0.45913	0.497;0.136	T	0.64952	-0.6286	10	0.30854	T	0.27	-10.1234	5.9647	0.19318	0.5737:0.0:0.0:0.4263	.	14;14	E9PDL7;Q9BYV1	.;AGT2_HUMAN	P	14	ENSP00000231420:L14P	ENSP00000231420:L14P	L	-	2	0	AGXT2	35083714	0.107000	0.21998	0.023000	0.16930	0.515000	0.34225	1.300000	0.33436	0.167000	0.19631	0.454000	0.30748	CTG		AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
GPR98	84059	hgsc.bcm.edu	37	5	90049411	90049411	+	Missense_Mutation	SNP	G	G	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:90049411G>C	ENST00000405460.2	+	54	11238	c.11142G>C	c.(11140-11142)caG>caC	p.Q3714H		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3714	Calx-beta 24. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTGAAGGCCAGGTACTGTCAA	0.318																																																	0			5											95.0	94.0	94.0					5																	90049411		1819	4076	5895	90085167	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11142G>C	5.37:g.90049411G>C	ENSP00000384582:p.Gln3714His	Somatic		Capture	Illumina HiSeq	Phase_I	90085167	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.66|15.66	2.899392|2.899392	0.52227|0.52227	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.33216|.	1.42|.	5.53|5.53	2.83|2.83	0.33086|0.33086	.|.	0.132302|.	0.52532|.	D|.	0.000062|.	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.996|.	D;P|.	0.69142|.	0.962;0.846|.	T|T	0.56214|0.56214	-0.8016|-0.8016	10|5	0.62326|.	D|.	0.03|.	.|.	8.3567|8.3567	0.32335|0.32335	0.3103:0.0:0.6897:0.0|0.3103:0.0:0.6897:0.0	.|.	3714;3714|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	H|T	3714|1280	ENSP00000384582:Q3714H|.	ENSP00000296619:Q3714H|.	Q|R	+|+	3|2	2|0	GPR98|GPR98	90085167|90085167	1.000000|1.000000	0.71417|0.71417	0.833000|0.833000	0.33012|0.33012	0.746000|0.746000	0.42486|0.42486	1.918000|1.918000	0.40006|0.40006	0.314000|0.314000	0.23086|0.23086	-0.262000|-0.262000	0.10625|0.10625	CAG|AGG		GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101834371	101834371	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:101834371T>C	ENST00000506729.1	-	1	349	c.178A>G	c.(178-180)Agg>Ggg	p.R60G	SLCO6A1_ENST00000379810.1_Missense_Mutation_p.R60G|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.R60G|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.R60G|SLCO6A1_ENST00000514551.1_5'Flank|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.R60G			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CCGCCGAACCTTATCAAGGCC	0.552																																																	0			5											153.0	169.0	164.0					5																	101834371		2203	4300	6503	101862270	SO:0001583	missense	133482			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.178A>G	5.37:g.101834371T>C	ENSP00000421339:p.Arg60Gly	Somatic		Capture	Illumina HiSeq	Phase_I	101862270	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.313220	0.23908	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.48836	0.87;0.87;0.88;0.8;0.8	3.41	0.995	0.19838	.	11.615200	0.00166	N	0.000000	T	0.34048	0.0884	N	0.19112	0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.21177	-1.0253	10	0.48119	T	0.1	.	5.0536	0.14522	0.0:0.2566:0.0:0.7434	.	60;60;60	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	G	60	ENSP00000421339:R60G;ENSP00000369135:R60G;ENSP00000373671:R60G;ENSP00000421990:R60G;ENSP00000369138:R60G	ENSP00000369135:R60G	R	-	1	2	SLCO6A1	101862270	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.710000	0.25748	0.210000	0.20664	0.397000	0.26171	AGG		SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
APC	324	hgsc.bcm.edu	37	5	112175118	112175118	+	Missense_Mutation	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175118C>T	ENST00000457016.1	+	16	4207	c.3827C>T	c.(3826-3828)tCa>tTa	p.S1276L	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.S1276L|APC_ENST00000257430.4_Missense_Mutation_p.S1276L			P25054	APC_HUMAN	adenomatous polyposis coli	1276	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.S1276*(5)|p.S1276L(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)		AGATGTAGTTCATTATCATCT	0.353		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)																											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"""	8	Substitution - Nonsense(5)|Substitution - Missense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(5)|soft_tissue(1)|breast(1)|skin(1)	5	GRCh37	CD086479|CM086472|CM990161	APC	D|M							53.0	56.0	55.0					5																	112175118		2202	4300	6502	112203017	SO:0001583	missense	324	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.3827C>T	5.37:g.112175118C>T	ENSP00000413133:p.Ser1276Leu	Somatic		Capture	Illumina HiSeq	Phase_I	112203017	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.809899	0.70797	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.97424	0.9157	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.96781	0.9575	9	.	.	.	-13.3116	20.1672	0.98154	0.0:1.0:0.0:0.0	.	1278;1276	Q4LE70;P25054	.;APC_HUMAN	L	1276	ENSP00000413133:S1276L;ENSP00000257430:S1276L;ENSP00000427089:S1276L;ENSP00000423828:S1276L	.	S	+	2	0	APC	112203017	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.861000	0.98227	0.655000	0.94253	TCA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175576	112175576	+	Nonsense_Mutation	SNP	C	C	T	rs74535574		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175576C>T	ENST00000457016.1	+	16	4665	c.4285C>T	c.(4285-4287)Caa>Taa	p.Q1429*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q1429*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1429*			P25054	APC_HUMAN	adenomatous polyposis coli	1429	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.Q1429*(35)|p.Q1429fs*8(4)|p.Y1376fs*41(1)|p.?(1)|p.P1424fs*19(1)|p.S1411fs*41(1)|p.K1192fs*3(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)		TAGCCCTGGACAAACCATGCC	0.468	Q1429*(NCIH747_LARGE_INTESTINE)|Q1429*(SW948_LARGE_INTESTINE)	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)																											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"""	44	Substitution - Nonsense(35)|Deletion - Frameshift(8)|Unknown(1)	large_intestine(42)|soft_tissue(1)|skin(1)	5	GRCh37	HM050024	APC	M	rs74535574						109.0	98.0	102.0					5																	112175576		2202	4300	6502	112203475	SO:0001587	stop_gained	324	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.4285C>T	5.37:g.112175576C>T	ENSP00000413133:p.Gln1429*	Somatic		Capture	Illumina HiSeq	Phase_I	112203475	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.799924	0.98958	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8813	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	1429	.	.	Q	+	1	0	APC	112203475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.884000	0.98904	0.655000	0.94253	CAA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175942	112175942	+	Missense_Mutation	SNP	A	A	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112175942A>G	ENST00000457016.1	+	16	5031	c.4651A>G	c.(4651-4653)Aaa>Gaa	p.K1551E	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.K1551E|APC_ENST00000257430.4_Missense_Mutation_p.K1551E			P25054	APC_HUMAN	adenomatous polyposis coli	1551	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.K1192fs*3(1)|p.?(1)|p.K1551*(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)		AAACCAAGAGAAAGAGGCAGA	0.343		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)																											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)	5											79.0	86.0	83.0					5																	112175942		2202	4300	6502	112203841	SO:0001583	missense	324	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.4651A>G	5.37:g.112175942A>G	ENSP00000413133:p.Lys1551Glu	Somatic		Capture	Illumina HiSeq	Phase_I	112203841	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	8.039	0.763515	0.15914	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88664	-2.41;-2.41;-2.41	6.16	5.01	0.66863	.	0.240065	0.49916	N	0.000138	T	0.82195	0.4984	L	0.35414	1.06	0.42707	D	0.993632	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.75280	-0.3373	9	.	.	.	-18.9638	12.1206	0.53889	0.9339:0.0:0.0661:0.0	.	1553;1551	Q4LE70;P25054	.;APC_HUMAN	E	1551	ENSP00000413133:K1551E;ENSP00000257430:K1551E;ENSP00000427089:K1551E	.	K	+	1	0	APC	112203841	1.000000	0.71417	0.987000	0.45799	0.956000	0.61745	3.319000	0.51983	1.163000	0.42636	0.528000	0.53228	AAA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
TSSK1B	83942	hgsc.bcm.edu	37	5	112769828	112769828	+	Missense_Mutation	SNP	G	G	A	rs55738530	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:112769828G>A	ENST00000390666.3	-	1	900	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> C (in dbSNP:rs55738530). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		TGCTTGGAGCGTGGGAAGTTG	0.587													G|||	4	0.000798722	0.0	0.0029	5008	,	,		21207	0.0		0.0	False		,,,				2504	0.002																0			5						G	,CYS/ARG	0,4404		0,0,2202	80.0	73.0	76.0		,709	0.9	0.3	5	dbSNP_129	76	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,180	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,possibly-damaging	,237/368	112769828	1,13003	2202	4300	6502	112797727	SO:0001583	missense	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.709C>T	5.37:g.112769828G>A	ENSP00000375081:p.Arg237Cys	Somatic		Capture	Illumina HiSeq	Phase_I	112797727	B2R8D9	Missense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	7.873	0.728635	0.15507	0.0	1.16E-4	ENSG00000212122	ENST00000390666	T	0.24723	1.84	0.9	0.9	0.19278	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.236472	0.21381	U	0.075478	T	0.24928	0.0605	L	0.50993	1.605	0.09310	N	0.999999	D	0.65815	0.995	P	0.58970	0.849	T	0.05451	-1.0884	10	0.72032	D	0.01	.	4.9573	0.14048	0.0:0.0:1.0:0.0	rs55738530	237	Q9BXA7	TSSK1_HUMAN	C	237	ENSP00000375081:R237C	ENSP00000375081:R237C	R	-	1	0	TSSK1B	112797727	0.004000	0.15560	0.313000	0.25210	0.177000	0.22998	0.069000	0.14552	0.308000	0.22923	0.313000	0.20887	CGC		TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203403	140203403	+	Silent	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:140203403G>A	ENST00000529859.1	+	1	2043	c.2043G>A	c.(2041-2043)gcG>gcA	p.A681A	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000378126.3_Silent_p.A681A|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Silent_p.A681A	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	681					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATCGCGGGCGTCGGCGGGCG	0.667																																																	0			5											42.0	49.0	46.0					5																	140203403		2203	4296	6499	140183587	SO:0001819	synonymous_variant	56143			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2043G>A	5.37:g.140203403G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140183587	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																				PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
CSF1R	1436	hgsc.bcm.edu	37	5	149453042	149453042	+	Missense_Mutation	SNP	T	T	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:149453042T>C	ENST00000286301.3	-	7	1195	c.904A>G	c.(904-906)Aac>Gac	p.N302D	CSF1R_ENST00000543093.1_Intron	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	302	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GAGCTCAAGTTCAAGTAGGCA	0.502																																																	0			5											104.0	95.0	98.0					5																	149453042		2203	4300	6503	149433235	SO:0001583	missense	1436			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.904A>G	5.37:g.149453042T>C	ENSP00000286301:p.Asn302Asp	Somatic		Capture	Illumina HiSeq	Phase_I	149433235	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	T	1.645	-0.515408	0.04200	.	.	ENSG00000182578	ENST00000286301;ENST00000394307	T	0.78003	-1.14	4.81	3.64	0.41730	Immunoglobulin-like fold (1);	0.239562	0.29100	N	0.013148	T	0.65883	0.2734	L	0.51422	1.61	0.80722	D	1	B;P	0.44627	0.007;0.839	B;B	0.35550	0.016;0.205	T	0.57774	-0.7753	10	0.22706	T	0.39	.	9.5487	0.39297	0.0:0.0926:0.0:0.9074	.	154;302	B4E2Y8;P07333	.;CSF1R_HUMAN	D	302;154	ENSP00000286301:N302D	ENSP00000286301:N302D	N	-	1	0	CSF1R	149433235	1.000000	0.71417	0.998000	0.56505	0.056000	0.15407	2.195000	0.42677	0.210000	0.20664	-1.139000	0.01908	AAC		CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
UIMC1	51720	hgsc.bcm.edu	37	5	176396701	176396701	+	Missense_Mutation	SNP	G	G	A	rs369146532		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:176396701G>A	ENST00000377227.4	-	5	496	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	UIMC1_ENST00000377219.2_Missense_Mutation_p.R122W|UIMC1_ENST00000506128.1_Missense_Mutation_p.R122W|UIMC1_ENST00000511320.1_Missense_Mutation_p.R122W|UIMC1_ENST00000503273.1_5'Flank			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	122	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGAAGGCCGGCAACTCTGA	0.493																																																	0			5											96.0	93.0	94.0					5																	176396701		2203	4300	6503	176329307	SO:0001583	missense	51720			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.364C>T	5.37:g.176396701G>A	ENSP00000366434:p.Arg122Trp	Somatic		Capture	Illumina HiSeq	Phase_I	176329307	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109611	0.56398	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000509236	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	5.64	3.82	0.43975	Ubiquitin interacting motif (1);	0.486110	0.19314	N	0.117319	T	0.15349	0.0370	N	0.08118	0	0.51012	D	0.999902	B	0.22211	0.066	B	0.14578	0.011	T	0.05419	-1.0886	10	0.39692	T	0.17	0.0817	9.1461	0.36933	0.0783:0.1467:0.775:0.0	.	122	Q96RL1	UIMC1_HUMAN	W	122;122;122;122;44;122	ENSP00000366434:R122W;ENSP00000366425:R122W;ENSP00000421926:R122W;ENSP00000427480:R122W;ENSP00000423885:R122W	ENSP00000366425:R122W	R	-	1	2	UIMC1	176329307	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.227000	0.58612	0.701000	0.31803	0.561000	0.74099	CGG		UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
CCM2	83605	hgsc.bcm.edu	37	7	45108041	45108041	+	Splice_Site	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr7:45108041G>A	ENST00000258781.6	+	5	621		c.e5-1		CCM2_ENST00000461377.1_Splice_Site|CCM2_ENST00000475551.1_Splice_Site|CCM2_ENST00000474617.1_Intron|CCM2_ENST00000541586.1_Splice_Site|CCM2_ENST00000544363.1_Intron|CCM2_ENST00000381112.3_Splice_Site	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2						blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TGACTTCTCAGCCCAGGACCC	0.607																																																	0			7											96.0	88.0	90.0					7																	45108041		2203	4300	6503	45074566	SO:0001630	splice_region_variant	83605			BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.473-1G>A	7.37:g.45108041G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45074566	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Splice_Site	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.111386	0.56398	.	.	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000475551;ENST00000381112	.	.	.	4.2	4.2	0.49525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.476	0.75481	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCM2	45074566	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	8.956000	0.93066	2.049000	0.60858	0.561000	0.74099	.		CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Intron
RNASEH2A	10535	hgsc.bcm.edu	37	19	12918232	12918232	+	Splice_Site	SNP	G	G	A			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr19:12918232G>A	ENST00000221486.4	+	4	417		c.e4-1			NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A						DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						CCCCACCACAGGGTCAAATAC	0.552																																																	0			19											146.0	125.0	132.0					19																	12918232		2203	4300	6503	12779232	SO:0001630	splice_region_variant	10535			Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"""ribonuclease H2, large subunit"", ""Aicardi-Goutieres syndrome 4"""			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.324-1G>A	19.37:g.12918232G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12779232	B2RCY1|Q96F11	Splice_Site	SNP	ENST00000221486.4	37	CCDS12282.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454974	0.63290	.	.	ENSG00000104889	ENST00000221486	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4625	0.75369	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNASEH2A	12779232	1.000000	0.71417	0.997000	0.53966	0.728000	0.41692	8.858000	0.92256	1.926000	0.55796	0.400000	0.26472	.		RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397	Intron
PDE5A	8654	hgsc.bcm.edu	37	4	120486475	120486475	+	Splice_Site	SNP	C	C	T	rs201028578		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr4:120486475C>T	ENST00000354960.3	-	5	1313		c.e5+1		PDE5A_ENST00000264805.5_Splice_Site|PDE5A_ENST00000394439.1_Splice_Site	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific						blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	ATCAGACTGACCTGATTTCTC	0.313																																																	0			4											67.0	62.0	63.0					4																	120486475		2203	4299	6502	120705923	SO:0001630	splice_region_variant	8654			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.993+1G>A	4.37:g.120486475C>T		Somatic		Capture	Illumina HiSeq	Phase_I	120705923	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Splice_Site	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.791214	0.90367	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7068	0.96076	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE5A	120705923	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.083000	0.76859	2.824000	0.97209	0.655000	0.94253	.		PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	Intron
GFRA3	2676	hgsc.bcm.edu	37	5	137589745	137589745	+	Splice_Site	SNP	C	C	T			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr5:137589745C>T	ENST00000274721.3	-	5	1136		c.e5+1		GFRA3_ENST00000378362.3_Splice_Site	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3						nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCAGCCTCACCAATCAGCCC	0.547																																																	0			5											148.0	130.0	136.0					5																	137589745		2203	4300	6503	137617644	SO:0001630	splice_region_variant	2676			AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.889+1G>A	5.37:g.137589745C>T		Somatic		Capture	Illumina HiSeq	Phase_I	137617644	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Splice_Site	SNP	ENST00000274721.3	37	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049834	0.75846	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2504	0.54595	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GFRA3	137617644	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.689000	0.61723	2.245000	0.73994	0.650000	0.86243	.		GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496	Intron
FMN2	56776	hgsc.bcm.edu	37	1	240371443	240371475	+	In_Frame_Del	DEL	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	-	rs200800873|rs199920451|rs112021213|rs367816204|rs199702261|rs200682272|rs201396397|rs181634878	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENST00000319653.9	+	5	3561_3593	c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	c.(3331-3363)ccccctctacccggagcgggcataccccctcctdel	p.PPLPGAGIPPP1133del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1133	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.A1259A(1)|p.G1260C(1)|p.P1262P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCTCCTCCGCCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCTCTAC	0.721																																																	3	Substitution - coding silent(2)|Substitution - Missense(1)	lung(2)|prostate(1)	1								366,2650		115,136,1257						-4.9	0.0			10	861,5641		256,349,2646	no	coding	FMN2	NM_020066.4		371,485,3903	A1A1,A1R,RR		13.2421,12.1353,12.8914				1227,8291				238438098	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	1.37:g.240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENSP00000318884:p.Pro1133_Pro1143del	Somatic		Capture	Illumina HiSeq	Phase_I	238438066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152236046	152236046	+	Stop_Codon_Del	DEL	A	A	-	rs71403164|rs35060021	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:152236046delA	ENST00000243347.3	+	0	908					NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6						cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	AGCCACTTATAAAAAAAAAAA	0.289													|||unknown(HR)	2457	0.490615	0.4425	0.4207	5008	,	,		15615	0.5208		0.5189	False		,,,				2504	0.545																0			2											20.0	21.0	21.0					2																	152236046		2160	4277	6437	151944292	SO:0001567	stop_retained_variant	7130				CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	Exception_encountered	2.37:g.152236046delA		Somatic		Capture	Illumina HiSeq	Phase_I	151944292	Q53TI7|Q8WWI9	Frame_Shift_Del	DEL	ENST00000243347.3	37	CCDS2193.1																																																																																				TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609239	32609241	+	In_Frame_Del	DEL	GGT	GGT	-	rs12722072|rs41556812|rs12722074|rs534654325	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	GGT	GGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609239_32609241delGGT	ENST00000343139.5	+	2	337_339	c.235_237delGGT	c.(235-237)ggtdel	p.G79del	HLA-DQA1_ENST00000374949.2_In_Frame_Del_p.G79del|HLA-DQA1_ENST00000395363.1_In_Frame_Del_p.G79del	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	78	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAAATTTGGAGGTTTTGACCCGC	0.502														1751	0.349641	0.3646	0.4236	5008	,	,		12241	0.2669		0.4046	False		,,,				2504	0.3057																0			6																																								32717219	SO:0001651	inframe_deletion	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.235_237delGGT	6.37:g.32609239_32609241delGGT	ENSP00000339398:p.Gly79del	Somatic		Capture	Illumina HiSeq	Phase_I	32717217	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	In_Frame_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609296	32609297	+	Frame_Shift_Ins	INS	-	-	G	rs9279910|rs9282026		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609296_32609297insG	ENST00000343139.5	+	2	394_395	c.292_293insG	c.(292-294)atcfs	p.I98fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Ins_p.I98fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Ins_p.I98fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	97	Alpha-1.		L -> M (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06 and allele DQA1*01:07).|L -> V (in allele DQA1*03:01, allele DQA1*03:02 and allele DQA1*03:03).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAACTTGAACATCATGATTAAA	0.480																																																	0			6								427,3759		87,253,1753						-3.9	0.0		dbSNP_118	83	1014,6964		244,526,3219	no	frameshift	HLA-DQA1	NM_002122.3		331,779,4972	A1A1,A1R,RR		12.71,10.2007,11.8464				1441,10723				32717275	SO:0001589	frameshift_variant	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	Exception_encountered	6.37:g.32609296_32609297insG	ENSP00000339398:p.Ile98fs	Somatic		Capture	Illumina HiSeq	Phase_I	32717274	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Frame_Shift_Ins	INS	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609299	32609299	+	Frame_Shift_Del	DEL	A	A	-	rs199556640|rs371894400|rs1064944	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609299delA	ENST00000343139.5	+	2	397	c.295delA	c.(295-297)atgfs	p.M99fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Del_p.M99fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Del_p.M99fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	98	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTTGAACATCATGATTAAACG	0.478																																																	0			6								349,3769		119,111,1829	95.0	82.0	86.0			2.2	0.0	6	dbSNP_118	84	786,7010		289,208,3401	no	frameshift	HLA-DQA1	NM_002122.3		408,319,5230	A1A1,A1R,RR		10.0821,8.475,9.5266			32609299	1135,10779	2029	3748	5777	32717277	SO:0001589	frameshift_variant	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.295delA	6.37:g.32609299delA	ENSP00000339398:p.Met99fs	Somatic		Capture	Illumina HiSeq	Phase_I	32717277	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Frame_Shift_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs	Somatic		Capture	Illumina HiSeq	Phase_I	1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FAM186A	121006	hgsc.bcm.edu	37	12	50745913	50745948	+	In_Frame_Del	DEL	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	-	rs34283706|rs538502101|rs34000017|rs35116763		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:50745913_50745948delTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	ENST00000327337.5	-	4	4666_4701	c.4667_4702delTCCCTCCGCAGGCTCAGGAATTGGAGATCCCTCTCA	c.(4666-4704)atccctccgcaggctcaggaattggagatccctctcacc>acc	p.IPPQAQELEIPL1556del	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_In_Frame_Del_p.IPPQAQELEIPL1556del	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1556																	TGCTGAGGGGTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGATGAGAGGGAT	0.665																																					NSCLC(138;1796 1887 12511 19463 37884)												0			12																																								49032215	SO:0001651	inframe_deletion	121006				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4667_4702delTCCCTCCGCAGGCTCAGGAATTGGAGATCCCTCTCA	12.37:g.50745913_50745948delTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	ENSP00000329995:p.Ile1556_Leu1567del	Somatic		Capture	Illumina HiSeq	Phase_I	49032180		In_Frame_Del	DEL	ENST00000327337.5	37	CCDS44878.1																																																																																				FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:55820959delA	ENST00000328314.3	+	1	922	c.922delA	c.(922-924)aaafs	p.K311fs		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCCCACAAAAAAAAAAA	0.338																																																	0			12											19.0	20.0	19.0					12																	55820959		2110	4120	6230	54107226	SO:0001589	frameshift_variant	390326				CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.922delA	12.37:g.55820959delA	ENSP00000328402:p.Lys311fs	Somatic		Capture	Illumina HiSeq	Phase_I	54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
PRR25	388199	hgsc.bcm.edu	37	16	863356	863372	+	Frame_Shift_Del	DEL	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC	-	rs367751056|rs199580467|rs371962006|rs200304320|rs138733834	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:863356_863372delGGACGCCGGACCGACAC	ENST00000301698.1	+	3	704_720	c.704_720delGGACGCCGGACCGACAC	c.(703-720)aggacgccggaccgacacfs	p.RTPDRH235fs		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	235										large_intestine(1)|lung(1)|skin(1)	3						GGACCGGCAAGGACGCCGGACCGACACGGCCTCCCCA	0.714														1307	0.260982	0.6876	0.2622	5008	,	,		14975	0.0675		0.0755	False		,,,				2504	0.0736																0			16																																								803373	SO:0001589	frameshift_variant	0			BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.704_720delGGACGCCGGACCGACAC	16.37:g.863356_863372delGGACGCCGGACCGACAC	ENSP00000301698:p.Arg235fs	Somatic		Capture	Illumina HiSeq	Phase_I	803357		Frame_Shift_Del	DEL	ENST00000301698.1	37	CCDS45372.1																																																																																				PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
DPEP1	1800	hgsc.bcm.edu	37	16	89702769	89702770	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:89702769_89702770insC	ENST00000393092.3	+	4	626_627	c.335_336insC	c.(334-339)tacccgfs	p.YP112fs	DPEP1_ENST00000261615.4_Frame_Shift_Ins_p.YP112fs|DPEP1_ENST00000421184.1_Frame_Shift_Ins_p.YP112fs	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	112					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	TGCCGGATGTACCCGGAGACCT	0.629																																																	0			16																																								88230271	SO:0001589	frameshift_variant	1800				CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.338dupC	16.37:g.89702772_89702772dupC	ENSP00000376807:p.Tyr112fs	Somatic		Capture	Illumina HiSeq	Phase_I	88230270	D3DX80|Q96AK2	Frame_Shift_Ins	INS	ENST00000393092.3	37	CCDS10982.1																																																																																				DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141	
MYH13	8735	hgsc.bcm.edu	37	17	10219217	10219218	+	Splice_Site	INS	-	-	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:10219217_10219218insG	ENST00000418404.3	-	27	4026_4027	c.3863_3864insC	c.(3862-3864)aat>aaCt	p.N1288fs	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Splice_Site_p.N1288fs			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1288					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CATTCTCACCATTTTGGGTCTG	0.530																																																	0			17																																								10159943	SO:0001630	splice_region_variant	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3865+1->C	17.37:g.10219217_10219218insG		Somatic		Capture	Illumina HiSeq	Phase_I	10159942	O95252|Q9P0U8	Frame_Shift_Ins	INS	ENST00000418404.3	37	CCDS45613.1																																																																																				MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	Frame_Shift_Ins
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
FMN2	56776	hgsc.bcm.edu	37	1	240371443	240371475	+	In_Frame_Del	DEL	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	-	rs200800873|rs199920451|rs112021213|rs367816204|rs199702261|rs200682272|rs201396397|rs181634878	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	CCCCCTCTACCCGGAGCGGGCATACCCCCTCCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr1:240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENST00000319653.9	+	5	3561_3593	c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	c.(3331-3363)ccccctctacccggagcgggcataccccctcctdel	p.PPLPGAGIPPP1133del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1133	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.A1259A(1)|p.G1260C(1)|p.P1262P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCTCCTCCGCCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCTCTAC	0.721																																																	3	Substitution - coding silent(2)|Substitution - Missense(1)	lung(2)|prostate(1)	1								366,2650		115,136,1257						-4.9	0.0			10	861,5641		256,349,2646	no	coding	FMN2	NM_020066.4		371,485,3903	A1A1,A1R,RR		13.2421,12.1353,12.8914				1227,8291				238438098	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3331_3363delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	1.37:g.240371443_240371475delCCCCCTCTACCCGGAGCGGGCATACCCCCTCCT	ENSP00000318884:p.Pro1133_Pro1143del	Somatic		Capture	Illumina HiSeq	Phase_I	238438066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152236046	152236046	+	Stop_Codon_Del	DEL	A	A	-	rs71403164|rs35060021	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr2:152236046delA	ENST00000243347.3	+	0	908					NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6						cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	AGCCACTTATAAAAAAAAAAA	0.289													|||unknown(HR)	2457	0.490615	0.4425	0.4207	5008	,	,		15615	0.5208		0.5189	False		,,,				2504	0.545																0			2											20.0	21.0	21.0					2																	152236046		2160	4277	6437	151944292	SO:0001567	stop_retained_variant	7130				CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	Exception_encountered	2.37:g.152236046delA		Somatic		Capture	Illumina HiSeq	Phase_I	151944292	Q53TI7|Q8WWI9	Frame_Shift_Del	DEL	ENST00000243347.3	37	CCDS2193.1																																																																																				TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609239	32609241	+	In_Frame_Del	DEL	GGT	GGT	-	rs12722072|rs41556812|rs12722074|rs534654325	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	GGT	GGT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609239_32609241delGGT	ENST00000343139.5	+	2	337_339	c.235_237delGGT	c.(235-237)ggtdel	p.G79del	HLA-DQA1_ENST00000374949.2_In_Frame_Del_p.G79del|HLA-DQA1_ENST00000395363.1_In_Frame_Del_p.G79del	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	78	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAAATTTGGAGGTTTTGACCCGC	0.502														1751	0.349641	0.3646	0.4236	5008	,	,		12241	0.2669		0.4046	False		,,,				2504	0.3057																0			6																																								32717219	SO:0001651	inframe_deletion	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.235_237delGGT	6.37:g.32609239_32609241delGGT	ENSP00000339398:p.Gly79del	Somatic		Capture	Illumina HiSeq	Phase_I	32717217	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	In_Frame_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609296	32609297	+	Frame_Shift_Ins	INS	-	-	G	rs9279910|rs9282026		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609296_32609297insG	ENST00000343139.5	+	2	394_395	c.292_293insG	c.(292-294)atcfs	p.I98fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Ins_p.I98fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Ins_p.I98fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	97	Alpha-1.		L -> M (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06 and allele DQA1*01:07).|L -> V (in allele DQA1*03:01, allele DQA1*03:02 and allele DQA1*03:03).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAACTTGAACATCATGATTAAA	0.480																																																	0			6								427,3759		87,253,1753						-3.9	0.0		dbSNP_118	83	1014,6964		244,526,3219	no	frameshift	HLA-DQA1	NM_002122.3		331,779,4972	A1A1,A1R,RR		12.71,10.2007,11.8464				1441,10723				32717275	SO:0001589	frameshift_variant	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	Exception_encountered	6.37:g.32609296_32609297insG	ENSP00000339398:p.Ile98fs	Somatic		Capture	Illumina HiSeq	Phase_I	32717274	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Frame_Shift_Ins	INS	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609299	32609299	+	Frame_Shift_Del	DEL	A	A	-	rs199556640|rs371894400|rs1064944	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr6:32609299delA	ENST00000343139.5	+	2	397	c.295delA	c.(295-297)atgfs	p.M99fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Del_p.M99fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Del_p.M99fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	98	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTTGAACATCATGATTAAACG	0.478																																																	0			6								349,3769		119,111,1829	95.0	82.0	86.0			2.2	0.0	6	dbSNP_118	84	786,7010		289,208,3401	no	frameshift	HLA-DQA1	NM_002122.3		408,319,5230	A1A1,A1R,RR		10.0821,8.475,9.5266			32609299	1135,10779	2029	3748	5777	32717277	SO:0001589	frameshift_variant	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.295delA	6.37:g.32609299delA	ENSP00000339398:p.Met99fs	Somatic		Capture	Illumina HiSeq	Phase_I	32717277	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Frame_Shift_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs	Somatic		Capture	Illumina HiSeq	Phase_I	1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FAM186A	121006	hgsc.bcm.edu	37	12	50745913	50745948	+	In_Frame_Del	DEL	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	-	rs34283706|rs538502101|rs34000017|rs35116763		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	TGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:50745913_50745948delTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	ENST00000327337.5	-	4	4666_4701	c.4667_4702delTCCCTCCGCAGGCTCAGGAATTGGAGATCCCTCTCA	c.(4666-4704)atccctccgcaggctcaggaattggagatccctctcacc>acc	p.IPPQAQELEIPL1556del	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_In_Frame_Del_p.IPPQAQELEIPL1556del	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1556																	TGCTGAGGGGTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGATGAGAGGGAT	0.665																																					NSCLC(138;1796 1887 12511 19463 37884)												0			12																																								49032215	SO:0001651	inframe_deletion	121006				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4667_4702delTCCCTCCGCAGGCTCAGGAATTGGAGATCCCTCTCA	12.37:g.50745913_50745948delTGAGAGGGATCTCCAATTCCTGAGCCTGCGGAGGGA	ENSP00000329995:p.Ile1556_Leu1567del	Somatic		Capture	Illumina HiSeq	Phase_I	49032180		In_Frame_Del	DEL	ENST00000327337.5	37	CCDS44878.1																																																																																				FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr12:55820959delA	ENST00000328314.3	+	1	922	c.922delA	c.(922-924)aaafs	p.K311fs		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCCCACAAAAAAAAAAA	0.338																																																	0			12											19.0	20.0	19.0					12																	55820959		2110	4120	6230	54107226	SO:0001589	frameshift_variant	390326				CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.922delA	12.37:g.55820959delA	ENSP00000328402:p.Lys311fs	Somatic		Capture	Illumina HiSeq	Phase_I	54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
PRR25	388199	hgsc.bcm.edu	37	16	863356	863372	+	Frame_Shift_Del	DEL	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC	-	rs367751056|rs199580467|rs371962006|rs200304320|rs138733834	byFrequency	TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:863356_863372delGGACGCCGGACCGACAC	ENST00000301698.1	+	3	704_720	c.704_720delGGACGCCGGACCGACAC	c.(703-720)aggacgccggaccgacacfs	p.RTPDRH235fs		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	235										large_intestine(1)|lung(1)|skin(1)	3						GGACCGGCAAGGACGCCGGACCGACACGGCCTCCCCA	0.714														1307	0.260982	0.6876	0.2622	5008	,	,		14975	0.0675		0.0755	False		,,,				2504	0.0736																0			16																																								803373	SO:0001589	frameshift_variant	0			BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.704_720delGGACGCCGGACCGACAC	16.37:g.863356_863372delGGACGCCGGACCGACAC	ENSP00000301698:p.Arg235fs	Somatic		Capture	Illumina HiSeq	Phase_I	803357		Frame_Shift_Del	DEL	ENST00000301698.1	37	CCDS45372.1																																																																																				PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
DPEP1	1800	hgsc.bcm.edu	37	16	89702769	89702770	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr16:89702769_89702770insC	ENST00000393092.3	+	4	626_627	c.335_336insC	c.(334-339)tacccgfs	p.YP112fs	DPEP1_ENST00000261615.4_Frame_Shift_Ins_p.YP112fs|DPEP1_ENST00000421184.1_Frame_Shift_Ins_p.YP112fs	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	112					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	TGCCGGATGTACCCGGAGACCT	0.629																																																	0			16																																								88230271	SO:0001589	frameshift_variant	1800				CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.338dupC	16.37:g.89702772_89702772dupC	ENSP00000376807:p.Tyr112fs	Somatic		Capture	Illumina HiSeq	Phase_I	88230270	D3DX80|Q96AK2	Frame_Shift_Ins	INS	ENST00000393092.3	37	CCDS10982.1																																																																																				DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141	
MYH13	8735	hgsc.bcm.edu	37	17	10219217	10219218	+	Splice_Site	INS	-	-	G			TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr17:10219217_10219218insG	ENST00000418404.3	-	27	4026_4027	c.3863_3864insC	c.(3862-3864)aat>aaCt	p.N1288fs	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Splice_Site_p.N1288fs			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1288					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CATTCTCACCATTTTGGGTCTG	0.530																																																	0			17																																								10159943	SO:0001630	splice_region_variant	8735			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3865+1->C	17.37:g.10219217_10219218insG		Somatic		Capture	Illumina HiSeq	Phase_I	10159942	O95252|Q9P0U8	Frame_Shift_Ins	INS	ENST00000418404.3	37	CCDS45613.1																																																																																				MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	Frame_Shift_Ins
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-DY-A1DC-01A-31D-A152-10	TCGA-DY-A1DC-10A-01D-A152-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3348da3-576f-42b0-a392-e0c2a49bd87a	70a4d555-69a2-437e-a2bb-5697a3f865ea	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
