#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	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_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ESPN	83715	hgsc.bcm.edu	37	1	6520166	6520166	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:6520166G>T	ENST00000377828.1	+	13	2693	c.2525G>T	c.(2524-2526)cGa>cTa	p.R842L	ESPN_ENST00000461727.1_Missense_Mutation_p.R276L|ESPN_ENST00000416731.1_Missense_Mutation_p.R276L	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	842					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		CCCTGGCAGCGACAGGTCATC	0.657																																					p.R842L		Atlas-SNP	.											.	ESPN	32	.	0			c.G2525T						.						46.0	47.0	47.0					1																	6520166		2203	4300	6503	SO:0001583	missense	83715	exon13			GGCAGCGACAGGT	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.2525G>T	chr1.hg19:g.6520166G>T	ENSP00000367059:p.Arg842Leu	164.0	0.0		203.0	38.0	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	hg19	CCDS70.1	.	.	.	.	.	.	.	.	.	.	g	26.2	4.712101	0.89112	.	.	ENSG00000187017	ENST00000377828;ENST00000416731	D;D	0.87887	-2.31;-2.31	4.32	4.32	0.51571	.	0.470861	0.18767	N	0.131731	D	0.90631	0.7062	M	0.67953	2.075	0.32685	N	0.514916	D;D	0.57571	0.98;0.98	P;P	0.56343	0.736;0.796	D	0.93084	0.6494	10	0.72032	D	0.01	-6.5359	14.3356	0.66586	0.0:0.0:1.0:0.0	.	276;842	B1AK53-2;B1AK53	.;ESPN_HUMAN	L	842;276	ENSP00000367059:R842L;ENSP00000399239:R276L	ENSP00000367059:R842L	R	+	2	0	ESPN	6442753	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.036000	0.70948	1.945000	0.56424	0.450000	0.29827	CGA	.	.		0.657	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
MAST2	23139	hgsc.bcm.edu	37	1	46485312	46485312	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:46485312G>A	ENST00000361297.2	+	11	1516	c.1233G>A	c.(1231-1233)caG>caA	p.Q411Q	MAST2_ENST00000372009.2_Silent_p.Q341Q	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TTGTGATGCAGCTGGTGAAAA	0.507																																					p.Q411Q		Atlas-SNP	.											.	MAST2	136	.	0			c.G1233A						.						88.0	87.0	87.0					1																	46485312		1976	4170	6146	SO:0001819	synonymous_variant	23139	exon11			GATGCAGCTGGTG	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1233G>A	chr1.hg19:g.46485312G>A		188.0	0.0		157.0	26.0	NM_015112		Silent	SNP	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.		0.507	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
ERICH3	127254	hgsc.bcm.edu	37	1	75037157	75037157	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:75037157C>A	ENST00000326665.5	-	14	4455	c.4237G>T	c.(4237-4239)Gag>Tag	p.E1413*	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1413	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GGCACTTCCTCCCCACTCCGT	0.552																																					p.E1413X		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4237T						.						99.0	99.0	99.0					1																	75037157		2203	4300	6503	SO:0001587	stop_gained	127254	exon14			CTTCCTCCCCACT																												ENST00000326665.5:c.4237G>T	chr1.hg19:g.75037157C>A	ENSP00000322609:p.Glu1413*	358.0	0.0		299.0	41.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Nonsense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	42	9.519403	0.99193	.	.	ENSG00000178965	ENST00000326665	.	.	.	4.58	3.64	0.41730	.	.	.	.	.	.	.	.	.	.	.	0.25645	N	0.986154	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-1.463	12.1663	0.54131	0.0:0.8257:0.1743:0.0	.	.	.	.	X	1413	.	ENSP00000322609:E1413X	E	-	1	0	C1orf173	74809745	0.087000	0.21565	0.027000	0.17364	0.032000	0.12392	2.336000	0.43938	0.888000	0.36160	0.561000	0.74099	GAG	.	.		0.552	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
NEXN	91624	hgsc.bcm.edu	37	1	78407772	78407772	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:78407772T>A	ENST00000334785.7	+	12	1722	c.1538T>A	c.(1537-1539)aTg>aAg	p.M513K	FUBP1_ENST00000489495.1_5'Flank|NEXN_ENST00000457030.1_Missense_Mutation_p.M499K|NEXN_ENST00000330010.8_Missense_Mutation_p.M449K|NEXN_ENST00000480732.2_3'UTR	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		AAAGTGAATATGAAAGCTAGA	0.388																																					p.M513K		Atlas-SNP	.											.	NEXN	77	.	0			c.T1538A						.						56.0	50.0	52.0					1																	78407772		1847	4095	5942	SO:0001583	missense	91624	exon12			TGAATATGAAAGC	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"""Immunoglobulin superfamily / I-set domain containing"""	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1538T>A	chr1.hg19:g.78407772T>A	ENSP00000333938:p.Met513Lys	339.0	0.0		299.0	43.0	NM_144573		Missense_Mutation	SNP	ENST00000334785.7	hg19	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.1|26.1	4.706696|4.706696	0.89018|0.89018	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000457030;ENST00000330010;ENST00000334785|ENST00000342754	T;T;T|.	0.60797|.	0.24;0.16;0.24|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	0.255168|.	0.29145|.	N|.	0.013004|.	T|.	0.67468|.	0.2896|.	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.999;0.995;0.992;0.999|.	D;D;D;D|.	0.79784|.	0.993;0.988;0.972;0.993|.	T|.	0.68614|.	-0.5362|.	10|.	0.07030|.	T|.	0.85|.	-17.1734|-17.1734	15.9818|15.9818	0.80116|0.80116	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	449;499;513;449|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	K|R	499;449;513|413	ENSP00000388048:M499K;ENSP00000327363:M449K;ENSP00000333938:M513K|.	ENSP00000327363:M449K|.	M|X	+|+	2|1	0|0	NEXN|NEXN	78180360|78180360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.022000|8.022000	0.88759|0.88759	2.172000|2.172000	0.68678|0.68678	0.477000|0.477000	0.44152|0.44152	ATG|TGA	.	.		0.388	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573	
S100A7A	338324	hgsc.bcm.edu	37	1	153390678	153390678	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:153390678C>A	ENST00000368729.4	+	2	177	c.120C>A	c.(118-120)ttC>ttA	p.F40L	S100A7A_ENST00000329256.2_Missense_Mutation_p.F40L|S100A7A_ENST00000368728.2_Missense_Mutation_p.F40L	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)	p.F40F(1)		cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGAGAACTTCCCCAATTTCC	0.488																																					p.F40L		Atlas-SNP	.											S100A7A,NS,carcinoma,0,1	S100A7A	24	.	1	Substitution - coding silent(1)	lung(1)	c.C120A						.						183.0	159.0	167.0					1																	153390678		2203	4300	6503	SO:0001583	missense	338324	exon2			GAACTTCCCCAAT	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	21657	protein-coding gene	gene with protein product			"""S100 calcium binding protein A15"", ""S100 calcium binding protein A7-like 1"""	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.120C>A	chr1.hg19:g.153390678C>A	ENSP00000357718:p.Phe40Leu	312.0	1.0		446.0	163.0	NM_176823	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	hg19	CCDS30872.1	.	.	.	.	.	.	.	.	.	.	.	17.41	3.382061	0.61845	.	.	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.04360	3.64;3.64;3.64	2.42	1.46	0.22682	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01627	0.0052	N	0.11364	0.135	0.24705	N	0.993231	D	0.89917	1.0	D	0.91635	0.999	T	0.28138	-1.0053	9	0.02654	T	1	.	5.5578	0.17125	0.0:0.8329:0.0:0.1671	.	40	Q86SG5	S1A7A_HUMAN	L	40	ENSP00000357718:F40L;ENSP00000357717:F40L;ENSP00000329008:F40L	ENSP00000329008:F40L	F	+	3	2	S100A7A	151657302	0.107000	0.21998	0.917000	0.36280	0.436000	0.31835	0.132000	0.15891	0.534000	0.28695	0.585000	0.79938	TTC	.	.		0.488	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823	
RGSL1	353299	hgsc.bcm.edu	37	1	182458241	182458241	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:182458241G>T	ENST00000294854.8	+	8	1641	c.1621G>T	c.(1621-1623)Gaa>Taa	p.E541*	RGSL1_ENST00000542961.1_Nonsense_Mutation_p.E576*	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	541					termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						TGACATGAAGGAAATGGACTA	0.438																																					p.E541X	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											.	RGSL1	111	.	0			c.G1621T						.						98.0	85.0	89.0					1																	182458241		692	1591	2283	SO:0001587	stop_gained	353299	exon8			ATGAAGGAAATGG	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.1621G>T	chr1.hg19:g.182458241G>T	ENSP00000457748:p.Glu541*	241.0	0.0		270.0	40.0	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Nonsense_Mutation	SNP	ENST00000294854.8	hg19	CCDS58049.1																																																																																			.	.		0.438	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
IVNS1ABP	10625	hgsc.bcm.edu	37	1	185274712	185274712	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:185274712C>A	ENST00000367498.3	-	8	1343	c.721G>T	c.(721-723)Gct>Tct	p.A241S	IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.A23S|IVNS1ABP_ENST00000459929.1_5'UTR	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	241	Sufficient for AHR interaction and signaling.				negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						AACACCTCAGCCTGTCCATCT	0.453																																					p.A241S		Atlas-SNP	.											.	IVNS1ABP	80	.	0			c.G721T						.						191.0	157.0	168.0					1																	185274712		2203	4300	6503	SO:0001583	missense	10625	exon8			CCTCAGCCTGTCC	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"""Kelch-like"", ""BTB/POZ domain containing"""	16951	protein-coding gene	gene with protein product	"""kelch-like family member 39"""	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.721G>T	chr1.hg19:g.185274712C>A	ENSP00000356468:p.Ala241Ser	259.0	0.0		297.0	107.0	NM_006469	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	hg19	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	C	8.607	0.888224	0.17540	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.75704	-0.96;-0.56	5.57	5.57	0.84162	.	0.147379	0.64402	D	0.000009	T	0.54532	0.1864	N	0.14661	0.345	0.46260	D	0.998957	B;B	0.14438	0.01;0.01	B;B	0.15052	0.012;0.005	T	0.51537	-0.8693	10	0.07325	T	0.83	.	12.8374	0.57782	0.0:0.9256:0.0:0.0744	.	23;241	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	S	241;23	ENSP00000356468:A241S;ENSP00000375864:A23S	ENSP00000356468:A241S	A	-	1	0	IVNS1ABP	183541335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.597000	0.54031	2.614000	0.88457	0.557000	0.71058	GCT	.	.		0.453	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469	
OR2T12	127064	hgsc.bcm.edu	37	1	248458244	248458244	+	Missense_Mutation	SNP	G	G	T	rs369151985		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr1:248458244G>T	ENST00000317996.1	-	1	636	c.637C>A	c.(637-639)Ctg>Atg	p.L213M		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TAGGAGGACAGGATGAGGGAA	0.542																																					p.L213M		Atlas-SNP	.											OR2T12,NS,carcinoma,0,1	OR2T12	113	.	0			c.C637A						.						80.0	68.0	72.0					1																	248458244		2203	4297	6500	SO:0001583	missense	127064	exon1			AGGACAGGATGAG	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.637C>A	chr1.hg19:g.248458244G>T	ENSP00000324583:p.Leu213Met	1449.0	2.0		1594.0	243.0	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	11.34	1.610495	0.28712	.	.	ENSG00000177201	ENST00000317996	T	0.00269	8.37	1.55	-2.43	0.06522	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29280	U	0.012616	T	0.00271	0.0008	L	0.51914	1.62	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.54964	-0.8214	10	0.41790	T	0.15	.	1.1523	0.01788	0.1468:0.1493:0.2893:0.4146	.	213	Q8NG77	O2T12_HUMAN	M	213	ENSP00000324583:L213M	ENSP00000324583:L213M	L	-	1	2	OR2T12	246524867	0.000000	0.05858	0.002000	0.10522	0.305000	0.27757	-2.179000	0.01259	-0.207000	0.10187	0.175000	0.17021	CTG	.	.		0.542	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
EGR4	1961	hgsc.bcm.edu	37	2	73518960	73518960	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73518960G>A	ENST00000545030.1	-	2	1469	c.1395C>T	c.(1393-1395)cgC>cgT	p.R465R	EGR4_ENST00000436467.2_Silent_p.R362R	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	465					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|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)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						ATTTGCCGCCGCGGCGCCCCT	0.731																																					p.R465R		Atlas-SNP	.											.	EGR4	52	.	0			c.C1395T						.						7.0	8.0	8.0					2																	73518960		2130	4139	6269	SO:0001819	synonymous_variant	1961	exon2			GCCGCCGCGGCGC		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1395C>T	chr2.hg19:g.73518960G>A		2.0	0.0		11.0	7.0	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	hg19	CCDS1925.2																																																																																			.	.		0.731	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
ALMS1	7840	hgsc.bcm.edu	37	2	73677972	73677972	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73677972C>T	ENST00000264448.6	+	8	4426	c.4315C>T	c.(4315-4317)Caa>Taa	p.Q1439*	ALMS1_ENST00000377715.1_Nonsense_Mutation_p.Q1439*|ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Q1397*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1439	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TAGTTTCTACCAACAGGTCTT	0.498																																					p.Q1439X		Atlas-SNP	.											.	ALMS1	384	.	0			c.C4315T						.						123.0	123.0	123.0					2																	73677972		1869	4109	5978	SO:0001587	stop_gained	7840	exon8			TTCTACCAACAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.4315C>T	chr2.hg19:g.73677972C>T	ENSP00000264448:p.Gln1439*	304.0	0.0		246.0	23.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	41	8.732772	0.98933	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	.	.	.	4.29	3.41	0.39046	.	1.331870	0.05417	N	0.543610	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	9.7911	0.40706	0.2048:0.7952:0.0:0.0	.	.	.	.	X	1397;1439;1439	.	ENSP00000264448:Q1439X	Q	+	1	0	ALMS1	73531480	0.001000	0.12720	0.004000	0.12327	0.001000	0.01503	0.974000	0.29436	1.382000	0.46385	-0.230000	0.12252	CAA	.	.		0.498	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ALMS1	7840	hgsc.bcm.edu	37	2	73800105	73800105	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:73800105C>T	ENST00000264448.6	+	16	11209	c.11098C>T	c.(11098-11100)Cat>Tat	p.H3700Y	ALMS1_ENST00000409009.1_Missense_Mutation_p.H3658Y	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3700					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GCTTTCTCATCATCGAGCTGG	0.333																																					p.H3700Y		Atlas-SNP	.											.	ALMS1	384	.	0			c.C11098T						.						44.0	44.0	44.0					2																	73800105		1818	4065	5883	SO:0001583	missense	7840	exon16			TCTCATCATCGAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.11098C>T	chr2.hg19:g.73800105C>T	ENSP00000264448:p.His3700Tyr	138.0	0.0		153.0	18.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	7.166	0.586628	0.13749	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.08193	3.12;3.12	4.89	2.0	0.26442	.	0.000000	0.47455	D	0.000234	T	0.12774	0.0310	L	0.38175	1.15	0.09310	N	0.999999	D;P;P	0.64830	0.994;0.578;0.578	P;B;B	0.62184	0.899;0.264;0.264	T	0.05321	-1.0892	10	0.66056	D	0.02	.	4.4163	0.11457	0.1781:0.6328:0.0:0.1891	.	3700;3658;3700	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	Y	3658;3700	ENSP00000386627:H3658Y;ENSP00000264448:H3700Y	ENSP00000264448:H3700Y	H	+	1	0	ALMS1	73653613	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	0.222000	0.17699	0.642000	0.30620	0.609000	0.83330	CAT	.	.		0.333	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
MYO7B	4648	hgsc.bcm.edu	37	2	128335798	128335798	+	Nonsense_Mutation	SNP	G	G	T	rs549327895		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:128335798G>T	ENST00000409816.2	+	8	972	c.940G>T	c.(940-942)Gag>Tag	p.E314*	MYO7B_ENST00000428314.1_Nonsense_Mutation_p.E314*|MYO7B_ENST00000389524.4_Nonsense_Mutation_p.E314*			Q6PIF6	MYO7B_HUMAN	myosin VIIB	314	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CTCCGACTCCGAGAGCTGGGA	0.607																																					p.E314X		Atlas-SNP	.											.	MYO7B	359	.	0			c.G940T						.						55.0	60.0	58.0					2																	128335798		2101	4219	6320	SO:0001587	stop_gained	4648	exon9			GACTCCGAGAGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.940G>T	chr2.hg19:g.128335798G>T	ENSP00000386461:p.Glu314*	140.0	0.0		171.0	24.0	NM_001080527	Q14786|Q8TEE1	Nonsense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	32	5.107329	0.94292	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	.	.	.	4.25	4.25	0.50352	.	0.060140	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	17.1863	0.86868	0.0:0.0:1.0:0.0	.	.	.	.	X	314	.	ENSP00000374175:E314X	E	+	1	0	MYO7B	128052268	1.000000	0.71417	0.935000	0.37517	0.289000	0.27227	7.682000	0.84083	2.365000	0.80145	0.563000	0.77884	GAG	.	.		0.607	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
MYO3B	140469	hgsc.bcm.edu	37	2	171260816	171260816	+	Silent	SNP	G	G	T	rs201316029		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr2:171260816G>T	ENST00000408978.4	+	20	2480	c.2337G>T	c.(2335-2337)ccG>ccT	p.P779P	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.P779P|MYO3B_ENST00000334231.6_Silent_p.P788P	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	779	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ACAACCGCCCGCTCTTGGACA	0.502																																					p.P779P		Atlas-SNP	.											.	MYO3B	320	.	0			c.G2337T						.						124.0	119.0	120.0					2																	171260816		1909	4115	6024	SO:0001819	synonymous_variant	140469	exon20			CCGCCCGCTCTTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2337G>T	chr2.hg19:g.171260816G>T		225.0	0.0		210.0	41.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	hg19	CCDS42773.1																																																																																			.	G|0.999;A|0.001		0.502	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
USP19	10869	hgsc.bcm.edu	37	3	49151699	49151699	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:49151699G>C	ENST00000398888.2	-	15	2320	c.2002C>G	c.(2002-2004)Ccg>Gcg	p.P668A	USP19_ENST00000453664.1_Missense_Mutation_p.P759A|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000434032.2_Missense_Mutation_p.P769A|USP19_ENST00000398898.2_Missense_Mutation_p.P708A|USP19_ENST00000398896.1_Missense_Mutation_p.P476A|USP19_ENST00000417901.1_Missense_Mutation_p.P771A|USP19_ENST00000398892.3_Missense_Mutation_p.P708A	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	668	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TAAAGAAACGGGTCAAAAGTG	0.537																																					p.P771A		Atlas-SNP	.											.	USP19	158	.	0			c.C2311G						.						71.0	77.0	75.0					3																	49151699		1977	4166	6143	SO:0001583	missense	10869	exon16			GAAACGGGTCAAA	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2002C>G	chr3.hg19:g.49151699G>C	ENSP00000381863:p.Pro668Ala	132.0	0.0		200.0	39.0	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	G	32	5.149690	0.94645	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36	6.17	6.17	0.99709	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.64538	0.2607	M	0.75150	2.29	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.996;0.983;0.992;0.994	T	0.63897	-0.6533	10	0.87932	D	0	-16.0913	20.8794	0.99867	0.0:0.0:1.0:0.0	.	769;759;668;708;476	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	A	476;708;771;759;708;668;769	ENSP00000381870:P476A;ENSP00000381872:P708A;ENSP00000395260:P771A;ENSP00000400090:P759A;ENSP00000381867:P708A;ENSP00000381863:P668A;ENSP00000401197:P769A	ENSP00000381863:P668A	P	-	1	0	USP19	49126703	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.896000	0.87350	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.537	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
STAB1	23166	hgsc.bcm.edu	37	3	52546358	52546358	+	Splice_Site	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:52546358C>T	ENST00000321725.6	+	27	2961	c.2885C>T	c.(2884-2886)gCc>gTc	p.A962V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	962	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCACCCCAGGCCACCTGCCGG	0.657																																					p.A962V		Atlas-SNP	.											.	STAB1	178	.	0			c.C2885T						.						62.0	69.0	67.0					3																	52546358		2203	4299	6502	SO:0001630	splice_region_variant	23166	exon27			CCCAGGCCACCTG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2884-1C>T	chr3.hg19:g.52546358C>T		75.0	0.0		68.0	9.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.924544	0.73213	.	.	ENSG00000010327	ENST00000321725	D	0.97710	-4.5	5.57	5.57	0.84162	EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98112	0.9377	L	0.60012	1.86	0.58432	D	0.999992	D	0.69078	0.997	D	0.68765	0.96	D	0.98740	1.0716	10	0.87932	D	0	.	15.0541	0.71897	0.0:1.0:0.0:0.0	.	962	Q9NY15	STAB1_HUMAN	V	962	ENSP00000312946:A962V	ENSP00000312946:A962V	A	+	2	0	STAB1	52521398	1.000000	0.71417	1.000000	0.80357	0.158000	0.22134	3.154000	0.50693	2.633000	0.89246	0.563000	0.77884	GCC	.	.		0.657	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	Missense_Mutation
MECOM	2122	hgsc.bcm.edu	37	3	168819859	168819859	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr3:168819859G>A	ENST00000464456.1	-	9	3369	c.2169C>T	c.(2167-2169)cgC>cgT	p.R723R	MECOM_ENST00000472280.1_Silent_p.R733R|MECOM_ENST00000468789.1_Silent_p.R732R|MECOM_ENST00000460814.1_Silent_p.R723R|MECOM_ENST00000392736.3_Silent_p.R732R|MECOM_ENST00000494292.1_Silent_p.R911R|MECOM_ENST00000433243.2_Silent_p.R733R|MECOM_ENST00000264674.3_Silent_p.R797R	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGCAGGTATAGCGCTCCTTTC	0.488																																					p.R920R		Atlas-SNP	.											.	MECOM	216	.	0			c.C2760T						.						66.0	63.0	64.0					3																	168819859		2203	4300	6503	SO:0001819	synonymous_variant	2122	exon11			GGTATAGCGCTCC	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2169C>T	chr3.hg19:g.168819859G>A		172.0	0.0		153.0	24.0	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	hg19	CCDS54669.1																																																																																			.	.		0.488	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
PPBP	5473	hgsc.bcm.edu	37	4	74853684	74853684	+	Missense_Mutation	SNP	G	G	T	rs201755460		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr4:74853684G>T	ENST00000296028.3	-	1	230	c.137C>A	c.(136-138)gCg>gAg	p.A46E		NM_002704.3	NP_002695.1	P02775	CXCL7_HUMAN	pro-platelet basic protein (chemokine (C-X-C motif) ligand 7)	46					blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|defense response to bacterium (GO:0042742)|glucose transport (GO:0015758)|immune response (GO:0006955)|leukocyte migration involved in inflammatory response (GO:0002523)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell division (GO:0051781)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)	glucose transmembrane transporter activity (GO:0005355)			breast(1)|central_nervous_system(1)|lung(1)|ovary(2)|skin(2)|stomach(1)|urinary_tract(2)	10	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			TTTGCCTTTCGCCAAGTTTCT	0.532																																					p.A46E		Atlas-SNP	.											.	PPBP	27	.	0			c.C137A						.						136.0	127.0	130.0					4																	74853684		2203	4300	6503	SO:0001583	missense	5473	exon1			CCTTTCGCCAAGT	M54995	CCDS3563.1	4q12-q13	2013-02-25	2002-08-22		ENSG00000163736	ENSG00000163736		"""Endogenous ligands"""	9240	protein-coding gene	gene with protein product	"""platelet basic protein"", ""beta-thromboglobulin"", ""connective tissue-activating peptide III"", ""neutrophil-activating peptide-2"""	121010		THBGB1		1826003	Standard	NM_002704		Approved	SCYB7, TGB, NAP-2-L1, LA-PF4, MDGF, LDGF, Beta-TG, CTAP3, CXCL7, PBP, b-TG1, TGB1, CTAPIII, NAP-2	uc003hhj.3	P02775	OTTHUMG00000130008	ENST00000296028.3:c.137C>A	chr4.hg19:g.74853684G>T	ENSP00000296028:p.Ala46Glu	291.0	0.0		229.0	51.0	NM_002704	B2R5F3|Q6IBJ8	Missense_Mutation	SNP	ENST00000296028.3	hg19	CCDS3563.1	.	.	.	.	.	.	.	.	.	.	G	2.782	-0.253372	0.05829	.	.	ENSG00000163736	ENST00000296028	T	0.44482	0.92	2.23	-1.96	0.07525	Chemokine interleukin-8-like domain (1);	5.599220	0.01243	U	0.008678	T	0.14270	0.0345	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05801	-1.0863	10	0.27082	T	0.32	.	0.3377	0.00328	0.1992:0.3118:0.2055:0.2835	.	46	P02775	CXCL7_HUMAN	E	46	ENSP00000296028:A46E	ENSP00000296028:A46E	A	-	2	0	PPBP	75072548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.482000	0.02320	-0.618000	0.05656	-1.398000	0.01145	GCG	.	.		0.532	PPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252281.2	NM_002704	
GFM2	84340	hgsc.bcm.edu	37	5	74047313	74047313	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:74047313C>T	ENST00000296805.3	-	6	767	c.310G>A	c.(310-312)Gat>Aat	p.D104N	GFM2_ENST00000509430.1_Missense_Mutation_p.D104N|GFM2_ENST00000427854.2_Missense_Mutation_p.D104N|GFM2_ENST00000345239.2_Missense_Mutation_p.D104N	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TCTCCATCATCAACATCTAGC	0.383																																					p.D104N		Atlas-SNP	.											.	GFM2	38	.	0			c.G310A						.						172.0	163.0	166.0					5																	74047313		2203	4300	6503	SO:0001583	missense	84340	exon6			CATCATCAACATC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.310G>A	chr5.hg19:g.74047313C>T	ENSP00000296805:p.Asp104Asn	168.0	0.0		188.0	24.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024543	0.93518	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000506778	T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85	5.84	4.98	0.66077	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.088118	0.85682	D	0.000000	D	0.88306	0.6401	M	0.89601	3.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.982;0.99;0.99;0.99	D	0.90761	0.4665	10	0.87932	D	0	-20.5045	14.9609	0.71156	0.0:0.9316:0.0:0.0684	.	104;104;104;104	Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;RRF2M_HUMAN	N	104;104;104;104;104;29	ENSP00000296805:D104N;ENSP00000296804:D104N;ENSP00000427004:D104N;ENSP00000405808:D104N;ENSP00000424877:D29N	ENSP00000296805:D104N	D	-	1	0	GFM2	74083069	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.691000	0.84191	1.474000	0.48178	0.650000	0.86243	GAT	.	.		0.383	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
PCDHA11	56138	hgsc.bcm.edu	37	5	140250371	140250371	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:140250371G>A	ENST00000398640.2	+	1	1683	c.1683G>A	c.(1681-1683)gcG>gcA	p.A561A	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	561	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGACAACGCGCCGGCACTGC	0.682																																					p.A561A		Atlas-SNP	.											.	PCDHA11	209	.	0			c.G1683A						.						86.0	95.0	92.0					5																	140250371		2203	4299	6502	SO:0001819	synonymous_variant	56138	exon1			CAACGCGCCGGCA	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1683G>A	chr5.hg19:g.140250371G>A		105.0	0.0		104.0	16.0	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	hg19	CCDS47284.1																																																																																			.	.		0.682	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149213132	149213132	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:149213132C>T	ENST00000309241.5	+	5	1528	c.1496C>T	c.(1495-1497)cCc>cTc	p.P499L	PPARGC1B_ENST00000394320.3_Missense_Mutation_p.P499L|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.P460L|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.P435L	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	499					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGCTGGTCCCCTCGGAGCCC	0.667																																					p.P499L		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C1496T						.						27.0	30.0	29.0					5																	149213132		2196	4298	6494	SO:0001583	missense	133522	exon5			TGGTCCCCTCGGA	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.1496C>T	chr5.hg19:g.149213132C>T	ENSP00000312649:p.Pro499Leu	89.0	0.0		102.0	21.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977948	0.53720	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	4.96	4.03	0.46877	.	0.745481	0.12560	N	0.458285	T	0.25121	0.0610	L	0.59436	1.845	0.20196	N	0.99993	D;D;D;D;D	0.76494	0.996;0.997;0.996;0.993;0.999	P;D;P;P;D	0.76575	0.9;0.913;0.9;0.796;0.988	T	0.02632	-1.1131	10	0.87932	D	0	-7.8559	13.1038	0.59235	0.0:0.8394:0.1606:0.0	.	478;478;460;499;499	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	L	460;499;499;435	ENSP00000353638:P460L;ENSP00000377855:P499L;ENSP00000312649:P499L;ENSP00000384403:P435L	ENSP00000312649:P499L	P	+	2	0	PPARGC1B	149193325	0.000000	0.05858	0.550000	0.28217	0.644000	0.38419	0.539000	0.23175	2.289000	0.77006	0.561000	0.74099	CCC	.	.		0.667	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
FNDC9	408263	hgsc.bcm.edu	37	5	156768087	156768087	+	IGR	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr5:156768087G>T	ENST00000312349.4	-	0	2125				CYFIP2_ENST00000377576.3_Silent_p.R865R|CYFIP2_ENST00000435847.2_Silent_p.R564R|CYFIP2_ENST00000541131.1_Silent_p.R790R|CYFIP2_ENST00000347377.6_Silent_p.R865R|CYFIP2_ENST00000522463.1_Silent_p.R669R|CYFIP2_ENST00000442283.2_Silent_p.R150R|CYFIP2_ENST00000318218.6_Silent_p.R890R|CYFIP2_ENST00000521420.1_Silent_p.R839R	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GTTTTGTGCGGACTGCCATTC	0.473																																					p.R865R		Atlas-SNP	.											.	CYFIP2	354	.	0			c.G2595T						.						125.0	120.0	122.0					5																	156768087		1916	4132	6048	SO:0001628	intergenic_variant	26999	exon23			TGTGCGGACTGCC	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"""Fibronectin type III domain containing"""	33547	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 40"""	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248		chr5.hg19:g.156768087G>T		245.0	0.0		251.0	42.0	NM_001037332	A8K0Y6	Silent	SNP	ENST00000312349.4	hg19	CCDS4337.1																																																																																			.	.		0.473	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343	
CUL7	9820	hgsc.bcm.edu	37	6	43012996	43012996	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr6:43012996C>T	ENST00000265348.3	-	15	3092	c.3007G>A	c.(3007-3009)Gac>Aac	p.D1003N	CUL7_ENST00000535468.1_Missense_Mutation_p.D1087N|CUL7_ENST00000478630.1_5'Flank			Q14999	CUL7_HUMAN	cullin 7	1003					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTCCTGCGGTCCTCTGCCATG	0.582																																					p.D1087N		Atlas-SNP	.											.	CUL7	133	.	0			c.G3259A						.						89.0	84.0	86.0					6																	43012996		2203	4300	6503	SO:0001583	missense	9820	exon15			TGCGGTCCTCTGC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3007G>A	chr6.hg19:g.43012996C>T	ENSP00000265348:p.Asp1003Asn	112.0	0.0		125.0	9.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	hg19	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570692	0.65765	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	D;D	0.83163	-1.66;-1.69	4.98	4.07	0.47477	.	0.150464	0.64402	N	0.000016	T	0.75199	0.3817	M	0.66939	2.045	0.80722	D	1	B;B;B	0.26258	0.145;0.124;0.129	B;B;B	0.37387	0.13;0.248;0.248	T	0.75861	-0.3168	10	0.59425	D	0.04	-16.9653	8.5871	0.33664	0.0:0.8162:0.0:0.1838	.	1087;1087;1003	F5H0L1;B4DYZ0;Q14999	.;.;CUL7_HUMAN	N	1003;1087	ENSP00000265348:D1003N;ENSP00000438788:D1087N	ENSP00000265348:D1003N	D	-	1	0	CUL7	43120974	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.877000	0.63086	1.018000	0.39521	0.563000	0.77884	GAC	.	.		0.582	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
HDAC9	9734	hgsc.bcm.edu	37	7	18633535	18633535	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:18633535G>A	ENST00000432645.2	+	5	538	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	HDAC9_ENST00000406451.4_Missense_Mutation_p.A180T|HDAC9_ENST00000524023.1_Missense_Mutation_p.A147T|HDAC9_ENST00000456174.2_Missense_Mutation_p.A152T|HDAC9_ENST00000441542.2_Missense_Mutation_p.A183T|HDAC9_ENST00000401921.1_Missense_Mutation_p.A183T|HDAC9_ENST00000428307.2_Missense_Mutation_p.A180T|HDAC9_ENST00000417496.2_Missense_Mutation_p.A222T|HDAC9_ENST00000405010.3_Missense_Mutation_p.A180T|HDAC9_ENST00000406072.1_Missense_Mutation_p.A211T	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	180	Interaction with MAPK10. {ECO:0000250}.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	TTCTAGGGCTGCCCACCACAC	0.448																																					p.A222T		Atlas-SNP	.											.	HDAC9	560	.	0			c.G664A						.						196.0	189.0	192.0					7																	18633535		1978	4147	6125	SO:0001583	missense	9734	exon8			AGGGCTGCCCACC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.538G>A	chr7.hg19:g.18633535G>A	ENSP00000410337:p.Ala180Thr	216.0	0.0		146.0	23.0	NM_001204144	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547390	0.45383	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.57752	0.96;0.98;0.38;0.99;0.97;0.39;0.38;0.38;0.98;0.94	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000008	T	0.62816	0.2459	L	0.31120	0.905	0.53005	D	0.999968	P;P;D;B;D;P;D;D;P;D;D;P;D	0.69078	0.851;0.954;0.975;0.02;0.958;0.851;0.975;0.975;0.533;0.997;0.975;0.946;0.958	B;P;P;B;B;B;P;P;B;D;P;P;B	0.77004	0.297;0.541;0.591;0.021;0.441;0.297;0.591;0.591;0.123;0.989;0.591;0.592;0.386	T	0.51834	-0.8655	10	0.17832	T	0.49	-13.9477	20.8794	0.99867	0.0:0.0:1.0:0.0	.	147;152;180;211;222;183;183;183;180;152;180;180;202	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	T	222;225;180;180;180;211;183;180;183;152;147;180	ENSP00000401669:A222T;ENSP00000384382:A180T;ENSP00000384657:A180T;ENSP00000395655:A180T;ENSP00000384017:A211T;ENSP00000383912:A183T;ENSP00000410337:A180T;ENSP00000408617:A183T;ENSP00000388568:A152T;ENSP00000430036:A147T	ENSP00000262069:A225T	A	+	1	0	HDAC9	18600060	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.018000	0.64054	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.448	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
ZP3	7784	hgsc.bcm.edu	37	7	76062261	76062261	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:76062261G>T	ENST00000394857.3	+	3	507	c.449G>T	c.(448-450)aGc>aTc	p.S150I	ZP3_ENST00000336517.4_Missense_Mutation_p.S99I|ZP3_ENST00000416245.1_5'UTR	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	150	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						AATGTGAGCAGCCAGGCCATC	0.582																																					p.S150I		Atlas-SNP	.											.	ZP3	32	.	0			c.G449T						.						89.0	74.0	79.0					7																	76062261		2203	4300	6503	SO:0001583	missense	7784	exon3			TGAGCAGCCAGGC	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.449G>T	chr7.hg19:g.76062261G>T	ENSP00000378326:p.Ser150Ile	95.0	0.0		103.0	19.0	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	hg19	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382218	0.82792	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121	D;D	0.82619	-1.63;-1.63	5.4	5.4	0.78164	Zona pellucida sperm-binding protein (3);	0.000000	0.85682	D	0.000000	D	0.92247	0.7541	M	0.91920	3.255	0.80722	D	1	D;P	0.62365	0.991;0.563	D;B	0.63381	0.914;0.345	D	0.93608	0.6936	10	0.66056	D	0.02	-41.2133	16.6568	0.85230	0.0:0.0:1.0:0.0	.	99;150	P21754-3;P21754	.;ZP3_HUMAN	I	99;150;150	ENSP00000337310:S99I;ENSP00000378326:S150I	ENSP00000337310:S99I	S	+	2	0	ZP3	75900197	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.459000	0.80802	2.536000	0.85505	0.561000	0.74099	AGC	.	.		0.582	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
PCLO	27445	hgsc.bcm.edu	37	7	82435139	82435139	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:82435139G>A	ENST00000333891.9	-	21	15135	c.14798C>T	c.(14797-14799)cCt>cTt	p.P4933L		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTGATTGGGAGGCTTTGCTGC	0.483																																					p.P4933L		Atlas-SNP	.											.	PCLO	1506	.	0			c.C14798T						.						39.0	41.0	41.0					7																	82435139		2022	4177	6199	SO:0001583	missense	27445	exon21			TTGGGAGGCTTTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14798C>T	chr7.hg19:g.82435139G>A	ENSP00000334319:p.Pro4933Leu	216.0	0.0		187.0	17.0	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790558	0.50102	.	.	ENSG00000186472	ENST00000333891	T	0.16073	2.37	5.69	5.69	0.88448	.	.	.	.	.	T	0.22627	0.0546	N	0.08118	0	0.80722	D	1	D	0.63046	0.992	P	0.59357	0.856	T	0.23797	-1.0178	9	0.87932	D	0	.	19.8069	0.96534	0.0:0.0:1.0:0.0	.	4933	Q9Y6V0-5	.	L	4933	ENSP00000334319:P4933L	ENSP00000334319:P4933L	P	-	2	0	PCLO	82273075	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	7.159000	0.77483	2.668000	0.90789	0.557000	0.71058	CCT	.	.		0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
EXOC4	60412	hgsc.bcm.edu	37	7	133314872	133314872	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr7:133314872G>T	ENST00000253861.4	+	10	1521	c.1492G>T	c.(1492-1494)Gtc>Ttc	p.V498F	EXOC4_ENST00000545148.1_Missense_Mutation_p.V108F|EXOC4_ENST00000539845.1_Missense_Mutation_p.V397F|EXOC4_ENST00000460346.1_3'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	498					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AAACATTACCGTCATATTCCA	0.368																																					p.V498F		Atlas-SNP	.											.	EXOC4	118	.	0			c.G1492T						.						123.0	118.0	120.0					7																	133314872		2203	4300	6503	SO:0001583	missense	60412	exon10			ATTACCGTCATAT	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1492G>T	chr7.hg19:g.133314872G>T	ENSP00000253861:p.Val498Phe	184.0	0.0		140.0	21.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	hg19	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706842	0.30232	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148	.	.	.	6.03	4.24	0.50183	.	0.140692	0.47852	D	0.000209	T	0.44477	0.1295	L	0.48642	1.525	0.80722	D	1	B;P;P	0.44877	0.01;0.845;0.664	B;P;B	0.44921	0.017;0.464;0.195	T	0.26503	-1.0101	9	0.15066	T	0.55	.	7.4852	0.27427	0.3458:0.0:0.6542:0.0	.	30;108;498	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	F	498;117;397;108	.	ENSP00000253861:V498F	V	+	1	0	EXOC4	132965412	1.000000	0.71417	0.860000	0.33809	0.866000	0.49608	4.254000	0.58798	0.893000	0.36288	0.655000	0.94253	GTC	.	.		0.368	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
EBF2	64641	hgsc.bcm.edu	37	8	25898461	25898461	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:25898461T>G	ENST00000520164.1	-	3	883	c.346A>C	c.(346-348)Agc>Cgc	p.S116R	EBF2_ENST00000408929.3_5'UTR	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	116					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TCACCGTTGCTGTAGAGGAGC	0.582																																					p.S116R	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	Atlas-SNP	.											.	EBF2	138	.	0			c.A346C						.						135.0	140.0	138.0					8																	25898461		2030	4202	6232	SO:0001583	missense	64641	exon3			CGTTGCTGTAGAG	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.346A>C	chr8.hg19:g.25898461T>G	ENSP00000430241:p.Ser116Arg	562.0	0.0		647.0	62.0	NM_022659	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	hg19	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	T	31	5.092377	0.94149	.	.	ENSG00000221818	ENST00000520164	T	0.49139	0.79	5.59	5.59	0.84812	.	0.000000	0.85682	U	0.000000	T	0.54382	0.1855	M	0.78049	2.395	0.80722	D	1	D	0.53312	0.959	P	0.44597	0.454	T	0.60622	-0.7227	10	0.44086	T	0.13	-4.0617	15.7811	0.78260	0.0:0.0:0.0:1.0	.	116	Q9HAK2	COE2_HUMAN	R	116	ENSP00000430241:S116R	ENSP00000430241:S116R	S	-	1	0	EBF2	25954378	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.040000	0.89188	2.123000	0.65237	0.533000	0.62120	AGC	.	.		0.582	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659	
STK3	6788	hgsc.bcm.edu	37	8	99560362	99560362	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:99560362T>A	ENST00000419617.2	-	9	1116	c.976A>T	c.(976-978)Atg>Ttg	p.M326L	STK3_ENST00000523601.1_Missense_Mutation_p.M354L	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	326					apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GTCTTCACCATGGTGTGGGAA	0.463																																					p.M354L		Atlas-SNP	.											.	STK3	47	.	0			c.A1060T						.						57.0	54.0	55.0					8																	99560362		1937	4146	6083	SO:0001583	missense	6788	exon11			TCACCATGGTGTG	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.976A>T	chr8.hg19:g.99560362T>A	ENSP00000390500:p.Met326Leu	188.0	0.0		152.0	34.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648917	0.67358	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.71222	-0.55;-0.54;0.27	5.74	5.74	0.90152	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.72827	0.3509	L	0.49455	1.56	0.80722	D	1	B;B;B	0.27068	0.167;0.011;0.026	B;B;B	0.41332	0.354;0.02;0.02	T	0.68349	-0.5432	10	0.27082	T	0.32	.	16.0502	0.80755	0.0:0.0:0.0:1.0	.	215;326;354	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	L	326;354;215	ENSP00000390500:M326L;ENSP00000429744:M354L;ENSP00000428014:M215L	ENSP00000390500:M326L	M	-	1	0	STK3	99629538	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.625000	0.83145	2.197000	0.70478	0.528000	0.53228	ATG	.	.		0.463	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281	
GRHL2	79977	hgsc.bcm.edu	37	8	102611376	102611376	+	Silent	SNP	G	G	A	rs267601683		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:102611376G>A	ENST00000251808.3	+	8	1433	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	GRHL2_ENST00000395927.1_Silent_p.A349A	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	365					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			ATGAAGAGGCGAAGGTGAGTG	0.378																																					p.A365A		Atlas-SNP	.											GRHL2,colon,carcinoma,0,1	GRHL2	68	.	0			c.G1095A						.						99.0	91.0	94.0					8																	102611376		2203	4300	6503	SO:0001819	synonymous_variant	79977	exon8			AGAGGCGAAGGTG	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.1095G>A	chr8.hg19:g.102611376G>A		304.0	0.0		298.0	60.0	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	hg19	CCDS34931.1																																																																																			.	.		0.378	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
COL22A1	169044	hgsc.bcm.edu	37	8	139838990	139838990	+	Missense_Mutation	SNP	C	C	A	rs372910376		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr8:139838990C>A	ENST00000303045.6	-	6	1326	c.880G>T	c.(880-882)Gcc>Tcc	p.A294S	COL22A1_ENST00000435777.1_Missense_Mutation_p.A294S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	294	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTGACAAAGGCGTACTCATCA	0.532										HNSCC(7;0.00092)																											p.A294S		Atlas-SNP	.											.	COL22A1	390	.	0			c.G880T						.						117.0	95.0	103.0					8																	139838990		2203	4300	6503	SO:0001583	missense	169044	exon6			CAAAGGCGTACTC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.880G>T	chr8.hg19:g.139838990C>A	ENSP00000303153:p.Ala294Ser	121.0	0.0		138.0	35.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633641	0.87660	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	T;T	0.13778	2.56;2.56	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.46758	U	0.000264	T	0.27559	0.0677	L	0.33485	1.01	0.58432	D	0.999997	D	0.89917	1.0	D	0.81914	0.995	T	0.01182	-1.1426	9	.	.	.	.	17.8006	0.88586	0.0:1.0:0.0:0.0	.	294	Q8NFW1	COMA1_HUMAN	S	294	ENSP00000303153:A294S;ENSP00000387655:A294S	.	A	-	1	0	COL22A1	139908172	1.000000	0.71417	0.999000	0.59377	0.827000	0.46813	4.718000	0.61930	2.452000	0.82932	0.644000	0.83932	GCC	.	.		0.532	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33567266	33567266	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr9:33567266G>T	ENST00000290943.6	+	14	2818	c.2722G>T	c.(2722-2724)Gca>Tca	p.A908S	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	908										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						GGAAGCCTTTGCAGTAGCATT	0.308																																					p.A907S		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.G2719T						.																																			SO:0001583	missense	441459	exon14			GCCTTTGCAGTAG			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2722G>T	chr9.hg19:g.33567266G>T	ENSP00000290943:p.Ala908Ser	372.0	0.0		436.0	59.0	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	hg19		.	.	.	.	.	.	.	.	.	.	g	0.406	-0.915995	0.02415	.	.	ENSG00000230453	ENST00000290943;ENST00000357927	T;T	0.31247	1.5;1.5	1.6	-0.706	0.11249	.	.	.	.	.	T	0.13970	0.0338	.	.	.	0.20403	N	0.999908	.	.	.	.	.	.	T	0.35475	-0.9787	5	0.14252	T	0.57	.	3.4396	0.07458	0.2695:0.422:0.3085:0.0	.	.	.	.	S	908;289	ENSP00000290943:A908S;ENSP00000350607:A289S	ENSP00000290943:A908S	A	+	1	0	ANKRD18B	33557266	0.006000	0.16342	0.002000	0.10522	0.001000	0.01503	-1.492000	0.02300	-0.194000	0.10399	-0.531000	0.04308	GCA	.	.		0.308	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
PFKP	5214	hgsc.bcm.edu	37	10	3146084	3146084	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr10:3146084G>A	ENST00000381125.4	+	5	644	c.568G>A	c.(568-570)Gcc>Acc	p.A190T	PFKP_ENST00000421751.1_3'UTR|PFKP_ENST00000381075.2_Missense_Mutation_p.A182T	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	190	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		CACGGACTCCGCCCTGCACAG	0.637																																					p.A190T		Atlas-SNP	.											.	PFKP	182	.	0			c.G568A						.						103.0	77.0	86.0					10																	3146084		2203	4300	6503	SO:0001583	missense	5214	exon5			GACTCCGCCCTGC	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.568G>A	chr10.hg19:g.3146084G>A	ENSP00000370517:p.Ala190Thr	60.0	0.0		72.0	17.0	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Missense_Mutation	SNP	ENST00000381125.4	hg19	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819537	0.71028	.	.	ENSG00000067057	ENST00000381125;ENST00000397834;ENST00000381075;ENST00000421751;ENST00000407806	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	4.64	4.64	0.57946	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.96917	0.8993	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98797	1.0738	10	0.72032	D	0.01	.	17.8892	0.88866	0.0:0.0:1.0:0.0	.	182;190	Q5VSR7;Q01813	.;K6PP_HUMAN	T	190;179;182;152;152	ENSP00000370517:A190T;ENSP00000370465:A182T;ENSP00000410590:A152T;ENSP00000385880:A152T	ENSP00000370465:A182T	A	+	1	0	PFKP	3136084	1.000000	0.71417	0.051000	0.19133	0.004000	0.04260	9.498000	0.97972	2.293000	0.77203	0.650000	0.86243	GCC	.	.		0.637	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
OR52R1	119695	hgsc.bcm.edu	37	11	4825512	4825512	+	Silent	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:4825512C>A	ENST00000356069.2	-	1	98	c.99G>T	c.(97-99)ccG>ccT	p.P33P	MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Silent_p.P112P|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCACAGAACGGAAAGGCAA	0.512																																					p.P33P		Atlas-SNP	.											OR52R1,NS,malignant_melanoma,-1,4	OR52R1	81	.	0			c.G99T						.						94.0	84.0	87.0					11																	4825512		2201	4298	6499	SO:0001819	synonymous_variant	119695	exon1			ACAGAACGGAAAG	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.99G>T	chr11.hg19:g.4825512C>A		148.0	1.0		132.0	20.0	NM_001005177	Q6IFI0	Silent	SNP	ENST00000356069.2	hg19	CCDS31360.2																																																																																			.	.		0.512	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
ZBED5	58486	hgsc.bcm.edu	37	11	10875696	10875696	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:10875696C>G	ENST00000432999.2	-	3	1295	c.797G>C	c.(796-798)aGa>aCa	p.R266T	ZBED5_ENST00000525350.1_Intron|ZBED5_ENST00000413761.2_Missense_Mutation_p.R266T	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	266							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						aattttcagtctacaaacaag	0.378																																					p.R266T		Atlas-SNP	.											.	ZBED5	50	.	0			c.G797C						.						117.0	95.0	102.0					11																	10875696		692	1591	2283	SO:0001583	missense	58486	exon3			TTCAGTCTACAAA	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.797G>C	chr11.hg19:g.10875696C>G	ENSP00000398106:p.Arg266Thr	216.0	0.0		215.0	12.0	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Missense_Mutation	SNP	ENST00000432999.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.34	2.207205	0.39003	.	.	ENSG00000236287	ENST00000432999;ENST00000413761	T;T	0.09073	3.02;3.02	4.18	3.26	0.37387	Ribonuclease H-like (1);	0.000000	0.35615	N	0.003090	T	0.11067	0.0270	L	0.56769	1.78	0.26159	N	0.980036	P	0.44090	0.826	B	0.43783	0.431	T	0.09509	-1.0671	10	0.33141	T	0.24	.	10.3058	0.43680	0.0:0.8013:0.1987:0.0	.	266	Q49AG3	ZBED5_HUMAN	T	266	ENSP00000398106:R266T;ENSP00000415939:R266T	ENSP00000415939:R266T	R	-	2	0	ZBED5	10832272	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.453000	0.35167	1.327000	0.45338	0.650000	0.86243	AGA	.	.		0.378	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
LRRC4C	57689	hgsc.bcm.edu	37	11	40137653	40137653	+	Silent	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:40137653G>T	ENST00000278198.2	-	2	2153	c.190C>A	c.(190-192)Cgg>Agg	p.R64R	LRRC4C_ENST00000527150.1_Silent_p.R64R|LRRC4C_ENST00000528697.1_Silent_p.R64R|LRRC4C_ENST00000530763.1_Silent_p.R64R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	64	LRRNT.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				AGGTTTTTCCGAACACAAATC	0.532																																					p.R64R		Atlas-SNP	.											.	LRRC4C	190	.	0			c.C190A						.						86.0	74.0	78.0					11																	40137653		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			TTTTCCGAACACA	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.190C>A	chr11.hg19:g.40137653G>T		157.0	0.0		155.0	20.0	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	hg19	CCDS31464.1																																																																																			.	.		0.532	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
OR4A15	81328	hgsc.bcm.edu	37	11	55135486	55135486	+	Silent	SNP	T	T	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:55135486T>C	ENST00000314706.3	+	1	127	c.127T>C	c.(127-129)Tta>Cta	p.L43L		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						ATTTATCCTCTTAGGGCTCAC	0.408																																					p.L43L		Atlas-SNP	.											.	OR4A15	161	.	0			c.T127C						.						66.0	63.0	64.0					11																	55135486		2201	4296	6497	SO:0001819	synonymous_variant	81328	exon1			ATCCTCTTAGGGC	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.127T>C	chr11.hg19:g.55135486T>C		262.0	0.0		220.0	35.0	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	hg19	CCDS31500.1																																																																																			.	.		0.408	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
OR5T2	219464	hgsc.bcm.edu	37	11	55999981	55999981	+	Silent	SNP	A	A	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:55999981A>C	ENST00000313264.4	-	1	756	c.681T>G	c.(679-681)tcT>tcG	p.S227S		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGTCAGAATAAGAAATAGCAA	0.423																																					p.S227S		Atlas-SNP	.											OR5T2,NS,carcinoma,0,4	OR5T2	107	.	0			c.T681G						.						140.0	130.0	133.0					11																	55999981		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			AGAATAAGAAATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.681T>G	chr11.hg19:g.55999981A>C		655.0	1.0		658.0	95.0	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.423	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
NXPE4	54827	hgsc.bcm.edu	37	11	114453455	114453455	+	Missense_Mutation	SNP	G	G	A	rs111330181		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:114453455G>A	ENST00000375478.3	-	3	565	c.385C>T	c.(385-387)Cgc>Tgc	p.R129C	NXPE4_ENST00000424261.2_Intron	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	129						extracellular vesicular exosome (GO:0070062)											TGCTTCCTGCGTCCCAAGTGG	0.587													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22557	0.0		0.0	False		,,,				2504	0.0				p.R129C		Atlas-SNP	.											FAM55D,right_upper_lobe,carcinoma,0,2	.	.	.	0			c.C385T						.	G	CYS/ARG,	0,4390		0,0,2195	109.0	110.0	110.0		385,	3.1	0.0	11	dbSNP_132	110	3,8581		0,3,4289	yes	missense,intron	FAM55D	NM_001077639.1,NM_017678.2	180,	0,3,6484	AA,AG,GG		0.0349,0.0,0.0231	benign,	129/545,	114453455	3,12971	2195	4292	6487	SO:0001583	missense	54827	exon3			TCCTGCGTCCCAA	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.385C>T	chr11.hg19:g.114453455G>A	ENSP00000364627:p.Arg129Cys	456.0	0.0		443.0	59.0	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	hg19	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	G	3.731	-0.055544	0.07362	0.0	3.49E-4	ENSG00000137634	ENST00000375478	T	0.14516	2.5	5.01	3.12	0.35913	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	1.043540	0.07504	N	0.907792	T	0.23249	0.0562	M	0.89840	3.065	0.09310	N	1	B	0.29481	0.245	B	0.27715	0.082	T	0.35076	-0.9803	10	0.54805	T	0.06	.	4.665	0.12660	0.1645:0.0:0.5301:0.3054	.	129	Q6UWF7	FA55D_HUMAN	C	129	ENSP00000364627:R129C	ENSP00000364627:R129C	R	-	1	0	FAM55D	113958665	0.005000	0.15991	0.007000	0.13788	0.003000	0.03518	1.457000	0.35212	0.607000	0.29982	-0.229000	0.12294	CGC	.	A|1.000;|0.000		0.587	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
TRAPPC4	51399	hgsc.bcm.edu	37	11	118896705	118896705	+	IGR	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:118896705C>A	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000330775.7_Missense_Mutation_p.R318L|SLC37A4_ENST00000538950.1_Missense_Mutation_p.R246L|SLC37A4_ENST00000525102.1_5'UTR|SLC37A4_ENST00000545985.1_Missense_Mutation_p.R319L|SLC37A4_ENST00000357590.5_Missense_Mutation_p.R319L	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		CACTGTTACCCGGAAGAGGTA	0.567																																					p.R319L		Atlas-SNP	.											.	SLC37A4	19	.	0			c.G956T						.						54.0	59.0	58.0					11																	118896705		2081	4220	6301	SO:0001628	intergenic_variant	2542	exon8			GTTACCCGGAAGA	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"""Trafficking protein particle complex"""	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			chr11.hg19:g.118896705C>A		140.0	0.0		134.0	14.0	NM_001467	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1																																																																																			.	.		0.567	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146	
ZNF202	7753	hgsc.bcm.edu	37	11	123598880	123598880	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:123598880A>G	ENST00000529691.1	-	5	1012	c.793T>C	c.(793-795)Tat>Cat	p.Y265H	ZNF202_ENST00000336139.4_Missense_Mutation_p.Y265H|ZNF202_ENST00000530393.1_Missense_Mutation_p.Y265H			O95125	ZN202_HUMAN	zinc finger protein 202	265	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		TCCAAGACATATTCTCCATAG	0.443																																					p.Y265H		Atlas-SNP	.											.	ZNF202	72	.	0			c.T793C						.						118.0	107.0	111.0					11																	123598880		2202	4299	6501	SO:0001583	missense	7753	exon7			AGACATATTCTCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.793T>C	chr11.hg19:g.123598880A>G	ENSP00000433881:p.Tyr265His	227.0	0.0		238.0	13.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.613970	0.66672	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.01767	4.65;4.65;4.65	4.58	4.58	0.56647	Krueppel-associated box (4);	0.000000	0.43579	D	0.000543	T	0.06600	0.0169	L	0.60455	1.87	0.35864	D	0.827721	D	0.76494	0.999	D	0.77004	0.989	T	0.46527	-0.9185	10	0.27082	T	0.32	-21.7355	10.2596	0.43419	1.0:0.0:0.0:0.0	.	265	O95125	ZN202_HUMAN	H	265	ENSP00000337724:Y265H;ENSP00000432504:Y265H;ENSP00000433881:Y265H	ENSP00000337724:Y265H	Y	-	1	0	ZNF202	123104090	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.524000	0.60552	1.929000	0.55896	0.459000	0.35465	TAT	.	.		0.443	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
ZNF202	7753	hgsc.bcm.edu	37	11	123600353	123600353	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:123600353C>A	ENST00000529691.1	-	3	802	c.583G>T	c.(583-585)Gaa>Taa	p.E195*	ZNF202_ENST00000336139.4_Nonsense_Mutation_p.E195*|ZNF202_ENST00000530393.1_Nonsense_Mutation_p.E195*			O95125	ZN202_HUMAN	zinc finger protein 202	195					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		AGCTCCTCTTCCTGGTGTGGA	0.617																																					p.E195X		Atlas-SNP	.											.	ZNF202	72	.	0			c.G583T						.						49.0	43.0	45.0					11																	123600353		2202	4299	6501	SO:0001587	stop_gained	7753	exon5			CCTCTTCCTGGTG	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.583G>T	chr11.hg19:g.123600353C>A	ENSP00000433881:p.Glu195*	140.0	0.0		123.0	10.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Nonsense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930758	0.92389	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	.	.	.	5.32	4.4	0.53042	.	0.143577	0.32093	N	0.006590	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-10.0485	8.9155	0.35579	0.0:0.9009:0.0:0.0991	.	.	.	.	X	195	.	ENSP00000337724:E195X	E	-	1	0	ZNF202	123105563	0.088000	0.21588	0.069000	0.20011	0.518000	0.34316	3.040000	0.49799	2.482000	0.83794	0.557000	0.71058	GAA	.	.		0.617	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
OVCH1	341350	hgsc.bcm.edu	37	12	29617463	29617463	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:29617463G>T	ENST00000318184.5	-	18	2101	c.2102C>A	c.(2101-2103)aCc>aAc	p.T701N	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	701	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TCCCCATCCGGTCACAGCACA	0.438																																					p.T701N		Atlas-SNP	.											.	OVCH1	195	.	0			c.C2102A						.						60.0	59.0	59.0					12																	29617463		1924	4131	6055	SO:0001583	missense	341350	exon18			CATCCGGTCACAG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2102C>A	chr12.hg19:g.29617463G>T	ENSP00000326708:p.Thr701Asn	148.0	0.0		142.0	20.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	G	15.85	2.955964	0.53293	.	.	ENSG00000187950	ENST00000318184	D	0.89552	-2.53	2.97	1.13	0.20643	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.92080	0.7490	M	0.78285	2.405	0.27105	N	0.962511	D	0.71674	0.998	D	0.63113	0.911	D	0.83443	0.0044	9	0.72032	D	0.01	.	6.8944	0.24247	0.2445:0.0:0.7555:0.0	.	701	Q7RTY7	OVCH1_HUMAN	N	701	ENSP00000326708:T701N	ENSP00000326708:T701N	T	-	2	0	OVCH1	29508730	1.000000	0.71417	0.048000	0.18961	0.993000	0.82548	4.138000	0.58017	0.301000	0.22738	0.655000	0.94253	ACC	.	.		0.438	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137832	32137832	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:32137832G>T	ENST00000312561.4	+	4	4357	c.3943G>T	c.(3943-3945)Gaa>Taa	p.E1315*	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1315																	AGCATCTTATGAACAAGCTTC	0.338																																					p.E1315X		Atlas-SNP	.											.	.	.	.	0			c.G3943T						.						82.0	85.0	84.0					12																	32137832		2203	4300	6503	SO:0001587	stop_gained	55196	exon4			TCTTATGAACAAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3943G>T	chr12.hg19:g.32137832G>T	ENSP00000310338:p.Glu1315*	118.0	0.0		153.0	20.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Nonsense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	43	10.299438	0.99378	.	.	ENSG00000174718	ENST00000312561	.	.	.	3.99	1.03	0.20045	.	0.844950	0.10220	N	0.701071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7252	0.23353	0.4378:0.0:0.5622:0.0	.	.	.	.	X	1315	.	.	E	+	1	0	C12orf35	32029099	0.279000	0.24239	0.001000	0.08648	0.145000	0.21501	1.027000	0.30115	0.148000	0.19059	-0.253000	0.11424	GAA	.	.		0.338	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
KIF21A	55605	hgsc.bcm.edu	37	12	39726715	39726715	+	Silent	SNP	C	C	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:39726715C>G	ENST00000361418.5	-	19	2697	c.2682G>C	c.(2680-2682)acG>acC	p.T894T	KIF21A_ENST00000395670.3_Silent_p.T894T|KIF21A_ENST00000361961.3_Silent_p.T881T|KIF21A_ENST00000544797.2_Silent_p.T881T|KIF21A_ENST00000541463.2_Silent_p.T858T			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	894					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TTGTTGCCGGCGTTGGTAAGG	0.458																																					p.T894T		Atlas-SNP	.											.	KIF21A	238	.	0			c.G2682C						.						70.0	72.0	71.0					12																	39726715		2203	4300	6503	SO:0001819	synonymous_variant	55605	exon19			TGCCGGCGTTGGT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2682G>C	chr12.hg19:g.39726715C>G		177.0	0.0		187.0	37.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	hg19	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.426334	0.01117	.	.	ENSG00000139116	ENST00000552961	.	.	.	5.58	-11.2	0.00127	.	.	.	.	.	T	0.24236	0.0587	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.17561	-1.0365	4	.	.	.	.	9.0399	0.36311	0.1905:0.0738:0.0656:0.6701	.	.	.	.	P	242	.	.	R	-	2	0	KIF21A	38012982	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-1.244000	0.02902	-2.383000	0.00592	-0.484000	0.04775	CGC	.	.		0.458	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
KMT2D	8085	hgsc.bcm.edu	37	12	49443882	49443882	+	Silent	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:49443882C>A	ENST00000301067.7	-	11	3488	c.3489G>T	c.(3487-3489)gtG>gtT	p.V1163V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1163	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCATAGGGGTCACAGGGGCCA	0.627																																					p.V1163V		Atlas-SNP	.											.	MLL2	1173	.	0			c.G3489T						.						53.0	58.0	56.0					12																	49443882		1942	4129	6071	SO:0001819	synonymous_variant	8085	exon11			AGGGGTCACAGGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3489G>T	chr12.hg19:g.49443882C>A		124.0	0.0		157.0	23.0	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.627	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
BCDIN3D	144233	hgsc.bcm.edu	37	12	50236856	50236856	+	Silent	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:50236856C>A	ENST00000333924.4	-	1	56	c.15G>T	c.(13-15)acG>acT	p.T5T	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	5					miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						CATCCAGTTCCGTGGGCACCG	0.642																																					p.T5T		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.G15T						.						40.0	38.0	39.0					12																	50236856		2202	4299	6501	SO:0001819	synonymous_variant	144233	exon1			CAGTTCCGTGGGC		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.15G>T	chr12.hg19:g.50236856C>A		55.0	0.0		88.0	16.0	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	hg19	CCDS8790.1																																																																																			.	.		0.642	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
ALDH1L2	160428	hgsc.bcm.edu	37	12	105464456	105464456	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:105464456A>G	ENST00000258494.9	-	3	460	c.320T>C	c.(319-321)tTc>tCc	p.F107S	ALDH1L2_ENST00000424857.2_Missense_Mutation_p.F107S|RP11-61E11.1_ENST00000547750.1_RNA	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	107	GART.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	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)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CTGAGTGCAGAAAGGGAGCAC	0.498																																					p.F107S		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T320C						.						168.0	137.0	147.0					12																	105464456		2203	4300	6503	SO:0001583	missense	160428	exon3			GTGCAGAAAGGGA	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.320T>C	chr12.hg19:g.105464456A>G	ENSP00000258494:p.Phe107Ser	307.0	0.0		335.0	62.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683030	0.88542	.	.	ENSG00000136010	ENST00000258494;ENST00000424857	T;T	0.75367	-0.93;-0.93	5.27	5.27	0.74061	Formyl transferase, N-terminal (3);	0.047094	0.85682	D	0.000000	T	0.80607	0.4655	L	0.45470	1.425	0.80722	D	1	D	0.59767	0.986	D	0.72075	0.976	T	0.81924	-0.0710	10	0.72032	D	0.01	.	10.6981	0.45911	0.8576:0.0:0.0:0.1424	.	107	Q3SY69	AL1L2_HUMAN	S	107	ENSP00000258494:F107S;ENSP00000389608:F107S	ENSP00000258494:F107S	F	-	2	0	ALDH1L2	103988586	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.217000	0.77982	2.133000	0.65898	0.533000	0.62120	TTC	.	.		0.498	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294	
DNAH10	196385	hgsc.bcm.edu	37	12	124387605	124387605	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr12:124387605G>A	ENST00000409039.3	+	56	9431	c.9406G>A	c.(9406-9408)Gag>Aag	p.E3136K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3136	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCCATCCTGGAGGCCGCCAA	0.572																																					p.E3136K		Atlas-SNP	.											.	DNAH10	888	.	0			c.G9406A						.						51.0	62.0	59.0					12																	124387605		2104	4226	6330	SO:0001583	missense	196385	exon56			ATCCTGGAGGCCG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9406G>A	chr12.hg19:g.124387605G>A	ENSP00000386770:p.Glu3136Lys	112.0	0.0		96.0	19.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311572	0.81358	.	.	ENSG00000197653	ENST00000409039	T	0.74002	-0.8	5.65	5.65	0.86999	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	D	0.88764	0.6525	M	0.89287	3.02	0.58432	D	0.999997	D	0.76494	0.999	D	0.75020	0.985	D	0.89316	0.3636	10	0.52906	T	0.07	.	19.7205	0.96142	0.0:0.0:1.0:0.0	.	3136	Q8IVF4	DYH10_HUMAN	K	3136	ENSP00000386770:E3136K	ENSP00000386770:E3136K	E	+	1	0	DNAH10	122953558	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	6.589000	0.74080	2.671000	0.90904	0.462000	0.41574	GAG	.	.		0.572	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
SACS	26278	hgsc.bcm.edu	37	13	23904756	23904756	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:23904756C>A	ENST00000382292.3	-	9	13532	c.13259G>T	c.(13258-13260)tGc>tTc	p.C4420F	SACS_ENST00000402364.1_Missense_Mutation_p.C3670F|SACS_ENST00000382298.3_Missense_Mutation_p.C4420F			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4420					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGAAGGGGGGCATTTTTCTTT	0.433																																					p.C4420F		Atlas-SNP	.											.	SACS	871	.	0			c.G13259T						.						81.0	85.0	84.0					13																	23904756		2203	4299	6502	SO:0001583	missense	26278	exon10			GGGGGGCATTTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.13259G>T	chr13.hg19:g.23904756C>A	ENSP00000371729:p.Cys4420Phe	129.0	0.0		151.0	35.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	0.058	-1.231456	0.01505	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86956	-2.04;-2.19;-2.04	5.85	5.85	0.93711	.	0.485149	0.26746	N	0.022708	T	0.71796	0.3382	N	0.02011	-0.69	0.24750	N	0.992988	B	0.02656	0.0	B	0.01281	0.0	T	0.63791	-0.6557	10	0.49607	T	0.09	.	14.9345	0.70944	0.143:0.857:0.0:0.0	.	4420	Q9NZJ4	SACS_HUMAN	F	4420;3670;4420	ENSP00000371729:C4420F;ENSP00000385844:C3670F;ENSP00000371735:C4420F	ENSP00000371729:C4420F	C	-	2	0	SACS	22802756	0.984000	0.35163	0.565000	0.28409	0.072000	0.16883	2.273000	0.43381	2.767000	0.95098	0.563000	0.77884	TGC	.	.		0.433	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
COMMD6	170622	hgsc.bcm.edu	37	13	76111799	76111799	+	Splice_Site	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:76111799C>A	ENST00000377615.3	-	3	219		c.e3+1		COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000377619.5_5'Flank|COMMD6_ENST00000406936.3_Splice_Site|COMMD6_ENST00000355801.4_Splice_Site			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6						negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		CGCTCACCCACCTGGTTGGTG	0.627																																					.		Atlas-SNP	.											.	COMMD6	4	.	0			c.54+1G>T						.						60.0	56.0	57.0					13																	76111799		2203	4300	6503	SO:0001630	splice_region_variant	170622	exon3			CACCCACCTGGTT	AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.54+1G>T	chr13.hg19:g.76111799C>A		63.0	0.0		78.0	13.0	NM_203497	A6NF28|B7ZLN0|Q5TBK4	Splice_Site	SNP	ENST00000377615.3	hg19	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898710	0.72639	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000355801	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5719	0.61851	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COMMD6	75009800	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.273000	0.51623	2.563000	0.86464	0.655000	0.94253	.	.	.		0.627	COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023	Intron
SLITRK6	84189	hgsc.bcm.edu	37	13	86370026	86370026	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:86370026G>T	ENST00000400286.2	-	2	1216	c.618C>A	c.(616-618)caC>caA	p.H206Q		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	206					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TTCGGCCAATGTGTTCGAGAA	0.408																																					p.H206Q		Atlas-SNP	.											.	SLITRK6	150	.	0			c.C618A						.						104.0	93.0	96.0					13																	86370026		1879	4104	5983	SO:0001583	missense	84189	exon2			GCCAATGTGTTCG	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.618C>A	chr13.hg19:g.86370026G>T	ENSP00000383143:p.His206Gln	120.0	0.0		131.0	24.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872355	0.51695	.	.	ENSG00000184564	ENST00000400286	T	0.51817	0.69	5.96	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	L	0.39467	1.215	0.49798	D	0.999829	D	0.76494	0.999	D	0.85130	0.997	T	0.52704	-0.8540	10	0.45353	T	0.12	-15.3126	9.8979	0.41329	0.2205:0.0:0.7795:0.0	.	206	Q9H5Y7	SLIK6_HUMAN	Q	206	ENSP00000383143:H206Q	ENSP00000383143:H206Q	H	-	3	2	SLITRK6	85268027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.524000	0.35942	0.870000	0.35726	0.655000	0.94253	CAC	.	.		0.408	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
SYT16	83851	hgsc.bcm.edu	37	14	62551067	62551067	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:62551067A>T	ENST00000430451.2	+	5	1785	c.1588A>T	c.(1588-1590)Agc>Tgc	p.S530C		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	530	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GATCAAAGGCAGCCATTTCCG	0.552																																					p.S530C		Atlas-SNP	.											.	SYT16	144	.	0			c.A1588T						.						59.0	58.0	59.0					14																	62551067		1961	4143	6104	SO:0001583	missense	83851	exon5			AAAGGCAGCCATT	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1588A>T	chr14.hg19:g.62551067A>T	ENSP00000394700:p.Ser530Cys	80.0	0.0		113.0	22.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631373	0.87660	.	.	ENSG00000139973	ENST00000430451	T	0.69806	-0.43	5.44	5.44	0.79542	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.84042	0.5385	M	0.88842	2.985	0.80722	D	1	D	0.62365	0.991	D	0.70487	0.969	D	0.87170	0.2220	10	0.72032	D	0.01	-7.4393	15.6783	0.77344	1.0:0.0:0.0:0.0	.	530	Q17RD7	SYT16_HUMAN	C	530	ENSP00000394700:S530C	ENSP00000394700:S530C	S	+	1	0	SYT16	61620820	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.752000	0.91632	2.284000	0.76573	0.523000	0.50628	AGC	.	.		0.552	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
SLC24A4	123041	hgsc.bcm.edu	37	14	92949118	92949118	+	Missense_Mutation	SNP	G	G	T	rs563681958		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:92949118G>T	ENST00000532405.1	+	13	1576	c.1350G>T	c.(1348-1350)gaG>gaT	p.E450D	SLC24A4_ENST00000298877.1_Missense_Mutation_p.E433D|SLC24A4_ENST00000351924.5_Missense_Mutation_p.E414D|SLC24A4_ENST00000393265.2_Missense_Mutation_p.E386D|SLC24A4_ENST00000531433.1_Missense_Mutation_p.E431D			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	450					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		CCCGCTGGGAGAAGTTCTTCA	0.602																																					p.E450D	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											.	SLC24A4	112	.	0			c.G1350T						.						117.0	96.0	103.0					14																	92949118		2203	4300	6503	SO:0001583	missense	123041	exon13			CTGGGAGAAGTTC	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"""Solute carriers"""	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1350G>T	chr14.hg19:g.92949118G>T	ENSP00000431840:p.Glu450Asp	146.0	0.0		135.0	20.0	NM_153646	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Missense_Mutation	SNP	ENST00000532405.1	hg19	CCDS9903.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.5|28.5	4.922728|4.922728	0.92319|0.92319	.|.	.|.	ENSG00000140090|ENSG00000140090	ENST00000393265;ENST00000531433;ENST00000532405;ENST00000298877;ENST00000351924;ENST00000318079|ENST00000525557	T;T;T;T;T|.	0.79845|.	0.44;-0.02;0.44;0.44;-1.31|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.71896|.	0.3394|.	M|M	0.84683|0.84683	2.71|2.71	0.58432|0.58432	D|D	0.999996|0.999996	P;P;B|.	0.39903|.	0.694;0.529;0.246|.	P;B;B|.	0.45406|.	0.479;0.331;0.331|.	T|.	0.68488|.	-0.5395|.	10|.	0.46703|0.08179	T|T	0.11|0.78	.|.	13.1576|13.1576	0.59527|0.59527	0.0728:0.0:0.9272:0.0|0.0728:0.0:0.9272:0.0	.|.	431;386;450|.	Q8NFF2-3;Q8NFF2-2;Q8NFF2|.	.;.;NCKX4_HUMAN|.	D|X	386;431;450;433;414;302|316	ENSP00000376948:E386D;ENSP00000433302:E431D;ENSP00000431840:E450D;ENSP00000298877:E433D;ENSP00000337789:E414D|.	ENSP00000298877:E433D|ENSP00000432464:E316X	E|E	+|+	3|1	2|0	SLC24A4|SLC24A4	92018871|92018871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.479000|6.479000	0.73600|0.73600	2.716000|2.716000	0.92895|0.92895	0.561000|0.561000	0.74099|0.74099	GAG|GAA	.	.		0.602	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103430853	103430853	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:103430853G>T	ENST00000361246.2	-	19	3000	c.2712C>A	c.(2710-2712)aaC>aaA	p.N904K		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CCAAGGTGAGGTTGGCGTCCT	0.652																																					p.N904K		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C2712A						.						72.0	65.0	67.0					14																	103430853		2203	4300	6503	SO:0001583	missense	9578	exon19			GGTGAGGTTGGCG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2712C>A	chr14.hg19:g.103430853G>T	ENSP00000355237:p.Asn904Lys	58.0	0.0		60.0	13.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	G	6.114	0.389289	0.11581	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.39056	1.1	5.51	-7.37	0.01412	Myotonic dystrophy protein kinase, coiled coil (2);	0.047074	0.85682	D	0.000000	T	0.39145	0.1067	M	0.71581	2.175	0.39011	D	0.959553	B;B	0.17465	0.022;0.022	B;B	0.35353	0.201;0.143	T	0.22312	-1.0220	10	0.30078	T	0.28	.	11.6997	0.51564	0.3722:0.0764:0.5514:0.0	.	904;904	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	K	904;41	ENSP00000355237:N904K	ENSP00000355237:N904K	N	-	3	2	CDC42BPB	102500606	0.996000	0.38824	0.000000	0.03702	0.141000	0.21300	0.383000	0.20651	-1.475000	0.01876	-0.253000	0.11424	AAC	.	.		0.652	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
TSC2	7249	hgsc.bcm.edu	37	16	2098719	2098719	+	Nonsense_Mutation	SNP	C	C	T	rs137854105		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:2098719C>T	ENST00000219476.3	+	2	733	c.103C>T	c.(103-105)Cag>Tag	p.Q35*	TSC2_ENST00000353929.4_Nonsense_Mutation_p.Q35*|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000439673.2_Nonsense_Mutation_p.Q35*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.Q46*|NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000401874.2_Nonsense_Mutation_p.Q35*|TSC2_ENST00000350773.4_Nonsense_Mutation_p.Q35*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	35	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AGAGGGTAAACAGACGGAGTT	0.493			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.Q35X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.C103T						.						172.0	145.0	154.0					16																	2098719		2198	4299	6497	SO:0001587	stop_gained	7249	exon2	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GGTAAACAGACGG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.103C>T	chr16.hg19:g.2098719C>T	ENSP00000219476:p.Gln35*	227.0	0.0		264.0	59.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768370	0.90020	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000350773;ENST00000445113	.	.	.	5.16	5.16	0.70880	.	0.211530	0.41294	D	0.000910	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-20.3627	18.6588	0.91465	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;35;35;35;46	.	ENSP00000219476:Q35X	Q	+	1	0	TSC2	2038720	1.000000	0.71417	0.921000	0.36526	0.909000	0.53808	5.108000	0.64609	2.403000	0.81681	0.563000	0.77884	CAG	.	.		0.493	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
DPEP2	64174	hgsc.bcm.edu	37	16	68027109	68027109	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:68027109G>T	ENST00000572888.1	-	1	657	c.7C>A	c.(7-9)Ccc>Acc	p.P3T	DPEP2_ENST00000412757.2_Missense_Mutation_p.P3T|DPEP2_ENST00000393847.1_Missense_Mutation_p.P3T			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	3					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		AGGCCGGAGGGCTGCATGTTG	0.687											OREG0023893	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P3T		Atlas-SNP	.											.	DPEP2	43	.	0			c.C7A						.						12.0	12.0	12.0					16																	68027109		2164	4269	6433	SO:0001583	missense	64174	exon2			CGGAGGGCTGCAT	AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.7C>A	chr16.hg19:g.68027109G>T	ENSP00000458977:p.Pro3Thr	47.0	0.0	1104	68.0	17.0	NM_022355	B2RCF8|Q6UX92|Q8TC95	Missense_Mutation	SNP	ENST00000572888.1	hg19	CCDS10857.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617733	0.46736	.	.	ENSG00000167261	ENST00000393847;ENST00000412757;ENST00000322384;ENST00000268795	T;T	0.23147	1.92;1.92	3.64	0.504	0.16946	.	2.002900	0.02667	N	0.108176	T	0.25082	0.0609	L	0.50333	1.59	0.09310	N	0.999995	B;B	0.24258	0.1;0.01	B;B	0.23018	0.043;0.006	T	0.28681	-1.0036	10	0.72032	D	0.01	-1.9434	4.2288	0.10592	0.1131:0.0:0.4785:0.4084	.	3;3	B4DNP7;Q9H4A9	.;DPEP2_HUMAN	T	3	ENSP00000377430:P3T;ENSP00000412549:P3T	ENSP00000268795:P3T	P	-	1	0	DPEP2	66584610	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.611000	0.24268	0.153000	0.19213	-0.314000	0.08810	CCC	.	.		0.687	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355	
PLCG2	5336	hgsc.bcm.edu	37	16	81927388	81927388	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr16:81927388G>T	ENST00000359376.3	+	12	1275	c.1061G>T	c.(1060-1062)cGc>cTc	p.R354L		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	354	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ATGGGCTGTCGCTGCATTGAA	0.542																																					p.R354L		Atlas-SNP	.											.	PLCG2	276	.	0			c.G1061T						.						63.0	65.0	64.0					16																	81927388		2182	4293	6475	SO:0001583	missense	5336	exon12			GCTGTCGCTGCAT		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1061G>T	chr16.hg19:g.81927388G>T	ENSP00000352336:p.Arg354Leu	90.0	0.0		74.0	13.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825445	0.90955	.	.	ENSG00000197943	ENST00000359376	T	0.81415	-1.49	3.71	3.71	0.42584	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.85682	D	0.000000	D	0.94463	0.8218	H	0.99650	4.68	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.913	D	0.97373	0.9977	10	0.87932	D	0	.	16.357	0.83239	0.0:0.0:1.0:0.0	.	221;354	B4E3H3;P16885	.;PLCG2_HUMAN	L	354	ENSP00000352336:R354L	ENSP00000352336:R354L	R	+	2	0	PLCG2	80484889	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.618000	0.98365	2.034000	0.60081	0.467000	0.42956	CGC	.	.		0.542	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
TP53	7157	hgsc.bcm.edu	37	17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	rs28934571		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S	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	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (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.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(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)	TGAGGATGGGCCTCCGGTTCA	0.572		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)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155.0	113.0	127.0					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	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;	GATGGGCCTCCGG	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.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	202.0	2.0		172.0	34.0	NM_000546	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	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
PHF12	57649	hgsc.bcm.edu	37	17	27251239	27251239	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:27251239C>A	ENST00000332830.4	-	4	1213	c.403G>T	c.(403-405)Gac>Tac	p.D135Y	RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000268756.3_Missense_Mutation_p.D135Y|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000577226.1_Missense_Mutation_p.D135Y|RP11-20B24.5_ENST00000582631.1_RNA	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			AAGTCAGTGTCACTGCTGGGG	0.537																																					p.D135Y		Atlas-SNP	.											.	PHF12	69	.	0			c.G403T						.						153.0	123.0	133.0					17																	27251239		2203	4300	6503	SO:0001583	missense	57649	exon4			CAGTGTCACTGCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.403G>T	chr17.hg19:g.27251239C>A	ENSP00000329933:p.Asp135Tyr	172.0	0.0		212.0	48.0	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667068	0.88251	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94828	-3.5;-3.53;-3.53	5.58	5.58	0.84498	.	0.095435	0.64402	D	0.000001	D	0.95937	0.8677	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.976;0.999	D;D;P;D	0.70935	0.936;0.971;0.656;0.936	D	0.96325	0.9239	10	0.72032	D	0.01	-7.893	18.1066	0.89521	0.0:1.0:0.0:0.0	.	117;135;135;135	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	Y	135	ENSP00000329933:D135Y;ENSP00000368157:D135Y;ENSP00000268756:D135Y	ENSP00000268756:D135Y	D	-	1	0	PHF12	24275365	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.252000	0.78309	2.609000	0.88269	0.655000	0.94253	GAC	.	.		0.537	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889	
KRT33B	3884	hgsc.bcm.edu	37	17	39522752	39522752	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:39522752C>A	ENST00000251646.3	-	3	607	c.558G>T	c.(556-558)gaG>gaT	p.E186D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	186	Coil 1B.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GGGACAGCAGCTCCTCCTTCA	0.562																																					p.E186D		Atlas-SNP	.											.	KRT33B	46	.	0			c.G558T						.						72.0	70.0	71.0					17																	39522752		2191	4300	6491	SO:0001583	missense	3884	exon3			CAGCAGCTCCTCC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.558G>T	chr17.hg19:g.39522752C>A	ENSP00000251646:p.Glu186Asp	128.0	0.0		95.0	19.0	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	hg19	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	16.08	3.022491	0.54683	.	.	ENSG00000131738	ENST00000251646	D	0.92249	-3.0	4.51	3.53	0.40419	Filament (1);	0.000000	0.64402	D	0.000004	D	0.92371	0.7579	M	0.76328	2.33	0.28712	N	0.903508	P	0.36125	0.538	B	0.43838	0.433	D	0.87459	0.2406	10	0.49607	T	0.09	.	11.4448	0.50116	0.0:0.8395:0.0:0.1605	.	186	Q14525	KT33B_HUMAN	D	186	ENSP00000251646:E186D	ENSP00000251646:E186D	E	-	3	2	KRT33B	36776278	0.998000	0.40836	0.997000	0.53966	0.912000	0.54170	0.636000	0.24644	0.654000	0.30846	-1.134000	0.01955	GAG	.	.		0.562	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
GOSR2	9570	hgsc.bcm.edu	37	17	45017921	45017921	+	IGR	SNP	G	G	T	rs147434599		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:45017921G>T	ENST00000393456.2	+	0	847				RP11-156P1.2_ENST00000571841.1_Intron|GOSR2_ENST00000439730.2_Intron|GOSR2_ENST00000225567.4_Splice_Site_p.G195V	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			TGTCCCCCAGGCACCCAAGGA	0.577																																					p.G195V		Atlas-SNP	.											.	GOSR2	38	.	0			c.G584T						.						135.0	128.0	130.0					17																	45017921		2203	4300	6503	SO:0001628	intergenic_variant	9570	exon7			CCCCAGGCACCCA	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653			chr17.hg19:g.45017921G>T		31.0	0.0		56.0	17.0	NM_054022	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	hg19	CCDS42355.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994802	0.35226	.	.	ENSG00000108433	ENST00000225567	D	0.82255	-1.59	4.15	1.12	0.20585	.	0.236625	0.42964	D	0.000630	D	0.84170	0.5413	L	0.56340	1.77	0.09310	N	0.999999	D	0.63880	0.993	P	0.62740	0.906	T	0.73251	-0.4042	9	.	.	.	.	6.0972	0.20027	0.3186:0.0:0.6814:0.0	.	195	O14653-2	.	V	195	ENSP00000225567:G195V	.	G	+	2	0	GOSR2	42372920	0.001000	0.12720	0.005000	0.12908	0.008000	0.06430	0.157000	0.16402	0.314000	0.23086	-0.258000	0.10820	GGC	.	G|0.999;C|0.001		0.577	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1		
MTMR4	9110	hgsc.bcm.edu	37	17	56582859	56582859	+	Silent	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:56582859C>A	ENST00000323456.5	-	11	1201	c.1077G>T	c.(1075-1077)gtG>gtT	p.V359V	MTMR4_ENST00000579925.1_Silent_p.V359V	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	359	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCTGGCTACACACAGCCCGGA	0.493																																					p.V359V		Atlas-SNP	.											.	MTMR4	91	.	0			c.G1077T						.						123.0	104.0	110.0					17																	56582859		2203	4300	6503	SO:0001819	synonymous_variant	9110	exon11			GCTACACACAGCC	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.1077G>T	chr17.hg19:g.56582859C>A		121.0	0.0		152.0	26.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Silent	SNP	ENST00000323456.5	hg19	CCDS11608.1																																																																																			.	.		0.493	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647292	34647292	+	Missense_Mutation	SNP	G	G	C	rs531868906		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:34647292G>C	ENST00000280020.5	+	7	1038	c.1016G>C	c.(1015-1017)cGg>cCg	p.R339P	KIAA1328_ENST00000435985.2_Missense_Mutation_p.R55P|KIAA1328_ENST00000591619.1_Missense_Mutation_p.R335P|KIAA1328_ENST00000543923.1_Missense_Mutation_p.R231P|KIAA1328_ENST00000586501.1_Missense_Mutation_p.R55P|KIAA1328_ENST00000586135.1_Missense_Mutation_p.R55P	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	339										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AGTTATTGTCGGCTTTCTTGG	0.463																																					p.R339P		Atlas-SNP	.											KIAA1328,NS,carcinoma,+1,1	KIAA1328	39	.	0			c.G1016C						.						94.0	89.0	91.0					18																	34647292		2050	4208	6258	SO:0001583	missense	57536	exon7			ATTGTCGGCTTTC	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1016G>C	chr18.hg19:g.34647292G>C	ENSP00000280020:p.Arg339Pro	538.0	0.0		435.0	68.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	8.834	0.940660	0.18281	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055;ENST00000435985	T;T;T	0.50277	0.75;0.75;0.75	6.17	3.25	0.37280	.	0.649434	0.16451	N	0.213853	T	0.35219	0.0924	L	0.34521	1.04	0.25823	N	0.98426	P;B;B;P	0.34757	0.467;0.195;0.195;0.467	B;B;B;B	0.38880	0.197;0.128;0.263;0.284	T	0.14172	-1.0482	10	0.28530	T	0.3	.	6.6411	0.22909	0.1392:0.0:0.6337:0.2272	.	55;339;55;339	Q86T90-4;A8K8C3;Q86T90-3;Q86T90	.;.;.;K1328_HUMAN	P	231;339;339;55	ENSP00000441359:R231P;ENSP00000280020:R339P;ENSP00000390515:R55P	ENSP00000280020:R339P	R	+	2	0	KIAA1328	32901290	0.731000	0.28111	1.000000	0.80357	0.601000	0.36947	0.710000	0.25748	1.635000	0.50512	0.655000	0.94253	CGG	.	.		0.463	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
EPG5	57724	hgsc.bcm.edu	37	18	43460188	43460188	+	Splice_Site	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:43460188C>A	ENST00000282041.5	-	32	5553	c.5519G>T	c.(5518-5520)aGc>aTc	p.S1840I	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1840					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CTCCGCGGAGCCTGCCAGCAG	0.547											OREG0024951	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1840I		Atlas-SNP	.											EPG5,NS,carcinoma,0,1	EPG5	199	.	0			c.G5519T						.						10.0	11.0	11.0					18																	43460188		1805	3991	5796	SO:0001630	splice_region_variant	57724	exon32			GCGGAGCCTGCCA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5519-1G>T	chr18.hg19:g.43460188C>A		53.0	0.0	916	63.0	12.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	18.25	3.583360	0.65992	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.11712	2.75	5.8	5.8	0.92144	.	.	.	.	.	T	0.31670	0.0804	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.66979	0.948	T	0.00402	-1.1762	9	0.72032	D	0.01	.	20.0466	0.97609	0.0:1.0:0.0:0.0	.	1840	Q9HCE0	EPG5_HUMAN	I	1840;715	ENSP00000282041:S1840I	ENSP00000282041:S1840I	S	-	2	0	EPG5	41714186	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	7.048000	0.76606	2.729000	0.93468	0.563000	0.77884	AGC	.	.		0.547	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	Missense_Mutation
MC4R	4160	hgsc.bcm.edu	37	18	58039123	58039123	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:58039123C>A	ENST00000299766.3	-	1	878	c.460G>T	c.(460-462)Gct>Tct	p.A154S		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	154					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|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)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				TACTGGAGAGCATAGAAGATA	0.418																																					p.A154S		Atlas-SNP	.											.	MC4R	49	.	0			c.G460T						.						93.0	83.0	86.0					18																	58039123		2203	4300	6503	SO:0001583	missense	4160	exon1			GGAGAGCATAGAA	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"""GPCR / Class A : Melanocortin receptors"""	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.460G>T	chr18.hg19:g.58039123C>A	ENSP00000299766:p.Ala154Ser	121.0	0.0		99.0	14.0	NM_005912	B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	hg19	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.823342	0.90873	.	.	ENSG00000166603	ENST00000299766	T	0.37584	1.19	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.72956	-0.4134	10	0.87932	D	0	.	17.6572	0.88181	0.0:1.0:0.0:0.0	.	154	P32245	MC4R_HUMAN	S	154	ENSP00000299766:A154S	ENSP00000299766:A154S	A	-	1	0	MC4R	56190103	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.818000	0.86416	2.773000	0.95371	0.655000	0.94253	GCT	.	.		0.418	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912	
SERPINB4	6318	hgsc.bcm.edu	37	18	61308143	61308143	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:61308143T>C	ENST00000341074.5	-	5	549	c.434A>G	c.(433-435)aAg>aGg	p.K145R	SERPINB4_ENST00000356424.6_Missense_Mutation_p.K145R	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	145					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GTTAATCTTCTTTCGACTTTC	0.408																																					p.K145R		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A434G						.						121.0	109.0	113.0					18																	61308143		2203	4300	6503	SO:0001583	missense	6318	exon5			ATCTTCTTTCGAC	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"""Serine (or cysteine) peptidase inhibitors"""	10570	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.434A>G	chr18.hg19:g.61308143T>C	ENSP00000343445:p.Lys145Arg	512.0	0.0		463.0	77.0	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	hg19	CCDS11986.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.26|13.26	2.183101|2.183101	0.38511|0.38511	.|.	.|.	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424;ENST00000436264|ENST00000413673	D;D;D|.	0.84944|.	-1.92;-1.92;-1.92|.	4.28|4.28	1.78|1.78	0.24846|0.24846	Serpin domain (3);|.	0.582093|.	0.14232|.	N|.	0.332645|.	T|T	0.54919|0.54919	0.1888|0.1888	M|M	0.78049|0.78049	2.395|2.395	0.09310|0.09310	N|N	1|1	B;P|.	0.49862|.	0.379;0.929|.	P;P|.	0.59825|.	0.496;0.864|.	T|T	0.46857|0.46857	-0.9161|-0.9161	10|5	0.62326|.	D|.	0.03|.	.|.	7.7402|7.7402	0.28837|0.28837	0.0:0.3425:0.0:0.6575|0.0:0.3425:0.0:0.6575	.|.	145;145|.	P48594;Q9BYF7|.	SPB4_HUMAN;.|.	R|G	145;145;102|147	ENSP00000343445:K145R;ENSP00000348795:K145R;ENSP00000399796:K102R|.	ENSP00000343445:K145R|.	K|R	-|-	2|1	0|2	SERPINB4|SERPINB4	59459123|59459123	0.000000|0.000000	0.05858|0.05858	0.760000|0.760000	0.31359|0.31359	0.539000|0.539000	0.34962|0.34962	0.618000|0.618000	0.24373|0.24373	0.683000|0.683000	0.31428|0.31428	0.491000|0.491000	0.48974|0.48974	AAG|AGA	.	.		0.408	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041	
ZNF407	55628	hgsc.bcm.edu	37	18	72775861	72775861	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr18:72775861C>T	ENST00000299687.5	+	8	6184	c.6184C>T	c.(6184-6186)Ccc>Tcc	p.P2062S		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2062					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GGTGGTCCATCCCTCAGCAGC	0.682																																					p.P2062S		Atlas-SNP	.											.	ZNF407	231	.	0			c.C6184T						.						38.0	44.0	42.0					18																	72775861		2085	4211	6296	SO:0001583	missense	55628	exon8			GTCCATCCCTCAG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6184C>T	chr18.hg19:g.72775861C>T	ENSP00000299687:p.Pro2062Ser	74.0	0.0		94.0	9.0	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	3.939	-0.014518	0.07681	.	.	ENSG00000215421	ENST00000299687	T	0.32988	1.43	4.42	3.53	0.40419	.	.	.	.	.	T	0.33933	0.0880	L	0.43757	1.38	0.58432	D	0.999997	P	0.50066	0.931	P	0.47673	0.554	T	0.32587	-0.9901	9	0.87932	D	0	.	14.3761	0.66879	0.0:0.8512:0.1487:0.0	.	2062	Q9C0G0	ZN407_HUMAN	S	2062	ENSP00000299687:P2062S	ENSP00000299687:P2062S	P	+	1	0	ZNF407	70904849	0.866000	0.29940	0.025000	0.17156	0.007000	0.05969	1.312000	0.33574	2.025000	0.59659	0.462000	0.41574	CCC	.	.		0.682	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
OR7D4	125958	hgsc.bcm.edu	37	19	9324917	9324917	+	Silent	SNP	C	C	T	rs377419980		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:9324917C>T	ENST00000308682.2	-	1	625	c.597G>A	c.(595-597)ttG>ttA	p.L199L		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L199L(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TGGCCACATACAAGACAATGT	0.522																																					p.L199L		Atlas-SNP	.											OR7D4,NS,carcinoma,0,1	OR7D4	66	.	1	Substitution - coding silent(1)	lung(1)	c.G597A						.						106.0	99.0	102.0					19																	9324917		2203	4300	6503	SO:0001819	synonymous_variant	125958	exon1			CACATACAAGACA		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.597G>A	chr19.hg19:g.9324917C>T		146.0	0.0		186.0	33.0	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Silent	SNP	ENST00000308682.2	hg19	CCDS32901.1																																																																																			.	.		0.522	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
LDLR	3949	hgsc.bcm.edu	37	19	11213382	11213382	+	Missense_Mutation	SNP	G	G	T	rs146675823		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:11213382G>T	ENST00000558518.1	+	3	420	c.233G>T	c.(232-234)cGt>cTt	p.R78L	LDLR_ENST00000557933.1_Missense_Mutation_p.R78L|LDLR_ENST00000455727.2_Missense_Mutation_p.R78L|LDLR_ENST00000545707.1_Missense_Mutation_p.R78L|LDLR_ENST00000535915.1_Intron|LDLR_ENST00000558013.1_Missense_Mutation_p.R78L	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	78	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		R -> C (in FH).		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TGTGGGGGCCGTGTCAACCGC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		19169	0.0		0.0	False		,,,				2504	0.001				p.R78L	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G233T						.						172.0	151.0	159.0					19																	11213382		2203	4300	6503	SO:0001583	missense	3949	exon3			GGGGCCGTGTCAA	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.233G>T	chr19.hg19:g.11213382G>T	ENSP00000454071:p.Arg78Leu	230.0	0.0		230.0	44.0	NM_001195800	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	hg19	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805102	0.70682	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000455727	D;D	0.91407	-2.84;-2.84	5.65	1.11	0.20524	.	0.118981	0.35677	N	0.003043	D	0.92961	0.7760	M	0.79614	2.46	0.43745	D	0.996243	B;B;P;D	0.76494	0.038;0.0;0.895;0.999	B;B;P;D	0.77557	0.033;0.006;0.793;0.99	D	0.88835	0.3308	10	0.22109	T	0.4	.	7.6124	0.28137	0.1636:0.0:0.7106:0.1258	.	78;78;90;78	B4DR00;B4DJZ8;Q59FQ1;P01130	.;.;.;LDLR_HUMAN	L	78	ENSP00000437639:R78L;ENSP00000397829:R78L	ENSP00000252444:R78L	R	+	2	0	LDLR	11074382	0.463000	0.25799	0.124000	0.21820	0.944000	0.59088	1.497000	0.35649	0.054000	0.16065	0.591000	0.81541	CGT	.	G|1.000;A|0.000		0.567	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ZNF536	9745	hgsc.bcm.edu	37	19	30935048	30935048	+	Silent	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:30935048C>T	ENST00000355537.3	+	2	726	c.579C>T	c.(577-579)cgC>cgT	p.R193R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	193					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GGCGTGTGCGCGAGGAGAACC	0.692																																					p.R193R		Atlas-SNP	.											ZNF536,right_upper_lobe,carcinoma,0,1	ZNF536	424	.	0			c.C579T						.						17.0	13.0	15.0					19																	30935048		2193	4290	6483	SO:0001819	synonymous_variant	9745	exon2			TGTGCGCGAGGAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.579C>T	chr19.hg19:g.30935048C>T		32.0	0.0		50.0	12.0	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.692	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
RYR1	6261	hgsc.bcm.edu	37	19	38974064	38974064	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:38974064G>A	ENST00000359596.3	+	33	4842	c.4842G>A	c.(4840-4842)gtG>gtA	p.V1614V	RYR1_ENST00000360985.3_Silent_p.V1614V|RYR1_ENST00000355481.4_Silent_p.V1614V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1614	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TCCTGCAGGTGGAGACGAGGC	0.697																																					p.V1614V		Atlas-SNP	.											.	RYR1	708	.	0			c.G4842A						.						13.0	14.0	13.0					19																	38974064		2193	4284	6477	SO:0001819	synonymous_variant	6261	exon33			GCAGGTGGAGACG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4842G>A	chr19.hg19:g.38974064G>A		91.0	0.0		76.0	13.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.697	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
CEACAM4	1089	hgsc.bcm.edu	37	19	42132051	42132051	+	Missense_Mutation	SNP	G	G	T	rs199959927		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:42132051G>T	ENST00000221954.2	-	2	458	c.348C>A	c.(346-348)gaC>gaA	p.D116E	CEACAM4_ENST00000600925.1_Missense_Mutation_p.D116E	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	116	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						AGGATCCTGCGTCCTCCAGGG	0.522																																					p.D116E		Atlas-SNP	.											.	CEACAM4	42	.	0			c.C348A						.						197.0	170.0	179.0					19																	42132051		2203	4300	6503	SO:0001583	missense	1089	exon2			TCCTGCGTCCTCC	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.348C>A	chr19.hg19:g.42132051G>T	ENSP00000221954:p.Asp116Glu	540.0	0.0		590.0	108.0	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	hg19	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399384	0.42512	.	.	ENSG00000105352	ENST00000221954	D	0.87729	-2.29	1.82	1.82	0.25136	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94056	0.8095	H	0.95679	3.705	0.09310	N	1	D;D	0.76494	0.999;0.976	D;P	0.69142	0.962;0.821	D	0.84347	0.0530	9	0.87932	D	0	.	7.103	0.25348	0.0:0.0:1.0:0.0	.	116;116	E7EMX3;O75871	.;CEAM4_HUMAN	E	116	ENSP00000221954:D116E	ENSP00000221954:D116E	D	-	3	2	CEACAM4	46823891	0.018000	0.18449	0.007000	0.13788	0.010000	0.07245	0.956000	0.29202	1.319000	0.45190	0.313000	0.20887	GAC	.	G|0.999;A|0.001		0.522	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
SMG9	56006	hgsc.bcm.edu	37	19	44238560	44238560	+	Silent	SNP	G	G	T	rs368481505		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:44238560G>T	ENST00000270066.6	-	10	1425	c.1083C>A	c.(1081-1083)acC>acA	p.T361T	SMG9_ENST00000601170.1_Silent_p.T361T	NM_019108.2	NP_061981.2	Q9H0W8	SMG9_HUMAN	SMG9 nonsense mediated mRNA decay factor	361					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|intracellular (GO:0005622)	identical protein binding (GO:0042802)			kidney(1)|large_intestine(5)|liver(1)|lung(7)|pancreas(1)|prostate(2)|urinary_tract(2)	19						GGTAGTACTCGGTGCCTTCAT	0.612																																					p.T361T		Atlas-SNP	.											.	SMG9	39	.	0			c.C1083A						.						33.0	28.0	30.0					19																	44238560		2188	4284	6472	SO:0001819	synonymous_variant	56006	exon10			GTACTCGGTGCCT	BC008869	CCDS33043.2	19q13.31	2013-07-02	2013-07-02	2011-06-21	ENSG00000105771	ENSG00000105771			25763	protein-coding gene	gene with protein product		613176	"""chromosome 19 open reading frame 61"", ""smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C19orf61		11230166, 19417104	Standard	NM_019108		Approved	FLJ12886	uc002oxj.2	Q9H0W8	OTTHUMG00000150337	ENST00000270066.6:c.1083C>A	chr19.hg19:g.44238560G>T		76.0	0.0		101.0	5.0	NM_019108	O60429|Q9H9A9	Silent	SNP	ENST00000270066.6	hg19	CCDS33043.2																																																																																			.	.		0.612	SMG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317668.1	NM_019108	
RSPH6A	81492	hgsc.bcm.edu	37	19	46318184	46318184	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:46318184C>A	ENST00000221538.3	-	1	393	c.251G>T	c.(250-252)gGc>gTc	p.G84V	RSPH6A_ENST00000597055.1_Missense_Mutation_p.G84V|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	84						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GTACTCCATGCCACCCAGCCG	0.607																																					p.G84V		Atlas-SNP	.											.	RSPH6A	70	.	0			c.G251T						.						51.0	46.0	47.0					19																	46318184		2203	4300	6503	SO:0001583	missense	81492	exon1			TCCATGCCACCCA	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.251G>T	chr19.hg19:g.46318184C>A	ENSP00000221538:p.Gly84Val	77.0	0.0		112.0	11.0	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.603976	0.28534	.	.	ENSG00000104941	ENST00000221538	T	0.15372	2.43	4.11	-5.72	0.02406	.	3.303470	0.00984	N	0.003424	T	0.09992	0.0245	L	0.29908	0.895	0.09310	N	1	B	0.26002	0.139	B	0.22386	0.039	T	0.18461	-1.0336	10	0.33141	T	0.24	-6.806	1.5802	0.02633	0.1887:0.2035:0.3962:0.2117	.	84	Q9H0K4	RSH6A_HUMAN	V	84	ENSP00000221538:G84V	ENSP00000221538:G84V	G	-	2	0	RSPH6A	51010024	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.057000	0.01395	-0.630000	0.05567	-0.310000	0.09108	GGC	.	.		0.607	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
CCDC155	147872	hgsc.bcm.edu	37	19	49920647	49920647	+	Silent	SNP	C	C	A	rs182291239	byFrequency	TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:49920647C>A	ENST00000447857.3	+	20	1774	c.1569C>A	c.(1567-1569)atC>atA	p.I523I		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	523						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						ATCCACTGATCCCAGCTCCTG	0.642																																					p.I523I		Atlas-SNP	.											.	CCDC155	46	.	0			c.C1569A						.						54.0	61.0	59.0					19																	49920647		2133	4220	6353	SO:0001819	synonymous_variant	147872	exon20			ACTGATCCCAGCT		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1569C>A	chr19.hg19:g.49920647C>A		104.0	0.0		137.0	30.0	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	hg19	CCDS46140.1																																																																																			.	C|1.000;T|0.000		0.642	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
VN1R2	317701	hgsc.bcm.edu	37	19	53761860	53761860	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:53761860T>G	ENST00000341702.3	+	1	316	c.232T>G	c.(232-234)Tct>Gct	p.S78A		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	78					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		ctctcttgtctctgcacacgg	0.468																																					p.S78A		Atlas-SNP	.											.	VN1R2	71	.	0			c.T232G						.						36.0	35.0	36.0					19																	53761860		2190	4283	6473	SO:0001583	missense	317701	exon1			CTTGTCTCTGCAC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.232T>G	chr19.hg19:g.53761860T>G	ENSP00000351244:p.Ser78Ala	90.0	0.0		135.0	26.0	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	T	4.435	0.080571	0.08533	.	.	ENSG00000196131	ENST00000341702	T	0.08984	3.03	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.40515	-0.9559	8	0.49607	T	0.09	.	.	.	.	.	78	Q8NFZ6	VN1R2_HUMAN	A	78	ENSP00000351244:S78A	ENSP00000351244:S78A	S	+	1	0	VN1R2	58453672	0.004000	0.15560	0.021000	0.16686	0.021000	0.10359	1.432000	0.34936	0.115000	0.18071	0.113000	0.15668	TCT	.	.		0.468	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
ZNF154	7710	hgsc.bcm.edu	37	19	58216279	58216279	+	Silent	SNP	A	A	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:58216279A>T	ENST00000512439.2	-	2	298	c.102T>A	c.(100-102)gcT>gcA	p.A34A	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron|ZNF154_ENST00000426889.1_Silent_p.A34A			Q13106	ZN154_HUMAN	zinc finger protein 154	34	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GGCATCTTTGAGCCTCATCAA	0.502																																					p.A34A		Atlas-SNP	.											.	ZNF154	34	.	0			c.T102A						.						181.0	171.0	175.0					19																	58216279		2203	4300	6503	SO:0001819	synonymous_variant	7710	exon2			TCTTTGAGCCTCA	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.102T>A	chr19.hg19:g.58216279A>T		314.0	0.0		266.0	30.0	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Silent	SNP	ENST00000512439.2	hg19	CCDS42639.1																																																																																			.	.		0.502	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
ZNF324B	388569	hgsc.bcm.edu	37	19	58967236	58967236	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:58967236G>T	ENST00000336614.4	+	4	1032	c.925G>T	c.(925-927)Ggc>Tgc	p.G309C	ZNF324B_ENST00000391696.1_Missense_Mutation_p.G299C|ZNF324B_ENST00000545523.1_Missense_Mutation_p.G309C	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CATCCACAGCGGCGAGACGCC	0.692																																					p.G309C		Atlas-SNP	.											.	ZNF324B	58	.	0			c.G925T						.						19.0	18.0	18.0					19																	58967236		2116	4167	6283	SO:0001583	missense	388569	exon4			CACAGCGGCGAGA	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"""Zinc fingers, C2H2-type"", ""-"""	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.925G>T	chr19.hg19:g.58967236G>T	ENSP00000337473:p.Gly309Cys	185.0	0.0		158.0	23.0	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	hg19	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877387	0.51801	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.01629	4.72;4.72;4.72	3.22	2.14	0.27477	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42682	D	0.000665	T	0.09291	0.0229	M	0.83118	2.625	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.01786	-1.1274	10	0.87932	D	0	.	9.6711	0.40013	0.0:0.0:0.7916:0.2084	.	309;299	Q6AW86;C9JTQ8	Z324B_HUMAN;.	C	309;309;299	ENSP00000337473:G309C;ENSP00000438930:G309C;ENSP00000375578:G299C	ENSP00000337473:G309C	G	+	1	0	ZNF324B	63659048	0.432000	0.25554	0.086000	0.20670	0.944000	0.59088	1.881000	0.39638	0.649000	0.30751	0.591000	0.81541	GGC	.	.		0.692	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395	
GNRH2	2797	hgsc.bcm.edu	37	20	3025397	3025397	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:3025397C>T	ENST00000245983.2	+	3	278	c.227C>T	c.(226-228)cCc>cTc	p.P76L	MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000380347.2_Missense_Mutation_p.P69L|GNRH2_ENST00000359100.2_Missense_Mutation_p.P69L|GNRH2_ENST00000380346.2_Missense_Mutation_p.P68L|GNRH2_ENST00000359987.1_Missense_Mutation_p.P68L	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2	76					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						GCCCTGGCTCCCCTGGACGAC	0.642																																					p.P76L		Atlas-SNP	.											.	GNRH2	15	.	0			c.C227T						.						36.0	34.0	35.0					20																	3025397		2201	4300	6501	SO:0001583	missense	2797	exon3			TGGCTCCCCTGGA	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.227C>T	chr20.hg19:g.3025397C>T	ENSP00000245983:p.Pro76Leu	96.0	0.0		110.0	12.0	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Missense_Mutation	SNP	ENST00000245983.2	hg19	CCDS13040.1	.	.	.	.	.	.	.	.	.	.	C	3.326	-0.137718	0.06711	.	.	ENSG00000125787	ENST00000245983;ENST00000359100;ENST00000359987;ENST00000380347;ENST00000380346	T;T;T;T;T	0.52295	0.77;0.75;0.67;0.75;0.67	4.38	-5.1	0.02911	.	1.743350	0.03660	N	0.242458	T	0.24967	0.0606	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.06917	-1.0800	10	0.32370	T	0.25	.	2.5	0.04631	0.111:0.331:0.325:0.2331	.	76;68;69	O43555;O43555-2;O43555-3	GON2_HUMAN;.;.	L	76;69;68;69;68	ENSP00000245983:P76L;ENSP00000352003:P69L;ENSP00000353077:P68L;ENSP00000369705:P69L;ENSP00000369704:P68L	ENSP00000245983:P76L	P	+	2	0	GNRH2	2973397	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.227000	0.02950	-1.051000	0.03226	-1.966000	0.00469	CCC	.	.		0.642	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
RALGAPB	57148	hgsc.bcm.edu	37	20	37154091	37154091	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:37154091G>C	ENST00000262879.6	+	12	2116	c.1832G>C	c.(1831-1833)cGa>cCa	p.R611P	RALGAPB_ENST00000397038.1_Missense_Mutation_p.R389P|RALGAPB_ENST00000397040.1_Missense_Mutation_p.R611P|RALGAPB_ENST00000397042.3_Missense_Mutation_p.R611P			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	611					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.R611P(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						ACAGAATTGCGAAGATCCTCC	0.328																																					p.R611P		Atlas-SNP	.											RALGAPB,NS,carcinoma,0,1	RALGAPB	134	.	1	Substitution - Missense(1)	lung(1)	c.G1832C						.						133.0	136.0	135.0					20																	37154091		2203	4300	6503	SO:0001583	missense	57148	exon12			AATTGCGAAGATC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1832G>C	chr20.hg19:g.37154091G>C	ENSP00000262879:p.Arg611Pro	711.0	0.0		607.0	105.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164602	0.94727	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.73363	-0.74;-0.74	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.86138	0.5861	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.998	D;D;D;D	0.87578	0.998;0.991;0.997;0.991	D	0.86502	0.1804	10	0.87932	D	0	.	20.0308	0.97536	0.0:0.0:1.0:0.0	.	439;611;611;611	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	P	611;611;611;389;611;439	ENSP00000262879:R611P;ENSP00000380233:R611P	ENSP00000262879:R611P	R	+	2	0	RALGAPB	36587505	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.732000	0.93576	0.585000	0.79938	CGA	.	.		0.328	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
NCOA3	8202	hgsc.bcm.edu	37	20	46279951	46279951	+	Missense_Mutation	SNP	G	G	T	rs376291640		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:46279951G>T	ENST00000371998.3	+	20	4068	c.3877G>T	c.(3877-3879)Gat>Tat	p.D1293Y	NCOA3_ENST00000371997.3_Missense_Mutation_p.D1284Y|NCOA3_ENST00000341724.6_Missense_Mutation_p.D1219Y|NCOA3_ENST00000372004.3_Missense_Mutation_p.D1289Y			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1293	Acetyltransferase.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CCCCAGCATGGATGGGCTTTT	0.522																																					p.D1293Y		Atlas-SNP	.											.	NCOA3	156	.	0			c.G3877T						.						111.0	104.0	106.0					20																	46279951		2203	4300	6503	SO:0001583	missense	8202	exon20			AGCATGGATGGGC	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3877G>T	chr20.hg19:g.46279951G>T	ENSP00000361066:p.Asp1293Tyr	139.0	0.0		133.0	22.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.877183	0.91664	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.26810	1.71;4.51;4.51;1.71	6.17	6.17	0.99709	Domain of unknown function DUF1518 (1);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.996;1.0;0.996;0.996;0.993;0.996	T	0.40059	-0.9583	10	0.56958	D	0.05	-28.1929	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1293;1284;1296;1288;1289;1293	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	Y	1289;1219;1289;1293;1284	ENSP00000342123:D1219Y;ENSP00000361073:D1289Y;ENSP00000361066:D1293Y;ENSP00000361065:D1284Y	ENSP00000345671:D1289Y	D	+	1	0	NCOA3	45713358	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.522	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
ZGPAT	84619	hgsc.bcm.edu	37	20	62340061	62340061	+	Silent	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:62340061G>T	ENST00000328969.5	+	2	256	c.129G>T	c.(127-129)ctG>ctT	p.L43L	ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000324228.2_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.L43L|ARFRP1_ENST00000609142.1_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.L43L|ZGPAT_ENST00000357119.4_Silent_p.L43L|ARFRP1_ENST00000440854.1_5'Flank|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.L43L|RP4-583P15.15_ENST00000490623.2_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	43					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					AGGGGGACCTGAAGGAGCTCA	0.672																																					p.L43L		Atlas-SNP	.											.	ZGPAT	57	.	0			c.G129T						.						38.0	41.0	40.0					20																	62340061		2203	4297	6500	SO:0001819	synonymous_variant	84619	exon2			GGACCTGAAGGAG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"""Zinc fingers, CCCH-type domain containing"", ""G patch domain containing"""	15948	protein-coding gene	gene with protein product			"""KIAA1847"""	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.129G>T	chr20.hg19:g.62340061G>T		63.0	0.0		59.0	11.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	hg19	CCDS13534.1																																																																																			.	.		0.672	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484	
KRTAP19-4	337971	hgsc.bcm.edu	37	21	31869199	31869199	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr21:31869199C>A	ENST00000334058.2	-	1	252	c.230G>T	c.(229-231)aGa>aTa	p.R77I		NM_181610.1	NP_853641.1	Q3LI73	KR194_HUMAN	keratin associated protein 19-4	77						intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATTGAATGATCTTCTTATGAC	0.373																																					p.R77I		Atlas-SNP	.											.	KRTAP19-4	22	.	0			c.G230T						.						175.0	173.0	174.0					21																	31869199		2203	4300	6503	SO:0001583	missense	337971	exon1			AATGATCTTCTTA	AP001708	CCDS33534.1	21q22.1	2011-02-10			ENSG00000186967	ENSG00000186967		"""Keratin associated proteins"""	18939	protein-coding gene	gene with protein product						12359730	Standard	NM_181610		Approved	KAP19.4	uc011acz.2	Q3LI73	OTTHUMG00000057767	ENST00000334058.2:c.230G>T	chr21.hg19:g.31869199C>A	ENSP00000335567:p.Arg77Ile	250.0	0.0		239.0	32.0	NM_181610	Q17RT4|Q17RT6	Missense_Mutation	SNP	ENST00000334058.2	hg19	CCDS33534.1	.	.	.	.	.	.	.	.	.	.	C	6.342	0.431173	0.12045	.	.	ENSG00000186967	ENST00000334058	T	0.21361	2.01	3.72	-0.509	0.11977	.	.	.	.	.	T	0.16342	0.0393	.	.	.	0.09310	N	1	P	0.52316	0.952	B	0.41571	0.36	T	0.15809	-1.0424	8	0.87932	D	0	.	6.3611	0.21429	0.0:0.4322:0.0:0.5678	.	77	Q3LI73	KR194_HUMAN	I	77	ENSP00000335567:R77I	ENSP00000335567:R77I	R	-	2	0	KRTAP19-4	30791070	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.249000	0.08842	-0.100000	0.12241	0.543000	0.68304	AGA	.	.		0.373	KRTAP19-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128219.2		
PLA2G3	50487	hgsc.bcm.edu	37	22	31534717	31534717	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:31534717G>T	ENST00000215885.3	-	2	835	c.583C>A	c.(583-585)Cag>Aag	p.Q195K		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	195	Phospholipase A2-like.				acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						TAGTTGTACTGCAAGGGTGAG	0.597																																					p.Q195K		Atlas-SNP	.											.	PLA2G3	85	.	0			c.C583A						.						309.0	240.0	263.0					22																	31534717		2203	4300	6503	SO:0001583	missense	50487	exon2			TGTACTGCAAGGG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.583C>A	chr22.hg19:g.31534717G>T	ENSP00000215885:p.Gln195Lys	593.0	1.0		544.0	95.0	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	hg19	CCDS13889.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491740	0.64074	.	.	ENSG00000100078	ENST00000215885	T	0.29142	1.58	5.41	4.35	0.52113	Phospholipase A2 (3);	0.370207	0.28871	N	0.013866	T	0.34366	0.0895	L	0.55990	1.75	0.32021	N	0.60077	P	0.47677	0.899	P	0.45610	0.487	T	0.49000	-0.8984	10	0.56958	D	0.05	-17.6393	12.855	0.57880	0.0:0.2879:0.7121:0.0	.	195	Q9NZ20	PA2G3_HUMAN	K	195	ENSP00000215885:Q195K	ENSP00000215885:Q195K	Q	-	1	0	PLA2G3	29864717	1.000000	0.71417	0.998000	0.56505	0.870000	0.49936	1.665000	0.37449	2.546000	0.85860	0.561000	0.74099	CAG	.	.		0.597	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
GRAP2	9402	hgsc.bcm.edu	37	22	40343142	40343142	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:40343142C>A	ENST00000344138.4	+	2	295	c.32C>A	c.(31-33)gCt>gAt	p.A11D	GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000544756.1_5'UTR|GRAP2_ENST00000407075.3_Missense_Mutation_p.A11D|GRAP2_ENST00000478445.1_Intron|GRAP2_ENST00000543252.1_Missense_Mutation_p.A11D|GRAP2_ENST00000540310.1_Intron	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	11	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GATTTCACTGCTTCAGGTGAG	0.502																																					p.A11D		Atlas-SNP	.											.	GRAP2	29	.	0			c.C32A						.						192.0	172.0	179.0					22																	40343142		2203	4300	6503	SO:0001583	missense	9402	exon2			TCACTGCTTCAGG	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"""SH2 domain containing"""	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.32C>A	chr22.hg19:g.40343142C>A	ENSP00000339186:p.Ala11Asp	338.0	0.0		263.0	68.0	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	hg19	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802409	0.90538	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000420971;ENST00000407075	T;T;T;T	0.58940	1.11;0.3;0.3;1.11	5.65	5.65	0.86999	Src homology-3 domain (4);	0.148621	0.64402	D	0.000011	D	0.83339	0.5233	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.87997	0.2753	10	0.87932	D	0	-29.0893	16.6526	0.85220	0.0:1.0:0.0:0.0	.	11;11	Q6FI14;O75791	.;GRAP2_HUMAN	D	11	ENSP00000339186:A11D;ENSP00000446350:A11D;ENSP00000396355:A11D;ENSP00000385607:A11D	ENSP00000339186:A11D	A	+	2	0	GRAP2	38673088	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.883000	0.63128	2.660000	0.90430	0.557000	0.71058	GCT	.	.		0.502	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810	
TLR8	51311	hgsc.bcm.edu	37	X	12939183	12939183	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:12939183T>C	ENST00000218032.6	+	2	2111	c.2024T>C	c.(2023-2025)aTg>aCg	p.M675T	TLR8_ENST00000311912.5_Missense_Mutation_p.M693T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	675					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	AATGATAATATGTTAAAGTTT	0.378																																					p.M675T		Atlas-SNP	.											.	TLR8	134	.	0			c.T2024C						.						49.0	50.0	50.0					X																	12939183		2202	4295	6497	SO:0001583	missense	51311	exon2			ATAATATGTTAAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2024T>C	chrX.hg19:g.12939183T>C	ENSP00000218032:p.Met675Thr	87.0	0.0		134.0	47.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.492083	0.00159	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56275	0.47;0.47	5.82	-11.6	0.00059	.	3.369210	0.00904	N	0.002384	T	0.35393	0.0930	L	0.39397	1.21	0.09310	N	1	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.14282	-1.0478	10	0.22706	T	0.39	.	6.4243	0.21760	0.4747:0.1082:0.3411:0.076	.	675;693	Q9NR97;D1CS70	TLR8_HUMAN;.	T	675;693	ENSP00000218032:M675T;ENSP00000312082:M693T	ENSP00000218032:M675T	M	+	2	0	TLR8	12849104	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.880000	0.01627	-4.010000	0.00082	-0.396000	0.06452	ATG	.	.		0.378	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
SPIN4	139886	hgsc.bcm.edu	37	X	62570624	62570624	+	Silent	SNP	G	G	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:62570624G>A	ENST00000335144.3	-	1	594	c.75C>T	c.(73-75)caC>caT	p.H25H	SPIN4_ENST00000374884.2_Silent_p.H7H|SPIN4-AS1_ENST00000451979.1_RNA	NM_001012968.2	NP_001012986.2	Q56A73	SPIN4_HUMAN	spindlin family, member 4	25					gamete generation (GO:0007276)					endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	11						GTTGCTTCCTGTGGGTGTGCC	0.582																																					p.H25H		Atlas-SNP	.											.	SPIN4	29	.	0			c.C75T						.						64.0	63.0	63.0					X																	62570624		2067	4173	6240	SO:0001819	synonymous_variant	139886	exon1			CTTCCTGTGGGTG	AK126931	CCDS43964.1	Xq11.1	2008-02-05			ENSG00000186767	ENSG00000186767			27040	protein-coding gene	gene with protein product						12477932	Standard	NM_001012968		Approved	FLJ44984	uc004dvf.3	Q56A73	OTTHUMG00000021696	ENST00000335144.3:c.75C>T	chrX.hg19:g.62570624G>A		89.0	0.0		84.0	44.0	NM_001012968	B3KX90|Q5JUL2	Silent	SNP	ENST00000335144.3	hg19	CCDS43964.1																																																																																			.	.		0.582	SPIN4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012968	
MAGEE2	139599	hgsc.bcm.edu	37	X	75004287	75004287	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:75004287C>T	ENST00000373359.2	-	1	792	c.600G>A	c.(598-600)tgG>tgA	p.W200*		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	200	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCAGCAAGTCCCAAATGGAGG	0.512																																					p.W200X		Atlas-SNP	.											.	MAGEE2	94	.	0			c.G600A						.						67.0	61.0	63.0					X																	75004287		2203	4300	6503	SO:0001587	stop_gained	139599	exon1			CAAGTCCCAAATG	AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.600G>A	chrX.hg19:g.75004287C>T	ENSP00000362457:p.Trp200*	69.0	0.0		110.0	26.0	NM_138703	Q5JSI5	Nonsense_Mutation	SNP	ENST00000373359.2	hg19	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.263087	0.39995	.	.	ENSG00000186675	ENST00000373359	.	.	.	3.1	2.21	0.28008	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1813	0.25774	0.0:0.7278:0.2722:0.0	.	.	.	.	X	200	.	ENSP00000362457:W200X	W	-	3	0	MAGEE2	74921012	1.000000	0.71417	0.289000	0.24876	0.026000	0.11368	1.172000	0.31908	0.664000	0.31047	0.422000	0.28245	TGG	.	.		0.512	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703	
NEFH	4744	hgsc.bcm.edu	37	22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	chr22.hg19:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	189.0	0.0		170.0	33.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
MED12	9968	hgsc.bcm.edu	37	X	70361159	70361160	+	In_Frame_Ins	INS	-	-	CCAGCAGCAACA	rs79912241		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:70361159_70361160insCCAGCAGCAACA	ENST00000374080.3	+	43	6379_6380	c.6347_6348insCCAGCAGCAACA	c.(6346-6351)caccag>caCCAGCAGCAACAccag	p.2116_2117HQ>HQQQHQ	MED12_ENST00000333646.6_In_Frame_Ins_p.2119_2120HQ>HQQQHQ|MED12_ENST00000374102.1_In_Frame_Ins_p.2115_2116HQ>HQQQHQ|AL590764.1_ENST00000579622.1_RNA			Q93074	MED12_HUMAN	mediator complex subunit 12	2116	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					caacagcaacaccagcagcaac	0.594			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.H2116delinsHQQQH		Atlas-INDEL	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.6347_6348insCCAGCAGCAACA						.																																			SO:0001652	inframe_insertion	9968	exon43			.	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6348_6359dupCCAGCAGCAACA	chrX.hg19:g.70361159_70361160insCCAGCAGCAACA	ENSP00000363193:p.Gln2113_His2116dup	138.0	0.0		243.0	94.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	In_Frame_Ins	INS	ENST00000374080.3	hg19	CCDS43970.1																																																																																			.	.		0.594	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
TRO	7216	hgsc.bcm.edu	37	X	54955568	54955598	+	Frame_Shift_Del	DEL	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	-	rs369090033		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	GTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chrX:54955568_54955598delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	ENST00000173898.7	+	12	2523_2553	c.2411_2441delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	c.(2410-2442)agtttcagcagtgaagccagcattagctttggtfs	p.SFSSEASISFG804fs	TRO_ENST00000375022.4_Intron|TRO_ENST00000375041.2_Frame_Shift_Del_p.SFSSEASISFG407fs|TRO_ENST00000399736.1_Intron|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Frame_Shift_Del_p.SFSSEASISFG335fs|TRO_ENST00000319167.8_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	804	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						ACCAGCACTAGTTTCAGCAGTGAAGCCAGCATTAGCTTTGGTGGCATGCCT	0.528																																					p.804_814del		Atlas-Indel,Pindel	.											.	TRO	246	.	0			c.2410_2440del						.																																			SO:0001589	frameshift_variant	7216	exon12			.	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2411_2441delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	chrX.hg19:g.54955568_54955598delGTTTCAGCAGTGAAGCCAGCATTAGCTTTGG	ENSP00000173898:p.Ser804fs	134.0	0.0		133.0	28.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Frame_Shift_Del	DEL	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.528	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157	
MYH6	4624	hgsc.bcm.edu	37	14	23859463	23859463	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:23859463delC	ENST00000356287.3	-	25	3564	c.3535delG	c.(3535-3537)gacfs	p.D1179fs	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Frame_Shift_Del_p.D1179fs			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1179					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCCTCCAGGTCCCGCCGCATC	0.682																																					p.D1179fs		Atlas-INDEL	.											.	MYH6	274	.	0			c.3536delA						.						6.0	7.0	7.0					14																	23859463		1974	3882	5856	SO:0001589	frameshift_variant	4624	exon26			.	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3535delG	chr14.hg19:g.23859463delC	ENSP00000348634:p.Asp1179fs	183.0	0.0		329.0	21.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Frame_Shift_Del	DEL	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.682	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
CRELD2	79174	hgsc.bcm.edu	37	22	50315943	50315980	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177	byFrequency	TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr22:50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPILTR198fs|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000444954.1_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTCTGTCTCT	0.618																																					p.198_207del		Atlas-INDEL	.											.	CRELD2	57	.	0			c.593_620del						.																																			SO:0001627	intron_variant	79174	exon6			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-280CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	chr22.hg19:g.50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		27.0	0.0		74.0	49.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.618	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
MSL1	339287	hgsc.bcm.edu	37	17	38289863	38289868	+	In_Frame_Del	DEL	CAGGAA	CAGGAA	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	CAGGAA	CAGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr17:38289863_38289868delCAGGAA	ENST00000398532.4	+	7	1948_1953	c.1633_1638delCAGGAA	c.(1633-1638)caggaadel	p.QE545del	MSL1_ENST00000578648.1_In_Frame_Del_p.QE529del|MSL1_ENST00000579565.1_In_Frame_Del_p.QE282del	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	545					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						GAAAGGAATTCAGGAATCTGAGCCTG	0.413																																					p.281_283del		Atlas-Indel,Pindel	.											.	MSL1	21	.	0			c.843_848del						.																																			SO:0001651	inframe_deletion	339287	exon8			.		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.1633_1638delCAGGAA	chr17.hg19:g.38289863_38289868delCAGGAA	ENSP00000381543:p.Gln545_Glu546del	125.0	0.0		103.0	17.0	NM_001012241	Q0VF46|Q69Z03	In_Frame_Del	DEL	ENST00000398532.4	hg19																																																																																				.	.		0.413	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
RBCK1	10616	hgsc.bcm.edu	37	20	400070	400071	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr20:400070_400071insC	ENST00000356286.5	+	5	1245_1246	c.540_541insC	c.(541-543)cccfs	p.P181fs	RBCK1_ENST00000382181.2_Frame_Shift_Ins_p.NP64fs|RBCK1_ENST00000353660.3_Frame_Shift_Ins_p.P139fs	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	181	Interaction with IRF3.|Interaction with TAB2.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				TCCCCCAGGAACCCGGACGGGG	0.678																																					p.E180fs		Atlas-INDEL	.											.	RBCK1	38	.	0			c.540_541insC						.																																			SO:0001589	frameshift_variant	10616	exon5			.	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, RAN-binding domain containing"""	15864	protein-coding gene	gene with protein product	"""heme-oxidized IRP2 ubiquitin ligase 1"""	610924	"""chromosome 20 open reading frame 18"""	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.543dupC	chr20.hg19:g.400073_400073dupC	ENSP00000348632:p.Pro181fs	140.0	0.0		156.0	13.0	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Frame_Shift_Ins	INS	ENST00000356286.5	hg19	CCDS13000.2																																																																																			.	.		0.678	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229	
ANO5	203859	hgsc.bcm.edu	37	11	22297639	22297639	+	Splice_Site	DEL	G	G	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:22297639delG	ENST00000324559.8	+	21	2731		c.e21-1		ANO5_ENST00000532043.1_Splice_Site	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCACTTTTCAGGTACAGAGAT	0.323																																					.		Atlas-Indel,Pindel	.											.	ANO5	162	.	0			c.2412-2G>-						.						70.0	67.0	68.0					11																	22297639		2203	4298	6501	SO:0001630	splice_region_variant	203859	exon21			.	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	27337	protein-coding gene	gene with protein product		608662	"""transmembrane protein 16E"", ""limb girdle muscular dystrophy 2L (autosomal recessive)"""	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2415-1G>-	chr11.hg19:g.22297639delG		199.0	0.0		286.0	31.0	NM_001142649		Splice_Site	DEL	ENST00000324559.8	hg19	CCDS31444.1																																																																																			.	.		0.323	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Intron
MYH7	4625	hgsc.bcm.edu	37	14	23889251	23889251	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr14:23889251delC	ENST00000355349.3	-	27	3691	c.3529delG	c.(3529-3531)gacfs	p.D1177fs	MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1177					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCCAGGTCCCGCCGCATC	0.682																																					p.D1177fs		Atlas-INDEL	.											.	MYH7	349	.	0			c.3530delA						.						6.0	7.0	7.0					14																	23889251		1994	3915	5909	SO:0001589	frameshift_variant	4625	exon27			.	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3529delG	chr14.hg19:g.23889251delC	ENSP00000347507:p.Asp1177fs	187.0	0.0		326.0	34.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Frame_Shift_Del	DEL	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.682	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
RASAL3	64926	hgsc.bcm.edu	37	19	15563967	15563968	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr19:15563967_15563968insG	ENST00000343625.7	-	15	2705_2706	c.2620_2621insC	c.(2620-2622)cagfs	p.Q874fs		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	874					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						GTCTTGCGGCTGGTCCATTTGG	0.693																																					p.Q874fs		Atlas-INDEL	.											.	RASAL3	49	.	0			c.2621_2622insC						.																																			SO:0001589	frameshift_variant	64926	exon15			.		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.2621dupC	chr19.hg19:g.15563969_15563969dupG	ENSP00000341905:p.Gln874fs	52.0	0.0		125.0	10.0	NM_022904	Q8N2T9|Q9H735	Frame_Shift_Ins	INS	ENST00000343625.7	hg19	CCDS46006.1																																																																																			.	.		0.693	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
LCOR	84458	hgsc.bcm.edu	37	10	98715171	98715171	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr10:98715171delG	ENST00000371097.4	+	8	1340	c.794delG	c.(793-795)tggfs	p.W265fs	LCOR_ENST00000371103.3_Frame_Shift_Del_p.W265fs|LCOR_ENST00000540664.1_Frame_Shift_Del_p.W265fs|LCOR_ENST00000356016.3_Frame_Shift_Del_p.W265fs|LCOR_ENST00000498444.1_Intron			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	265					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		GATCTTTCTTGGGAGTCTCGC	0.408																																					p.W265fs		Atlas-Indel,Pindel	.											.	LCOR	32	.	0			c.793delT						.						82.0	85.0	84.0					10																	98715171		2203	4300	6503	SO:0001589	frameshift_variant	84458	exon8			.		CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233			29503	protein-coding gene	gene with protein product		607698				12535528, 15193453	Standard	NM_001170765		Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000371097.4:c.794delG	chr10.hg19:g.98715171delG	ENSP00000360138:p.Trp265fs	157.0	0.0		138.0	23.0	NM_001170766	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	Frame_Shift_Del	DEL	ENST00000371097.4	hg19	CCDS7451.1																																																																																			.	.		0.408	LCOR-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049628.2		
TRIM49	57093	hgsc.bcm.edu	37	11	89537604	89537604	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:89537604delC	ENST00000329758.1	-	3	362	c.34delG	c.(34-36)gaafs	p.E12fs	TRIM49_ENST00000532501.2_Frame_Shift_Del_p.E12fs	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	12						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CAGATGAGTTCCCCCTGAAAG	0.463																																					p.E12fs		Atlas-INDEL	.											.	TRIM49	45	.	0			c.35delA						.						14.0	15.0	15.0					11																	89537604		2155	4245	6400	SO:0001589	frameshift_variant	57093	exon3			.	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13431	protein-coding gene	gene with protein product		606124	"""ring finger protein 18"", ""tripartite motif-containing 49"""	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.34delG	chr11.hg19:g.89537604delC	ENSP00000327604:p.Glu12fs	435.0	0.0		392.0	36.0	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Frame_Shift_Del	DEL	ENST00000329758.1	hg19	CCDS8287.1																																																																																			.	.		0.463	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
RB1	5925	hgsc.bcm.edu	37	13	49030478	49030479	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr13:49030478_49030479insA	ENST00000267163.4	+	19	2091_2092	c.1953_1954insA	c.(1954-1956)aaafs	p.K652fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	652	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|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 during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.V654fs*4(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CACTGTTTTATAAAAAAGGTTA	0.401		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.Y651fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.	RB1	1068	.	26	Whole gene deletion(15)|Unknown(10)|Deletion - Frameshift(1)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|soft_tissue(2)|adrenal_gland(1)|eye(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	c.1953_1954insA						.																																			SO:0001589	frameshift_variant	5925	exon19	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1959dupA	chr13.hg19:g.49030484_49030484dupA	ENSP00000267163:p.Lys652fs	126.0	0.0		103.0	19.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.401	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
ANO5	203859	hgsc.bcm.edu	37	11	22297638	22297659	+	Splice_Site	DEL	TGCATTTACTTCCACTTTTCAG	TGCATTTACTTCCACTTTTCAG	-	rs367604910		TCGA-DD-A114-01A-11D-A12Z-10	TCGA-DD-A114-10A-01D-A12Z-10	TGCATTTACTTCCACTTTTCAG	TGCATTTACTTCCACTTTTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	90fc6786-22dd-4122-9622-6cd05c0f9f96	9d9f0180-5872-4882-ab29-986b29f4af7d	g.chr11:22297638_22297659delTGCATTTACTTCCACTTTTCAG	ENST00000324559.8	+	21	2731_2751	c.2414_2434delTGCATTTACTTCCACTTTTCAG	c.(2413-2436)atgcatttacttccacttttcagc>agc	p.MHLLPLF805fs	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	805					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCACTTTTCAGGTACAGAGATTACAGATATCCTCCTGATGA	0.324																																					.		Pindel	.											.	ANO5	162	.	0			.						.																																			SO:0001630	splice_region_variant	203859	.			.	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	27337	protein-coding gene	gene with protein product		608662	"""transmembrane protein 16E"", ""limb girdle muscular dystrophy 2L (autosomal recessive)"""	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2415-1TGCATTTACTTCCACTTTTCAG>-	chr11.hg19:g.22297638_22297659delTGCATTTACTTCCACTTTTCAG		156.0	0.0		236.0	10.0	.		Splice_Site	DEL	ENST00000324559.8	hg19	CCDS31444.1																																																																																			.	.		0.324	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Frame_Shift_Del
