#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
ACTRT2	140625	hgsc.bcm.edu	37	1	2938945	2938945	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:2938945C>T	ENST00000378404.2	+	1	900	c.695C>T	c.(694-696)tCc>tTc	p.S232F		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	232						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		AAGGAGCTTTCCCGGAGGCCG	0.652																																					p.S232F		Atlas-SNP	.											.	ACTRT2	69	.	0			c.C695T						.						36.0	41.0	39.0					1																	2938945		2203	4300	6503	SO:0001583	missense	140625	exon1			AGCTTTCCCGGAG	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.695C>T	chr1.hg19:g.2938945C>T	ENSP00000367658:p.Ser232Phe	171.0	0.0		152.0	25.0	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Missense_Mutation	SNP	ENST00000378404.2	hg19	CCDS45.1	.	.	.	.	.	.	.	.	.	.	C	8.373	0.835796	0.16820	.	.	ENSG00000169717	ENST00000378404;ENST00000543312	D	0.94723	-3.5	4.85	-0.658	0.11428	.	1.896970	0.02817	N	0.125078	D	0.95004	0.8383	M	0.62723	1.935	0.09310	N	1	P	0.37573	0.6	P	0.46110	0.504	D	0.85943	0.1459	10	0.87932	D	0	.	10.8114	0.46549	0.196:0.1629:0.6411:0.0	.	232	Q8TDY3	ACTT2_HUMAN	F	232	ENSP00000367658:S232F	ENSP00000367658:S232F	S	+	2	0	ACTRT2	2928805	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.662000	0.05305	-0.468000	0.06922	-1.083000	0.02208	TCC	.	.		0.652	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
UBXN10	127733	hgsc.bcm.edu	37	1	20517360	20517360	+	Silent	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:20517360A>G	ENST00000375099.3	+	2	390	c.306A>G	c.(304-306)caA>caG	p.Q102Q		NM_152376.3	NP_689589.1	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	102										endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2)	14						TGCAGCAGCAAGTACCCACTG	0.517																																					p.Q102Q		Atlas-SNP	.											.	UBXN10	29	.	0			c.A306G						.						54.0	59.0	57.0					1																	20517360		2203	4300	6503	SO:0001819	synonymous_variant	127733	exon2			GCAGCAAGTACCC	AK058158	CCDS205.1	1p36.13	2008-07-25	2008-07-25	2008-07-25	ENSG00000162543	ENSG00000162543		"""UBX domain containing"""	26354	protein-coding gene	gene with protein product			"""UBX domain containing 3"""	UBXD3		12477932	Standard	NM_152376		Approved	FLJ25429	uc001bdb.3	Q96LJ8	OTTHUMG00000002708	ENST00000375099.3:c.306A>G	chr1.hg19:g.20517360A>G		137.0	0.0		151.0	27.0	NM_152376	Q5R386	Silent	SNP	ENST00000375099.3	hg19	CCDS205.1																																																																																			.	.		0.517	UBXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007693.1	NM_152376	
FAM69A	388650	hgsc.bcm.edu	37	1	93309540	93309540	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:93309540T>A	ENST00000370310.4	-	5	757	c.687A>T	c.(685-687)gaA>gaT	p.E229D	SNORA51_ENST00000384295.1_RNA	NM_001006605.4|NM_001252269.1|NM_001252271.1	NP_001006606.2|NP_001239198.1|NP_001239200.1	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	229						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		ATTCAACACTTTCCATCACAT	0.388																																					p.E229D		Atlas-SNP	.											.	FAM69A	30	.	0			c.A687T						.						137.0	112.0	120.0					1																	93309540		692	1591	2283	SO:0001583	missense	388650	exon5			AACACTTTCCATC	AK027146	CCDS44173.1, CCDS72822.1, CCDS72823.1, CCDS72824.1, CCDS72825.1	1p22	2014-06-25			ENSG00000154511	ENSG00000154511			32213	protein-coding gene	gene with protein product		614542				21334309	Standard	NM_001006605		Approved	FLJ23493	uc001dpg.3	Q5T7M9	OTTHUMG00000010894	ENST00000370310.4:c.687A>T	chr1.hg19:g.93309540T>A	ENSP00000359333:p.Glu229Asp	127.0	0.0		125.0	27.0	NM_001006605	Q6IRV2	Missense_Mutation	SNP	ENST00000370310.4	hg19	CCDS44173.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911830	0.72983	.	.	ENSG00000154511	ENST00000370310	T	0.63913	-0.07	5.82	4.69	0.59074	.	0.044304	0.85682	D	0.000000	T	0.73337	0.3574	M	0.81942	2.565	0.58432	D	0.999997	D;D	0.76494	0.997;0.999	D;D	0.80764	0.992;0.994	T	0.77656	-0.2506	10	0.72032	D	0.01	-15.1303	11.7636	0.51918	0.0:0.0705:0.0:0.9295	.	222;229	B4E174;Q5T7M9	.;FA69A_HUMAN	D	229	ENSP00000359333:E229D	ENSP00000359333:E229D	E	-	3	2	FAM69A	93082128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.864000	0.56024	2.218000	0.71995	0.533000	0.62120	GAA	.	.		0.388	FAM69A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030046.2	NM_001006605	
CLK2	1196	hgsc.bcm.edu	37	1	155238148	155238148	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:155238148C>A	ENST00000368361.4	-	5	805	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	CLK2_ENST00000536801.1_Nonsense_Mutation_p.E164*|CLK2_ENST00000355560.4_Nonsense_Mutation_p.E162*|CLK2_ENST00000361168.5_Nonsense_Mutation_p.E163*|CLK2_ENST00000497188.1_5'UTR			P49760	CLK2_HUMAN	CDC-like kinase 2	164	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTAACGATTTCATCTGAAATG	0.527								Other conserved DNA damage response genes																													p.E163X		Atlas-SNP	.											.	CLK2	55	.	0			c.G487T						.						51.0	51.0	51.0					1																	155238148		2203	4300	6503	SO:0001587	stop_gained	1196	exon5			CGATTTCATCTGA	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.490G>T	chr1.hg19:g.155238148C>A	ENSP00000357345:p.Glu164*	122.0	0.0		109.0	17.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Nonsense_Mutation	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	.	26.1	4.703077	0.88924	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	.	.	.	5.41	5.41	0.78517	.	0.046935	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	17.9201	0.88963	0.0:1.0:0.0:0.0	.	.	.	.	X	163;164;162;164	.	ENSP00000347759:E162X	E	-	1	0	CLK2	153504772	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.651000	0.83577	2.815000	0.96918	0.561000	0.74099	GAA	.	.		0.527	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	
IQGAP3	128239	hgsc.bcm.edu	37	1	156498714	156498714	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:156498714T>C	ENST00000361170.2	-	35	4575	c.4565A>G	c.(4564-4566)gAc>gGc	p.D1522G	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1522					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTACTTGGAGTCGGGGGCCAG	0.572																																					p.D1522G		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A4565G						.						87.0	87.0	87.0					1																	156498714		2203	4300	6503	SO:0001583	missense	128239	exon35			TTGGAGTCGGGGG	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4565A>G	chr1.hg19:g.156498714T>C	ENSP00000354451:p.Asp1522Gly	69.0	0.0		73.0	45.0	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	T	9.060	0.994334	0.19043	.	.	ENSG00000183856	ENST00000361170	T	0.42131	0.98	4.41	2.47	0.30058	RasGAP protein, C-terminal (1);	0.761500	0.12908	N	0.429198	T	0.07908	0.0198	N	0.08118	0	0.25885	N	0.983547	B	0.02656	0.0	B	0.01281	0.0	T	0.32079	-0.9920	10	0.37606	T	0.19	-0.256	6.6198	0.22796	0.0:0.6774:0.0:0.3226	.	1522	Q86VI3	IQGA3_HUMAN	G	1522	ENSP00000354451:D1522G	ENSP00000354451:D1522G	D	-	2	0	IQGAP3	154765338	0.230000	0.23740	0.961000	0.40146	0.320000	0.28249	0.568000	0.23623	0.564000	0.29238	-0.415000	0.06103	GAC	.	.		0.572	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
DARS2	55157	hgsc.bcm.edu	37	1	173806173	173806173	+	Silent	SNP	C	C	T	rs149916824		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:173806173C>T	ENST00000361951.4	+	8	1486	c.759C>T	c.(757-759)ggC>ggT	p.G253G	DARS2_ENST00000239457.5_5'UTR	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	253					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	TGATGGTTGGCGGTTTAGACA	0.403																																					p.G253G		Atlas-SNP	.											.	DARS2	61	.	0			c.C759T						.						133.0	149.0	143.0					1																	173806173		2203	4300	6503	SO:0001819	synonymous_variant	55157	exon8			GGTTGGCGGTTTA	AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	25538	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 2, mitochondrial"""	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.759C>T	chr1.hg19:g.173806173C>T		111.0	0.0		105.0	22.0	NM_018122		Silent	SNP	ENST00000361951.4	hg19	CCDS1311.1																																																																																			.	C|1.000;A|0.000		0.403	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122	
BRINP3	339479	hgsc.bcm.edu	37	1	190250737	190250737	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:190250737A>T	ENST00000367462.3	-	3	611	c.380T>A	c.(379-381)cTt>cAt	p.L127H	RP11-547I7.1_ENST00000452178.1_RNA|BRINP3_ENST00000534846.1_Intron	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	127	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TTTCTTGATAAGGTTTTCTGT	0.458																																					p.L127H		Atlas-SNP	.											.	FAM5C	343	.	0			c.T380A						.						91.0	89.0	90.0					1																	190250737		2203	4300	6503	SO:0001583	missense	339479	exon3			TTGATAAGGTTTT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.380T>A	chr1.hg19:g.190250737A>T	ENSP00000356432:p.Leu127His	293.0	0.0		270.0	173.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.690914	0.88735	.	.	ENSG00000162670	ENST00000367462	D	0.87256	-2.23	5.67	5.67	0.87782	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.64402	D	0.000001	D	0.89357	0.6692	L	0.59436	1.845	0.80722	D	1	D	0.55172	0.97	P	0.53266	0.722	D	0.90431	0.4424	10	0.87932	D	0	.	13.8533	0.63510	1.0:0.0:0.0:0.0	.	127	Q76B58	FAM5C_HUMAN	H	127	ENSP00000356432:L127H	ENSP00000356432:L127H	L	-	2	0	FAM5C	188517360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.309000	0.96252	2.162000	0.67917	0.477000	0.44152	CTT	.	.		0.458	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051	
CHRM3	1131	hgsc.bcm.edu	37	1	240071289	240071289	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:240071289C>G	ENST00000255380.4	+	5	1317	c.538C>G	c.(538-540)Cga>Gga	p.R180G		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	180					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCGAGCCAAACGAACAACAAA	0.488																																					p.R180G		Atlas-SNP	.											.	CHRM3	118	.	0			c.C538G						.						162.0	165.0	164.0					1																	240071289		2203	4300	6503	SO:0001583	missense	1131	exon5			GCCAAACGAACAA	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.538C>G	chr1.hg19:g.240071289C>G	ENSP00000255380:p.Arg180Gly	79.0	0.0		94.0	18.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328672	0.60743	.	.	ENSG00000133019	ENST00000255380	T	0.39406	1.08	5.9	0.454	0.16644	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.65893	0.2735	M	0.83012	2.62	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.72207	-0.4360	10	0.87932	D	0	-7.6239	16.5734	0.84631	0.5576:0.4424:0.0:0.0	.	180	P20309	ACM3_HUMAN	G	180	ENSP00000255380:R180G	ENSP00000255380:R180G	R	+	1	2	CHRM3	238137912	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	0.835000	0.27531	-0.161000	0.10983	0.650000	0.86243	CGA	.	.		0.488	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
APOB	338	hgsc.bcm.edu	37	2	21229519	21229519	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:21229519C>A	ENST00000233242.1	-	26	10348	c.10221G>T	c.(10219-10221)gaG>gaT	p.E3407D		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3407	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGACTACCCTCCACAAATT	0.408																																					p.E3407D		Atlas-SNP	.											.	APOB	761	.	0			c.G10221T						.						164.0	163.0	163.0					2																	21229519		2203	4300	6503	SO:0001583	missense	338	exon26			ACTACCCTCCACA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10221G>T	chr2.hg19:g.21229519C>A	ENSP00000233242:p.Glu3407Asp	95.0	0.0		86.0	53.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.469527	0.26423	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.39787	1.06	5.74	-2.06	0.07298	.	0.307999	0.27811	N	0.017751	T	0.42268	0.1195	M	0.84585	2.705	0.80722	D	1	P	0.34780	0.468	B	0.36464	0.225	T	0.35871	-0.9771	10	0.42905	T	0.14	.	8.1747	0.31275	0.0:0.446:0.1206:0.4334	.	3407	P04114	APOB_HUMAN	D	3407	ENSP00000233242:E3407D	ENSP00000233242:E3407D	E	-	3	2	APOB	21083024	0.772000	0.28567	0.772000	0.31596	0.117000	0.20001	-0.005000	0.12855	-0.127000	0.11661	-0.302000	0.09304	GAG	.	.		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CLIP4	79745	hgsc.bcm.edu	37	2	29366802	29366802	+	Silent	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:29366802A>T	ENST00000320081.5	+	7	1131	c.876A>T	c.(874-876)gcA>gcT	p.A292A	CLIP4_ENST00000404424.1_Silent_p.A292A|CLIP4_ENST00000401605.1_Silent_p.A292A|CLIP4_ENST00000401617.2_Silent_p.A185A	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	292										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTGTTATTGCAGGACAGAAGG	0.443																																					p.A292A		Atlas-SNP	.											.	CLIP4	69	.	0			c.A876T						.						236.0	212.0	220.0					2																	29366802		2203	4300	6503	SO:0001819	synonymous_variant	79745	exon7			TATTGCAGGACAG	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.876A>T	chr2.hg19:g.29366802A>T		144.0	0.0		144.0	86.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.		0.443	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
DHX57	90957	hgsc.bcm.edu	37	2	39053721	39053721	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:39053721T>A	ENST00000295373.6	-	15	2876	c.2750A>T	c.(2749-2751)gAg>gTg	p.E917V		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	917	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TATGGATGTCTCAGCAATGTT	0.408																																					p.E917V	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A2750T						.						161.0	145.0	150.0					2																	39053721		2203	4300	6503	SO:0001583	missense	90957	exon15			GATGTCTCAGCAA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.2750A>T	chr2.hg19:g.39053721T>A	ENSP00000295373:p.Glu917Val	116.0	0.0		99.0	53.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.2|27.2	4.810992|4.810992	0.90707|0.90707	.|.	.|.	ENSG00000163214|ENSG00000163214	ENST00000295373|ENST00000452978	T|.	0.77877|.	-1.13|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Helicase, C-terminal (3);|.	0.000000|.	0.52532|.	D|.	0.000062|.	D|.	0.90943|.	0.7153|.	H|H	0.99286|0.99286	4.5|4.5	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|.	0.94682|.	0.7866|.	10|.	0.87932|.	D|.	0|.	.|.	15.3782|15.3782	0.74630|0.74630	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	917;917;309|.	Q6P158;B4DKW2;Q59G60|.	DHX57_HUMAN;.;.|.	V|C	917|240	ENSP00000295373:E917V|.	ENSP00000295373:E917V|.	E|X	-|-	2|3	0|0	DHX57|DHX57	38907225|38907225	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.930000|7.930000	0.87610|0.87610	2.026000|2.026000	0.59711|0.59711	0.460000|0.460000	0.39030|0.39030	GAG|TGA	.	.		0.408	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
R3HDM1	23518	hgsc.bcm.edu	37	2	136481727	136481727	+	Silent	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:136481727C>G	ENST00000264160.4	+	26	3535	c.3165C>G	c.(3163-3165)gtC>gtG	p.V1055V	R3HDM1_ENST00000409606.1_Silent_p.V1056V|R3HDM1_ENST00000409478.1_Silent_p.V927V|R3HDM1_ENST00000410054.1_Silent_p.V1000V|R3HDM1_ENST00000329971.3_Silent_p.V926V	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	1055							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		CCTACACCGTCTTAGCCACAT	0.502																																					p.V1055V		Atlas-SNP	.											.	R3HDM1	84	.	0			c.C3165G						.						91.0	87.0	88.0					2																	136481727		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon26			CACCGTCTTAGCC	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.3165C>G	chr2.hg19:g.136481727C>G		170.0	0.0		206.0	48.0	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	hg19	CCDS2177.1	.	.	.	.	.	.	.	.	.	.	C	3.741	-0.053617	0.07362	.	.	ENSG00000048991	ENST00000429703	.	.	.	5.74	3.92	0.45320	.	.	.	.	.	T	0.56031	0.1958	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53436	-0.8439	4	.	.	.	-7.4794	6.8462	0.23990	0.0:0.6622:0.0:0.3378	.	.	.	.	V	779	.	.	L	+	1	0	R3HDM1	136198197	0.987000	0.35691	1.000000	0.80357	0.981000	0.71138	1.067000	0.30616	1.574000	0.49760	0.561000	0.74099	CTT	.	.		0.502	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	
DARS	1615	hgsc.bcm.edu	37	2	136691481	136691481	+	Splice_Site	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:136691481T>A	ENST00000264161.4	-	6	718	c.503A>T	c.(502-504)gAg>gTg	p.E168V	DARS_ENST00000537273.1_Splice_Site_p.E68V	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	168					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	AATTTTTACCTCTTCTCCTTC	0.403																																					p.E168V		Atlas-SNP	.											.	DARS	44	.	0			c.A503T						.						48.0	48.0	48.0					2																	136691481		2203	4300	6503	SO:0001630	splice_region_variant	1615	exon6			TTTACCTCTTCTC	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	2678	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 1, cytoplasmic"""	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.504+1A>T	chr2.hg19:g.136691481T>A		331.0	0.0		347.0	212.0	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	ENST00000264161.4	hg19	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901975	0.72754	.	.	ENSG00000115866	ENST00000264161;ENST00000537273;ENST00000441323;ENST00000456565;ENST00000449218	D;T	0.83755	-1.76;-1.37	4.94	4.94	0.65067	.	0.139089	0.64402	D	0.000004	D	0.83940	0.5363	M	0.72576	2.205	0.80722	D	1	B	0.26845	0.161	B	0.35182	0.197	T	0.82782	-0.0287	10	0.45353	T	0.12	-12.7829	14.4276	0.67227	0.0:0.0:0.0:1.0	.	168	P14868	SYDC_HUMAN	V	168;68;135;135;135	ENSP00000264161:E168V;ENSP00000444192:E68V	ENSP00000264161:E168V	E	-	2	0	DARS	136407951	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.572000	0.82409	2.086000	0.62901	0.472000	0.43445	GAG	.	.		0.403	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	Missense_Mutation
COBLL1	22837	hgsc.bcm.edu	37	2	165559721	165559721	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:165559721T>C	ENST00000392717.2	-	10	1353	c.1349A>G	c.(1348-1350)cAc>cGc	p.H450R	COBLL1_ENST00000194871.6_Missense_Mutation_p.H478R|COBLL1_ENST00000342193.4_Missense_Mutation_p.H412R|COBLL1_ENST00000491126.2_Intron|COBLL1_ENST00000409184.3_Intron|COBLL1_ENST00000375458.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	450						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						AAGCCCAGGGTGAAAGGTTTC	0.478																																					p.H412R		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1235G						.						92.0	88.0	89.0					2																	165559721		2203	4300	6503	SO:0001583	missense	22837	exon9			CCAGGGTGAAAGG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1349A>G	chr2.hg19:g.165559721T>C	ENSP00000376478:p.His450Arg	85.0	0.0		51.0	11.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.457	-0.891058	0.02491	.	.	ENSG00000082438	ENST00000342193;ENST00000392717;ENST00000194871	.	.	.	4.68	2.88	0.33553	.	0.299368	0.28996	N	0.013465	T	0.16085	0.0387	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.19976	-1.0289	9	0.21014	T	0.42	-0.8433	7.2693	0.26248	0.0:0.7987:0.0:0.2013	.	478	B7Z2P5	.	R	412;450;478	.	ENSP00000194871:H478R	H	-	2	0	COBLL1	165267967	0.438000	0.25602	0.271000	0.24616	0.009000	0.06853	0.164000	0.16542	0.706000	0.31912	-0.766000	0.03442	CAC	.	.		0.478	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
ARMC9	80210	hgsc.bcm.edu	37	2	232123721	232123721	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr2:232123721C>T	ENST00000349938.4	+	11	1126	c.932C>T	c.(931-933)cCa>cTa	p.P311L	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	311						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AAGGATGTCCCATTACTGCCC	0.453																																					p.P311L		Atlas-SNP	.											ARMC9_ENST00000359743,NS,neuroblastoma,0,2	ARMC9	129	.	0			c.C932T						.						157.0	143.0	148.0					2																	232123721		2203	4300	6503	SO:0001583	missense	80210	exon11			ATGTCCCATTACT	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.932C>T	chr2.hg19:g.232123721C>T	ENSP00000258417:p.Pro311Leu	76.0	0.0		91.0	59.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.273584|4.273584	0.80580|0.80580	.|.	.|.	ENSG00000135931|ENSG00000135931	ENST00000424740|ENST00000349938;ENST00000359743;ENST00000436339	.|T	.|0.19669	.|2.13	4.7|4.7	4.7|4.7	0.59300|0.59300	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.69307	.|0.963	T|T	0.22417|0.22417	-1.0217|-1.0217	5|10	.|0.59425	.|D	.|0.04	-13.3684|-13.3684	16.7969|16.7969	0.85604|0.85604	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|311	.|Q7Z3E5	.|ARMC9_HUMAN	Y|L	14|311;311;28	.|ENSP00000258417:P311L	.|ENSP00000258417:P311L	H|P	+|+	1|2	0|0	ARMC9|ARMC9	231831965|231831965	1.000000|1.000000	0.71417|0.71417	0.936000|0.936000	0.37596|0.37596	0.989000|0.989000	0.77384|0.77384	6.553000|6.553000	0.73918|0.73918	2.344000|2.344000	0.79699|0.79699	0.561000|0.561000	0.74099|0.74099	CAT|CCA	.	.		0.453	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
SLC6A11	6538	hgsc.bcm.edu	37	3	10970945	10970945	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:10970945C>T	ENST00000254488.2	+	10	1357	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	431					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	CAAGGTTTTCCGGAGGGGTTA	0.542																																					p.R431W		Atlas-SNP	.											SLC6A11,NS,adenocarcinoma,-1,1	SLC6A11	87	.	0			c.C1291T						.						212.0	206.0	208.0					3																	10970945		2203	4300	6503	SO:0001583	missense	6538	exon10			GTTTTCCGGAGGG	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1291C>T	chr3.hg19:g.10970945C>T	ENSP00000254488:p.Arg431Trp	148.0	0.0		173.0	58.0	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	hg19	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201112	0.79015	.	.	ENSG00000132164	ENST00000254488	T	0.76316	-1.01	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.89863	0.6838	M	0.91090	3.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91822	0.5468	10	0.87932	D	0	.	13.5363	0.61648	0.1558:0.8442:0.0:0.0	.	431	P48066	S6A11_HUMAN	W	431	ENSP00000254488:R431W	ENSP00000254488:R431W	R	+	1	2	SLC6A11	10945945	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.379000	0.34340	2.376000	0.81061	0.462000	0.41574	CGG	.	.		0.542	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
COLQ	8292	hgsc.bcm.edu	37	3	15507879	15507879	+	Silent	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:15507879G>T	ENST00000383788.5	-	12	908	c.783C>A	c.(781-783)ggC>ggA	p.G261G	COLQ_ENST00000383785.2_3'UTR|COLQ_ENST00000435459.2_Silent_p.G251G|COLQ_ENST00000603808.1_Silent_p.G261G|COLQ_ENST00000383781.4_Silent_p.G251G|COLQ_ENST00000383786.5_Silent_p.G227G|COLQ_ENST00000383787.2_Silent_p.G252G	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	261	Collagen-like 1.				acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						GCCCCGGACGGCCAGGTTGAC	0.602																																					p.G261G		Atlas-SNP	.											.	COLQ	82	.	0			c.C783A						.						50.0	54.0	53.0					3																	15507879		2203	4300	6503	SO:0001819	synonymous_variant	8292	exon12			CGGACGGCCAGGT	AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"""single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase"", ""collagenic tail of endplate acetylcholinesterase"", ""AChE Q subunit"", ""acetylcholinesterase-associated collagen"""	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.783C>A	chr3.hg19:g.15507879G>T		298.0	0.0		376.0	62.0	NM_005677	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Silent	SNP	ENST00000383788.5	hg19	CCDS33709.1																																																																																			.	.		0.602	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677	
TOP2B	7155	hgsc.bcm.edu	37	3	25686805	25686805	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:25686805C>G	ENST00000264331.4	-	2	225	c.226G>C	c.(226-228)Gag>Cag	p.E76Q	TOP2B_ENST00000435706.2_Missense_Mutation_p.E71Q	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	76					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GTCAATGGCTCCACTGACCCA	0.313																																					p.E71Q		Atlas-SNP	.											.	TOP2B	98	.	0			c.G211C						.						179.0	166.0	170.0					3																	25686805		1859	4099	5958	SO:0001583	missense	7155	exon2			ATGGCTCCACTGA	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.226G>C	chr3.hg19:g.25686805C>G	ENSP00000264331:p.Glu76Gln	188.0	0.0		934.0	334.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	C	21.8	4.208803	0.79240	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225;ENST00000535930	T;T	0.53423	0.62;0.62	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.64034	0.2562	M	0.73372	2.23	0.80722	D	1	D	0.53151	0.958	P	0.54060	0.741	T	0.67047	-0.5769	10	0.87932	D	0	-0.4432	19.8426	0.96695	0.0:1.0:0.0:0.0	.	71	Q02880-2	.	Q	71;76;71;53	ENSP00000396704:E71Q;ENSP00000264331:E76Q	ENSP00000264331:E76Q	E	-	1	0	TOP2B	25661809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.775000	0.95449	0.655000	0.94253	GAG	.	.		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
SCN11A	11280	hgsc.bcm.edu	37	3	38904741	38904741	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:38904741T>A	ENST00000302328.3	-	24	4199	c.4001A>T	c.(4000-4002)aAt>aTt	p.N1334I	SCN11A_ENST00000444237.2_Missense_Mutation_p.N1334I|SCN11A_ENST00000450244.1_Missense_Mutation_p.N1334I|SCN11A_ENST00000456224.3_Missense_Mutation_p.N1296I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1334					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTCATTGCATTATAGTATTT	0.328																																					p.N1334I		Atlas-SNP	.											.	SCN11A	296	.	0			c.A4001T						.						143.0	130.0	134.0					3																	38904741		2203	4300	6503	SO:0001583	missense	11280	exon24			ATTGCATTATAGT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4001A>T	chr3.hg19:g.38904741T>A	ENSP00000307599:p.Asn1334Ile	54.0	0.0		82.0	36.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.351754	0.82132	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.96554	-4.05;-4.05;-4.02;-3.93	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.98529	0.9509	M	0.93150	3.385	0.52099	D	0.999946	D	0.89917	1.0	D	0.71184	0.972	D	0.99671	1.0996	10	0.87932	D	0	.	15.6082	0.76692	0.0:0.0:0.0:1.0	.	1334	Q9UI33	SCNBA_HUMAN	I	1334;1334;1296;1334	ENSP00000307599:N1334I;ENSP00000400945:N1334I;ENSP00000416757:N1296I;ENSP00000408028:N1334I	ENSP00000307599:N1334I	N	-	2	0	SCN11A	38879745	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.217000	0.72218	2.169000	0.68431	0.533000	0.62120	AAT	.	.		0.328	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
ZNF502	91392	hgsc.bcm.edu	37	3	44763599	44763599	+	Silent	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:44763599T>A	ENST00000296091.4	+	4	1546	c.1290T>A	c.(1288-1290)acT>acA	p.T430T	ZNF502_ENST00000436624.2_Silent_p.T430T|ZNF502_ENST00000449836.1_Silent_p.T430T	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		GAAGTCACACTGGAGAAAAAC	0.428																																					p.T430T		Atlas-SNP	.											.	ZNF502	58	.	0			c.T1290A						.						73.0	78.0	76.0					3																	44763599		2203	4300	6503	SO:0001819	synonymous_variant	91392	exon4			TCACACTGGAGAA	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"""Zinc fingers, C2H2-type"""	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.1290T>A	chr3.hg19:g.44763599T>A		122.0	0.0		146.0	58.0	NM_001134440		Silent	SNP	ENST00000296091.4	hg19	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	T	8.715	0.912974	0.17907	.	.	ENSG00000196653	ENST00000427783	.	.	.	4.42	-1.48	0.08745	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54768	-0.8244	5	0.87932	D	0	-10.8818	1.4648	0.02403	0.3845:0.082:0.2621:0.2714	.	.	.	.	Q	430	.	ENSP00000397812:L430Q	L	+	2	0	ZNF502	44738603	0.001000	0.12720	0.996000	0.52242	0.998000	0.95712	-2.759000	0.00787	-0.305000	0.08831	0.533000	0.62120	CTG	.	.		0.428	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
SETD2	29072	hgsc.bcm.edu	37	3	47165225	47165225	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:47165225T>A	ENST00000409792.3	-	3	943	c.901A>T	c.(901-903)Agc>Tgc	p.S301C		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	301					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTTTTACAGCTCAGACTAATC	0.353			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.S301C		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A901T						.						136.0	107.0	116.0					3																	47165225		692	1591	2283	SO:0001583	missense	29072	exon3			TACAGCTCAGACT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.901A>T	chr3.hg19:g.47165225T>A	ENSP00000386759:p.Ser301Cys	102.0	0.0		87.0	34.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	4.103	0.017112	0.07959	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	T;T	0.16073	2.37;2.37	4.88	-0.167	0.13347	.	.	.	.	.	T	0.08714	0.0216	N	0.19112	0.55	0.28774	N	0.900188	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37526	-0.9702	8	.	.	.	.	4.9808	0.14164	0.3411:0.1273:0.0:0.5316	.	301;301	F2Z317;Q9BYW2	.;SETD2_HUMAN	C	301;301;301;257	ENSP00000386759:S301C;ENSP00000416401:S257C	.	S	-	1	0	SETD2	47140229	0.002000	0.14202	0.998000	0.56505	0.975000	0.68041	0.257000	0.18369	0.150000	0.19136	-0.433000	0.05886	AGC	.	.		0.353	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
SPICE1	152185	hgsc.bcm.edu	37	3	113212129	113212129	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:113212129G>T	ENST00000295872.4	-	6	675	c.416C>A	c.(415-417)tCc>tAc	p.S139Y		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	139					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						ACCCTGAGAGGAATCAGGAGC	0.398																																					p.S139Y		Atlas-SNP	.											.	SPICE1	130	.	0			c.C416A						.						98.0	93.0	95.0					3																	113212129		2203	4300	6503	SO:0001583	missense	152185	exon6			TGAGAGGAATCAG	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.416C>A	chr3.hg19:g.113212129G>T	ENSP00000295872:p.Ser139Tyr	82.0	0.0		104.0	43.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645383	0.67358	.	.	ENSG00000163611	ENST00000295872;ENST00000495812;ENST00000480527	T	0.37058	1.22	5.22	4.28	0.50868	.	0.161352	0.56097	D	0.000028	T	0.53738	0.1815	L	0.60455	1.87	0.43907	D	0.996544	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.55560	-0.8122	10	0.72032	D	0.01	-6.5994	12.8312	0.57746	0.0:0.1645:0.8355:0.0	.	35;139	B3KX77;Q8N0Z3	.;SPICE_HUMAN	Y	139	ENSP00000295872:S139Y	ENSP00000295872:S139Y	S	-	2	0	SPICE1	114694819	1.000000	0.71417	0.995000	0.50966	0.931000	0.56810	2.960000	0.49161	2.577000	0.86979	0.563000	0.77884	TCC	.	.		0.398	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
PLXND1	23129	hgsc.bcm.edu	37	3	129282004	129282004	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:129282004G>C	ENST00000324093.4	-	26	4779	c.4601C>G	c.(4600-4602)aCa>aGa	p.T1534R	PLXND1_ENST00000393239.1_Missense_Mutation_p.T1534R	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1534					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGCCTTGCCTGTGATGGCGTC	0.637																																					p.T1534R	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C4601G						.						72.0	64.0	67.0					3																	129282004		2203	4300	6503	SO:0001583	missense	23129	exon26			TTGCCTGTGATGG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4601C>G	chr3.hg19:g.129282004G>C	ENSP00000317128:p.Thr1534Arg	66.0	0.0		51.0	22.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449403	0.84101	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.16324	2.35;2.35	5.25	5.25	0.73442	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.182670	0.47852	D	0.000219	T	0.50154	0.1599	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.997;0.999	T	0.58934	-0.7548	10	0.87932	D	0	.	18.8662	0.92293	0.0:0.0:1.0:0.0	.	129;1534	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	R	1534	ENSP00000317128:T1534R;ENSP00000376931:T1534R	ENSP00000317128:T1534R	T	-	2	0	PLXND1	130764694	1.000000	0.71417	0.944000	0.38274	0.539000	0.34962	6.813000	0.75231	2.454000	0.82982	0.462000	0.41574	ACA	.	.		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
ACPP	55	hgsc.bcm.edu	37	3	132086623	132086623	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr3:132086623G>C	ENST00000351273.7	+	11	1264	c.1214G>C	c.(1213-1215)cGc>cCc	p.R405P		NM_001134194.1	NP_001127666.1	P15309	PPAP_HUMAN	acid phosphatase, prostate	0					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ATCCACATTCGCCGTGGACTC	0.468																																					p.R405P		Atlas-SNP	.											ACPP_ENST00000351273,NS,carcinoma,0,1	ACPP	118	.	0			c.G1214C						.						394.0	334.0	352.0					3																	132086623		1568	3582	5150	SO:0001583	missense	55	exon11			ACATTCGCCGTGG		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000351273.7:c.1214G>C	chr3.hg19:g.132086623G>C	ENSP00000323036:p.Arg405Pro	53.0	0.0		73.0	8.0	NM_001134194	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000351273.7	hg19	CCDS46916.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067088	0.36470	.	.	ENSG00000014257	ENST00000351273	T	0.07444	3.19	4.96	3.13	0.36017	.	0.424638	0.22602	N	0.057947	T	0.18341	0.0440	.	.	.	0.19300	N	0.999974	D	0.67145	0.996	D	0.65443	0.935	T	0.04811	-1.0925	9	0.30078	T	0.28	.	9.3876	0.38352	0.1456:0.0:0.8544:0.0	.	405	P15309-2	.	P	405	ENSP00000323036:R405P	ENSP00000323036:R405P	R	+	2	0	ACPP	133569313	0.891000	0.30450	0.498000	0.27564	0.192000	0.23643	1.862000	0.39448	0.765000	0.33221	0.655000	0.94253	CGC	.	.		0.468	ACPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356701.1	NM_001099	
ZNF518B	85460	hgsc.bcm.edu	37	4	10446373	10446373	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr4:10446373A>T	ENST00000326756.3	-	3	2018	c.1580T>A	c.(1579-1581)tTa>tAa	p.L527*		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	527					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						AAATGGGAGTAACTGCTGTGA	0.408																																					p.L527X		Atlas-SNP	.											ZNF518B,colon,carcinoma,0,1	ZNF518B	116	.	0			c.T1580A						.						93.0	93.0	93.0					4																	10446373		2203	4300	6503	SO:0001587	stop_gained	85460	exon3			GGGAGTAACTGCT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1580T>A	chr4.hg19:g.10446373A>T	ENSP00000317614:p.Leu527*	247.0	0.0		164.0	58.0	NM_053042	Q96LN8	Nonsense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	A	38	7.267662	0.98175	.	.	ENSG00000178163	ENST00000326756	.	.	.	5.36	1.72	0.24424	.	1.629630	0.04159	N	0.322733	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-0.0026	0.8378	0.01143	0.4076:0.164:0.2709:0.1574	.	.	.	.	X	527	.	ENSP00000317614:L527X	L	-	2	0	ZNF518B	10055471	0.003000	0.15002	0.000000	0.03702	0.032000	0.12392	1.112000	0.31172	0.503000	0.28060	0.496000	0.49642	TTA	.	.		0.408	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
N4BP2	55728	hgsc.bcm.edu	37	4	40154482	40154482	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr4:40154482C>G	ENST00000261435.6	+	17	5642	c.5226C>G	c.(5224-5226)atC>atG	p.I1742M		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1742	Smr. {ECO:0000255|PROSITE- ProRule:PRU00321}.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTGCTCGCATCAAACCAGCTG	0.423																																					p.I1742M		Atlas-SNP	.											.	N4BP2	166	.	0			c.C5226G						.						161.0	143.0	149.0					4																	40154482		2203	4300	6503	SO:0001583	missense	55728	exon17			TCGCATCAAACCA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.5226C>G	chr4.hg19:g.40154482C>G	ENSP00000261435:p.Ile1742Met	121.0	0.0		172.0	42.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.77|15.77	2.931636|2.931636	0.52866|0.52866	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.28454|.	1.61|.	5.83|5.83	5.0|5.0	0.66597|0.66597	Smr protein/MutS2 C-terminal (2);|.	0.079922|.	0.64402|.	D|.	0.000019|.	T|T	0.75882|0.75882	0.3910|0.3910	M|M	0.84683|0.84683	2.71|2.71	0.52501|0.52501	D|D	0.999959|0.999959	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.78048|0.78048	-0.2356|-0.2356	10|5	0.87932|.	D|.	0|.	-9.2451|-9.2451	11.0507|11.0507	0.47884|0.47884	0.0:0.8589:0.0:0.1411|0.0:0.8589:0.0:0.1411	.|.	1725;1742|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	M|E	1742;1662|1372	ENSP00000261435:I1742M|.	ENSP00000261435:I1742M|.	I|Q	+|+	3|1	3|0	N4BP2|N4BP2	39830877|39830877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.435000|0.435000	0.31806|0.31806	2.834000|2.834000	0.48167|0.48167	1.485000|1.485000	0.48380|0.48380	-0.140000|-0.140000	0.14226|0.14226	ATC|CAA	.	.		0.423	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
GYPE	2996	hgsc.bcm.edu	37	4	144796663	144796663	+	Splice_Site	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr4:144796663C>A	ENST00000437468.2	-	4	302		c.e4-1		GYPE_ENST00000358615.4_Intron	NM_002102.3	NP_002093.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					atcctcatgcctgtgataaaa	0.512																																					.		Atlas-SNP	.											.	GYPE	21	.	0			c.247-1G>T						.																																			SO:0001630	splice_region_variant	2996	exon5			TCATGCCTGTGAT		CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"""Blood group antigens"""	4705	protein-coding gene	gene with protein product		138590	"""glycophorin E"""				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000437468.2:c.235-1G>T	chr4.hg19:g.144796663C>A		186.0	0.0		127.0	41.0	NM_002102	D3DNZ5	Splice_Site	SNP	ENST00000437468.2	hg19	CCDS47138.1																																																																																			.	.		0.512	GYPE-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364782.1	NM_002102	Intron
PRDM9	56979	hgsc.bcm.edu	37	5	23526821	23526821	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:23526821C>A	ENST00000296682.3	+	11	1806	c.1624C>A	c.(1624-1626)Cac>Aac	p.H542N		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	542					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TGTTATTACACACCAAAGGAC	0.468										HNSCC(3;0.000094)																											p.H542N		Atlas-SNP	.											.	PRDM9	344	.	0			c.C1624A						.						93.0	99.0	97.0					5																	23526821		2160	4288	6448	SO:0001583	missense	56979	exon11			ATTACACACCAAA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1624C>A	chr5.hg19:g.23526821C>A	ENSP00000296682:p.His542Asn	174.0	0.0		304.0	79.0	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	hg19	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	5.291	0.239000	0.10023	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	D	0.86865	-2.18	2.39	1.48	0.22813	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.89518	0.6738	H	0.94264	3.515	0.40517	D	0.980796	B	0.18863	0.031	B	0.26517	0.07	D	0.86779	0.1978	9	0.62326	D	0.03	-9.746	8.3235	0.32142	0.2374:0.7626:0.0:0.0	.	542	Q9NQV7	PRDM9_HUMAN	N	542;336	ENSP00000296682:H542N	ENSP00000253473:H336N	H	+	1	0	PRDM9	23562578	0.396000	0.25262	0.522000	0.27862	0.066000	0.16364	1.723000	0.38053	0.521000	0.28445	0.400000	0.26472	CAC	.	.		0.468	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
PLCXD3	345557	hgsc.bcm.edu	37	5	41382470	41382470	+	Silent	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:41382470A>T	ENST00000377801.3	-	2	344	c.270T>A	c.(268-270)gcT>gcA	p.A90A	PLCXD3_ENST00000328457.3_Silent_p.A90A			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	90	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						AACGAATTCCAGCTCCTAGCT	0.438																																					p.A90A		Atlas-SNP	.											.	PLCXD3	86	.	0			c.T270A						.						65.0	70.0	68.0					5																	41382470		2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			AATTCCAGCTCCT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.270T>A	chr5.hg19:g.41382470A>T		134.0	0.0		220.0	129.0	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	hg19	CCDS34150.1																																																																																			.	.		0.438	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875	
C5orf28	64417	hgsc.bcm.edu	37	5	43446574	43446574	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:43446574T>C	ENST00000500337.2	-	5	729	c.398A>G	c.(397-399)cAc>cGc	p.H133R	C5orf28_ENST00000397080.3_Missense_Mutation_p.H133R|C5orf28_ENST00000512085.1_Missense_Mutation_p.H133R|C5orf28_ENST00000510130.1_Missense_Mutation_p.H31R|C5orf28_ENST00000511525.1_5'UTR|C5orf28_ENST00000537319.1_Missense_Mutation_p.H2R			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	133						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					CTTGAAAAGGTGCATAGTAAA	0.458																																					p.H133R		Atlas-SNP	.											.	C5orf28	25	.	0			c.A398G						.						97.0	89.0	92.0					5																	43446574		2203	4300	6503	SO:0001583	missense	64417	exon3			AAAAGGTGCATAG	AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.398A>G	chr5.hg19:g.43446574T>C	ENSP00000426067:p.His133Arg	104.0	0.0		174.0	108.0	NM_022483	B2RDA6|Q9H6Z2	Missense_Mutation	SNP	ENST00000500337.2	hg19	CCDS3945.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.242650	0.39598	.	.	ENSG00000151881	ENST00000500337;ENST00000537319;ENST00000397080;ENST00000512085;ENST00000510130;ENST00000506860	.	.	.	5.95	5.95	0.96441	.	0.316960	0.42420	D	0.000707	T	0.59321	0.2185	L	0.56396	1.775	0.37729	D	0.925205	B	0.17667	0.023	B	0.23852	0.049	T	0.58657	-0.7598	9	0.13108	T	0.6	-23.8459	16.4025	0.83647	0.0:0.0:0.0:1.0	.	133	Q0VDI3	CE028_HUMAN	R	133;2;133;133;31;133	.	ENSP00000380270:H133R	H	-	2	0	C5orf28	43482331	1.000000	0.71417	0.916000	0.36221	0.970000	0.65996	4.658000	0.61497	2.268000	0.75426	0.533000	0.62120	CAC	.	.		0.458	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1	NM_022483	
CEP120	153241	hgsc.bcm.edu	37	5	122754208	122754208	+	Splice_Site	SNP	A	A	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:122754208A>C	ENST00000306467.5	-	2	355	c.51T>G	c.(49-51)ggT>ggG	p.G17G	CEP120_ENST00000306481.6_5'UTR|CEP120_ENST00000328236.5_Splice_Site_p.G17G|CEP120_ENST00000395431.2_Splice_Site_p.G17G|CEP120_ENST00000515110.1_Splice_Site_p.S54A			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	17					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GGAAATGCCGACCTGGAGAAA	0.383																																					p.G17G		Atlas-SNP	.											.	CEP120	72	.	0			c.T51G						.						85.0	76.0	79.0					5																	122754208		1848	4085	5933	SO:0001630	splice_region_variant	153241	exon3			ATGCCGACCTGGA	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.50-1T>G	chr5.hg19:g.122754208A>C		85.0	0.0		79.0	16.0	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	hg19	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	A	9.890	1.203870	0.22121	.	.	ENSG00000168944	ENST00000515110	.	.	.	5.18	2.51	0.30379	.	.	.	.	.	T	0.50871	0.1641	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54529	-0.8280	5	0.87932	D	0	.	1.1814	0.01846	0.3153:0.2666:0.0854:0.3327	.	.	.	.	A	54	.	ENSP00000428303:S54A	S	-	1	0	CEP120	122782107	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	0.881000	0.28173	0.859000	0.35456	0.533000	0.62120	TCG	.	.		0.383	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	Silent
PDE6A	5145	hgsc.bcm.edu	37	5	149247346	149247346	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr5:149247346G>T	ENST00000255266.5	-	19	2335	c.2216C>A	c.(2215-2217)gCt>gAt	p.A739D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	739					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GAATTCAGCAGCCACCAGCAG	0.572																																					p.A739D		Atlas-SNP	.											.	PDE6A	98	.	0			c.C2216A						.						96.0	69.0	78.0					5																	149247346		2203	4300	6503	SO:0001583	missense	5145	exon19			TCAGCAGCCACCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2216C>A	chr5.hg19:g.149247346G>T	ENSP00000255266:p.Ala739Asp	53.0	0.0		60.0	14.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884058	0.91814	.	.	ENSG00000132915	ENST00000255266	D	0.82081	-1.57	5.42	5.42	0.78866	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.178771	0.47852	D	0.000220	D	0.91546	0.7330	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91889	0.5522	10	0.52906	T	0.07	.	16.72	0.85408	0.0:0.0:1.0:0.0	.	739	P16499	PDE6A_HUMAN	D	739	ENSP00000255266:A739D	ENSP00000255266:A739D	A	-	2	0	PDE6A	149227539	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.994000	0.93529	2.544000	0.85801	0.407000	0.27541	GCT	.	.		0.572	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
DDX39B	7919	hgsc.bcm.edu	37	6	31507007	31507007	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:31507007G>C	ENST00000396172.1	-	3	886	c.256C>G	c.(256-258)Ctg>Gtg	p.L86V	SNORD117_ENST00000364915.1_RNA|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|DDX39B_ENST00000449074.2_Missense_Mutation_p.L86V|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000417556.2_Missense_Mutation_p.L86V|DDX39B_ENST00000376177.2_Missense_Mutation_p.L86V|DDX39B_ENST00000458640.1_Missense_Mutation_p.L86V|DDX39B_ENST00000453105.2_Intron|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000415382.2_Intron	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	86	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						GCCTGGCACAGGACATCCATT	0.517																																					p.L86V		Atlas-SNP	.											.	DDX39B	38	.	0			c.C256G						.						137.0	138.0	138.0					6																	31507007		1511	2709	4220	SO:0001583	missense	7919	exon3			GGCACAGGACATC	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.256C>G	chr6.hg19:g.31507007G>C	ENSP00000379475:p.Leu86Val	102.0	0.0		81.0	40.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699928	0.48307	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.49720	0.77;2.23;2.23;2.23;0.77;0.77;0.77;2.23;0.77;0.77;0.77;2.23;2.23;0.77	5.53	4.47	0.54385	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.64402	D	0.000016	T	0.26955	0.0660	L	0.31664	0.95	0.58432	D	0.999998	B;B;B	0.26363	0.147;0.012;0.087	B;B;B	0.35607	0.206;0.092;0.13	T	0.12863	-1.0531	10	0.41790	T	0.15	-10.6604	12.514	0.56021	0.0953:0.0:0.9047:0.0	.	106;86;86	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	V	86;86;86;86;86;86;86;86;86;86;109;86;101;86;86	ENSP00000365347:L86V;ENSP00000416269:L86V;ENSP00000379475:L86V;ENSP00000412582:L86V;ENSP00000399371:L86V;ENSP00000392672:L86V;ENSP00000410313:L86V;ENSP00000416350:L86V;ENSP00000391946:L86V;ENSP00000405707:L86V;ENSP00000409426:L109V;ENSP00000393984:L86V;ENSP00000399841:L101V;ENSP00000405245:L86V	ENSP00000365347:L86V	L	-	1	2	DDX39B	31614986	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.430000	0.52807	2.592000	0.87571	0.563000	0.77884	CTG	.	.		0.517	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
NCR3	259197	hgsc.bcm.edu	37	6	31555456	31555456	+	IGR	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:31555456C>T	ENST00000340027.5	-	0	1042				LST1_ENST00000303757.8_Silent_p.L20L|LST1_ENST00000376086.3_Intron|LST1_ENST00000339530.4_Silent_p.L20L|NCR3_ENST00000491161.1_5'Flank|LST1_ENST00000396101.3_Silent_p.L20L|LST1_ENST00000376111.4_5'UTR|LST1_ENST00000376092.3_Intron|LST1_ENST00000376099.1_Intron|LST1_ENST00000376096.1_Intron|LST1_ENST00000418507.2_Intron|LST1_ENST00000438075.2_Silent_p.L20L|LST1_ENST00000376090.2_Intron|LST1_ENST00000376089.2_Intron|LST1_ENST00000376093.2_Silent_p.L20L|LST1_ENST00000376110.3_Intron|LST1_ENST00000211921.7_Intron|LST1_ENST00000376102.3_Silent_p.S14S|LST1_ENST00000419073.1_3'UTR|LST1_ENST00000376100.3_Intron	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3						cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)				cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						GGGCGGGCTCCTGCTTCTGGC	0.627																																					p.L20L		Atlas-SNP	.											.	LST1	6	.	0			c.C58T						.						12.0	14.0	13.0					6																	31555456		1980	4138	6118	SO:0001628	intergenic_variant	7940	exon2			GGGCTCCTGCTTC	AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19077	protein-coding gene	gene with protein product		611550	"""lymphocyte antigen 117"""	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123		chr6.hg19:g.31555456C>T		46.0	0.0		42.0	12.0	NM_205840	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Silent	SNP	ENST00000340027.5	hg19	CCDS34397.1	.	.	.	.	.	.	.	.	.	.	C	7.548	0.662115	0.14645	.	.	ENSG00000204482	ENST00000464044	.	.	.	4.47	4.47	0.54385	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53995	-0.8359	4	.	.	.	-5.8203	12.5067	0.55986	0.0:1.0:0.0:0.0	.	.	.	.	L	4	.	.	P	+	2	0	LST1	31663435	0.975000	0.34042	0.326000	0.25389	0.069000	0.16628	1.878000	0.39608	2.310000	0.77875	0.561000	0.74099	CCT	.	.		0.627	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076210.2		
PIM1	5292	hgsc.bcm.edu	37	6	37139141	37139141	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:37139141T>A	ENST00000373509.5	+	4	854	c.481T>A	c.(481-483)Tgc>Agc	p.C161S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	252	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	CTGCCACAACTGCGGGGTGCT	0.612			T	BCL6	NHL																																p.C252S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.T754A						.						46.0	51.0	49.0					6																	37139141		2203	4300	6503	SO:0001583	missense	5292	exon4			CACAACTGCGGGG		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.481T>A	chr6.hg19:g.37139141T>A	ENSP00000362608:p.Cys161Ser	165.0	0.0		174.0	69.0	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	hg19	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	T	10.47	1.360168	0.24598	.	.	ENSG00000137193	ENST00000373509	T	0.63744	-0.06	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.126933	0.56097	D	0.000040	T	0.22126	0.0533	N	0.11106	0.095	0.47065	D	0.999301	B	0.21753	0.06	B	0.20384	0.029	T	0.12192	-1.0557	10	0.11794	T	0.64	.	12.658	0.56797	0.0:0.0:0.0:1.0	.	252	P11309	PIM1_HUMAN	S	161	ENSP00000362608:C161S	ENSP00000362608:C161S	C	+	1	0	PIM1	37247119	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.844000	0.55873	1.827000	0.53221	0.368000	0.22195	TGC	.	.		0.612	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
XPO5	57510	hgsc.bcm.edu	37	6	43492327	43492327	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:43492327T>A	ENST00000265351.7	-	31	3569	c.3359A>T	c.(3358-3360)gAa>gTa	p.E1120V	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1120					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			CTTCTGTATTTCAGGGATTTG	0.493																																					p.E1120V		Atlas-SNP	.											.	XPO5	79	.	0			c.A3359T						.						149.0	151.0	150.0					6																	43492327		1919	4124	6043	SO:0001583	missense	57510	exon31			TGTATTTCAGGGA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.3359A>T	chr6.hg19:g.43492327T>A	ENSP00000265351:p.Glu1120Val	112.0	0.0		120.0	48.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.026845|4.026845	0.75390|0.75390	.|.	.|.	ENSG00000124571|ENSG00000124571	ENST00000265351;ENST00000372258;ENST00000439465|ENST00000455285	T|.	0.68903|.	-0.36|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Armadillo-type fold (1);|.	0.160919|.	0.56097|.	D|.	0.000028|.	T|.	0.52273|.	0.1724|.	L|L	0.44542|0.44542	1.39|1.39	0.47476|0.47476	D|D	0.999434|0.999434	B|.	0.27068|.	0.167|.	B|.	0.25614|.	0.062|.	T|.	0.50294|.	-0.8845|.	10|.	0.54805|.	T|.	0.06|.	-9.1451|-9.1451	16.6093|16.6093	0.84858|0.84858	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1120|.	Q9HAV4|.	XPO5_HUMAN|.	V|X	1120;660;748|235	ENSP00000265351:E1120V|.	ENSP00000265351:E1120V|.	E|K	-|-	2|1	0|0	XPO5|XPO5	43600305|43600305	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.499000|7.499000	0.81566|0.81566	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.493	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
TFAP2B	7021	hgsc.bcm.edu	37	6	50803905	50803905	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:50803905A>G	ENST00000393655.3	+	4	902	c.733A>G	c.(733-735)Aag>Gag	p.K245E	TFAP2B_ENST00000263046.4_Missense_Mutation_p.K254E	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	245					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					TTCAACTTCGAAGTACAAAGT	0.537																																					p.K245E	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.A733G						.						67.0	65.0	66.0					6																	50803905		2203	4300	6503	SO:0001583	missense	7021	exon4			ACTTCGAAGTACA	X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"""			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.733A>G	chr6.hg19:g.50803905A>G	ENSP00000377265:p.Lys245Glu	74.0	0.0		83.0	36.0	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	hg19	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	A	18.85	3.711761	0.68730	.	.	ENSG00000008196	ENST00000393655;ENST00000263046	D;D	0.97831	-4.56;-4.56	5.44	5.44	0.79542	Transcription factor AP-2, C-terminal (1);	0.098510	0.64402	D	0.000002	D	0.98324	0.9444	M	0.91561	3.22	0.80722	D	1	D	0.59767	0.986	P	0.53490	0.727	D	0.98968	1.0800	10	0.87932	D	0	-15.3874	15.5056	0.75739	1.0:0.0:0.0:0.0	.	245	Q92481	AP2B_HUMAN	E	245;254	ENSP00000377265:K245E;ENSP00000263046:K254E	ENSP00000263046:K254E	K	+	1	0	TFAP2B	50911864	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	9.339000	0.96797	2.071000	0.62044	0.528000	0.53228	AAG	.	.		0.537	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221	
SIM1	6492	hgsc.bcm.edu	37	6	100896528	100896528	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:100896528C>A	ENST00000369208.3	-	7	1352	c.570G>T	c.(568-570)aaG>aaT	p.K190N	SIM1_ENST00000262901.4_Missense_Mutation_p.K190N			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	190					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		ACTGGCGGATCTTCAAGTAGC	0.627																																					p.K190N		Atlas-SNP	.											.	SIM1	173	.	0			c.G570T						.						35.0	37.0	37.0					6																	100896528		2203	4300	6503	SO:0001583	missense	6492	exon6			GCGGATCTTCAAG	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.570G>T	chr6.hg19:g.100896528C>A	ENSP00000358210:p.Lys190Asn	21.0	0.0		24.0	7.0	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	33	5.288765	0.95517	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.70749	-0.51;-0.51	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.86493	0.5946	M	0.91872	3.25	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.88940	0.3379	10	0.87932	D	0	.	19.5581	0.95361	0.0:1.0:0.0:0.0	.	190	P81133	SIM1_HUMAN	N	190	ENSP00000358210:K190N;ENSP00000262901:K190N	ENSP00000262901:K190N	K	-	3	2	SIM1	101003249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.328000	0.52052	2.614000	0.88457	0.655000	0.94253	AAG	.	.		0.627	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
PTPRK	5796	hgsc.bcm.edu	37	6	128403764	128403764	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:128403764C>A	ENST00000368215.3	-	10	1594	c.1595G>T	c.(1594-1596)aGa>aTa	p.R532I	RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368207.3_Missense_Mutation_p.R532I|PTPRK_ENST00000532331.1_Missense_Mutation_p.R532I|PTPRK_ENST00000368210.3_Missense_Mutation_p.R532I|PTPRK_ENST00000368226.4_Missense_Mutation_p.R532I|PTPRK_ENST00000368213.5_Missense_Mutation_p.R532I|PTPRK_ENST00000368227.3_Missense_Mutation_p.R532I|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	532	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATCAAATGATCTTATACTGCT	0.363																																					p.R532I		Atlas-SNP	.											.	PTPRK	330	.	0			c.G1595T						.						81.0	72.0	75.0					6																	128403764		2203	4300	6503	SO:0001583	missense	5796	exon10			AATGATCTTATAC	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.1595G>T	chr6.hg19:g.128403764C>A	ENSP00000357198:p.Arg532Ile	97.0	0.0		118.0	26.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.77	3.888976	0.72524	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.097739	0.64402	D	0.000002	T	0.41650	0.1168	N	0.19112	0.55	0.53688	D	0.999977	B;P;P;B;P;P	0.48834	0.371;0.916;0.898;0.451;0.857;0.828	B;P;P;B;P;B	0.54026	0.31;0.74;0.622;0.306;0.508;0.374	T	0.40739	-0.9547	10	0.51188	T	0.08	.	14.8552	0.70332	0.0:0.9288:0.0:0.0712	.	532;532;532;389;532;532	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	I	532;532;532;532;532;532;532;389	ENSP00000357209:R532I;ENSP00000357210:R532I;ENSP00000432973:R532I;ENSP00000357196:R532I;ENSP00000357193:R532I;ENSP00000357198:R532I;ENSP00000357190:R532I	ENSP00000357190:R532I	R	-	2	0	PTPRK	128445457	0.972000	0.33761	0.989000	0.46669	0.966000	0.64601	2.407000	0.44565	2.718000	0.92993	0.650000	0.86243	AGA	.	.		0.363	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
WIPF3	644150	hgsc.bcm.edu	37	7	29874406	29874406	+	Silent	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:29874406C>G	ENST00000409290.1	+	1	66	c.66C>G	c.(64-66)ccC>ccG	p.P22P	WIPF3_ENST00000242140.5_Silent_p.P22P|WIPF3_ENST00000409123.1_Silent_p.P22P	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	22					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						gggctcctccccctcccccac	0.552																																					p.P22P		Atlas-SNP	.											.	WIPF3	46	.	0			c.C66G						.						13.0	14.0	13.0					7																	29874406		931	2074	3005	SO:0001819	synonymous_variant	644150	exon2			TCCTCCCCCTCCC	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.66C>G	chr7.hg19:g.29874406C>G		288.0	0.0		332.0	81.0	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	hg19	CCDS56472.1																																																																																			.	.		0.552	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
MYO1G	64005	hgsc.bcm.edu	37	7	45016656	45016656	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:45016656C>T	ENST00000258787.7	-	2	246	c.110G>A	c.(109-111)cGc>cAc	p.R37H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	37	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GGTGTAGATGCGGCCCTTCTC	0.637																																					p.R37H		Atlas-SNP	.											.	MYO1G	86	.	0			c.G110A						.						58.0	54.0	56.0					7																	45016656		2203	4300	6503	SO:0001583	missense	64005	exon2			TAGATGCGGCCCT	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.110G>A	chr7.hg19:g.45016656C>T	ENSP00000258787:p.Arg37His	68.0	0.0		82.0	5.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518945	0.44866	.	.	ENSG00000136286	ENST00000258787	T	0.71698	-0.59	3.93	2.02	0.26589	Myosin head, motor domain (2);	0.000000	0.37437	N	0.002082	T	0.68485	0.3006	N	0.25789	0.76	0.49389	D	0.999789	D	0.69078	0.997	D	0.63283	0.913	T	0.66614	-0.5879	10	0.59425	D	0.04	.	7.4484	0.27223	0.1644:0.744:0.0:0.0915	.	37	B0I1T2	MYO1G_HUMAN	H	37	ENSP00000258787:R37H	ENSP00000258787:R37H	R	-	2	0	MYO1G	44983181	0.978000	0.34361	0.998000	0.56505	0.791000	0.44710	2.517000	0.45529	0.402000	0.25451	0.655000	0.94253	CGC	.	.		0.637	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
POM121L12	285877	hgsc.bcm.edu	37	7	53104142	53104142	+	Missense_Mutation	SNP	G	G	A	rs202031574	byFrequency	TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:53104142G>A	ENST00000408890.4	+	1	794	c.778G>A	c.(778-780)Gcc>Acc	p.A260T		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	260										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTCCAGCCCGCCCCATCCGC	0.657																																					p.A260T		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	.	0			c.G778A						.						50.0	57.0	54.0					7																	53104142		2017	4174	6191	SO:0001583	missense	285877	exon1			CAGCCCGCCCCAT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.778G>A	chr7.hg19:g.53104142G>A	ENSP00000386133:p.Ala260Thr	26.0	0.0		37.0	15.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	7.673	0.687324	0.14973	.	.	ENSG00000221900	ENST00000408890	T	0.25912	1.77	2.16	-4.31	0.03698	.	.	.	.	.	T	0.09335	0.0230	N	0.08118	0	0.09310	N	1	B	0.28419	0.211	B	0.19391	0.025	T	0.12889	-1.0530	9	0.56958	D	0.05	.	2.3928	0.04382	0.1725:0.1362:0.5107:0.1807	.	260	Q8N7R1	P1L12_HUMAN	T	260	ENSP00000386133:A260T	ENSP00000386133:A260T	A	+	1	0	POM121L12	53071636	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.248000	0.00541	-2.674000	0.00412	-0.410000	0.06199	GCC	.	.		0.657	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
CPA4	51200	hgsc.bcm.edu	37	7	129962512	129962512	+	Missense_Mutation	SNP	A	A	T	rs376985428		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:129962512A>T	ENST00000222482.4	+	11	1290	c.1262A>T	c.(1261-1263)tAc>tTc	p.Y421F	CPA4_ENST00000493259.1_Missense_Mutation_p.Y317F|CPA4_ENST00000445470.2_Missense_Mutation_p.Y388F	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	421					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GACAACCTCTACTAGGCGATG	0.537																																					p.Y421F		Atlas-SNP	.											.	CPA4	47	.	0			c.A1262T						.						181.0	147.0	159.0					7																	129962512		2203	4300	6503	SO:0001583	missense	51200	exon11			ACCTCTACTAGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1262A>T	chr7.hg19:g.129962512A>T	ENSP00000222482:p.Tyr421Phe	70.0	0.0		61.0	24.0	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089189	0.55968	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.14144	2.74;2.8;2.53	5.63	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	M	0.79258	2.445	0.47511	D	0.999444	D;D	0.71674	0.998;0.994	D;D	0.87578	0.998;0.989	T	0.15435	-1.0437	10	0.66056	D	0.02	.	12.1272	0.53922	0.8563:0.1437:0.0:0.0	.	388;421	B7Z576;Q9UI42	.;CBPA4_HUMAN	F	388;421;226;317	ENSP00000412947:Y388F;ENSP00000222482:Y421F;ENSP00000419660:Y317F	ENSP00000222482:Y421F	Y	+	2	0	CPA4	129749748	1.000000	0.71417	1.000000	0.80357	0.094000	0.18550	3.959000	0.56744	0.947000	0.37659	0.460000	0.39030	TAC	.	.		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
CREB3L2	64764	hgsc.bcm.edu	37	7	137567230	137567230	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:137567230T>A	ENST00000330387.6	-	11	1766	c.1415A>T	c.(1414-1416)gAt>gTt	p.D472V		NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	472					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						ATGGGGAAGATCCACATCCGG	0.592			T	FUS	fibromyxoid sarcoma																																p.D472V		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.A1415T						.						78.0	73.0	74.0					7																	137567230		2203	4300	6503	SO:0001583	missense	64764	exon11			GGAAGATCCACAT	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"""basic leucine zipper proteins"""	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.1415A>T	chr7.hg19:g.137567230T>A	ENSP00000329140:p.Asp472Val	129.0	0.0		180.0	74.0	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.920532	0.52653	.	.	ENSG00000182158	ENST00000330387	T	0.59638	0.25	5.59	3.15	0.36227	.	0.519429	0.21454	N	0.074281	T	0.38268	0.1034	N	0.22421	0.69	0.80722	D	1	B	0.23735	0.09	B	0.18263	0.021	T	0.13926	-1.0491	10	0.31617	T	0.26	-0.3458	7.5117	0.27577	0.0:0.0728:0.1409:0.7863	.	472	Q70SY1	CR3L2_HUMAN	V	472	ENSP00000329140:D472V	ENSP00000329140:D472V	D	-	2	0	CREB3L2	137217770	0.932000	0.31603	0.997000	0.53966	0.989000	0.77384	2.435000	0.44811	0.935000	0.37341	0.454000	0.30748	GAT	.	.		0.592	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071	
KLRG2	346689	hgsc.bcm.edu	37	7	139168233	139168233	+	Silent	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:139168233C>G	ENST00000340940.4	-	1	225	c.156G>C	c.(154-156)ggG>ggC	p.G52G	KLRG2_ENST00000393039.2_Silent_p.G52G	NM_198508.2	NP_940910.1	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G, member 2	52	Pro-rich.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|large_intestine(2)|lung(3)	6	Melanoma(164;0.233)					TCTCCACGGCCCCGGCCGGAC	0.731																																					p.G52G		Atlas-SNP	.											.	KLRG2	22	.	0			c.G156C						.						12.0	14.0	14.0					7																	139168233		1932	4005	5937	SO:0001819	synonymous_variant	346689	exon1			CACGGCCCCGGCC	AK126174	CCDS5854.1	7q34	2011-08-30			ENSG00000188883	ENSG00000188883		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	24778	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member B"""						Standard	XM_005250311		Approved	FLJ44186, CLEC15B	uc003vvb.3	A4D1S0	OTTHUMG00000157705	ENST00000340940.4:c.156G>C	chr7.hg19:g.139168233C>G		47.0	0.0		63.0	10.0	NM_198508	Q2NL79|Q6ZTV6	Silent	SNP	ENST00000340940.4	hg19	CCDS5854.1																																																																																			.	.		0.731	KLRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349433.1	NM_198508	
ZNF282	8427	hgsc.bcm.edu	37	7	148907790	148907790	+	Missense_Mutation	SNP	A	A	G	rs141109561		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr7:148907790A>G	ENST00000262085.3	+	5	1051	c.946A>G	c.(946-948)Att>Gtt	p.I316V	ZNF282_ENST00000479907.1_Missense_Mutation_p.I316V	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	316					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TACGGAATCCATTACCGGTGA	0.637																																					p.I316V		Atlas-SNP	.											.	ZNF282	42	.	0			c.A946G						.	A	VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	54.0	47.0	49.0		946	3.0	0.1	7	dbSNP_134	49	0,8598		0,0,4299	no	missense	ZNF282	NM_003575.2	29	0,1,6501	GG,GA,AA		0.0,0.0227,0.0077	benign	316/672	148907790	1,13003	2203	4299	6502	SO:0001583	missense	8427	exon5			GAATCCATTACCG	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"""Zinc fingers, C2H2-type"", ""-"""	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.946A>G	chr7.hg19:g.148907790A>G	ENSP00000262085:p.Ile316Val	260.0	0.0		275.0	127.0	NM_003575	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	hg19	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	A	3.715	-0.058831	0.07317	2.27E-4	0.0	ENSG00000170265	ENST00000262085;ENST00000479907	T;T	0.05580	3.42;5.25	5.29	2.95	0.34219	.	0.335009	0.21348	N	0.076011	T	0.03739	0.0106	N	0.21448	0.665	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43734	-0.9373	10	0.18710	T	0.47	-7.401	4.7612	0.13110	0.7082:0.0:0.2918:0.0	.	316;288;316	B4DRI5;Q7Z2V4;Q9UDV7	.;.;ZN282_HUMAN	V	316	ENSP00000262085:I316V;ENSP00000418840:I316V	ENSP00000262085:I316V	I	+	1	0	ZNF282	148538723	0.020000	0.18652	0.126000	0.21872	0.471000	0.32888	0.601000	0.24119	0.857000	0.35407	0.460000	0.39030	ATT	.	A|1.000;G|0.000		0.637	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575	
NUDT18	79873	hgsc.bcm.edu	37	8	21965221	21965221	+	Missense_Mutation	SNP	C	C	T	rs554932005		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr8:21965221C>T	ENST00000309188.6	-	5	680	c.562G>A	c.(562-564)Gtc>Atc	p.V188I	NUDT18_ENST00000521807.2_3'UTR|NUDT18_ENST00000522405.1_Missense_Mutation_p.V111I	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	188					dADP catabolic process (GO:0046057)|dGDP catabolic process (GO:0046067)|GDP catabolic process (GO:0046712)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-hydroxy-dADP phosphatase activity (GO:0044717)|8-oxo-dGDP phosphatase activity (GO:0044715)|8-oxo-GDP phosphatase activity (GO:0044716)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|lung(2)	4				Colorectal(74;0.00185)|COAD - Colon adenocarcinoma(73;0.0608)|READ - Rectum adenocarcinoma(5;0.0986)		CGCTGGCAGACCAGATCACAG	0.612																																					p.V188I		Atlas-SNP	.											.	NUDT18	13	.	0			c.G562A						.						64.0	76.0	72.0					8																	21965221		2141	4232	6373	SO:0001583	missense	79873	exon5			GGCAGACCAGATC		CCDS75706.1	8p21.3	2012-07-31				ENSG00000275074		"""Nudix motif containing"""	26194	protein-coding gene	gene with protein product	"""mutT human homolog 3"""	615791				22556419	Standard	NM_024815		Approved	FLJ22494, MTH3	uc003xaq.1	Q6ZVK8		ENST00000309188.6:c.562G>A	chr8.hg19:g.21965221C>T	ENSP00000307852:p.Val188Ile	94.0	0.0		28.0	15.0	NM_024815	Q8IZ75|Q9H687	Missense_Mutation	SNP	ENST00000309188.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.600|9.600	1.128556|1.128556	0.21041|0.21041	.|.	.|.	ENSG00000173566|ENSG00000173566	ENST00000522379|ENST00000522405;ENST00000309188	.|.	.|.	.|.	5.37|5.37	3.32|3.32	0.38043|0.38043	.|.	.|0.312145	.|0.30320	.|N	.|0.009883	T|T	0.34395|0.34395	0.0896|0.0896	L|L	0.39633|0.39633	1.23|1.23	0.32039|0.32039	N|N	0.598503|0.598503	.|B	.|0.10296	.|0.003	.|B	.|0.08055	.|0.003	T|T	0.33650|0.33650	-0.9860|-0.9860	5|9	.|0.33141	.|T	.|0.24	-18.3948|-18.3948	7.4638|7.4638	0.27310|0.27310	0.0:0.7468:0.0:0.2532|0.0:0.7468:0.0:0.2532	.|.	.|188	.|Q6ZVK8	.|NUD18_HUMAN	D|I	223|111;188	.|.	.|ENSP00000307852:V188I	G|V	-|-	2|1	0|0	NUDT18|NUDT18	22021166|22021166	0.003000|0.003000	0.15002|0.15002	1.000000|1.000000	0.80357|0.80357	0.806000|0.806000	0.45545|0.45545	-0.111000|-0.111000	0.10807|0.10807	1.260000|1.260000	0.44134|0.44134	0.655000|0.655000	0.94253|0.94253	GGT|GTC	.	.		0.612	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815	
EYA1	2138	hgsc.bcm.edu	37	8	72182014	72182014	+	Silent	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr8:72182014G>A	ENST00000340726.3	-	11	1650	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	EYA1_ENST00000388742.4_Silent_p.H337H|EYA1_ENST00000303824.7_Silent_p.H331H|EYA1_ENST00000388740.3_Silent_p.H304H|EYA1_ENST00000388741.2_Silent_p.H303H|EYA1_ENST00000388743.2_Silent_p.H336H|EYA1_ENST00000419131.1_Silent_p.H332H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	337					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TAAGCAAGGAGTGGAAAACAA	0.403																																					p.H337H		Atlas-SNP	.											.	EYA1	108	.	0			c.C1011T						.						172.0	156.0	161.0					8																	72182014		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon11			CAAGGAGTGGAAA	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3519	protein-coding gene	gene with protein product		601653	"""eyes absent (Drosophila) homolog 1"", ""eyes absent homolog 1 (Drosophila)"""	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1011C>T	chr8.hg19:g.72182014G>A		94.0	0.0		130.0	31.0	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.		0.403	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060	
KIAA2026	158358	hgsc.bcm.edu	37	9	5921873	5921873	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:5921873G>A	ENST00000399933.3	-	8	4122	c.4123C>T	c.(4123-4125)Cac>Tac	p.H1375Y	KIAA2026_ENST00000381461.2_Missense_Mutation_p.H1345Y	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1375	Ser-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CCAGTGGTGTGGCCTAATGTA	0.443																																					p.H1375Y		Atlas-SNP	.											.	KIAA2026	231	.	0			c.C4123T						.						155.0	150.0	151.0					9																	5921873		1883	4120	6003	SO:0001583	missense	158358	exon8			TGGTGTGGCCTAA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4123C>T	chr9.hg19:g.5921873G>A	ENSP00000382815:p.His1375Tyr	79.0	0.0		54.0	45.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.013	-1.630739	0.00813	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	3.9	2.98	0.34508	.	0.273622	0.24568	N	0.037402	T	0.20170	0.0485	N	0.08118	0	0.18873	N	0.999989	B	0.22851	0.076	B	0.19946	0.027	T	0.23762	-1.0179	9	0.02654	T	1	0.4025	14.2375	0.65937	0.0827:0.0:0.9173:0.0	.	1375	Q5HYC2	K2026_HUMAN	Y	1375;1345	.	ENSP00000370870:H1345Y	H	-	1	0	KIAA2026	5911873	1.000000	0.71417	0.235000	0.24058	0.073000	0.16967	4.572000	0.60886	0.342000	0.23796	-1.233000	0.01565	CAC	.	.		0.443	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
MVB12B	89853	hgsc.bcm.edu	37	9	129148868	129148868	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:129148868A>G	ENST00000361171.3	+	4	421	c.340A>G	c.(340-342)Atg>Gtg	p.M114V	MVB12B_ENST00000545391.1_Missense_Mutation_p.M114V|MVB12B_ENST00000535766.1_Missense_Mutation_p.M107V|MVB12B_ENST00000436593.3_Missense_Mutation_p.M99V	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	114	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										GTTAGTAGATATGAAGCTCAT	0.453																																					p.M114V		Atlas-SNP	.											.	.	.	.	0			c.A340G						.						121.0	95.0	104.0					9																	129148868		2203	4300	6503	SO:0001583	missense	89853	exon4			GTAGATATGAAGC	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 28"", ""family with sequence similarity 125, member B"""	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.340A>G	chr9.hg19:g.129148868A>G	ENSP00000354772:p.Met114Val	51.0	0.0		58.0	18.0	NM_001011703	Q8N6S7	Missense_Mutation	SNP	ENST00000361171.3	hg19	CCDS35142.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.456758	0.43634	.	.	ENSG00000196814	ENST00000361171;ENST00000545391;ENST00000402437;ENST00000436593;ENST00000535766	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.29	5.29	0.74685	MABP domain (1);	0.000000	0.85682	D	0.000000	T	0.41073	0.1143	L	0.58101	1.795	0.58432	D	0.999996	P;P;P	0.39535	0.677;0.476;0.476	B;B;B	0.40199	0.322;0.223;0.223	T	0.23691	-1.0181	10	0.13470	T	0.59	-1.0168	15.2378	0.73443	1.0:0.0:0.0:0.0	.	107;99;114	B7Z4X0;B7Z1P9;Q9H7P6	.;.;F125B_HUMAN	V	114;114;99;99;107	ENSP00000354772:M114V;ENSP00000441988:M114V;ENSP00000384751:M99V;ENSP00000401379:M99V;ENSP00000442846:M107V	ENSP00000354772:M114V	M	+	1	0	FAM125B	128188689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.088000	0.76901	2.003000	0.58678	0.528000	0.53228	ATG	.	.		0.453	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525	
RALGDS	5900	hgsc.bcm.edu	37	9	135985072	135985072	+	Silent	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:135985072T>C	ENST00000372050.3	-	4	546	c.525A>G	c.(523-525)agA>agG	p.R175R	RALGDS_ENST00000393157.3_Silent_p.R174R|RALGDS_ENST00000372047.3_Splice_Site_p.R163R|RALGDS_ENST00000393160.3_Silent_p.R120R|RALGDS_ENST00000542690.1_Silent_p.R246R|RALGDS_ENST00000469972.1_5'Flank|RALGDS_ENST00000372062.3_Splice_Site_p.R146R	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	175	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TGCAGCCGTATCTAGAGGAGG	0.567			T	CIITA	"""PMBL, Hodgkin Lymphona, """																																p.R175R	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.A525G						.						178.0	138.0	152.0					9																	135985072		2202	4300	6502	SO:0001819	synonymous_variant	5900	exon4			GCCGTATCTAGAG	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.525A>G	chr9.hg19:g.135985072T>C		88.0	0.0		90.0	34.0	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.		0.567	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
KCNT1	57582	hgsc.bcm.edu	37	9	138660742	138660742	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:138660742A>G	ENST00000263604.3	+	15	1412	c.1412A>G	c.(1411-1413)cAg>cGg	p.Q471R	KCNT1_ENST00000487664.1_Missense_Mutation_p.Q445R|KCNT1_ENST00000488444.2_Missense_Mutation_p.Q471R|KCNT1_ENST00000371757.2_Missense_Mutation_p.Q490R|KCNT1_ENST00000486577.2_Missense_Mutation_p.Q451R|KCNT1_ENST00000491806.2_Missense_Mutation_p.Q457R|KCNT1_ENST00000490355.2_Missense_Mutation_p.Q471R|KCNT1_ENST00000298480.5_Missense_Mutation_p.Q490R			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	471					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CTCTACGTCCAGATCCTCAAA	0.617																																					p.Q490R		Atlas-SNP	.											.	KCNT1	139	.	0			c.A1469G						.						122.0	105.0	111.0					9																	138660742		2201	4300	6501	SO:0001583	missense	57582	exon15			ACGTCCAGATCCT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1412A>G	chr9.hg19:g.138660742A>G	ENSP00000263604:p.Gln471Arg	39.0	0.0		33.0	13.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.083107	0.76642	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.75	3.75	0.43078	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000001	T	0.78799	0.4340	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.67145	0.983;0.996;0.99;0.983	D;D;D;P	0.70487	0.917;0.969;0.948;0.889	T	0.82325	-0.0513	10	0.87932	D	0	-10.1884	11.7981	0.52112	1.0:0.0:0.0:0.0	.	457;490;445;471	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	R	445;490;490;451;457;471;471;471	ENSP00000417851:Q445R;ENSP00000298480:Q490R;ENSP00000360822:Q490R;ENSP00000263604:Q471R	ENSP00000263604:Q471R	Q	+	2	0	KCNT1	137800563	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.919000	0.92770	1.550000	0.49438	0.402000	0.26972	CAG	.	.		0.617	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
GBF1	8729	hgsc.bcm.edu	37	10	104140434	104140434	+	Missense_Mutation	SNP	G	G	C	rs142268101		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:104140434G>C	ENST00000369983.3	+	38	5421	c.5161G>C	c.(5161-5163)Gtc>Ctc	p.V1721L		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1721					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CAAGCAGACCGTCATCCAGGG	0.577																																					p.V1721L		Atlas-SNP	.											.	GBF1	142	.	0			c.G5161C						.						165.0	183.0	177.0					10																	104140434		2203	4300	6503	SO:0001583	missense	8729	exon38			CAGACCGTCATCC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.5161G>C	chr10.hg19:g.104140434G>C	ENSP00000359000:p.Val1721Leu	69.0	0.0		53.0	34.0	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.979964	0.53827	.	.	ENSG00000107862	ENST00000369983	T	0.09911	2.93	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.31167	0.0788	L	0.57536	1.79	0.80722	D	1	P;D;D	0.63880	0.495;0.993;0.993	B;D;D	0.72075	0.062;0.976;0.976	T	0.00141	-1.1999	10	0.28530	T	0.3	-22.5885	20.2985	0.98592	0.0:0.0:1.0:0.0	.	1717;1717;1721	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	L	1721	ENSP00000359000:V1721L	ENSP00000359000:V1721L	V	+	1	0	GBF1	104130424	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.836000	0.86788	2.793000	0.96121	0.655000	0.94253	GTC	.	G|1.000;A|0.000		0.577	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
ARL3	403	hgsc.bcm.edu	37	10	104465227	104465227	+	Missense_Mutation	SNP	C	C	T	rs368901451		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:104465227C>T	ENST00000260746.5	-	2	154	c.23G>A	c.(22-24)cGc>cAc	p.R8H		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	8					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TTTCAACTTGCGCAAAATTGA	0.463																																					p.R8H		Atlas-SNP	.											.	ARL3	13	.	0			c.G23A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	107.0	90.0	96.0		23	4.2	1.0	10		96	0,8600		0,0,4300	no	missense	ARL3	NM_004311.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	8/183	104465227	1,13005	2203	4300	6503	SO:0001583	missense	403	exon2			AACTTGCGCAAAA	U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.23G>A	chr10.hg19:g.104465227C>T	ENSP00000260746:p.Arg8His	84.0	0.0		61.0	31.0	NM_004311	B2R6C7|Q53X83|Q5JSM2	Missense_Mutation	SNP	ENST00000260746.5	hg19	CCDS7538.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066753	0.93898	2.27E-4	0.0	ENSG00000138175	ENST00000260746	T	0.64618	-0.11	6.03	4.17	0.49024	.	0.882556	0.09697	N	0.767547	T	0.79240	0.4412	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	P	0.58210	0.835	T	0.78250	-0.2277	10	0.62326	D	0.03	-22.8469	13.1907	0.59709	0.0:0.8695:0.0:0.1305	.	8	P36405	ARL3_HUMAN	H	8	ENSP00000260746:R8H	ENSP00000260746:R8H	R	-	2	0	ARL3	104455217	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.060000	0.71141	1.572000	0.49736	0.555000	0.69702	CGC	.	.		0.463	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311	
DMBT1	1755	hgsc.bcm.edu	37	10	124336218	124336218	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:124336218A>G	ENST00000338354.3	+	7	693	c.587A>G	c.(586-588)gAt>gGt	p.D196G	DMBT1_ENST00000368956.2_Missense_Mutation_p.D196G|DMBT1_ENST00000344338.3_Missense_Mutation_p.D196G|DMBT1_ENST00000359586.6_Missense_Mutation_p.D196G|DMBT1_ENST00000330163.4_Missense_Mutation_p.D196G|DMBT1_ENST00000368955.3_Missense_Mutation_p.D196G|DMBT1_ENST00000368909.3_Missense_Mutation_p.D196G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	196	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CATGGTGAAGATGCTGGTGTT	0.562																																					p.D196G	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A587G						.						113.0	111.0	112.0					10																	124336218		2056	4193	6249	SO:0001583	missense	1755	exon7			GTGAAGATGCTGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.587A>G	chr10.hg19:g.124336218A>G	ENSP00000342210:p.Asp196Gly	95.0	0.0		84.0	20.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	a	33	5.207083	0.95033	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.63	4.63	0.57726	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.83069	0.5174	H	0.98701	4.305	0.44175	D	0.996983	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	0.997;1.0;1.0;0.994;0.999;1.0	D	0.89635	0.3858	9	0.62326	D	0.03	.	14.3417	0.66630	1.0:0.0:0.0:0.0	.	196;196;196;196;196;196	F8WEF7;Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	G	196	ENSP00000342210:D196G;ENSP00000343175:D196G;ENSP00000327747:D196G;ENSP00000357905:D196G;ENSP00000357951:D196G;ENSP00000357952:D196G;ENSP00000352593:D196G	ENSP00000331522:D196G	D	+	2	0	DMBT1	124326208	1.000000	0.71417	0.034000	0.17996	0.728000	0.41692	7.112000	0.77086	1.853000	0.53794	0.533000	0.62120	GAT	.	.		0.562	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
MKI67	4288	hgsc.bcm.edu	37	10	129913465	129913465	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:129913465C>G	ENST00000368654.3	-	7	1582	c.1207G>C	c.(1207-1209)Gct>Cct	p.A403P	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	403					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TCAACTTTAGCTGGTGTTCGA	0.438																																					p.A403P		Atlas-SNP	.											.	MKI67	363	.	0			c.G1207C						.						91.0	93.0	92.0					10																	129913465		2203	4300	6503	SO:0001583	missense	4288	exon7			CTTTAGCTGGTGT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1207G>C	chr10.hg19:g.129913465C>G	ENSP00000357643:p.Ala403Pro	118.0	0.0		110.0	31.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.436079	0.43224	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.01516	4.81	4.0	-5.46	0.02608	.	3.288320	0.00866	N	0.001962	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	D	0.61080	0.989	P	0.50708	0.648	T	0.40213	-0.9575	10	0.87932	D	0	.	12.4406	0.55623	0.0:0.2242:0.0:0.7758	.	403	P46013	KI67_HUMAN	P	403	ENSP00000357643:A403P	ENSP00000357643:A403P	A	-	1	0	MKI67	129803455	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-2.827000	0.00746	-1.180000	0.02734	-0.302000	0.09304	GCT	.	.		0.438	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
CYP2E1	1571	hgsc.bcm.edu	37	10	135352460	135352460	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr10:135352460C>T	ENST00000463117.2	+	11	1746	c.1474C>T	c.(1474-1476)Cgc>Tgc	p.R492C	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Missense_Mutation_p.R492C			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	492					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	TGTCATTCCCCGCTCATGAGT	0.453									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.R492C		Atlas-SNP	.											.	CYP2E1	69	.	0			c.C1474T						.						103.0	84.0	90.0					10																	135352460		2203	4300	6503	SO:0001583	missense	1571	exon9	Familial Cancer Database	incl.: Familial Head and Neck Cancer	ATTCCCCGCTCAT	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"""Cytochrome P450s"""	2631	protein-coding gene	gene with protein product		124040	"""cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"""	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.1474C>T	chr10.hg19:g.135352460C>T	ENSP00000440689:p.Arg492Cys	77.0	0.0		53.0	23.0	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	Missense_Mutation	SNP	ENST00000463117.2	hg19	CCDS7686.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.372590	0.42003	.	.	ENSG00000130649	ENST00000463117;ENST00000252945	T;T	0.66638	-0.22;-0.22	4.64	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.77903	0.4200	M	0.64170	1.965	0.41488	D	0.988206	D	0.89917	1.0	D	0.85130	0.997	T	0.80132	-0.1510	10	0.72032	D	0.01	.	12.1856	0.54236	0.1721:0.8279:0.0:0.0	.	492	P05181	CP2E1_HUMAN	C	492	ENSP00000440689:R492C;ENSP00000252945:R492C	ENSP00000252945:R492C	R	+	1	0	CYP2E1	135202450	0.064000	0.20934	0.549000	0.28204	0.064000	0.16182	1.363000	0.34159	1.299000	0.44798	0.491000	0.48974	CGC	.	.		0.453	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773	
HBD	3045	hgsc.bcm.edu	37	11	5254217	5254217	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:5254217C>A	ENST00000380299.3	-	3	635	c.421G>T	c.(421-423)Gcc>Tcc	p.A141S	HBD_ENST00000292901.3_Intron	NM_000519.3	NP_000510.1	P02042	HBD_HUMAN	hemoglobin, delta	141			A -> V (in Bagheria). {ECO:0000269|PubMed:17145605}.		blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			endometrium(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	16		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;5.69e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGAGCCAGGGCATTAGCCACA	0.493																																					p.A141S		Atlas-SNP	.											.	HBD	35	.	0			c.G421T						.						158.0	138.0	145.0					11																	5254217		2201	4298	6499	SO:0001583	missense	3045	exon3			CCAGGGCATTAGC	AY034468	CCDS31376.1	11p15.5	2012-10-02			ENSG00000223609	ENSG00000223609			4829	protein-coding gene	gene with protein product		142000				2649166	Standard	NM_000519		Approved		uc001maf.1	P02042	OTTHUMG00000066674	ENST00000380299.3:c.421G>T	chr11.hg19:g.5254217C>A	ENSP00000369654:p.Ala141Ser	91.0	0.0		87.0	18.0	NM_000519	Q3Y5H3|Q8WXT7	Missense_Mutation	SNP	ENST00000380299.3	hg19	CCDS31376.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.13|14.13	2.442754|2.442754	0.43326|0.43326	.|.	.|.	ENSG00000223609|ENSG00000223609	ENST00000380299|ENST00000417377	D|D	0.94537|0.86432	-3.45|-2.12	4.8|4.8	2.92|2.92	0.33932|0.33932	Globin-like (1);Globin, structural domain (1);|.	.|.	.|.	.|.	.|.	D|D	0.91229|0.91229	0.7236|0.7236	M|M	0.88310|0.88310	2.945|2.945	0.22001|0.22001	N|N	0.999425|0.999425	D|.	0.61697|.	0.99|.	D|.	0.75484|.	0.986|.	D|D	0.83916|0.83916	0.0298|0.0298	9|7	0.87932|0.87932	D|D	0|0	.|.	7.8913|7.8913	0.29680|0.29680	0.0:0.8148:0.0:0.1852|0.0:0.8148:0.0:0.1852	.|.	141|.	P02042|.	HBD_HUMAN|.	S|I	141|66	ENSP00000369654:A141S|ENSP00000414741:M66I	ENSP00000369654:A141S|ENSP00000414741:M66I	A|M	-|-	1|3	0|0	HBD|HBD	5210793|5210793	0.236000|0.236000	0.23804|0.23804	0.017000|0.017000	0.16124|0.16124	0.491000|0.491000	0.33493|0.33493	1.473000|1.473000	0.35387|0.35387	0.737000|0.737000	0.32582|0.32582	0.650000|0.650000	0.86243|0.86243	GCC|ATG	.	.		0.493	HBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142970.1	NM_000519	
CD44	960	hgsc.bcm.edu	37	11	35208383	35208383	+	Silent	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:35208383A>T	ENST00000428726.2	+	4	495	c.372A>T	c.(370-372)ccA>ccT	p.P124P	CD44_ENST00000526669.2_Intron|CD44_ENST00000434472.2_Silent_p.P124P|CD44_ENST00000263398.6_Silent_p.P124P|CD44_ENST00000433354.2_Silent_p.P124P|CD44_ENST00000278386.6_Intron|CD44_ENST00000437706.2_Silent_p.P124P|CD44_ENST00000352818.4_Silent_p.P124P|CD44_ENST00000360158.4_Silent_p.P124P|CD44_ENST00000433892.2_Silent_p.P124P|CD44_ENST00000449691.2_Silent_p.P124P|CD44_ENST00000415148.2_Silent_p.P124P	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	124					blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TCATAGCTCCACCTGAAGAAG	0.348																																					p.P124P		Atlas-SNP	.											.	CD44	48	.	0			c.A372T						.						147.0	140.0	143.0					11																	35208383		2202	4298	6500	SO:0001819	synonymous_variant	960	exon4			AGCTCCACCTGAA	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.372A>T	chr11.hg19:g.35208383A>T		79.0	0.0		78.0	29.0	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	hg19	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.12|13.12	2.142421|2.142421	0.37825|0.37825	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000527889;ENST00000531873|ENST00000442151;ENST00000528455	.|.	.|.	.|.	4.76|4.76	-6.03|-6.03	0.02185|0.02185	.|.	.|.	.|.	.|.	.|.	T|T	0.47284|0.47284	0.1437|0.1437	.|.	.|.	.|.	0.33917|0.33917	D|D	0.64039|0.64039	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.58880|0.58880	-0.7558|-0.7558	4|5	.|0.87932	.|D	.|0	-1.0333|-1.0333	4.403|4.403	0.11395|0.11395	0.3457:0.0:0.3983:0.256|0.3457:0.0:0.3983:0.256	.|.	.|.	.|.	.|.	L|S	80;45|124;61	.|.	.|ENSP00000395953:T80S	H|T	+|+	2|1	0|0	CD44|CD44	35164959|35164959	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.007000|0.007000	0.05969|0.05969	-0.790000|-0.790000	0.04604|0.04604	-1.146000|-1.146000	0.02854|0.02854	-0.366000|-0.366000	0.07423|0.07423	CAC|ACC	.	.		0.348	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
GLYATL1	92292	hgsc.bcm.edu	37	11	58723497	58723497	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:58723497T>G	ENST00000317391.4	+	8	1246	c.906T>G	c.(904-906)ttT>ttG	p.F302L	GLYATL1_ENST00000300079.5_Missense_Mutation_p.F333L|RP11-142C4.6_ENST00000533954.1_RNA|RP11-142C4.6_ENST00000525714.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	302						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	TAGTTCCATTTTAGACAATGA	0.423																																					p.F333L		Atlas-SNP	.											.	GLYATL1	89	.	0			c.T999G						.						46.0	47.0	47.0					11																	58723497		2201	4292	6493	SO:0001583	missense	92292	exon7			TCCATTTTAGACA	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.906T>G	chr11.hg19:g.58723497T>G	ENSP00000322223:p.Phe302Leu	75.0	0.0		80.0	36.0	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	3.217	-0.160382	0.06502	.	.	ENSG00000166840	ENST00000444580;ENST00000317391;ENST00000300079	T;T	0.20598	2.55;2.06	1.67	-0.859	0.10685	.	1.074110	0.07478	N	0.903386	T	0.10508	0.0257	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38090	-0.9677	10	0.19147	T	0.46	.	4.1596	0.10277	0.0:0.4767:0.0:0.5233	.	333;302	Q969I3-2;Q969I3	.;GLYL1_HUMAN	L	279;302;333	ENSP00000322223:F302L;ENSP00000300079:F333L	ENSP00000300079:F333L	F	+	3	2	GLYATL1	58480073	0.021000	0.18746	0.004000	0.12327	0.116000	0.19942	1.550000	0.36223	-0.063000	0.13065	0.338000	0.21704	TTT	.	.		0.423	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661	
MS4A7	58475	hgsc.bcm.edu	37	11	60157018	60157018	+	Silent	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:60157018T>C	ENST00000300184.3	+	5	691	c.495T>C	c.(493-495)taT>taC	p.Y165Y	MS4A7_ENST00000534016.1_Silent_p.Y120Y|MS4A7_ENST00000530234.2_Intron|MS4A7_ENST00000358246.1_Silent_p.Y120Y|MS4A14_ENST00000531787.1_Intron	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	165						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						CGGAGTACTATTATCCAATAT	0.418																																					p.Y165Y		Atlas-SNP	.											.	MS4A7	38	.	0			c.T495C						.						124.0	115.0	118.0					11																	60157018		2203	4300	6503	SO:0001819	synonymous_variant	58475	exon5			GTACTATTATCCA	AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.495T>C	chr11.hg19:g.60157018T>C		60.0	0.0		58.0	18.0	NM_021201	A6NP53|Q6IAG8	Silent	SNP	ENST00000300184.3	hg19	CCDS7985.1																																																																																			.	.		0.418	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1		
AMOTL1	154810	hgsc.bcm.edu	37	11	94603926	94603926	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:94603926T>C	ENST00000433060.2	+	13	2978	c.2837T>C	c.(2836-2838)tTc>tCc	p.F946S	AMOTL1_ENST00000317829.8_Missense_Mutation_p.F896S|AMOTL1_ENST00000317837.9_Missense_Mutation_p.F533S	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	946					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AAGCCCGAGTTCCCTGATGGA	0.522																																					p.F946S		Atlas-SNP	.											.	AMOTL1	95	.	0			c.T2837C						.						34.0	36.0	35.0					11																	94603926		1954	4145	6099	SO:0001583	missense	154810	exon13			CCGAGTTCCCTGA	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2837T>C	chr11.hg19:g.94603926T>C	ENSP00000387739:p.Phe946Ser	47.0	0.0		45.0	17.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811101	0.70797	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.61392	1.75;0.11;1.7	5.56	5.56	0.83823	.	0.152891	0.45867	D	0.000329	T	0.70404	0.3220	L	0.57536	1.79	0.24328	N	0.995018	D;P	0.69078	0.997;0.771	P;B	0.62184	0.899;0.226	T	0.65606	-0.6127	10	0.56958	D	0.05	-10.5661	15.7213	0.77713	0.0:0.0:0.0:1.0	.	896;946	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	S	896;533;946	ENSP00000320968:F896S;ENSP00000323474:F533S;ENSP00000387739:F946S	ENSP00000320968:F896S	F	+	2	0	AMOTL1	94243574	1.000000	0.71417	0.989000	0.46669	0.413000	0.31143	5.322000	0.65852	2.127000	0.65507	0.379000	0.24179	TTC	.	.		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
USP2	9099	hgsc.bcm.edu	37	11	119243744	119243744	+	Silent	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:119243744A>G	ENST00000260187.2	-	2	741	c.447T>C	c.(445-447)gaT>gaC	p.D149D	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	149	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GGCTGGAGAAATCCCGGGCCA	0.627																																					p.D149D		Atlas-SNP	.											.	USP2	71	.	0			c.T447C						.						55.0	63.0	61.0					11																	119243744		2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			GGAGAAATCCCGG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.447T>C	chr11.hg19:g.119243744A>G		84.0	0.0		70.0	26.0	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	hg19	CCDS8422.1																																																																																			.	.		0.627	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
VWF	7450	hgsc.bcm.edu	37	12	6182863	6182863	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:6182863G>A	ENST00000261405.5	-	8	1173	c.919C>T	c.(919-921)Cct>Tct	p.P307S		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	307	TIL 1.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.P307S(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CTGGCGCAAGGGGACACACAC	0.557																																					p.P307S		Atlas-SNP	.											VWF,NS,carcinoma,0,1	VWF	338	.	1	Substitution - Missense(1)	lung(1)	c.C919T						.						124.0	101.0	109.0					12																	6182863		2203	4300	6503	SO:0001583	missense	7450	exon8			CGCAAGGGGACAC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.919C>T	chr12.hg19:g.6182863G>A	ENSP00000261405:p.Pro307Ser	28.0	0.0		39.0	18.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304563	0.60305	.	.	ENSG00000110799	ENST00000261405	D	0.90133	-2.62	5.07	5.07	0.68467	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.000000	0.41097	D	0.000949	D	0.90762	0.7100	N	0.17082	0.46	0.80722	D	1	P;D	0.89917	0.623;1.0	B;D	0.87578	0.401;0.998	D	0.89663	0.3878	10	0.26408	T	0.33	.	17.0171	0.86422	0.0:0.0:1.0:0.0	.	307;307	B4DNX0;P04275	.;VWF_HUMAN	S	307	ENSP00000261405:P307S	ENSP00000261405:P307S	P	-	1	0	VWF	6053124	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	4.058000	0.57463	2.352000	0.79861	0.491000	0.48974	CCT	.	.		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
CLEC9A	283420	hgsc.bcm.edu	37	12	10205329	10205329	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:10205329C>G	ENST00000355819.1	+	4	656	c.43C>G	c.(43-45)Cca>Gca	p.P15A	CLEC9A_ENST00000544751.1_3'UTR	NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	15					positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						GTGGGATAGCCCAGCACCAGA	0.418																																					p.P15A		Atlas-SNP	.											.	CLEC9A	41	.	0			c.C43G						.						118.0	109.0	112.0					12																	10205329		2203	4300	6503	SO:0001583	missense	283420	exon4			GATAGCCCAGCAC		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"""C-type lectin domain containing"""	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.43C>G	chr12.hg19:g.10205329C>G	ENSP00000348074:p.Pro15Ala	103.0	0.0		54.0	26.0	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	hg19	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	C	8.653	0.898740	0.17686	.	.	ENSG00000197992	ENST00000355819	T	0.01438	4.89	4.2	3.31	0.37934	.	0.380726	0.19384	N	0.115570	T	0.02230	0.0069	L	0.50333	1.59	0.09310	N	1	P	0.48834	0.916	P	0.45712	0.491	T	0.47433	-0.9118	10	0.45353	T	0.12	.	7.8528	0.29464	0.0:0.8894:0.0:0.1106	.	15	Q6UXN8	CLC9A_HUMAN	A	15	ENSP00000348074:P15A	ENSP00000348074:P15A	P	+	1	0	CLEC9A	10096596	0.001000	0.12720	0.005000	0.12908	0.056000	0.15407	0.454000	0.21827	1.361000	0.45981	0.655000	0.94253	CCA	.	.		0.418	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345	
KIAA1551	55196	hgsc.bcm.edu	37	12	32136720	32136720	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:32136720A>G	ENST00000312561.4	+	4	3245	c.2831A>G	c.(2830-2832)gAt>gGt	p.D944G	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	944																	AAACAATTAGATAATACCACT	0.378																																					p.D944G		Atlas-SNP	.											.	.	.	.	0			c.A2831G						.						38.0	37.0	38.0					12																	32136720		2203	4300	6503	SO:0001583	missense	55196	exon4			AATTAGATAATAC	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.2831A>G	chr12.hg19:g.32136720A>G	ENSP00000310338:p.Asp944Gly	79.0	0.0		42.0	19.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079373	0.55753	.	.	ENSG00000174718	ENST00000312561	T	0.12879	2.64	5.67	4.54	0.55810	.	1.377390	0.04380	N	0.360631	T	0.25975	0.0633	L	0.54323	1.7	0.09310	N	1	D	0.56746	0.977	P	0.51016	0.656	T	0.12863	-1.0531	9	.	.	.	.	9.7098	0.40238	0.9214:0.0:0.0786:0.0	.	944	Q9HCM1	CL035_HUMAN	G	944	ENSP00000310338:D944G	.	D	+	2	0	C12orf35	32027987	0.025000	0.19082	0.001000	0.08648	0.011000	0.07611	1.719000	0.38011	0.993000	0.38866	0.459000	0.35465	GAT	.	.		0.378	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
PDZRN4	29951	hgsc.bcm.edu	37	12	41900359	41900359	+	Silent	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:41900359T>C	ENST00000402685.2	+	4	953	c.945T>C	c.(943-945)ccT>ccC	p.P315P	PDZRN4_ENST00000298919.7_Silent_p.P55P|PDZRN4_ENST00000539469.2_Silent_p.P57P	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	315							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GGCGAACACCTCTTAGTAGAC	0.512																																					p.P315P		Atlas-SNP	.											.	PDZRN4	346	.	0			c.T945C						.						140.0	118.0	126.0					12																	41900359		2203	4300	6503	SO:0001819	synonymous_variant	29951	exon4			AACACCTCTTAGT	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.945T>C	chr12.hg19:g.41900359T>C		87.0	0.0		59.0	39.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.		0.512	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
LRP1	4035	hgsc.bcm.edu	37	12	57594875	57594875	+	Silent	SNP	C	C	T	rs551393670		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:57594875C>T	ENST00000243077.3	+	65	10750	c.10284C>T	c.(10282-10284)ccC>ccT	p.P3428P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3428	LDL-receptor class A 23. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCTGTATTCCCGGCATCTTCC	0.597																																					p.P3428P		Atlas-SNP	.											.	LRP1	428	.	0			c.C10284T						.						241.0	200.0	214.0					12																	57594875		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon65			TATTCCCGGCATC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10284C>T	chr12.hg19:g.57594875C>T		55.0	0.0		60.0	15.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.597	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CIT	11113	hgsc.bcm.edu	37	12	120220408	120220408	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr12:120220408C>T	ENST00000261833.7	-	13	1631	c.1579G>A	c.(1579-1581)Gag>Aag	p.E527K	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.E527K	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	527					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TGGGACACCTCCATCCGTGCT	0.473																																					p.E527K		Atlas-SNP	.											.	CIT	535	.	0			c.G1579A						.						106.0	96.0	99.0					12																	120220408		2203	4300	6503	SO:0001583	missense	11113	exon13			ACACCTCCATCCG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1579G>A	chr12.hg19:g.120220408C>T	ENSP00000261833:p.Glu527Lys	65.0	0.0		49.0	27.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.380699|5.380699	0.95945|0.95945	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|.	0.64438|.	-0.1;-0.1|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.59280|.	0.2182|.	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;P;P|.	0.60575|.	0.988;0.851;0.908|.	P;B;B|.	0.55508|.	0.777;0.253;0.436|.	T|.	0.49173|.	-0.8967|.	10|.	0.33940|.	T|.	0.23|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	527;527;60|.	Q2M5E1;O14578;O14578-3|.	.;CTRO_HUMAN;.|.	K|X	527|154	ENSP00000376306:E527K;ENSP00000261833:E527K|.	ENSP00000261833:E527K|.	E|W	-|-	1|3	0|0	CIT|CIT	118704791|118704791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.999000|5.999000	0.70665|0.70665	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GAG|TGG	.	.		0.473	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
CCDC169	728591	hgsc.bcm.edu	37	13	36827982	36827982	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr13:36827982C>A	ENST00000239859.7	-	6	457	c.426G>T	c.(424-426)aaG>aaT	p.K142N	CCDC169_ENST00000510088.1_Missense_Mutation_p.K40N|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.K42N|CCDC169_ENST00000379864.2_Missense_Mutation_p.K40N|SOHLH2_ENST00000554962.1_Missense_Mutation_p.K42N|CCDC169_ENST00000491049.2_Missense_Mutation_p.K40N|CCDC169_ENST00000239860.6_Missense_Mutation_p.K42N|CCDC169_ENST00000503173.1_Missense_Mutation_p.K142N|CCDC169_ENST00000379862.2_Missense_Mutation_p.K40N			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	142										breast(1)|endometrium(1)	2						CATTGTTGATCTTCTGGTAAG	0.348																																					p.K142N		Atlas-SNP	.											.	CCDC169	20	.	0			c.G426T						.						198.0	164.0	174.0					13																	36827982		692	1591	2283	SO:0001583	missense	728591	exon6			GTTGATCTTCTGG		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000239859.7:c.426G>T	chr13.hg19:g.36827982C>A	ENSP00000239859:p.Lys142Asn	119.0	0.0		56.0	20.0	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Missense_Mutation	SNP	ENST00000239859.7	hg19	CCDS45028.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.750247	0.49257	.	.	ENSG00000120669;ENSG00000250709;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715	ENST00000554962;ENST00000511166;ENST00000491049;ENST00000503173;ENST00000239860;ENST00000379864;ENST00000510088;ENST00000379862;ENST00000239859	T;T;D;D;T;D;D;D;D	0.85088	0.58;0.58;-1.94;-1.94;0.58;-1.94;-1.94;-1.94;-1.94	4.8	3.96	0.45880	.	0.272379	0.26792	N	0.022480	D	0.82490	0.5048	L	0.41492	1.28	0.09310	N	1	P;P;P;P;P	0.49783	0.787;0.928;0.928;0.622;0.928	B;B;B;B;P	0.50659	0.372;0.426;0.426;0.265;0.647	T	0.74768	-0.3553	10	0.72032	D	0.01	-5.4086	7.3701	0.26796	0.0:0.8071:0.0:0.1929	.	142;42;40;42;142	A6NNP5-4;B7ZW49;A6NNP5-3;B4DX90;A6NNP5	.;.;.;.;CC169_HUMAN	N	42;42;40;142;42;40;40;40;142	ENSP00000451542:K42N;ENSP00000421868:K42N;ENSP00000425252:K40N;ENSP00000426174:K142N;ENSP00000239860:K42N;ENSP00000369193:K40N;ENSP00000427495:K40N;ENSP00000369191:K40N;ENSP00000239859:K142N	ENSP00000239859:K142N	K	-	3	2	CCDC169-SOHLH2;SOHLH2;CCDC169	35725982	1.000000	0.71417	0.036000	0.18154	0.068000	0.16541	0.828000	0.27435	1.367000	0.46095	0.561000	0.74099	AAG	.	.		0.348	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
IRG1	730249	hgsc.bcm.edu	37	13	77531898	77531898	+	Silent	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr13:77531898C>T	ENST00000377462.1	+	5	1286	c.1224C>T	c.(1222-1224)caC>caT	p.H408H	IRG1_ENST00000449753.1_Silent_p.H408H	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	408					cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to progesterone stimulus (GO:0071393)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of type I interferon production (GO:0032480)|positive regulation of antimicrobial humoral response (GO:0002760)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|propionate catabolic process (GO:0019543)|tolerance induction to lipopolysaccharide (GO:0072573)	mitochondrion (GO:0005739)	2-methylcitrate dehydratase activity (GO:0047547)|aconitate decarboxylase activity (GO:0047613)										TCTATGGGCACTGGAGAAAAC	0.488																																					p.H404H		Atlas-SNP	.											.	IRG1	1	.	0			c.C1212T						.																																			SO:0001819	synonymous_variant	730249	exon4			TGGGCACTGGAGA		CCDS58299.1	13q22.3	2013-04-29			ENSG00000102794	ENSG00000102794			33904	protein-coding gene	gene with protein product		615275				23610393	Standard	NM_001258406		Approved		uc031qmi.1	A6NK06	OTTHUMG00000017098	ENST00000377462.1:c.1224C>T	chr13.hg19:g.77531898C>T		120.0	0.0		60.0	27.0	NM_001258406		Silent	SNP	ENST00000377462.1	hg19	CCDS58299.1																																																																																			.	.		0.488	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
TMTC4	84899	hgsc.bcm.edu	37	13	101289831	101289831	+	Silent	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr13:101289831C>A	ENST00000376234.3	-	8	1092	c.903G>T	c.(901-903)gtG>gtT	p.V301V	TMTC4_ENST00000342624.5_Silent_p.V320V|TMTC4_ENST00000328767.5_Silent_p.V190V|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	301						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCGGGTTGTCCACCTCGGTGA	0.637																																					p.V320V		Atlas-SNP	.											.	TMTC4	103	.	0			c.G960T						.						61.0	67.0	65.0					13																	101289831		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon9			GTTGTCCACCTCG		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.903G>T	chr13.hg19:g.101289831C>A		88.0	0.0		65.0	24.0	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	hg19	CCDS41904.1																																																																																			.	.		0.637	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
PRPF39	55015	hgsc.bcm.edu	37	14	45571737	45571737	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr14:45571737T>G	ENST00000355765.6	+	5	745	c.575T>G	c.(574-576)tTt>tGt	p.F192C		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	192					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TTCAGAACTTTTGAGCATGCT	0.313																																					p.F192C		Atlas-SNP	.											.	PRPF39	46	.	0			c.T575G						.						52.0	55.0	54.0					14																	45571737		2202	4300	6502	SO:0001583	missense	55015	exon5			GAACTTTTGAGCA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.575T>G	chr14.hg19:g.45571737T>G	ENSP00000348010:p.Phe192Cys	74.0	0.0		43.0	23.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560757	0.65538	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.36878	1.23	5.62	5.62	0.85841	.	0.157792	0.64402	D	0.000018	T	0.55337	0.1914	M	0.68317	2.08	0.41612	D	0.988919	D;D	0.76494	0.999;0.998	D;P	0.70016	0.967;0.891	T	0.60000	-0.7348	10	0.87932	D	0	-24.4203	10.5592	0.45135	0.1806:0.0:0.0:0.8193	.	192;71	Q86UA1;F5H1P0	PRP39_HUMAN;.	C	192;71	ENSP00000348010:F192C	ENSP00000348010:F192C	F	+	2	0	PRPF39	44641487	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.403000	0.59729	2.137000	0.66172	0.533000	0.62120	TTT	.	.		0.313	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
PRPF39	55015	hgsc.bcm.edu	37	14	45571769	45571769	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr14:45571769T>G	ENST00000355765.6	+	5	777	c.607T>G	c.(607-609)Ttc>Gtc	p.F203V		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	203					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AGGAACAGATTTCCGTTCTGA	0.333																																					p.F203V		Atlas-SNP	.											.	PRPF39	46	.	0			c.T607G						.						89.0	92.0	91.0					14																	45571769		2203	4300	6503	SO:0001583	missense	55015	exon5			ACAGATTTCCGTT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.607T>G	chr14.hg19:g.45571769T>G	ENSP00000348010:p.Phe203Val	106.0	0.0		58.0	23.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	T	25.9	4.681776	0.88542	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.34275	1.37	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.63307	0.2500	M	0.84948	2.725	0.80722	D	1	D;P	0.71674	0.998;0.638	D;B	0.77004	0.989;0.225	T	0.64719	-0.6341	10	0.31617	T	0.26	-7.2579	15.4843	0.75551	0.0:0.0:0.0:1.0	.	203;82	Q86UA1;F5H1P0	PRP39_HUMAN;.	V	203;82	ENSP00000348010:F203V	ENSP00000348010:F203V	F	+	1	0	PRPF39	44641519	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.137000	0.66172	0.533000	0.62120	TTC	.	.		0.333	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
NPAP1	23742	hgsc.bcm.edu	37	15	24922750	24922750	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:24922750A>T	ENST00000329468.2	+	1	2210	c.1736A>T	c.(1735-1737)gAt>gTt	p.D579V		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	579					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GTTAATATGGATACTACTGCC	0.468																																					p.D579V		Atlas-SNP	.											.	.	.	.	0			c.A1736T						.						114.0	107.0	109.0					15																	24922750		2203	4300	6503	SO:0001583	missense	23742	exon1			ATATGGATACTAC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1736A>T	chr15.hg19:g.24922750A>T	ENSP00000333735:p.Asp579Val	98.0	0.0		84.0	20.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.306848	0.40795	.	.	ENSG00000185823	ENST00000329468	T	0.18502	2.21	2.12	2.12	0.27331	.	0.333628	0.21904	N	0.067419	T	0.20129	0.0484	L	0.34521	1.04	0.18873	N	0.999988	D	0.89917	1.0	D	0.66351	0.943	T	0.11324	-1.0592	10	0.12103	T	0.63	.	6.205	0.20598	1.0:0.0:0.0:0.0	.	579	Q9NZP6	CO002_HUMAN	V	579	ENSP00000333735:D579V	ENSP00000333735:D579V	D	+	2	0	C15orf2	22473843	0.036000	0.19791	0.089000	0.20774	0.196000	0.23810	0.076000	0.14712	1.223000	0.43536	0.172000	0.16884	GAT	.	.		0.468	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
DUOX2	50506	hgsc.bcm.edu	37	15	45388244	45388244	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:45388244G>T	ENST00000603300.1	-	30	4064	c.3862C>A	c.(3862-3864)Caa>Aaa	p.Q1288K	DUOX2_ENST00000389039.6_Missense_Mutation_p.Q1288K	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1288	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTCTGGAATTGCAGGTAGGTC	0.577																																					p.Q1288K		Atlas-SNP	.											.	DUOX2	137	.	0			c.C3862A						.						67.0	57.0	60.0					15																	45388244		2198	4298	6496	SO:0001583	missense	50506	exon30			GGAATTGCAGGTA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3862C>A	chr15.hg19:g.45388244G>T	ENSP00000475084:p.Gln1288Lys	89.0	0.0		71.0	17.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	G	0.674	-0.800649	0.02841	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.69	2.61	0.31194	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.426166	0.27618	N	0.018571	T	0.28532	0.0706	N	0.16862	0.45	0.29131	N	0.879665	B	0.02656	0.0	B	0.06405	0.002	T	0.19484	-1.0304	9	0.02654	T	1	-5.0647	16.6592	0.85237	0.0:0.5324:0.4676:0.0	.	1288	Q9NRD8	DUOX2_HUMAN	K	1288	.	ENSP00000373691:Q1288K	Q	-	1	0	DUOX2	43175536	0.999000	0.42202	0.972000	0.41901	0.436000	0.31835	1.551000	0.36233	0.723000	0.32274	0.561000	0.74099	CAA	.	.		0.577	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
DIS3L	115752	hgsc.bcm.edu	37	15	66599227	66599227	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:66599227A>G	ENST00000319212.4	+	3	409	c.359A>G	c.(358-360)gAa>gGa	p.E120G	DIS3L_ENST00000319194.5_Missense_Mutation_p.E37G|DIS3L_ENST00000441424.2_Intron	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	120					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TTTGCTAATGAATTCCAGCAA	0.473																																					p.E120G		Atlas-SNP	.											.	DIS3L	175	.	0			c.A359G						.						135.0	108.0	117.0					15																	66599227		2201	4299	6500	SO:0001583	missense	115752	exon3			CTAATGAATTCCA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"""DIS3 mitotic control homolog (S. cerevisiae)-like"""			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.359A>G	chr15.hg19:g.66599227A>G	ENSP00000321711:p.Glu120Gly	48.0	0.0		61.0	21.0	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	hg19	CCDS45286.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.937762	0.92458	.	.	ENSG00000166938	ENST00000319194;ENST00000525134;ENST00000319212;ENST00000532580;ENST00000530615	T;T	0.39997	1.05;1.14	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.69540	0.3122	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.972;0.994	T	0.75479	-0.3303	10	0.87932	D	0	-8.2493	15.6296	0.76893	1.0:0.0:0.0:0.0	.	120;120	Q8TF46;Q8TF46-3	DI3L1_HUMAN;.	G	37;37;120;37;37	ENSP00000321583:E37G;ENSP00000321711:E120G	ENSP00000321583:E37G	E	+	2	0	DIS3L	64386281	1.000000	0.71417	0.890000	0.34922	0.780000	0.44128	8.494000	0.90477	2.285000	0.76669	0.533000	0.62120	GAA	.	.		0.473	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
ISLR2	57611	hgsc.bcm.edu	37	15	74426696	74426696	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:74426696C>T	ENST00000361742.3	+	4	2370	c.1601C>T	c.(1600-1602)cCa>cTa	p.P534L	ISLR2_ENST00000453268.2_Missense_Mutation_p.P534L|ISLR2_ENST00000435464.1_Missense_Mutation_p.P534L|ISLR2_ENST00000445793.1_Missense_Mutation_p.P534L|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Missense_Mutation_p.P534L|ISLR2_ENST00000419208.1_Missense_Mutation_p.P534L|ISLR2_ENST00000565540.1_Missense_Mutation_p.P534L	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	534					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						TATCTGTGTCCAGCGGGGGGC	0.746																																					p.P534L		Atlas-SNP	.											.	ISLR2	78	.	0			c.C1601T						.						5.0	7.0	6.0					15																	74426696		2034	4098	6132	SO:0001583	missense	57611	exon4			TGTGTCCAGCGGG		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1601C>T	chr15.hg19:g.74426696C>T	ENSP00000355402:p.Pro534Leu	35.0	0.0		44.0	30.0	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	hg19	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.487186	0.26686	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000419208	T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5	4.83	3.91	0.45181	.	0.371892	0.27549	N	0.018869	T	0.03827	0.0108	N	0.14661	0.345	0.31337	N	0.684065	B	0.27351	0.176	B	0.20184	0.028	T	0.11372	-1.0590	10	0.59425	D	0.04	.	7.3605	0.26744	0.1658:0.7452:0.0:0.089	.	534	Q6UXK2	ISLR2_HUMAN	L	534	ENSP00000403244:P534L;ENSP00000355402:P534L;ENSP00000411443:P534L;ENSP00000411834:P534L;ENSP00000408872:P534L	ENSP00000355402:P534L	P	+	2	0	ISLR2	72213749	0.669000	0.27502	0.954000	0.39281	0.874000	0.50279	1.709000	0.37909	1.017000	0.39495	0.313000	0.20887	CCA	.	.		0.746	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851	
ZNF592	9640	hgsc.bcm.edu	37	15	85327987	85327987	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:85327987C>T	ENST00000560079.2	+	4	2369	c.2081C>T	c.(2080-2082)cCt>cTt	p.P694L	ZNF592_ENST00000299927.3_Missense_Mutation_p.P694L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	694					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGTCCCCCTCCTCCAGCCTTG	0.592																																					p.P694L		Atlas-SNP	.											.	ZNF592	95	.	0			c.C2081T						.						85.0	78.0	80.0					15																	85327987		2203	4299	6502	SO:0001583	missense	9640	exon4			CCCCTCCTCCAGC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2081C>T	chr15.hg19:g.85327987C>T	ENSP00000452877:p.Pro694Leu	71.0	0.0		59.0	26.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.439993	0.43326	.	.	ENSG00000166716	ENST00000299927	T	0.30981	1.51	5.93	1.11	0.20524	.	0.594857	0.18557	N	0.137746	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24693	-1.0153	10	0.26408	T	0.33	0.3876	8.7519	0.34620	0.0:0.597:0.0:0.403	.	694	Q92610	ZN592_HUMAN	L	694	ENSP00000299927:P694L	ENSP00000299927:P694L	P	+	2	0	ZNF592	83128991	0.011000	0.17503	0.000000	0.03702	0.881000	0.50899	1.032000	0.30178	-0.080000	0.12685	-0.136000	0.14681	CCT	.	.		0.592	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
ARRDC4	91947	hgsc.bcm.edu	37	15	98512602	98512602	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr15:98512602C>A	ENST00000268042.6	+	5	1039	c.875C>A	c.(874-876)tCc>tAc	p.S292Y	ARRDC4_ENST00000538249.1_Missense_Mutation_p.S205Y	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	292					positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			GTGGACTATTCCTTAGCTGTA	0.393																																					p.S292Y		Atlas-SNP	.											.	ARRDC4	30	.	0			c.C875A						.						88.0	80.0	83.0					15																	98512602		2197	4298	6495	SO:0001583	missense	91947	exon5			ACTATTCCTTAGC	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.875C>A	chr15.hg19:g.98512602C>A	ENSP00000268042:p.Ser292Tyr	99.0	0.0		85.0	44.0	NM_183376	Q6NSI9	Missense_Mutation	SNP	ENST00000268042.6	hg19	CCDS10377.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.263852	0.80358	.	.	ENSG00000140450	ENST00000538249;ENST00000268042	T;T	0.15718	2.4;2.4	5.22	4.29	0.51040	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.078649	0.53938	D	0.000041	T	0.28699	0.0711	L	0.43152	1.355	0.58432	D	0.999998	D;D	0.60160	0.987;0.984	P;P	0.59115	0.852;0.656	T	0.01074	-1.1460	10	0.72032	D	0.01	-25.6166	13.5324	0.61629	0.0:0.9242:0.0:0.0758	.	292;205	Q8NCT1;F5H824	ARRD4_HUMAN;.	Y	205;292	ENSP00000443774:S205Y;ENSP00000268042:S292Y	ENSP00000268042:S292Y	S	+	2	0	ARRDC4	96313606	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.666000	0.68059	2.597000	0.87782	0.591000	0.81541	TCC	.	.		0.393	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376	
TP53	7157	hgsc.bcm.edu	37	17	7578275	7578275	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:7578275G>A	ENST00000269305.4	-	6	763	c.574C>T	c.(574-576)Cag>Tag	p.Q192*	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q192*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q192*	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	192	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> L (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; 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.Q192*(83)|p.0?(8)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191del(4)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(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)	ATAAGATGCTGAGGAGGGGCC	0.557		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.Q192X	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_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	144	Substitution - Nonsense(95)|Deletion - In frame(19)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(6)|Unknown(6)|Insertion - Frameshift(1)|Complex - frameshift(1)|Substitution - Missense(1)	breast(26)|ovary(20)|urinary_tract(15)|lung(12)|upper_aerodigestive_tract(10)|skin(8)|biliary_tract(7)|oesophagus(7)|large_intestine(6)|kidney(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)	c.C574T						.						89.0	80.0	83.0					17																	7578275		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	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;	GATGCTGAGGAGG	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.574C>T	chr17.hg19:g.7578275G>A	ENSP00000269305:p.Gln192*	153.0	0.0		87.0	64.0	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	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269040	0.40095	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	3.36	0.38483	.	0.242461	0.43260	D	0.000594	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.6404	8.6971	0.34303	0.0:0.1484:0.545:0.3066	.	.	.	.	X	192;192;192;192;192;192;181;99;60;99;60	.	ENSP00000269305:Q192X	Q	-	1	0	TP53	7519000	1.000000	0.71417	0.987000	0.45799	0.035000	0.12851	2.163000	0.42377	0.732000	0.32470	0.655000	0.94253	CAG	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
RARA	5914	hgsc.bcm.edu	37	17	38508601	38508601	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:38508601C>A	ENST00000254066.5	+	6	1104	c.649C>A	c.(649-651)Cgt>Agt	p.R217S	RARA_ENST00000394089.2_Missense_Mutation_p.R217S|RARA_ENST00000394086.3_Missense_Mutation_p.R233S|RARA_ENST00000394081.3_Missense_Mutation_p.R212S|RARA_ENST00000425707.3_Missense_Mutation_p.R120S|RARA_ENST00000420042.1_3'UTR	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	217	Ligand-binding.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CTCAGAACAACGTGTCTCTCT	0.582			T	"""PML, ZNF145, TIF1, NUMA1, NPM1"""	APL																																p.R217S		Atlas-SNP	.		Dom	yes		17	17q12	5914	"""retinoic acid receptor, alpha"""		L	.	RARA	52	.	0			c.C649A						.						171.0	147.0	155.0					17																	38508601		2203	4300	6503	SO:0001583	missense	5914	exon6			GAACAACGTGTCT	X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"""Nuclear hormone receptors"""	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.649C>A	chr17.hg19:g.38508601C>A	ENSP00000254066:p.Arg217Ser	59.0	0.0		50.0	12.0	NM_000964	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Missense_Mutation	SNP	ENST00000254066.5	hg19	CCDS11366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.396|8.396	0.840786|0.840786	0.16891|0.16891	.|.	.|.	ENSG00000131759|ENSG00000131759	ENST00000319149|ENST00000254066;ENST00000425707;ENST00000394089;ENST00000394086;ENST00000394081;ENST00000420042	.|T;D;T;T;T	.|0.92699	.|1.48;-3.09;1.48;1.48;1.48	4.34|4.34	4.34|4.34	0.51931|0.51931	.|Nuclear hormone receptor, ligand-binding (2);	0.378221|.	0.27595|.	N|.	0.018673|.	D|D	0.93416|0.93416	0.7900|0.7900	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D;P;D	.|0.89917	.|1.0;0.513;1.0	.|D;B;D	.|0.91635	.|0.997;0.284;0.999	D|D	0.93060|0.93060	0.6473|0.6473	7|9	0.22109|0.40728	T|T	0.4|0.16	.|.	15.7766|15.7766	0.78224|0.78224	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|120;212;217	.|B8Y636;F1D8N9;P10276	.|.;.;RARA_HUMAN	K|S	210|217;120;217;233;212;104	.|ENSP00000254066:R217S;ENSP00000389993:R120S;ENSP00000377649:R217S;ENSP00000377648:R233S;ENSP00000377643:R212S	ENSP00000316769:N210K|ENSP00000254066:R217S	N|R	+|+	3|1	2|0	RARA|RARA	35762127|35762127	1.000000|1.000000	0.71417|0.71417	0.260000|0.260000	0.24451|0.24451	0.018000|0.018000	0.09664|0.09664	5.906000|5.906000	0.69900|0.69900	2.219000|2.219000	0.72066|0.72066	0.460000|0.460000	0.39030|0.39030	AAC|CGT	.	.		0.582	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2		
KRT13	3860	hgsc.bcm.edu	37	17	39659035	39659036	+	Missense_Mutation	DNP	GG	GG	TT			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:39659035_39659036GG>TT	ENST00000246635.3	-	5	972_973	c.926_927CC>AA	c.(925-927)aCC>aAA	p.T309K	KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Missense_Mutation_p.T309K|KRT13_ENST00000587544.1_Missense_Mutation_p.T309K	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	309	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.T309T(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				TGGCAGTGTTGGTAGACACCTC	0.569																																					p.T309T|p.T309N		Atlas-SNP	.											KRT13,bladder,carcinoma,0,1|.	KRT13	72	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.C927A|c.C926A						.																																			SO:0001583	missense	3860	exon5			AGTGTTGGTAGAC|GTGTTGGTAGACA		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.926_927delinsTT	chr17.hg19:g.39659035_39659036delinsTT	ENSP00000246635:p.Thr309Lys	52.0	0.0		68.0	26.0|27.0	NM_002274	Q53G54|Q6AZK5|Q8N240	Silent|Missense_Mutation	SNP	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.		0.569	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490	
SOX9	6662	hgsc.bcm.edu	37	17	70117638	70117638	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:70117638C>T	ENST00000245479.2	+	1	478	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	36					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CTCGCCCTGCCCGTCGGGCTC	0.672																																					p.P36S	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.C106T						.						13.0	14.0	14.0					17																	70117638		2196	4288	6484	SO:0001583	missense	6662	exon1			CCCTGCCCGTCGG	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.106C>T	chr17.hg19:g.70117638C>T	ENSP00000245479:p.Pro36Ser	244.0	0.0		272.0	111.0	NM_000346	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	hg19	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026531	0.75390	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	T	0.75050	-0.9	4.39	4.39	0.52855	.	0.120496	0.56097	U	0.000025	D	0.85504	0.5712	M	0.77406	2.37	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84697	0.0726	10	0.29301	T	0.29	.	16.9671	0.86288	0.0:1.0:0.0:0.0	.	36	P48436	SOX9_HUMAN	S	36	ENSP00000245479:P36S	ENSP00000245479:P36S	P	+	1	0	SOX9	67629233	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	4.489000	0.60309	1.997000	0.58415	0.491000	0.48974	CCG	.	.		0.672	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346	
CBX4	8535	hgsc.bcm.edu	37	17	77808306	77808306	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:77808306G>A	ENST00000269397.4	-	5	1312	c.1135C>T	c.(1135-1137)Ccg>Tcg	p.P379S		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	379	His-rich.|Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			tgTGAGGGCGGGTGCGTGTTC	0.697																																					p.P379S		Atlas-SNP	.											.	CBX4	40	.	0			c.C1135T						.						11.0	13.0	12.0					17																	77808306		2190	4282	6472	SO:0001583	missense	8535	exon5			AGGGCGGGTGCGT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1135C>T	chr17.hg19:g.77808306G>A	ENSP00000269397:p.Pro379Ser	44.0	0.0		51.0	17.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	g	1.031	-0.681816	0.03353	.	.	ENSG00000141582	ENST00000269397	.	.	.	3.67	2.66	0.31614	.	555.879000	0.00166	N	0.000003	T	0.50017	0.1591	L	0.48642	1.525	0.80722	D	1	B	0.26935	0.164	B	0.19946	0.027	T	0.28933	-1.0028	9	0.09338	T	0.73	.	8.8709	0.35316	0.0:0.2315:0.7685:0.0	.	379	O00257	CBX4_HUMAN	S	379	.	ENSP00000269397:P379S	P	-	1	0	CBX4	75422901	0.902000	0.30710	0.020000	0.16555	0.022000	0.10575	1.431000	0.34925	0.487000	0.27698	0.306000	0.20318	CCG	.	.		0.697	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29488760	29488760	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr18:29488760A>G	ENST00000283351.4	-	7	1414	c.1079T>C	c.(1078-1080)cTt>cCt	p.L360P	TRAPPC8_ENST00000582513.1_Missense_Mutation_p.L360P|TRAPPC8_ENST00000582539.1_Missense_Mutation_p.L306P	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	360					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						ATGTGGCAAAAGGCCCCGAAA	0.294																																					p.L360P		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.T1079C						.						57.0	53.0	54.0					18																	29488760		2203	4300	6503	SO:0001583	missense	22878	exon7			GGCAAAAGGCCCC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1079T>C	chr18.hg19:g.29488760A>G	ENSP00000283351:p.Leu360Pro	82.0	0.0		86.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317904	0.40996	.	.	ENSG00000153339	ENST00000283351	T	0.26810	1.71	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000001	T	0.56761	0.2007	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.64063	-0.6495	10	0.87932	D	0	.	15.97	0.80008	1.0:0.0:0.0:0.0	.	360;360	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	P	360	ENSP00000283351:L360P	ENSP00000283351:L360P	L	-	2	0	TRAPPC8	27742758	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.615000	0.90920	2.181000	0.69327	0.459000	0.35465	CTT	.	.		0.294	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
SALL3	27164	hgsc.bcm.edu	37	18	76755362	76755362	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr18:76755362C>A	ENST00000537592.2	+	2	3371	c.3371C>A	c.(3370-3372)tCg>tAg	p.S1124*	SALL3_ENST00000536229.3_Nonsense_Mutation_p.S919*|SALL3_ENST00000575389.2_Nonsense_Mutation_p.S1052*	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1124					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ACCTTCTCCTCGGCCAGCGCC	0.692																																					p.S1124X		Atlas-SNP	.											SALL3,colon,carcinoma,0,1	SALL3	162	.	0			c.C3371A						.						10.0	10.0	10.0					18																	76755362		2159	4238	6397	SO:0001587	stop_gained	27164	exon2			TCTCCTCGGCCAG	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3371C>A	chr18.hg19:g.76755362C>A	ENSP00000441823:p.Ser1124*	23.0	0.0		28.0	10.0	NM_171999	Q9UGH1	Nonsense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.679248	0.96774	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	.	.	.	5.35	3.56	0.40772	.	0.137147	0.33057	N	0.005322	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.8292	10.9437	0.47289	0.0:0.7997:0.1301:0.0701	.	.	.	.	X	1124;1052;784	.	ENSP00000299466:S1124X	S	+	2	0	SALL3	74856350	1.000000	0.71417	0.811000	0.32455	0.912000	0.54170	5.990000	0.70595	0.628000	0.30357	0.655000	0.94253	TCG	.	.		0.692	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
ZNF208	7757	hgsc.bcm.edu	37	19	22154761	22154761	+	Silent	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:22154761T>C	ENST00000397126.4	-	4	3223	c.3075A>G	c.(3073-3075)ggA>ggG	p.G1025G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1025					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGGGTGTCTCTCCAGTGTGAA	0.413																																					p.G1025G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A3075G						.						98.0	106.0	103.0					19																	22154761		2135	4254	6389	SO:0001819	synonymous_variant	7757	exon4			TGTCTCTCCAGTG	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.3075A>G	chr19.hg19:g.22154761T>C		138.0	0.0		292.0	46.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.413	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
SIX5	147912	hgsc.bcm.edu	37	19	46268971	46268972	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:46268971_46268972CC>AA	ENST00000317578.6	-	3	2388_2389	c.2007_2008GG>TT	c.(2005-2010)ctGGaa>ctTTaa	p.E670*	AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	670					lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		GCGCTTAGTTCCAGCCCTGCTG	0.688																																					p.E670X|p.L669L		Atlas-SNP	.											.	SIX5	35	.	0			c.G2008T|c.G2007T						.																																			SO:0001587	stop_gained	147912	exon3			TTAGTTCCAGCCC|TAGTTCCAGCCCT	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.2007_2008delinsAA	chr19.hg19:g.46268971_46268972delinsAA	ENSP00000316842:p.Glu670*	56.0	0.0		112.0|111.0	79.0|78.0	NM_175875		Nonsense_Mutation|Silent	SNP	ENST00000317578.6	hg19	CCDS12673.1																																																																																			.	.		0.688	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
SEL1L2	80343	hgsc.bcm.edu	37	20	13912332	13912332	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:13912332A>G	ENST00000284951.5	-	3	274	c.200T>C	c.(199-201)cTc>cCc	p.L67P	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.L67P			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	67						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TTTCTCCAGGAGATTTTCTCT	0.259																																					p.L67P		Atlas-SNP	.											.	SEL1L2	103	.	0			c.T200C						.						69.0	61.0	64.0					20																	13912332		1779	4041	5820	SO:0001583	missense	80343	exon3			TCCAGGAGATTTT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.200T>C	chr20.hg19:g.13912332A>G	ENSP00000284951:p.Leu67Pro	84.0	0.0		99.0	48.0	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	hg19		.	.	.	.	.	.	.	.	.	.	A	6.378	0.437767	0.12104	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23348	1.91;2.23	5.34	1.35	0.21983	.	1.324090	0.05221	N	0.508542	T	0.12774	0.0310	N	0.08118	0	0.25756	N	0.985008	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26677	-1.0096	10	0.31617	T	0.26	2.4044	3.8076	0.08783	0.513:0.2536:0.2334:0.0	.	67;67	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	P	67	ENSP00000367312:L67P;ENSP00000284951:L67P	ENSP00000284951:L67P	L	-	2	0	SEL1L2	13860332	0.981000	0.34729	0.403000	0.26384	0.602000	0.36980	0.953000	0.29162	0.420000	0.25954	0.533000	0.62120	CTC	.	.		0.259	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
ZFP64	55734	hgsc.bcm.edu	37	20	50781292	50781292	+	Silent	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:50781292G>A	ENST00000216923.4	-	4	802	c.453C>T	c.(451-453)tgC>tgT	p.C151C	ZFP64_ENST00000346617.4_Silent_p.C97C|ZFP64_ENST00000477786.1_5'UTR|ZFP64_ENST00000361387.2_Silent_p.C151C|ZFP64_ENST00000371518.2_Silent_p.C151C|ZFP64_ENST00000371515.4_Silent_p.C149C	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TCTTGAATTGGCAACCTAAAA	0.378																																					p.C151C		Atlas-SNP	.											.	ZFP64	240	.	0			c.C453T						.						87.0	81.0	83.0					20																	50781292		2203	4300	6503	SO:0001819	synonymous_variant	55734	exon4			GAATTGGCAACCT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.453C>T	chr20.hg19:g.50781292G>A		39.0	0.0		43.0	15.0	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	hg19	CCDS13440.1																																																																																			.	.		0.378	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
OGFR	11054	hgsc.bcm.edu	37	20	61443981	61443981	+	Silent	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr20:61443981G>T	ENST00000290291.6	+	7	1039	c.1014G>T	c.(1012-1014)ggG>ggT	p.G338G	OGFR_ENST00000370461.1_Silent_p.G286G	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	338					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					GCAAGGGTGGGGGCAGGGTGG	0.721																																					p.G338G		Atlas-SNP	.											.	OGFR	63	.	0			c.G1014T						.						3.0	4.0	4.0					20																	61443981		1956	3966	5922	SO:0001819	synonymous_variant	11054	exon7			GGGTGGGGGCAGG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1014G>T	chr20.hg19:g.61443981G>T		142.0	0.0		110.0	41.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.		0.721	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
BRWD1	54014	hgsc.bcm.edu	37	21	40568678	40568678	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr21:40568678T>C	ENST00000333229.2	-	41	6644	c.6317A>G	c.(6316-6318)aAg>aGg	p.K2106R	BRWD1_ENST00000380800.3_Missense_Mutation_p.K2106R|BRWD1_ENST00000342449.3_Missense_Mutation_p.K2106R	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2106					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AAAAGGAGCCTTTCCATAGGT	0.413																																					p.K2106R	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A6317G						.						174.0	166.0	169.0					21																	40568678		2203	4299	6502	SO:0001583	missense	54014	exon41			GGAGCCTTTCCAT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6317A>G	chr21.hg19:g.40568678T>C	ENSP00000330753:p.Lys2106Arg	58.0	0.0		42.0	11.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.194740	0.58017	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.58797	0.31;0.49;0.43	5.53	4.39	0.52855	.	0.256906	0.34178	N	0.004189	T	0.47911	0.1471	L	0.46885	1.475	0.80722	D	1	B;B	0.19583	0.037;0.022	B;B	0.19148	0.024;0.011	T	0.47686	-0.9098	10	0.44086	T	0.13	-14.0862	9.1127	0.36737	0.0:0.141:0.0:0.859	.	2106;2106	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	R	2106	ENSP00000330753:K2106R;ENSP00000344333:K2106R;ENSP00000370178:K2106R	ENSP00000330753:K2106R	K	-	2	0	BRWD1	39490548	0.471000	0.25862	1.000000	0.80357	0.995000	0.86356	1.058000	0.30504	2.100000	0.63781	0.533000	0.62120	AAG	.	.		0.413	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
SLC37A1	54020	hgsc.bcm.edu	37	21	43955639	43955639	+	Missense_Mutation	SNP	A	A	G	rs564499706		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr21:43955639A>G	ENST00000352133.2	+	5	1311	c.329A>G	c.(328-330)tAt>tGt	p.Y110C	SLC37A1_ENST00000398341.3_Missense_Mutation_p.Y110C			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	110					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						CTGTGCGCCTATGCCGTGGGG	0.507													A|||	1	0.000199681	0.0	0.0	5008	,	,		20100	0.0		0.001	False		,,,				2504	0.0				p.Y110C		Atlas-SNP	.											.	SLC37A1	48	.	0			c.A329G						.						174.0	167.0	169.0					21																	43955639		2203	4300	6503	SO:0001583	missense	54020	exon6			GCGCCTATGCCGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.329A>G	chr21.hg19:g.43955639A>G	ENSP00000344648:p.Tyr110Cys	93.0	0.0		69.0	29.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.087246	0.55968	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.61742	0.08;0.08	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.81945	0.4930	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87380	0.2356	10	0.87932	D	0	-15.6574	14.3838	0.66929	1.0:0.0:0.0:0.0	.	110	P57057	GLPT_HUMAN	C	110	ENSP00000381383:Y110C;ENSP00000344648:Y110C	ENSP00000344648:Y110C	Y	+	2	0	SLC37A1	42828708	1.000000	0.71417	0.034000	0.17996	0.341000	0.28922	8.763000	0.91715	1.858000	0.53909	0.460000	0.39030	TAT	.	.		0.507	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
CCDC116	164592	hgsc.bcm.edu	37	22	21989329	21989329	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:21989329G>C	ENST00000292779.3	+	4	1138	c.977G>C	c.(976-978)gGc>gCc	p.G326A	CCDC116_ENST00000607942.1_Missense_Mutation_p.G326A	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	326										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AAGCTCCGTGGCGCCCACTGC	0.662																																					p.G326A		Atlas-SNP	.											.	CCDC116	56	.	0			c.G977C						.						36.0	38.0	37.0					22																	21989329		2203	4300	6503	SO:0001583	missense	164592	exon4			TCCGTGGCGCCCA	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.977G>C	chr22.hg19:g.21989329G>C	ENSP00000292779:p.Gly326Ala	72.0	0.0		70.0	38.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	G	9.629	1.135800	0.21123	.	.	ENSG00000161180	ENST00000292779	T	0.11712	2.75	3.83	-0.833	0.10782	.	1.489690	0.03821	N	0.267551	T	0.09862	0.0242	L	0.39898	1.24	0.09310	N	1	B;B	0.27882	0.093;0.192	B;B	0.27170	0.077;0.029	T	0.37126	-0.9719	10	0.62326	D	0.03	-22.3123	3.5073	0.07695	0.3558:0.197:0.4472:0.0	.	326;326	B7Z7H5;Q8IYX3-2	.;.	A	326	ENSP00000292779:G326A	ENSP00000292779:G326A	G	+	2	0	CCDC116	20319329	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.113000	0.10774	-0.046000	0.13446	0.561000	0.74099	GGC	.	.		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
LARGE	9215	hgsc.bcm.edu	37	22	33733771	33733771	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:33733771G>C	ENST00000354992.2	-	11	1719	c.1148C>G	c.(1147-1149)tCc>tGc	p.S383C	LARGE_ENST00000402320.1_Intron|LARGE_ENST00000437602.2_Missense_Mutation_p.S383C|LARGE_ENST00000452586.2_Missense_Mutation_p.S182C|LARGE_ENST00000397394.2_Missense_Mutation_p.S383C|LARGE_ENST00000337431.2_Intron	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	383					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CTTCTTGGGGGAGTTCCAGTG	0.557																																					p.S383C	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.C1148G						.						62.0	58.0	59.0					22																	33733771		2203	4300	6503	SO:0001583	missense	9215	exon11			TTGGGGGAGTTCC	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1148C>G	chr22.hg19:g.33733771G>C	ENSP00000347088:p.Ser383Cys	155.0	0.0		118.0	50.0	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	hg19	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660247	0.88154	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000445431;ENST00000354992;ENST00000397394;ENST00000452586;ENST00000437602;ENST00000421768	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.80764	0.994;0.985;0.992	T	0.70669	-0.4808	10	0.87932	D	0	-5.7369	18.8007	0.92015	0.0:0.0:1.0:0.0	.	383;182;383	B7Z2I9;E9PH73;O95461	.;.;LARGE_HUMAN	C	60;60;60;383;383;182;383;182	ENSP00000347088:S383C;ENSP00000380549:S383C;ENSP00000407917:S182C;ENSP00000388544:S383C;ENSP00000403841:S182C	ENSP00000347088:S383C	S	-	2	0	LARGE	32063771	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.171000	0.94802	2.437000	0.82529	0.655000	0.94253	TCC	.	.		0.557	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
PRR5	55615	hgsc.bcm.edu	37	22	45132994	45132994	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:45132994C>T	ENST00000336985.6	+	8	1311	c.1034C>T	c.(1033-1035)cCg>cTg	p.P345L	ARHGAP8_ENST00000517296.3_Intron|PRR5-ARHGAP8_ENST00000361473.5_Intron|ARHGAP8_ENST00000389773.5_Intron|PRR5_ENST00000006251.7_Missense_Mutation_p.P336L|PRR5_ENST00000477331.1_3'UTR|PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000403581.1_Missense_Mutation_p.P368L	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	345					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CGCTCCAGCCCGGAGAACCTG	0.667																																					p.P368L		Atlas-SNP	.											.	PRR5	75	.	0			c.C1103T						.						25.0	29.0	28.0					22																	45132994		2203	4296	6499	SO:0001583	missense	55615	exon10			CCAGCCCGGAGAA	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.1034C>T	chr22.hg19:g.45132994C>T	ENSP00000337464:p.Pro345Leu	93.0	0.0		85.0	40.0	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	hg19	CCDS14058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.1|20.1	3.932598|3.932598	0.73442|0.73442	.|.	.|.	ENSG00000186654|ENSG00000186654	ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985|ENST00000455389	T;T;T|.	0.38560|.	1.18;1.13;1.18|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	.|.	.|.	.|.	.|.	T|T	0.74741|0.74741	0.3756|0.3756	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;P;D;P;P|.	0.89917|.	1.0;0.822;1.0;0.696;0.696|.	D;B;D;B;B|.	0.83275|.	0.991;0.171;0.996;0.099;0.099|.	T|T	0.71303|0.71303	-0.4633|-0.4633	8|5	.|.	.|.	.|.	.|.	19.6803|19.6803	0.95960|0.95960	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	309;368;244;345;345|.	B1AHF5;B1AHF6;P85299-2;P85299;A8K699|.	.;.;.;PRR5_HUMAN;.|.	L|W	336;309;368;345|305	ENSP00000006251:P336L;ENSP00000384848:P368L;ENSP00000337464:P345L|.	.|.	P|R	+|+	2|1	0|2	PRR5|PRR5	43511658|43511658	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.491000|0.491000	0.33493|0.33493	5.369000|5.369000	0.66138|0.66138	2.756000|2.756000	0.94617|0.94617	0.561000|0.561000	0.74099|0.74099	CCG|CGG	.	.		0.667	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528	
SHANK3	85358	hgsc.bcm.edu	37	22	51113605	51113605	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr22:51113605G>T	ENST00000414786.2	+	2	420	c.193G>T	c.(193-195)Ggc>Tgc	p.G65C	SHANK3_ENST00000262795.3_Missense_Mutation_p.G65C|SHANK3_ENST00000445220.2_Missense_Mutation_p.G65C			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	65	Intramolecular interaction with the ANK repeats. {ECO:0000250}.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GGGCCGCGCCGGCAAGTTCCT	0.701																																					p.G65C		Atlas-SNP	.											.	SHANK3	96	.	0			c.G193T						.						5.0	6.0	6.0					22																	51113605		1713	3725	5438	SO:0001583	missense	85358	exon2			CGCGCCGGCAAGT	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.193G>T	chr22.hg19:g.51113605G>T	ENSP00000464552:p.Gly65Cys	105.0	0.0		87.0	5.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	20.2	3.944295	0.73672	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.17213	2.29;2.29	3.91	1.58	0.23477	.	.	.	.	.	T	0.37999	0.1024	M	0.79123	2.44	0.30951	N	0.72475	D	0.89917	1.0	D	0.85130	0.997	T	0.34750	-0.9816	9	0.87932	D	0	.	7.2035	0.25895	0.1041:0.1703:0.7256:0.0	.	65	F2Z3L0	.	C	65	ENSP00000442518:G65C;ENSP00000446078:G65C	ENSP00000442518:G65C	G	+	1	0	SHANK3	49460471	1.000000	0.71417	0.994000	0.49952	0.905000	0.53344	5.229000	0.65316	0.620000	0.30215	0.185000	0.17295	GGC	.	.		0.701	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
UBA1	7317	hgsc.bcm.edu	37	X	47065414	47065414	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:47065414A>G	ENST00000335972.6	+	15	1826	c.1643A>G	c.(1642-1644)cAc>cGc	p.H548R	UBA1_ENST00000377269.3_5'Flank|UBA1_ENST00000377351.4_Missense_Mutation_p.H548R|INE1_ENST00000456273.1_RNA|UBA1_ENST00000490869.1_Intron	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	548	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GTGACAAGCCACCAGAACCGT	0.527																																					p.H548R		Atlas-SNP	.											.	UBA1	89	.	0			c.A1643G						.						54.0	39.0	44.0					X																	47065414		2202	4300	6502	SO:0001583	missense	7317	exon15			CAAGCCACCAGAA	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1643A>G	chrX.hg19:g.47065414A>G	ENSP00000338413:p.His548Arg	120.0	0.0		113.0	52.0	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.170785	0.38315	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.44881	0.91;0.91	4.63	4.63	0.57726	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.50701	0.1631	M	0.68728	2.09	0.80722	D	1	P	0.38767	0.646	P	0.49012	0.598	T	0.44498	-0.9324	10	0.21540	T	0.41	-22.4795	12.3933	0.55370	1.0:0.0:0.0:0.0	.	548	P22314	UBA1_HUMAN	R	548	ENSP00000366568:H548R;ENSP00000338413:H548R	ENSP00000338413:H548R	H	+	2	0	UBA1	46950358	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.443000	0.59994	1.630000	0.50440	0.483000	0.47432	CAC	.	.		0.527	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
RBMX2	51634	hgsc.bcm.edu	37	X	129546795	129546795	+	Silent	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:129546795G>T	ENST00000305536.6	+	6	1006	c.942G>T	c.(940-942)tcG>tcT	p.S314S		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	314	Arg-rich.			SSDAHSSWYNGRSEGRSYRSRSRSRDKSHRHKRARRSRERE SSNPSDRWRH -> LQMHILAGIMGVLKGVVIEVEVGAEIN PIGIKGPDAPGRGVLRIPVTVGVTEDFSCTVDLEIIMFFKC SQIQLGGYYFCI (in Ref. 1; AAD34074). {ECO:0000305}.			nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						GGGAGTCTTCGAATCCCAGTG	0.473																																					p.S314S		Atlas-SNP	.											.	RBMX2	46	.	0			c.G942T						.						29.0	30.0	29.0					X																	129546795		1815	4061	5876	SO:0001819	synonymous_variant	51634	exon6			GTCTTCGAATCCC	AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"""RNA binding motif (RRM) containing"""	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.942G>T	chrX.hg19:g.129546795G>T		124.0	0.0		121.0	5.0	NM_016024	A8K9Z0|Q5JY82|Q9Y3I8	Silent	SNP	ENST00000305536.6	hg19	CCDS43993.1																																																																																			.	.		0.473	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024	
MAGEC3	139081	hgsc.bcm.edu	37	X	140984732	140984732	+	Silent	SNP	C	C	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:140984732C>A	ENST00000298296.1	+	7	1188	c.1188C>A	c.(1186-1188)ccC>ccA	p.P396P	MAGEC3_ENST00000443323.2_Silent_p.P18P|MAGEC3_ENST00000544766.1_Silent_p.P98P|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000409007.1_Silent_p.P98P|MAGEC3_ENST00000536088.1_Silent_p.P98P	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	396	Pro-rich.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					AGATtcctccccagggtcctc	0.577																																					p.P396P		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C1188A						.						34.0	31.0	32.0					X																	140984732		2189	4271	6460	SO:0001819	synonymous_variant	139081	exon7			TCCTCCCCAGGGT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1188C>A	chrX.hg19:g.140984732C>A		48.0	0.0		44.0	39.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.577	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
MAGEC1	9947	hgsc.bcm.edu	37	X	140994996	140994996	+	Silent	SNP	G	G	T			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrX:140994996G>T	ENST00000285879.4	+	4	2092	c.1806G>T	c.(1804-1806)ggG>ggT	p.G602G	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	602										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTCCTCAGGGGGAGGACTCCA	0.582										HNSCC(15;0.026)																											p.G602G		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G1806T						.						205.0	219.0	214.0					X																	140994996		2203	4300	6503	SO:0001819	synonymous_variant	9947	exon4			TCAGGGGGAGGAC	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1806G>T	chrX.hg19:g.140994996G>T		100.0	0.0		102.0	39.0	NM_005462	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	hg19	CCDS35417.1																																																																																			.	.		0.582	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
MT-ND5	4540	hgsc.bcm.edu	37	M	13633	13633	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chrM:13633G>A	ENST00000361567.2	+	1	1297	c.1297G>A	c.(1297-1299)Ggt>Agt	p.G433S	MT-TP_ENST00000387461.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	433					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCACCCTAACAGGTCAACCTC	0.478																																					p.G433S		Atlas-SNP	.											.	.	.	.	0			c.G1297A						.																																			SO:0001583	missense	0	exon1			CTAACAGGTCAAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1297G>A	chrM.hg19:g.13633G>A	ENSP00000354813:p.Gly433Ser	17.0	0.0		30.0	6.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.478	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
SLFN12	55106	hgsc.bcm.edu	37	17	33749492	33749493	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr17:33749492_33749493insA	ENST00000394562.1	-	4	1078_1079	c.555_556insT	c.(553-558)tttgatfs	p.D186fs	SLFN12_ENST00000452764.3_Frame_Shift_Ins_p.D186fs|SLFN12_ENST00000304905.5_Frame_Shift_Ins_p.D186fs|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	186							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCTGTTCTATCAAAAAAAACCC	0.366																																					p.D186_R187delinsX		Atlas-INDEL	.											.,3	SLFN12	56	.	0			c.556_557insT						.			7,4195		1,5,2095						-0.7	0.0			58	10,8220		0,10,4105	no	frameshift	SLFN12	NM_018042.3		1,15,6200	A1A1,A1R,RR		0.1215,0.1666,0.1367				17,12415				SO:0001589	frameshift_variant	55106	exon2			.	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.556dupT	chr17.hg19:g.33749500_33749500dupA	ENSP00000378063:p.Asp186fs	100.0	0.0		101.0	17.0	NM_018042	A8K711|Q9NP47	Frame_Shift_Ins	INS	ENST00000394562.1	hg19	CCDS11295.1																																																																																			.	.		0.366	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
SCP2	6342	hgsc.bcm.edu	37	1	53504627	53504637	+	Frame_Shift_Del	DEL	TGCCTTCAAGG	TGCCTTCAAGG	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	TGCCTTCAAGG	TGCCTTCAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:53504627_53504637delTGCCTTCAAGG	ENST00000528311.1	+	13	1430_1440	c.1134_1144delTGCCTTCAAGG	c.(1132-1146)tttgccttcaaggtgfs	p.AFKV379fs	SCP2_ENST00000488965.1_Intron|SCP2_ENST00000435345.2_Frame_Shift_Del_p.AFKV56fs|SCP2_ENST00000408941.3_Intron|SCP2_ENST00000371509.4_Frame_Shift_Del_p.AFKV416fs|SCP2_ENST00000430330.2_Frame_Shift_Del_p.AFKV53fs|SCP2_ENST00000371514.3_Frame_Shift_Del_p.AFKV460fs|SCP2_ENST00000407246.2_Frame_Shift_Del_p.AFKV436fs	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	1252					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						GTGGTATTTTTGCCTTCAAGGTGAAAGATGG	0.455																																					p.459_462del		Atlas-INDEL	.											.	SCP2	44	.	0			c.1376_1386del						.																																			SO:0001589	frameshift_variant	6342	exon14			.	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.1134_1144delTGCCTTCAAGG	chr1.hg19:g.53504627_53504637delTGCCTTCAAGG	ENSP00000434132:p.Ala379fs	141.0	0.0		128.0	14.0	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Del	DEL	ENST00000528311.1	hg19	CCDS53319.1																																																																																			.	.		0.455	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979	
ARID1A	8289	hgsc.bcm.edu	37	1	27023218	27023222	+	Frame_Shift_Del	DEL	CCCTA	CCCTA	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	CCCTA	CCCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr1:27023218_27023222delCCCTA	ENST00000324856.7	+	1	695_699	c.324_328delCCCTA	c.(322-330)ggccctaggfs	p.PR109fs	RP5-968P14.2_ENST00000569378.1_RNA|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.PR109fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	109					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.A107fs*4(1)|p.N106fs*4(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGAACGCGGGCCCTAGGCCCGCCCT	0.771			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.108_109del		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	2	Deletion - Frameshift(2)	liver(2)	c.323_327del						.																																			SO:0001589	frameshift_variant	8289	exon1			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.324_328delCCCTA	chr1.hg19:g.27023218_27023222delCCCTA	ENSP00000320485:p.Pro109fs	29.0	0.0		18.0	11.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.771	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
NCBP1	4686	hgsc.bcm.edu	37	9	100423350	100423375	+	Splice_Site	DEL	GGTAAGTGGAATTCAGTATTTCTTAA	GGTAAGTGGAATTCAGTATTTCTTAA	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GGTAAGTGGAATTCAGTATTTCTTAA	GGTAAGTGGAATTCAGTATTTCTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:100423350_100423375delGGTAAGTGGAATTCAGTATTTCTTAA	ENST00000375147.3	+	16	1856	c.1600delGGTAAGTGGAATTCAGTATTTCTTAA	c.(1600-1602)ggt>gt	p.G534fs		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	534					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TGATGACGACGGTAAGTGGAATTCAGTATTTCTTAAGTGGAACTAT	0.376																																					p.533_534del	Ovarian(36;879 898 2893 44212 50307)	Atlas-INDEL	.											.	NCBP1	64	.	0			c.1599_1600del						.																																			SO:0001630	splice_region_variant	4686	exon16			.	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"""nuclear cap binding protein subunit 1, 80kD"""	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1600+1GGTAAGTGGAATTCAGTATTTCTTAA>-	chr9.hg19:g.100423350_100423375delGGTAAGTGGAATTCAGTATTTCTTAA		40.0	0.0		41.0	11.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Frame_Shift_Del	DEL	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.376	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486	Frame_Shift_Del
CEP164	22897	hgsc.bcm.edu	37	11	117251354	117251359	+	In_Frame_Del	DEL	GACAAG	GACAAG	-	rs144135343		TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GACAAG	GACAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:117251354_117251359delGACAAG	ENST00000278935.3	+	12	1489_1494	c.1342_1347delGACAAG	c.(1342-1347)gacaagdel	p.DK448del	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	448					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GGGAATAGAAGACAAGGATGACAGCC	0.549																																					p.447_449del		Atlas-INDEL	.											.	CEP164	121	.	0			c.1341_1346del						.																																			SO:0001651	inframe_deletion	22897	exon11			.	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.1342_1347delGACAAG	chr11.hg19:g.117251354_117251359delGACAAG	ENSP00000278935:p.Asp448_Lys449del	68.0	0.0		54.0	19.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	In_Frame_Del	DEL	ENST00000278935.3	hg19	CCDS31683.1																																																																																			.	.		0.549	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151161379	151161380	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:151161379_151161380delAA	ENST00000358517.2	+	16	3716_3717	c.3505_3506delAA	c.(3505-3507)aaafs	p.K1169fs	PLEKHG1_ENST00000367328.1_Frame_Shift_Del_p.K1169fs			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1169							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTTGGGTCGGAAAGGGATCAGC	0.495																																					p.1168_1169del		Atlas-INDEL	.											.	PLEKHG1	97	.	0			c.3504_3505del						.																																			SO:0001589	frameshift_variant	57480	exon17			.	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3505_3506delAA	chr6.hg19:g.151161379_151161380delAA	ENSP00000351318:p.Lys1169fs	83.0	0.0		77.0	28.0	NM_001029884	Q5T1F2	Frame_Shift_Del	DEL	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.495	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
PTPMT1	114971	hgsc.bcm.edu	37	11	47591365	47591365	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr11:47591365delG	ENST00000326674.9	+	3	391	c.369delG	c.(367-369)tcgfs	p.S123fs	PTPMT1_ENST00000426530.2_Intron|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000534775.1_Frame_Shift_Del_p.A160fs|PTPMT1_ENST00000326656.8_Intron|NDUFS3_ENST00000533507.1_Intron	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	123	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						AGTACCAGTCGCTGGGCCAGT	0.547																																					p.S123fs		Atlas-INDEL	.											.	PTPMT1	17	.	0			c.368delC						.						110.0	112.0	112.0					11																	47591365		2013	4163	6176	SO:0001589	frameshift_variant	114971	exon3			.	BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.369delG	chr11.hg19:g.47591365delG	ENSP00000325958:p.Ser123fs	86.0	0.0		89.0	33.0	NM_175732	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Frame_Shift_Del	DEL	ENST00000326674.9	hg19	CCDS41643.1																																																																																			.	.		0.547	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879	
COL11A2	1302	hgsc.bcm.edu	37	6	33135050	33135051	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr6:33135050_33135051insG	ENST00000374708.4	-	55	4166_4167	c.3908_3909insC	c.(3907-3909)ccafs	p.P1303fs	COL11A2_ENST00000357486.1_Frame_Shift_Ins_p.P1368fs|COL11A2_ENST00000374714.1_Frame_Shift_Ins_p.P1363fs|COL11A2_ENST00000395197.1_Frame_Shift_Ins_p.P1329fs|COL11A2_ENST00000341947.2_Frame_Shift_Ins_p.P1389fs|COL11A2_ENST00000374712.1_Frame_Shift_Ins_p.P1308fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Frame_Shift_Ins_p.P1342fs|COL11A2_ENST00000361917.1_Frame_Shift_Ins_p.P1282fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1389	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCACAGGACCTGGGGGCCCAGC	0.649																																					p.P1389fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.4167_4168insC						.																																			SO:0001589	frameshift_variant	1302	exon57			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3909dupC	chr6.hg19:g.33135055_33135055dupG	ENSP00000363840:p.Pro1303fs	119.0	0.0		122.0	50.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Ins	INS	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.649	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
ZNF317	57693	hgsc.bcm.edu	37	19	9271261	9271281	+	In_Frame_Del	DEL	GCTTACGGCCGGAGCTGCCAC	GCTTACGGCCGGAGCTGCCAC	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	GCTTACGGCCGGAGCTGCCAC	GCTTACGGCCGGAGCTGCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr19:9271261_9271281delGCTTACGGCCGGAGCTGCCAC	ENST00000247956.6	+	7	1245_1265	c.940_960delGCTTACGGCCGGAGCTGCCAC	c.(940-960)gcttacggccggagctgccacdel	p.AYGRSCH314del	ZNF317_ENST00000360385.3_In_Frame_Del_p.AYGRSCH282del	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R317Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GTGCGGGAAGGCTTACGGCCGGAGCTGCCACCTCATCGCAC	0.579																																					p.313_320del		Atlas-INDEL	.											.	ZNF317	61	.	1	Substitution - Missense(1)	endometrium(1)	c.939_959del						.																																			SO:0001651	inframe_deletion	57693	exon7			.	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"""Zinc fingers, C2H2-type"", ""-"""	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.940_960delGCTTACGGCCGGAGCTGCCAC	chr19.hg19:g.9271261_9271281delGCTTACGGCCGGAGCTGCCAC	ENSP00000247956:p.Ala314_His320del	64.0	0.0		26.0	18.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	In_Frame_Del	DEL	ENST00000247956.6	hg19	CCDS12210.1																																																																																			.	.		0.579	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933	
SHB	6461	hgsc.bcm.edu	37	9	38068423	38068428	+	In_Frame_Del	DEL	TGTCGT	TGTCGT	-			TCGA-DD-AACG-01A-11D-A40R-10	TCGA-DD-AACG-10A-01D-A40U-10	TGTCGT	TGTCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c6ddfbe-37e1-413a-b7f2-03b4ec624939	f02542e5-142c-4397-812e-dc8806103f40	g.chr9:38068423_38068428delTGTCGT	ENST00000377707.3	-	1	780_785	c.215_220delACGACA	c.(214-222)gacgacagc>ggc	p.72_74DDS>G	RP11-613M10.9_ENST00000540557.1_In_Frame_Del_p.72_74DDS>G|SHB_ENST00000377700.4_In_Frame_Del_p.72_74DDS>G	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	72	Mediates interaction with LAT, PTK2/FAK1, JAK1 and JAK3.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		GTGCTGCCGCTGTCGTCGGGCAGCGA	0.728																																					p.72_74del		Atlas-INDEL	.											.	SHB	31	.	0			c.216_221del						.																																			SO:0001651	inframe_deletion	6461	exon1			.		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"""SH2 domain containing"""	10838	protein-coding gene	gene with protein product		600314	"""SHB adaptor protein (a Src homology 2 protein)"", ""SHB (Src homology 2 domain containing) adaptor protein B"""			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.215_220delACGACA	chr9.hg19:g.38068423_38068428delTGTCGT	ENSP00000366936:p.Asp72_Ser74delinsGly	81.0	0.0		72.0	26.0	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	In_Frame_Del	DEL	ENST00000377707.3	hg19	CCDS43806.1																																																																																			.	.		0.728	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1		
