#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
ACAP3	116983	hgsc.bcm.edu	37	1	1231249	1231249	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:1231249T>C	ENST00000354700.5	-	18	1774	c.1572A>G	c.(1570-1572)gcA>gcG	p.A524A	ACAP3_ENST00000379037.2_5'Flank|ACAP3_ENST00000353662.3_Silent_p.A482A	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	524	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						CCAGGGCTGGTGCCATGGGCG	0.657																																					p.A524A		Atlas-SNP	.											.	ACAP3	87	.	0			c.A1572G						.						49.0	61.0	57.0					1																	1231249		2201	4298	6499	SO:0001819	synonymous_variant	116983	exon18			GGCTGGTGCCATG	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16754	protein-coding gene	gene with protein product			"""centaurin, beta 5"""	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.1572A>G	chr1.hg19:g.1231249T>C		110.0	0.0		83.0	4.0	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Silent	SNP	ENST00000354700.5	hg19	CCDS19.2																																																																																			.	.		0.657	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649	
NADK	65220	hgsc.bcm.edu	37	1	1685559	1685559	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:1685559C>A	ENST00000341426.5	-	10	1253	c.1032G>T	c.(1030-1032)atG>atT	p.M344I	NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.M489I|NADK_ENST00000344463.4_Missense_Mutation_p.M489I|NADK_ENST00000342348.5_Missense_Mutation_p.M312I|NADK_ENST00000341991.3_Missense_Mutation_p.M344I	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	344					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TGGGCGTGATCATGATGGCCG	0.662																																					p.M489I		Atlas-SNP	.											.	NADK	79	.	0			c.G1467T						.						52.0	63.0	59.0					1																	1685559		2203	4300	6503	SO:0001583	missense	65220	exon12			CGTGATCATGATG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1032G>T	chr1.hg19:g.1685559C>A	ENSP00000341679:p.Met344Ile	190.0	0.0		117.0	5.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	hg19	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.943976	0.92593	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.27	4.33	0.51752	ATP-NAD kinase, PpnK-type, all-beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.44850	0.1313	N	0.21545	0.675	0.58432	D	0.999995	P;P;P	0.51240	0.86;0.939;0.943	P;P;P	0.57548	0.661;0.771;0.823	T	0.40079	-0.9582	10	0.44086	T	0.13	-56.1128	14.1061	0.65091	0.1517:0.8483:0.0:0.0	.	312;489;344	F5GXR5;Q5QPS4;O95544	.;.;NADK_HUMAN	I	344;344;489;489;312	ENSP00000341679:M344I;ENSP00000344340:M344I;ENSP00000367890:M489I;ENSP00000340925:M489I;ENSP00000339727:M312I	ENSP00000341679:M344I	M	-	3	0	NADK	1675419	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.288000	0.78691	1.309000	0.44985	0.561000	0.74099	ATG	.	.		0.662	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
PANK4	55229	hgsc.bcm.edu	37	1	2451799	2451799	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:2451799T>C	ENST00000378466.3	-	5	673	c.661A>G	c.(661-663)Acc>Gcc	p.T221A	PANK4_ENST00000435556.3_Missense_Mutation_p.T182A|PANK4_ENST00000491212.1_5'Flank	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	221					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCCCAGAAGGTGCCGCCTCCA	0.647																																					p.T221A		Atlas-SNP	.											.	PANK4	64	.	0			c.A661G						.						53.0	52.0	52.0					1																	2451799		2202	4300	6502	SO:0001583	missense	55229	exon5			AGAAGGTGCCGCC	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.661A>G	chr1.hg19:g.2451799T>C	ENSP00000367727:p.Thr221Ala	104.0	0.0		82.0	4.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	hg19	CCDS42.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.687746	0.68157	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.99652	-6.3;-6.3	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	D	0.99405	0.9790	M	0.90198	3.095	0.80722	D	1	P;P	0.45569	0.861;0.861	P;P	0.48840	0.592;0.592	D	0.98376	1.0556	10	0.72032	D	0.01	-33.4976	13.4557	0.61197	0.0:0.0:0.0:1.0	.	182;221	E9PHT6;Q9NVE7	.;PANK4_HUMAN	A	221;182	ENSP00000367727:T221A;ENSP00000421433:T182A	ENSP00000367727:T221A	T	-	1	0	PANK4	2441659	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.595000	0.67563	1.784000	0.52394	0.455000	0.32223	ACC	.	.		0.647	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
TPRG1L	127262	hgsc.bcm.edu	37	1	3544177	3544177	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:3544177C>A	ENST00000378344.2	+	4	655	c.584C>A	c.(583-585)cCg>cAg	p.P195Q	RP11-46F15.2_ENST00000435049.1_RNA|TPRG1L_ENST00000344579.5_Missense_Mutation_p.P136Q	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	195						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		ACAGAACACCCGATGGCTGGC	0.537																																					p.P195Q		Atlas-SNP	.											.	TPRG1L	24	.	0			c.C584A						.						144.0	145.0	145.0					1																	3544177		2203	4300	6503	SO:0001583	missense	127262	exon4			AACACCCGATGGC	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"""family with sequence similarity 79, member A"""	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.584C>A	chr1.hg19:g.3544177C>A	ENSP00000367595:p.Pro195Gln	118.0	0.0		95.0	4.0	NM_182752	A8K1K4|Q8WV04	Missense_Mutation	SNP	ENST00000378344.2	hg19	CCDS47.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343531	0.82022	.	.	ENSG00000158109	ENST00000378344;ENST00000456805;ENST00000344579	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86311	0.1686	9	0.87932	D	0	-0.7616	17.1228	0.86706	0.0:1.0:0.0:0.0	.	136;195	Q5T0D9-2;Q5T0D9	.;TPRGL_HUMAN	Q	195;152;136	.	ENSP00000339714:P136Q	P	+	2	0	TPRG1L	3534037	1.000000	0.71417	0.980000	0.43619	0.972000	0.66771	5.803000	0.69129	2.282000	0.76494	0.563000	0.77884	CCG	.	.		0.537	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752	
H6PD	9563	hgsc.bcm.edu	37	1	9324411	9324411	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:9324411A>G	ENST00000377403.2	+	5	2161	c.1859A>G	c.(1858-1860)gAc>gGc	p.D620G	H6PD_ENST00000602477.1_Missense_Mutation_p.D631G	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	620	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGGCTGGTTGACGAGCGCTGC	0.682																																					p.D620G		Atlas-SNP	.											H6PD,NS,carcinoma,0,1	H6PD	71	.	0			c.A1859G						.						19.0	20.0	20.0					1																	9324411		2193	4287	6480	SO:0001583	missense	9563	exon5			TGGTTGACGAGCG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1859A>G	chr1.hg19:g.9324411A>G	ENSP00000366620:p.Asp620Gly	109.0	2.0		60.0	4.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.149643	0.78001	.	.	ENSG00000049239	ENST00000377403	T	0.73575	-0.76	5.16	5.16	0.70880	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.000000	0.85682	D	0.000000	D	0.91676	0.7369	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94719	0.7899	10	0.87932	D	0	-40.0579	14.1988	0.65688	1.0:0.0:0.0:0.0	.	620	O95479	G6PE_HUMAN	G	620	ENSP00000366620:D620G	ENSP00000366620:D620G	D	+	2	0	H6PD	9246998	1.000000	0.71417	0.894000	0.35097	0.950000	0.60333	8.774000	0.91767	1.961000	0.56991	0.459000	0.35465	GAC	.	.		0.682	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
TMEM201	199953	hgsc.bcm.edu	37	1	9662234	9662234	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:9662234T>C	ENST00000340381.6	+	6	1073	c.1064T>C	c.(1063-1065)cTc>cCc	p.L355P	TMEM201_ENST00000377376.4_Missense_Mutation_p.L355P|TMEM201_ENST00000340305.5_Missense_Mutation_p.L355P	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	355					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CTAGACACGCTCAAGTTCAGC	0.652																																					p.L355P		Atlas-SNP	.											.	TMEM201	63	.	0			c.T1064C						.						44.0	38.0	40.0					1																	9662234		2203	4300	6503	SO:0001583	missense	199953	exon6			ACACGCTCAAGTT		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1064T>C	chr1.hg19:g.9662234T>C	ENSP00000344503:p.Leu355Pro	185.0	0.0		97.0	4.0	NM_001010866	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	t	10.85	1.467908	0.26335	.	.	ENSG00000188807	ENST00000377376;ENST00000340305;ENST00000340381	.	.	.	4.65	3.52	0.40303	.	0.414815	0.22632	N	0.057562	T	0.31857	0.0810	L	0.27053	0.805	0.46028	D	0.998826	B;P	0.42123	0.005;0.771	B;B	0.39840	0.017;0.311	T	0.07481	-1.0770	9	0.56958	D	0.05	-21.7504	5.9072	0.19008	0.0:0.2218:0.0:0.7782	.	355;355	E9PBR6;Q5SNT2-2	.;.	P	355	.	ENSP00000344772:L355P	L	+	2	0	TMEM201	9584821	0.991000	0.36638	0.926000	0.36857	0.719000	0.41307	2.453000	0.44970	0.658000	0.30925	0.375000	0.23000	CTC	.	.		0.652	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866	
MTOR	2475	hgsc.bcm.edu	37	1	11186822	11186822	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:11186822G>A	ENST00000361445.4	-	46	6459	c.6383C>T	c.(6382-6384)cCa>cTa	p.P2128L	MTOR_ENST00000376838.1_Missense_Mutation_p.P333L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2128	Sufficient for interaction with the FKBP1A/rapamycin complex. {ECO:0000250}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CAGAAGTTTTGGGGAAACATA	0.428																																					p.P2128L		Atlas-SNP	.											.	MTOR	327	.	0			c.C6383T						.						107.0	105.0	106.0					1																	11186822		2203	4300	6503	SO:0001583	missense	2475	exon46			AGTTTTGGGGAAA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6383C>T	chr1.hg19:g.11186822G>A	ENSP00000354558:p.Pro2128Leu	125.0	0.0		93.0	4.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086473	0.94100	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.80909	-1.43;-1.43	5.4	5.4	0.78164	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93115	0.7808	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94890	0.8047	10	0.87932	D	0	-19.6508	19.196	0.93689	0.0:0.0:1.0:0.0	.	2128	P42345	MTOR_HUMAN	L	2128;333	ENSP00000354558:P2128L;ENSP00000366034:P333L	ENSP00000354558:P2128L	P	-	2	0	MTOR	11109409	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.434000	0.97515	2.531000	0.85337	0.650000	0.86243	CCA	.	.		0.428	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
VPS13D	55187	hgsc.bcm.edu	37	1	12516140	12516140	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:12516140C>A	ENST00000358136.3	+	66	12550	c.12420C>A	c.(12418-12420)gcC>gcA	p.A4140A	VPS13D_ENST00000356315.4_Silent_p.A4115A|VPS13D_ENST00000496628.1_Intron|VPS13D_ENST00000543766.1_Silent_p.A138A	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ACCATGCAGCCACAAGTGGTG	0.527																																					p.A4140A		Atlas-SNP	.											.	VPS13D	316	.	0			c.C12420A						.						112.0	83.0	93.0					1																	12516140		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon66			TGCAGCCACAAGT	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.12420C>A	chr1.hg19:g.12516140C>A		84.0	0.0		62.0	4.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	9.015	0.983490	0.18889	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.84	0.112	0.14623	.	.	.	.	.	T	0.42268	0.1195	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21245	-1.0251	4	.	.	.	.	2.0973	0.03671	0.3234:0.3773:0.0836:0.2157	.	.	.	.	Q	2962	.	.	P	+	2	0	VPS13D	12438727	1.000000	0.71417	0.932000	0.37286	0.788000	0.44548	1.310000	0.33551	-0.099000	0.12263	-0.813000	0.03139	CCA	.	.		0.527	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
CROCC	9696	hgsc.bcm.edu	37	1	17265407	17265407	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:17265407G>A	ENST00000375541.5	+	12	1447	c.1378G>A	c.(1378-1380)Gtc>Atc	p.V460I	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCCTCAGGCCGTCTTGTCAGA	0.687																																					p.V460I		Atlas-SNP	.											.	CROCC	185	.	0			c.G1378A						.						29.0	28.0	29.0					1																	17265407		2200	4293	6493	SO:0001583	missense	9696	exon12			CAGGCCGTCTTGT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1378G>A	chr1.hg19:g.17265407G>A	ENSP00000364691:p.Val460Ile	129.0	0.0		80.0	4.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955289	0.34471	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.14640	2.49	5.39	5.39	0.77823	.	.	.	.	.	T	0.15998	0.0385	L	0.38838	1.175	0.35922	D	0.831901	P;D;P	0.58620	0.839;0.983;0.939	B;P;B	0.44696	0.186;0.458;0.357	T	0.05666	-1.0871	9	0.39692	T	0.17	.	18.0808	0.89440	0.0:0.0:1.0:0.0	.	323;323;460	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	I	460;341	ENSP00000364691:V460I	ENSP00000364691:V460I	V	+	1	0	CROCC	17137994	1.000000	0.71417	0.845000	0.33349	0.037000	0.13140	6.294000	0.72738	2.702000	0.92279	0.561000	0.74099	GTC	.	.		0.687	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
PADI4	23569	hgsc.bcm.edu	37	1	17674451	17674451	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:17674451G>T	ENST00000375448.4	+	10	1089	c.1063G>T	c.(1063-1065)Ggc>Tgc	p.G355C	PADI4_ENST00000487048.1_3'UTR|AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	355					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	AATGGAGATCGGCTACATCCA	0.587																																					p.G355C		Atlas-SNP	.											.	PADI4	70	.	0			c.G1063T						.						108.0	91.0	97.0					1																	17674451		2203	4300	6503	SO:0001583	missense	23569	exon10			GAGATCGGCTACA	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1063G>T	chr1.hg19:g.17674451G>T	ENSP00000364597:p.Gly355Cys	119.0	0.0		65.0	4.0	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	-	20.7	4.033983	0.75504	.	.	ENSG00000159339	ENST00000375448	T	0.39787	1.06	5.47	5.47	0.80525	Protein-arginine deiminase, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.67163	0.2864	M	0.83692	2.655	0.44539	D	0.997494	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67647	-0.5617	10	0.39692	T	0.17	-37.6537	16.1026	0.81194	0.0:0.0:1.0:0.0	.	355;355	A8K392;Q9UM07	.;PADI4_HUMAN	C	355	ENSP00000364597:G355C	ENSP00000364597:G355C	G	+	1	0	PADI4	17547038	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	8.773000	0.91762	2.582000	0.87167	0.518000	0.50308	GGC	.	.		0.587	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807714	18807714	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:18807714C>T	ENST00000400664.1	+	1	291	c.239C>T	c.(238-240)cCa>cTa	p.P80L		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	80						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGAGGGGGCCAAGACGTCGG	0.647																																					p.P80L		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C239T						.						18.0	21.0	20.0					1																	18807714		1994	4158	6152	SO:0001583	missense	127707	exon1			GGGGGCCAAGACG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.239C>T	chr1.hg19:g.18807714C>T	ENSP00000383505:p.Pro80Leu	125.0	0.0		97.0	4.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	C	2.644	-0.283498	0.05642	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.69685	-0.42	5.63	-4.18	0.03846	.	.	.	.	.	T	0.39572	0.1083	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.19778	-1.0295	9	0.27082	T	0.32	.	8.0909	0.30801	0.0:0.3593:0.1094:0.5313	.	80	Q5VTJ3	KLD7A_HUMAN	L	80;17	ENSP00000383505:P80L	ENSP00000383505:P80L	P	+	2	0	KLHDC7A	18680301	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-1.542000	0.02196	-0.764000	0.04651	0.591000	0.81541	CCA	.	.		0.647	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
UBR4	23352	hgsc.bcm.edu	37	1	19407897	19407897	+	Missense_Mutation	SNP	C	C	T	rs372882903		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19407897C>T	ENST00000375254.3	-	103	15206	c.15179G>A	c.(15178-15180)cGg>cAg	p.R5060Q	UBR4_ENST00000375225.3_Missense_Mutation_p.R135Q|AL137127.1_ENST00000582644.1_RNA|UBR4_ENST00000375217.2_Missense_Mutation_p.R5053Q|UBR4_ENST00000375226.2_Missense_Mutation_p.R5036Q|UBR4_ENST00000375267.2_Missense_Mutation_p.R5060Q|UBR4_ENST00000375224.1_Missense_Mutation_p.R767Q|UBR4_ENST00000543981.1_Missense_Mutation_p.R724Q|UBR4_ENST00000429347.2_Missense_Mutation_p.R583Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5060					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAACAGCCTCCGCAAGATTTC	0.587																																					p.R5060Q		Atlas-SNP	.											.	UBR4	415	.	0			c.G15179A						.	C	GLN/ARG	0,4406		0,0,2203	99.0	104.0	103.0		15179	2.5	1.0	1		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	UBR4	NM_020765.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	5060/5184	19407897	1,13005	2203	4300	6503	SO:0001583	missense	23352	exon103			AGCCTCCGCAAGA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.15179G>A	chr1.hg19:g.19407897C>T	ENSP00000364403:p.Arg5060Gln	93.0	0.0		103.0	11.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.255837	0.80135	0.0	1.16E-4	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375225;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.69	2.48	0.30137	.	0.060957	0.64402	N	0.000002	T	0.19446	0.0467	L	0.27053	0.805	0.50313	D	0.999865	B;B;B;B	0.15719	0.001;0.001;0.014;0.003	B;B;B;B	0.08055	0.002;0.002;0.002;0.003	T	0.05419	-1.0886	10	0.25106	T	0.35	.	10.6625	0.45710	0.0:0.744:0.0:0.256	.	724;583;5060;5036	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	Q	5060;5060;5053;5036;135;767;583;724	ENSP00000364403:R5060Q;ENSP00000364416:R5060Q;ENSP00000364365:R5053Q;ENSP00000364374:R5036Q;ENSP00000364373:R135Q;ENSP00000364372:R767Q;ENSP00000394173:R583Q;ENSP00000444070:R724Q	ENSP00000364365:R5053Q	R	-	2	0	UBR4	19280484	0.691000	0.27709	1.000000	0.80357	0.984000	0.73092	1.169000	0.31871	0.630000	0.30394	0.462000	0.41574	CGG	.	.		0.587	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
UBR4	23352	hgsc.bcm.edu	37	1	19433073	19433073	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19433073C>A	ENST00000375254.3	-	83	12410	c.12383G>T	c.(12382-12384)tGg>tTg	p.W4128L	UBR4_ENST00000375217.2_Missense_Mutation_p.W4121L|UBR4_ENST00000375226.2_Missense_Mutation_p.W4104L|UBR4_ENST00000375267.2_Missense_Mutation_p.W4128L|UBR4_ENST00000375224.1_5'Flank	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4128					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTGTCGCAGCCAGTTGTTATG	0.552																																					p.W4128L		Atlas-SNP	.											.	UBR4	415	.	0			c.G12383T						.						90.0	83.0	85.0					1																	19433073		2203	4300	6503	SO:0001583	missense	23352	exon83			CGCAGCCAGTTGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.12383G>T	chr1.hg19:g.19433073C>A	ENSP00000364403:p.Trp4128Leu	46.0	0.0		30.0	4.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.902347	0.92035	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.49139	0.8;0.79;0.85;0.86	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.65026	0.2652	M	0.64997	1.995	0.80722	D	1	D	0.54601	0.967	P	0.62382	0.901	T	0.67154	-0.5742	10	0.87932	D	0	.	17.5745	0.87944	0.0:1.0:0.0:0.0	.	4128	Q5T4S7	UBR4_HUMAN	L	4128;4128;4121;4104	ENSP00000364403:W4128L;ENSP00000364416:W4128L;ENSP00000364365:W4121L;ENSP00000364374:W4104L	ENSP00000364365:W4121L	W	-	2	0	UBR4	19305660	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.320000	0.79064	2.733000	0.93635	0.561000	0.74099	TGG	.	.		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
UBR4	23352	hgsc.bcm.edu	37	1	19501462	19501462	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19501462G>T	ENST00000375254.3	-	21	2866	c.2839C>A	c.(2839-2841)Cga>Aga	p.R947R	UBR4_ENST00000375217.2_Silent_p.R947R|UBR4_ENST00000375226.2_Silent_p.R947R|UBR4_ENST00000375267.2_Silent_p.R947R	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	947					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAATCAAGTCGGTTCAAATCA	0.443																																					p.R947R		Atlas-SNP	.											.	UBR4	415	.	0			c.C2839A						.						102.0	94.0	97.0					1																	19501462		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon21			CAAGTCGGTTCAA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2839C>A	chr1.hg19:g.19501462G>T		133.0	0.0		109.0	5.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.443	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
PLA2G2F	64600	hgsc.bcm.edu	37	1	20466705	20466705	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:20466705G>A	ENST00000375102.3	+	2	265	c.163G>A	c.(163-165)Ggc>Agc	p.G55S		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	12					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CATCCTTGCTGGCAGCGGTGA	0.592																																					p.G55S		Atlas-SNP	.											.	PLA2G2F	28	.	0			c.G163A						.						138.0	122.0	128.0					1																	20466705		2203	4300	6503	SO:0001583	missense	64600	exon2			CTTGCTGGCAGCG	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.163G>A	chr1.hg19:g.20466705G>A	ENSP00000364243:p.Gly55Ser	108.0	0.0		64.0	4.0	NM_022819	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	hg19	CCDS204.2	.	.	.	.	.	.	.	.	.	.	G	2.466	-0.323005	0.05350	.	.	ENSG00000158786	ENST00000375102	T	0.27890	1.64	4.76	-2.07	0.07276	.	0.459946	0.20406	N	0.092947	T	0.12774	0.0310	N	0.14661	0.345	0.09310	N	0.999998	P	0.35628	0.513	B	0.26202	0.067	T	0.16394	-1.0404	10	0.26408	T	0.33	-10.5336	10.6333	0.45549	0.5084:0.0:0.4916:0.0	.	55	Q9BZM2-2	.	S	55	ENSP00000364243:G55S	ENSP00000364243:G55S	G	+	1	0	PLA2G2F	20339292	0.006000	0.16342	0.016000	0.15963	0.000000	0.00434	-0.216000	0.09266	-1.046000	0.03246	-2.069000	0.00389	GGC	.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819	
PINK1	65018	hgsc.bcm.edu	37	1	20971140	20971140	+	Missense_Mutation	SNP	C	C	T	rs536146282		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:20971140C>T	ENST00000321556.4	+	4	1028	c.934C>T	c.(934-936)Cgg>Tgg	p.R312W	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	312	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGCCATGGCCGGACGCTGTT	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		18286	0.0		0.0	False		,,,				2504	0.001				p.R312W	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											PINK1,NS,carcinoma,0,1	PINK1	37	.	0			c.C934T						.						63.0	58.0	60.0					1																	20971140		2203	4300	6503	SO:0001583	missense	65018	exon4			CATGGCCGGACGC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.934C>T	chr1.hg19:g.20971140C>T	ENSP00000364204:p.Arg312Trp	57.0	0.0		47.0	2.0	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	hg19	CCDS211.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.711168	0.89112	.	.	ENSG00000158828	ENST00000321556	T	0.74421	-0.84	6.07	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.104529	0.64402	D	0.000002	D	0.86510	0.5950	M	0.85041	2.73	0.49915	D	0.999839	D	0.89917	1.0	D	0.77004	0.989	D	0.88162	0.2858	10	0.66056	D	0.02	-21.5917	12.5324	0.56122	0.1666:0.8334:0.0:0.0	.	312	Q9BXM7	PINK1_HUMAN	W	312	ENSP00000364204:R312W	ENSP00000364204:R312W	R	+	1	2	PINK1	20843727	1.000000	0.71417	0.912000	0.35992	0.982000	0.71751	4.948000	0.63590	1.533000	0.49186	0.655000	0.94253	CGG	.	.		0.647	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
ALPL	249	hgsc.bcm.edu	37	1	21902359	21902359	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:21902359G>T	ENST00000374840.3	+	10	1381	c.1131G>T	c.(1129-1131)gcG>gcT	p.A377A	ALPL_ENST00000374829.1_Silent_p.A23A|ALPL_ENST00000374832.1_Silent_p.A377A|ALPL_ENST00000539907.1_Silent_p.A300A|ALPL_ENST00000374830.1_Silent_p.A23A|ALPL_ENST00000540617.1_Silent_p.A322A|ALPL_ENST00000425315.2_Silent_p.A377A	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	377					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	TGGTCACTGCGGACCATTCCC	0.607																																					p.A377A		Atlas-SNP	.											.	ALPL	50	.	0			c.G1131T						.						167.0	158.0	161.0					1																	21902359		2203	4300	6503	SO:0001819	synonymous_variant	249	exon10			CACTGCGGACCAT	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.1131G>T	chr1.hg19:g.21902359G>T		129.0	0.0		108.0	5.0	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	hg19	CCDS217.1																																																																																			.	.		0.607	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
HSPG2	3339	hgsc.bcm.edu	37	1	22170757	22170757	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:22170757A>G	ENST00000374695.3	-	65	8579	c.8500T>C	c.(8500-8502)Tcc>Ccc	p.S2834P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2834	Ig-like C2-type 14.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CGGGAGGAGGAGGGCTCGATG	0.677																																					p.S2834P		Atlas-SNP	.											.	HSPG2	311	.	0			c.T8500C						.						57.0	59.0	58.0					1																	22170757		2203	4300	6503	SO:0001583	missense	3339	exon65			AGGAGGAGGGCTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8500T>C	chr1.hg19:g.22170757A>G	ENSP00000363827:p.Ser2834Pro	184.0	0.0		105.0	5.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389311	0.61956	.	.	ENSG00000142798	ENST00000374695	T	0.68479	-0.33	4.65	4.65	0.58169	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37577	N	0.002034	T	0.79246	0.4413	M	0.79614	2.46	0.43211	D	0.995072	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.77175	-0.2684	10	0.21540	T	0.41	.	12.0553	0.53531	1.0:0.0:0.0:0.0	.	774;2834	Q59EG0;P98160	.;PGBM_HUMAN	P	2834	ENSP00000363827:S2834P	ENSP00000363827:S2834P	S	-	1	0	HSPG2	22043344	1.000000	0.71417	0.970000	0.41538	0.893000	0.52053	4.846000	0.62860	1.724000	0.51502	0.459000	0.35465	TCC	.	.		0.677	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
HSPG2	3339	hgsc.bcm.edu	37	1	22175467	22175467	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:22175467C>T	ENST00000374695.3	-	58	7583	c.7504G>A	c.(7504-7506)Gtg>Atg	p.V2502M	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2502	Ig-like C2-type 10.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACACGGCACACGTACTCCCCT	0.642																																					p.V2502M		Atlas-SNP	.											.	HSPG2	311	.	0			c.G7504A						.						146.0	138.0	140.0					1																	22175467		2203	4300	6503	SO:0001583	missense	3339	exon58			GGCACACGTACTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.7504G>A	chr1.hg19:g.22175467C>T	ENSP00000363827:p.Val2502Met	130.0	0.0		97.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.219229	0.39201	.	.	ENSG00000142798	ENST00000374695	T	0.16073	2.37	4.96	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276156	0.19533	N	0.111990	T	0.35740	0.0942	M	0.66378	2.025	0.26627	N	0.97254	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.09640	-1.0665	10	0.52906	T	0.07	.	7.8077	0.29213	0.0:0.8108:0.0:0.1892	.	442;2502	Q59EG0;P98160	.;PGBM_HUMAN	M	2502	ENSP00000363827:V2502M	ENSP00000363827:V2502M	V	-	1	0	HSPG2	22048054	0.943000	0.32029	0.980000	0.43619	0.097000	0.18754	1.915000	0.39976	1.080000	0.41073	0.561000	0.74099	GTG	.	.		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
EPHB2	2048	hgsc.bcm.edu	37	1	23110887	23110887	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:23110887G>T	ENST00000400191.3	+	3	147	c.129G>T	c.(127-129)tgG>tgT	p.W43C	EPHB2_ENST00000544305.1_Missense_Mutation_p.W43C|EPHB2_ENST00000374627.1_Missense_Mutation_p.W37C|EPHB2_ENST00000374630.3_Missense_Mutation_p.W43C|EPHB2_ENST00000374632.3_Missense_Mutation_p.W43C	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	43	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		ACCCACAGTGGGAAGAGGTGA	0.542																																					p.W43C		Atlas-SNP	.											.	EPHB2	257	.	0			c.G129T						.						87.0	74.0	78.0					1																	23110887		2203	4300	6503	SO:0001583	missense	2048	exon3			ACAGTGGGAAGAG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.129G>T	chr1.hg19:g.23110887G>T	ENSP00000383053:p.Trp43Cys	151.0	0.0		97.0	4.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.79	3.893633	0.72639	.	.	ENSG00000133216	ENST00000374625;ENST00000544305;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.19	5.19	0.71726	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.58623	0.2135	M	0.93978	3.48	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.69928	-0.5012	10	0.87932	D	0	.	17.4346	0.87548	0.0:0.0:1.0:0.0	.	43;43;61;43	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	C	43;43;43;43;43;37	ENSP00000444174:W43C;ENSP00000363761:W43C;ENSP00000383053:W43C;ENSP00000363763:W43C;ENSP00000363758:W37C	ENSP00000363755:W43C	W	+	3	0	EPHB2	22983474	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.578000	0.98200	2.704000	0.92352	0.484000	0.47621	TGG	.	.		0.542	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
TCEA3	6920	hgsc.bcm.edu	37	1	23710837	23710837	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:23710837A>G	ENST00000450454.2	-	10	1145		c.e10+1			NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3						regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		AAACATACAGACCTTCCAGCG	0.507																																					.		Atlas-SNP	.											.	TCEA3	20	.	0			c.1038+2T>C						.						159.0	161.0	161.0					1																	23710837		2143	4265	6408	SO:0001630	splice_region_variant	6920	exon11			ATACAGACCTTCC	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.1038+1T>C	chr1.hg19:g.23710837A>G		91.0	0.0		55.0	4.0	NM_003196	A8K2K7|Q5DR83	Splice_Site	SNP	ENST00000450454.2	hg19	CCDS44086.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.252025	0.80135	.	.	ENSG00000204219	ENST00000450454	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5294	0.67915	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TCEA3	23583424	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	8.804000	0.91921	2.189000	0.69895	0.459000	0.35465	.	.	.		0.507	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	Intron
FUCA1	2517	hgsc.bcm.edu	37	1	24186295	24186295	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:24186295G>T	ENST00000374479.3	-	4	768	c.761C>A	c.(760-762)cCt>cAt	p.P254H		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	254					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TACCTTGACAGGGCTGTCATT	0.418																																					p.P254H		Atlas-SNP	.											.	FUCA1	24	.	0			c.C761A						.						93.0	87.0	89.0					1																	24186295		2203	4300	6503	SO:0001583	missense	2517	exon4			TTGACAGGGCTGT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.761C>A	chr1.hg19:g.24186295G>T	ENSP00000363603:p.Pro254His	90.0	0.0		73.0	4.0	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	hg19	CCDS244.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437118	0.62955	.	.	ENSG00000179163	ENST00000374479;ENST00000374475	T	0.66638	-0.22	6.16	6.16	0.99307	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88081	0.6341	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89805	0.3978	10	0.87932	D	0	-15.2455	20.8598	0.99761	0.0:0.0:1.0:0.0	.	254	P04066	FUCO_HUMAN	H	254;43	ENSP00000363603:P254H	ENSP00000363599:P43H	P	-	2	0	FUCA1	24058882	1.000000	0.71417	0.954000	0.39281	0.054000	0.15201	9.283000	0.95860	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.418	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147	
WDTC1	23038	hgsc.bcm.edu	37	1	27627864	27627864	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:27627864A>G	ENST00000319394.3	+	13	1915	c.1380A>G	c.(1378-1380)aaA>aaG	p.K460K	WDTC1_ENST00000361771.3_Silent_p.K459K	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	460					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		ACGACTTCAAAGGGAAATTTC	0.572											OREG0013280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K460K		Atlas-SNP	.											.	WDTC1	69	.	0			c.A1380G						.						70.0	68.0	69.0					1																	27627864		2203	4300	6503	SO:0001819	synonymous_variant	23038	exon13			CTTCAAAGGGAAA	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.1380A>G	chr1.hg19:g.27627864A>G		116.0	0.0	795	74.0	4.0	NM_001276252	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Silent	SNP	ENST00000319394.3	hg19																																																																																				.	.		0.572	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
AHDC1	27245	hgsc.bcm.edu	37	1	27876114	27876114	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:27876114C>T	ENST00000247087.5	-	5	3109	c.2513G>A	c.(2512-2514)gGc>gAc	p.G838D	AHDC1_ENST00000374011.2_Missense_Mutation_p.G838D			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	838							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGAAAGTAGCCGGTGAAGAG	0.627																																					p.G838D		Atlas-SNP	.											.	AHDC1	98	.	0			c.G2513A						.						46.0	51.0	50.0					1																	27876114		2193	4286	6479	SO:0001583	missense	27245	exon6			AAGTAGCCGGTGA	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2513G>A	chr1.hg19:g.27876114C>T	ENSP00000247087:p.Gly838Asp	170.0	0.0		99.0	4.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308244	0.81247	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.71222	-0.55;-0.55	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000010	T	0.76399	0.3982	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76462	-0.2950	10	0.44086	T	0.13	-16.5503	18.7552	0.91830	0.0:1.0:0.0:0.0	.	838	Q5TGY3	AHDC1_HUMAN	D	838	ENSP00000247087:G838D;ENSP00000363123:G838D	ENSP00000247087:G838D	G	-	2	0	AHDC1	27748701	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.987000	0.76206	2.723000	0.93209	0.655000	0.94253	GGC	.	.		0.627	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
CSMD2	114784	hgsc.bcm.edu	37	1	34033348	34033348	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34033348G>T	ENST00000373381.4	-	53	8401	c.8225C>A	c.(8224-8226)cCt>cAt	p.P2742H		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2719	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AATGGGCTCAGGAGTCCCACA	0.532																																					p.P2719H		Atlas-SNP	.											.	CSMD2	946	.	0			c.C8156A						.						98.0	83.0	88.0					1																	34033348		2203	4300	6503	SO:0001583	missense	114784	exon54			GGCTCAGGAGTCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8225C>A	chr1.hg19:g.34033348G>T	ENSP00000362479:p.Pro2742His	142.0	0.0		125.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	G	18.06	3.540138	0.65085	.	.	ENSG00000121904	ENST00000373381	D	0.84873	-1.91	5.07	5.07	0.68467	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.95881	0.8659	H	0.98701	4.305	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.991;1.0	D	0.97764	1.0222	10	0.87932	D	0	.	17.7969	0.88575	0.0:0.0:1.0:0.0	.	2719;2742	Q7Z408;E7EUA6	CSMD2_HUMAN;.	H	2742	ENSP00000362479:P2742H	ENSP00000241312:P2719H	P	-	2	0	CSMD2	33805935	1.000000	0.71417	0.868000	0.34077	0.776000	0.43924	9.809000	0.99208	2.539000	0.85634	0.655000	0.94253	CCT	.	.		0.532	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
CSMD2	114784	hgsc.bcm.edu	37	1	34080170	34080170	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34080170C>A	ENST00000373380.1	-	19	2906	c.2686G>T	c.(2686-2688)Ggc>Tgc	p.G896C	CSMD2_ENST00000373381.4_Missense_Mutation_p.G2023C|CSMD2_ENST00000373388.2_Missense_Mutation_p.G122C|CSMD2_ENST00000373377.1_Missense_Mutation_p.G122C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1983	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G1983S(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCTGGGAAGCCGGGGCTCAGG	0.572																																					p.G1983C		Atlas-SNP	.											CSMD2,caecum,carcinoma,0,1	CSMD2	946	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5947T						.						90.0	83.0	85.0					1																	34080170		2203	4300	6503	SO:0001583	missense	114784	exon40			GGAAGCCGGGGCT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2686G>T	chr1.hg19:g.34080170C>A	ENSP00000362478:p.Gly896Cys	71.0	1.0		61.0	3.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	C	29.0	4.966772	0.92855	.	.	ENSG00000121904	ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.47	5.47	0.80525	CUB (5);	0.000000	0.85682	D	0.000000	T	0.68742	0.3034	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75795	-0.3192	10	0.87932	D	0	.	18.323	0.90244	0.0:1.0:0.0:0.0	.	896;1983;2023	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	2023;896;122;122	ENSP00000362479:G2023C;ENSP00000362478:G896C;ENSP00000362475:G122C;ENSP00000362486:G122C	ENSP00000241312:G1983C	G	-	1	0	CSMD2	33852757	1.000000	0.71417	0.930000	0.37139	0.992000	0.81027	7.818000	0.86416	2.570000	0.86706	0.655000	0.94253	GGC	.	.		0.572	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
CSMD2	114784	hgsc.bcm.edu	37	1	34089068	34089068	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34089068T>C	ENST00000373380.1	-	15	2465		c.e15-2		CSMD2_ENST00000373381.4_Splice_Site|CSMD2_ENST00000373388.2_Splice_Site|CSMD2_ENST00000373377.1_Splice_Site			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACTTGGATCTGGGAAGGGAG	0.483																																					.		Atlas-SNP	.											.	CSMD2	946	.	0			c.5506-2A>G						.						100.0	86.0	91.0					1																	34089068		2203	4300	6503	SO:0001630	splice_region_variant	114784	exon37			TGGATCTGGGAAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2245-2A>G	chr1.hg19:g.34089068T>C		136.0	0.0		113.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Splice_Site	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.26	2.481768	0.44147	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7749	0.69724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD2	33861655	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	7.669000	0.83911	2.170000	0.68504	0.459000	0.35465	.	.	.		0.483	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	Intron
MAP7D1	55700	hgsc.bcm.edu	37	1	36636731	36636731	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:36636731A>G	ENST00000373151.2	+	2	422	c.206A>G	c.(205-207)gAg>gGg	p.E69G	MAP7D1_ENST00000373150.4_Missense_Mutation_p.E69G|MAP7D1_ENST00000316156.4_Missense_Mutation_p.E69G	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	69	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CTGGAACCAGAGAGCCCCTCA	0.652																																					p.E69G		Atlas-SNP	.											.	MAP7D1	62	.	0			c.A206G						.						52.0	58.0	56.0					1																	36636731		2203	4300	6503	SO:0001583	missense	55700	exon2			AACCAGAGAGCCC	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.206A>G	chr1.hg19:g.36636731A>G	ENSP00000362244:p.Glu69Gly	119.0	0.0		77.0	4.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049010	0.36181	.	.	ENSG00000116871	ENST00000429533;ENST00000316156;ENST00000373150;ENST00000373151;ENST00000530729	T;T;T;T;T	0.05319	3.46;3.46;3.46;3.46;3.46	4.62	-0.754	0.11065	.	0.351134	0.20847	N	0.084582	T	0.02494	0.0076	N	0.08118	0	0.80722	D	1	B;B;B	0.15719	0.0;0.0;0.014	B;B;B	0.09377	0.001;0.001;0.004	T	0.48790	-0.9004	10	0.40728	T	0.16	-5.5227	2.306	0.04174	0.4741:0.2962:0.0843:0.1455	.	69;69;69	Q3KQU3-2;Q3KQU3-4;Q3KQU3	.;.;MA7D1_HUMAN	G	30;69;69;69;30	ENSP00000390091:E30G;ENSP00000320228:E69G;ENSP00000362243:E69G;ENSP00000362244:E69G;ENSP00000435126:E30G	ENSP00000320228:E69G	E	+	2	0	MAP7D1	36409318	0.511000	0.26179	0.687000	0.30102	0.929000	0.56500	0.815000	0.27253	-0.199000	0.10317	0.379000	0.24179	GAG	.	.		0.652	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
SH3D21	79729	hgsc.bcm.edu	37	1	36785547	36785547	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:36785547T>C	ENST00000426732.2	+	13	1220	c.935T>C	c.(934-936)aTc>aCc	p.I312T	SH3D21_ENST00000312808.4_Missense_Mutation_p.I74T|SH3D21_ENST00000453908.2_Missense_Mutation_p.I428T|SH3D21_ENST00000505871.1_Missense_Mutation_p.I317T|EVA1B_ENST00000490466.1_5'Flank			A4FU49	SH321_HUMAN	SH3 domain containing 21	312						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						AAGGCTTCTATCCCAGAGAAC	0.572																																					p.I428T		Atlas-SNP	.											.	SH3D21	73	.	0			c.T1283C						.						55.0	60.0	59.0					1																	36785547		2203	4300	6503	SO:0001583	missense	79729	exon14			CTTCTATCCCAGA	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 113"""	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.935T>C	chr1.hg19:g.36785547T>C	ENSP00000408613:p.Ile312Thr	83.0	0.0		69.0	5.0	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Missense_Mutation	SNP	ENST00000426732.2	hg19		.	.	.	.	.	.	.	.	.	.	T	5.827	0.336767	0.11013	.	.	ENSG00000214193	ENST00000453908;ENST00000426732;ENST00000312808;ENST00000505871	T;T;T;T	0.45276	1.43;1.88;0.9;1.89	2.83	-4.09	0.03951	.	.	.	.	.	T	0.23451	0.0567	N	0.22421	0.69	0.09310	N	1	B;B	0.22346	0.068;0.018	B;B	0.17098	0.017;0.005	T	0.22906	-1.0203	8	.	.	.	.	8.9418	0.35733	0.0:0.3146:0.5794:0.106	.	317;312	A4FU49-3;A4FU49	.;SH321_HUMAN	T	428;312;74;317	ENSP00000403476:I428T;ENSP00000408613:I312T;ENSP00000321936:I74T;ENSP00000421294:I317T	.	I	+	2	0	SH3D21	36558134	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.065000	0.01386	-0.907000	0.03862	0.260000	0.18958	ATC	.	.		0.572	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676	
KCNQ4	9132	hgsc.bcm.edu	37	1	41285131	41285131	+	Missense_Mutation	SNP	T	T	C	rs80358276		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:41285131T>C	ENST00000347132.5	+	5	903	c.821T>C	c.(820-822)cTc>cCc	p.L274P	KCNQ4_ENST00000509682.2_Missense_Mutation_p.L274P|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	274			L -> H (in DFNA2A). {ECO:0000269|PubMed:10925378}.		inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	GCCGACTCGCTCTGGTGGGGG	0.622																																					p.L274P		Atlas-SNP	.											.	KCNQ4	58	.	0			c.T821C	GRCh37	CM001721	KCNQ4	M	rs80358276	.						116.0	101.0	106.0					1																	41285131		2203	4300	6503	SO:0001583	missense	9132	exon5			ACTCGCTCTGGTG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.821T>C	chr1.hg19:g.41285131T>C	ENSP00000262916:p.Leu274Pro	237.0	0.0		137.0	6.0	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	hg19	CCDS456.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621136	0.87460	.	.	ENSG00000117013	ENST00000347132;ENST00000509682	D;D	0.98926	-5.24;-5.24	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99254	0.9740	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99150	1.0858	10	0.87932	D	0	-28.9565	12.801	0.57586	0.0:0.0:0.0:1.0	.	274;274	P56696-2;P56696	.;KCNQ4_HUMAN	P	274	ENSP00000262916:L274P;ENSP00000423756:L274P	ENSP00000262916:L274P	L	+	2	0	KCNQ4	41057718	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	1.907000	0.55213	0.460000	0.39030	CTC	.	.		0.622	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
PTPRF	5792	hgsc.bcm.edu	37	1	44083444	44083444	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:44083444C>A	ENST00000359947.4	+	25	4573	c.4233C>A	c.(4231-4233)atC>atA	p.I1411I	PTPRF_ENST00000438120.1_Silent_p.I1402I|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.I770I|PTPRF_ENST00000372413.3_Silent_p.I1402I|PTPRF_ENST00000372414.3_Silent_p.I1411I	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1411	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCAACTACATCGATGGCTACC	0.602																																					p.I1411I		Atlas-SNP	.											PTPRF,colon,carcinoma,0,1	PTPRF	172	.	0			c.C4233A						.						63.0	62.0	62.0					1																	44083444		2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			CTACATCGATGGC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4233C>A	chr1.hg19:g.44083444C>A		144.0	0.0		116.0	6.0	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	hg19	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	9.798	1.179769	0.21787	.	.	ENSG00000142949	ENST00000429895	.	.	.	5.58	-0.477	0.12097	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.5273	0.11988	0.226:0.3766:0.0:0.3974	.	.	.	.	X	1057	.	.	S	+	2	0	PTPRF	43856031	0.000000	0.05858	1.000000	0.80357	0.977000	0.68977	-2.533000	0.00942	0.237000	0.21200	-0.727000	0.03589	TCG	.	.		0.602	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
RNF220	55182	hgsc.bcm.edu	37	1	45115396	45115396	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:45115396A>G	ENST00000355387.2	+	13	1959	c.1509A>G	c.(1507-1509)gaA>gaG	p.E503E	TMEM53_ENST00000372244.3_Intron|RNF220_ENST00000361799.2_Silent_p.E503E|RNF220_ENST00000372247.2_Silent_p.E503E|RNF220_ENST00000443020.2_Silent_p.E290E|TMEM53_ENST00000372242.3_Intron|RNF220_ENST00000480686.1_3'UTR|TMEM53_ENST00000372243.3_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220	503					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						GAGAACTTGAACGGCAGCTAT	0.547																																					p.E503E		Atlas-SNP	.											.	RNF220	56	.	0			c.A1509G						.						139.0	131.0	134.0					1																	45115396		2203	4300	6503	SO:0001819	synonymous_variant	55182	exon13			ACTTGAACGGCAG	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"""RING-type (C3HC4) zinc fingers"""	25552	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 164"""	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1509A>G	chr1.hg19:g.45115396A>G		122.0	0.0		97.0	4.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Silent	SNP	ENST00000355387.2	hg19	CCDS510.1																																																																																			.	.		0.547	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150	
MUTYH	4595	hgsc.bcm.edu	37	1	45797951	45797951	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:45797951G>T	ENST00000372098.3	-	10	944	c.811C>A	c.(811-813)Cgg>Agg	p.R271R	MUTYH_ENST00000372104.1_Silent_p.R246R|MUTYH_ENST00000372110.3_Silent_p.R261R|MUTYH_ENST00000528013.2_Silent_p.R260R|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000355498.2_Silent_p.R246R|MUTYH_ENST00000448481.1_Silent_p.R257R|MUTYH_ENST00000456914.2_Silent_p.R246R|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000354383.6_Silent_p.R247R|MUTYH_ENST00000372100.5_Silent_p.R257R|MUTYH_ENST00000450313.1_Silent_p.R274R|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000372115.3_Silent_p.R260R			Q9UIF7	MUTYH_HUMAN	mutY homolog	271					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TCTCCTGGCCGGGCTGGGTCC	0.612			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.R274R		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	MUTYH,NS,chondrosarcoma,0,1	MUTYH	38	.	0			c.C820A	GRCh37	CM053996	MUTYH	M		.						29.0	31.0	30.0					1																	45797951		2203	4300	6503	SO:0001819	synonymous_variant	4595	exon10	Familial Cancer Database	MAP, MYH-associated polyposis	CTGGCCGGGCTGG	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.811C>A	chr1.hg19:g.45797951G>T		87.0	0.0		51.0	3.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.		0.612	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
CYP4B1	1580	hgsc.bcm.edu	37	1	47264911	47264911	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:47264911G>A	ENST00000271153.4	+	1	194	c.158G>A	c.(157-159)tGg>tAg	p.W53*	CYP4B1_ENST00000371919.4_Nonsense_Mutation_p.W53*|CYP4B1_ENST00000371923.4_Nonsense_Mutation_p.W53*|CYP4B1_ENST00000546128.1_Intron			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	53					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.W53*(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	CCCACCCACTGGCTTTTTGGA	0.557																																					p.W53X		Atlas-SNP	.											CYP4B1,extremity,malignant_melanoma,0,1	CYP4B1	81	.	1	Substitution - Nonsense(1)	skin(1)	c.G158A						.						35.0	31.0	33.0					1																	47264911		2203	4300	6503	SO:0001587	stop_gained	1580	exon1			CCCACTGGCTTTT	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.158G>A	chr1.hg19:g.47264911G>A	ENSP00000271153:p.Trp53*	137.0	0.0		70.0	25.0	NM_000779	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Nonsense_Mutation	SNP	ENST00000271153.4	hg19	CCDS542.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707124	0.68615	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5952	0.76574	0.0:0.0:1.0:0.0	.	.	.	.	X	53	.	ENSP00000271153:W53X	W	+	2	0	CYP4B1	47037498	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	4.702000	0.61817	2.753000	0.94483	0.467000	0.42956	TGG	.	.		0.557	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
C8B	732	hgsc.bcm.edu	37	1	57399139	57399139	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:57399139A>G	ENST00000371237.4	-	10	1487	c.1421T>C	c.(1420-1422)gTg>gCg	p.V474A	C8B_ENST00000543257.1_Missense_Mutation_p.V422A|C8B_ENST00000535057.1_Missense_Mutation_p.V412A	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	474	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						TGTGGCTGTCACTAGTTCATA	0.438																																					p.V474A		Atlas-SNP	.											.	C8B	107	.	0			c.T1421C						.						78.0	70.0	73.0					1																	57399139		2203	4300	6503	SO:0001583	missense	732	exon10			GCTGTCACTAGTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1421T>C	chr1.hg19:g.57399139A>G	ENSP00000360281:p.Val474Ala	100.0	0.0		88.0	5.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094834	0.56075	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.86030	-2.06;-2.06;-2.06	5.08	3.88	0.44766	Membrane attack complex component/perforin (MACPF) domain (3);	0.117394	0.56097	D	0.000024	D	0.87989	0.6317	M	0.82517	2.595	0.58432	D	0.999999	P;D;P	0.55385	0.868;0.971;0.892	B;P;P	0.48488	0.443;0.562;0.579	D	0.90070	0.4162	10	0.87932	D	0	-20.4023	12.5995	0.56489	0.8624:0.1376:0.0:0.0	.	422;412;474	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	A	474;422;412	ENSP00000360281:V474A;ENSP00000442548:V422A;ENSP00000440113:V412A	ENSP00000360281:V474A	V	-	2	0	C8B	57171727	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	5.809000	0.69172	2.264000	0.75181	0.533000	0.62120	GTG	.	.		0.438	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
KANK4	163782	hgsc.bcm.edu	37	1	62739434	62739434	+	Silent	SNP	G	G	T	rs370065609		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:62739434G>T	ENST00000371153.4	-	3	1720	c.1342C>A	c.(1342-1344)Cga>Aga	p.R448R	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	448						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						TCCTCTCCTCGGTGCCCCCAG	0.557																																					p.R448R		Atlas-SNP	.											.	KANK4	135	.	0			c.C1342A						.						164.0	161.0	162.0					1																	62739434		2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			CTCCTCGGTGCCC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1342C>A	chr1.hg19:g.62739434G>T		140.0	0.0		113.0	5.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.		0.557	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
PGM1	5236	hgsc.bcm.edu	37	1	64114221	64114221	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:64114221G>T	ENST00000371084.3	+	8	1391	c.1178G>T	c.(1177-1179)tGg>tTg	p.W393L	PGM1_ENST00000540265.1_Missense_Mutation_p.W196L|PGM1_ENST00000371083.4_Missense_Mutation_p.W411L	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	393					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						GATGGACTGTGGGCTGTCCTT	0.522																																					p.W411L		Atlas-SNP	.											.	PGM1	75	.	0			c.G1232T						.						83.0	69.0	74.0					1																	64114221		2203	4300	6503	SO:0001583	missense	5236	exon8			GACTGTGGGCTGT	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1178G>T	chr1.hg19:g.64114221G>T	ENSP00000360125:p.Trp393Leu	70.0	0.0		59.0	4.0	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	hg19	CCDS625.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.726226	0.89298	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.38077	1.16;1.16;1.16	6.06	6.06	0.98353	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (1);	0.000000	0.85682	D	0.000000	T	0.58652	0.2137	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.59402	-0.7461	10	0.87932	D	0	-33.0953	20.6208	0.99490	0.0:0.0:1.0:0.0	.	411;393	P36871-2;P36871	.;PGM1_HUMAN	L	369;393;196;411	ENSP00000360125:W393L;ENSP00000443449:W196L;ENSP00000360124:W411L	ENSP00000360124:W411L	W	+	2	0	PGM1	63886809	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	TGG	.	.		0.522	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
DIRAS3	9077	hgsc.bcm.edu	37	1	68512864	68512864	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:68512864G>A	ENST00000370981.1	-	4	753	c.117C>T	c.(115-117)cgC>cgT	p.R39R	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Silent_p.R39R			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	39					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CTACCACGACGCGGTAATCTC	0.582																																					p.R39R		Atlas-SNP	.											.	DIRAS3	31	.	0			c.C117T						.						68.0	72.0	71.0					1																	68512864		2203	4300	6503	SO:0001819	synonymous_variant	9077	exon2			CACGACGCGGTAA	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"""ras homolog gene family, member I"""	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.117C>T	chr1.hg19:g.68512864G>A		147.0	0.0		106.0	30.0	NM_004675	B3KMP3	Silent	SNP	ENST00000370981.1	hg19	CCDS641.1																																																																																			.	.		0.582	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675	
LRRC7	57554	hgsc.bcm.edu	37	1	70504859	70504859	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:70504859C>A	ENST00000035383.5	+	19	3268	c.3238C>A	c.(3238-3240)Cca>Aca	p.P1080T	LRRC7_ENST00000310961.5_Missense_Mutation_p.P1085T|LRRC7_ENST00000415775.2_Missense_Mutation_p.P364T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1080						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAGAGGATACCCACCGATGGA	0.512																																					p.P1080T		Atlas-SNP	.											.	LRRC7	400	.	0			c.C3238A						.						68.0	72.0	71.0					1																	70504859		2203	4300	6503	SO:0001583	missense	57554	exon19			GGATACCCACCGA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3238C>A	chr1.hg19:g.70504859C>A	ENSP00000035383:p.Pro1080Thr	121.0	0.0		93.0	4.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006281	0.19199	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.39406	1.08;1.15;2.26	5.76	2.77	0.32553	.	0.118903	0.64402	D	0.000020	T	0.44787	0.1310	L	0.40543	1.245	0.47659	D	0.999489	P;B;D	0.89917	0.952;0.221;1.0	P;B;D	0.80764	0.732;0.244;0.994	T	0.47812	-0.9088	10	0.49607	T	0.09	.	17.496	0.87717	0.0:0.526:0.474:0.0	.	364;1080;1080	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	T	1085;1080;364;903	ENSP00000309245:P1085T;ENSP00000035383:P1080T;ENSP00000394867:P364T	ENSP00000035383:P1080T	P	+	1	0	LRRC7	70277447	1.000000	0.71417	0.951000	0.38953	0.001000	0.01503	3.007000	0.49536	0.319000	0.23209	-0.955000	0.02649	CCA	.	.		0.512	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	
SRSF11	9295	hgsc.bcm.edu	37	1	70710417	70710417	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:70710417G>T	ENST00000370950.3	+	9	933	c.851G>T	c.(850-852)cGg>cTg	p.R284L	SRSF11_ENST00000484162.1_3'UTR|SRSF11_ENST00000405432.1_Missense_Mutation_p.R284L|SRSF11_ENST00000370949.1_Missense_Mutation_p.R224L|SRSF11_ENST00000370951.1_Missense_Mutation_p.R284L			Q05519	SRS11_HUMAN	serine/arginine-rich splicing factor 11	284	10 X 8 AA approximate repeats of R-R-S-R- S-R-S-R.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|ovary(2)|skin(1)	6						TCTAGGAGTCGGCGACGATCC	0.443																																					p.R284L		Atlas-SNP	.											.	SRSF11	68	.	0			c.G851T						.						94.0	90.0	91.0					1																	70710417		2203	4300	6503	SO:0001583	missense	9295	exon9			GGAGTCGGCGACG	M74002	CCDS647.1, CCDS53332.1	1p31.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000116754	ENSG00000116754		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10782	protein-coding gene	gene with protein product	"""SR splicing factor 11"""	602010	"""splicing factor, arginine/serine-rich 11"""	SFRS11		1896467, 20516191	Standard	NM_004768		Approved	p54, NET2	uc001des.3	Q05519	OTTHUMG00000009342	ENST00000370950.3:c.851G>T	chr1.hg19:g.70710417G>T	ENSP00000359988:p.Arg284Leu	129.0	0.0		115.0	6.0	NM_001190987	Q5T758|Q8IWE6	Missense_Mutation	SNP	ENST00000370950.3	hg19	CCDS647.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201992	0.79127	.	.	ENSG00000116754	ENST00000370951;ENST00000370950;ENST00000405432;ENST00000395136;ENST00000370949	D;D;D;T;T	0.82167	-1.58;-1.58;-1.58;2.56;-0.45	5.53	5.53	0.82687	.	0.038654	0.85682	D	0.000000	D	0.89591	0.6759	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.60575	0.988;0.983;0.983;0.958	P;P;P;P	0.57911	0.829;0.549;0.549;0.451	D	0.90381	0.4388	10	0.87932	D	0	.	19.8223	0.96603	0.0:0.0:1.0:0.0	.	224;284;284;284	Q5T757;Q6PJB9;Q8IWE6;Q05519	.;.;.;SRS11_HUMAN	L	284;284;284;284;224	ENSP00000359989:R284L;ENSP00000359988:R284L;ENSP00000384357:R284L;ENSP00000378568:R284L;ENSP00000359987:R224L	ENSP00000359987:R224L	R	+	2	0	SRSF11	70483005	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.281000	0.72632	2.763000	0.94921	0.555000	0.69702	CGG	.	.		0.443	SRSF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025889.1	NM_004768	
LPAR3	23566	hgsc.bcm.edu	37	1	85331068	85331068	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:85331068C>A	ENST00000440886.1	-	1	774	c.736G>T	c.(736-738)Ggg>Tgg	p.G246W	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Splice_Site_p.G246W			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	246					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TCTTACCTACCTAAGACAGTC	0.498																																					p.G246W		Atlas-SNP	.											.	LPAR3	53	.	0			c.G736T						.						54.0	41.0	46.0					1																	85331068		2203	4300	6503	SO:0001630	splice_region_variant	23566	exon2			ACCTACCTAAGAC	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	14298	protein-coding gene	gene with protein product		605106	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"""	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.736+1G>T	chr1.hg19:g.85331068C>A		118.0	0.0		71.0	4.0	NM_012152	A0AVA3	Missense_Mutation	SNP	ENST00000440886.1	hg19	CCDS700.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142484	0.77888	.	.	ENSG00000171517	ENST00000440886;ENST00000370611	T;T	0.38560	1.13;1.13	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.110306	0.64402	D	0.000008	T	0.73651	0.3614	H	0.97077	3.935	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.83863	0.0269	9	.	.	.	.	18.7607	0.91849	0.0:1.0:0.0:0.0	.	246	Q9UBY5	LPAR3_HUMAN	W	246	ENSP00000395389:G246W;ENSP00000359643:G246W	.	G	-	1	0	LPAR3	85103656	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.792000	0.85828	2.437000	0.82529	0.650000	0.86243	GGG	.	.		0.498	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152	Missense_Mutation
COL24A1	255631	hgsc.bcm.edu	37	1	86340972	86340972	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:86340972T>C	ENST00000370571.2	-	34	3438	c.3072A>G	c.(3070-3072)gaA>gaG	p.E1024E	COL24A1_ENST00000436319.1_Silent_p.E1024E	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1024	Collagen-like 9.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTGCACCTGGTTCACCTTGCA	0.413																																					p.E1024E		Atlas-SNP	.											.	COL24A1	202	.	0			c.A3072G						.						79.0	77.0	78.0					1																	86340972		1875	4107	5982	SO:0001819	synonymous_variant	255631	exon34			ACCTGGTTCACCT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3072A>G	chr1.hg19:g.86340972T>C		220.0	0.0		108.0	5.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.413	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
GBP7	388646	hgsc.bcm.edu	37	1	89607318	89607318	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:89607318A>G	ENST00000294671.2	-	9	1517	c.1379T>C	c.(1378-1380)cTc>cCc	p.L460P		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	460						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		GAAGCTCTGGAGGACCTCGTC	0.498																																					p.L460P		Atlas-SNP	.											.	GBP7	57	.	0			c.T1379C						.						113.0	104.0	107.0					1																	89607318		2203	4300	6503	SO:0001583	missense	388646	exon9			CTCTGGAGGACCT	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1379T>C	chr1.hg19:g.89607318A>G	ENSP00000294671:p.Leu460Pro	148.0	0.0		100.0	4.0	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	hg19	CCDS720.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241778	0.79912	.	.	ENSG00000213512	ENST00000294671	T	0.73152	-0.72	4.14	4.14	0.48551	Guanylate-binding protein, C-terminal (3);	0.000000	0.64402	D	0.000003	D	0.85128	0.5626	H	0.95539	3.685	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.88657	0.3186	10	0.87932	D	0	.	11.1443	0.48422	1.0:0.0:0.0:0.0	.	460	Q8N8V2	GBP7_HUMAN	P	460	ENSP00000294671:L460P	ENSP00000294671:L460P	L	-	2	0	GBP7	89379906	1.000000	0.71417	0.930000	0.37139	0.704000	0.40688	5.607000	0.67648	1.745000	0.51790	0.477000	0.44152	CTC	.	.		0.498	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
GLMN	11146	hgsc.bcm.edu	37	1	92712653	92712653	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:92712653T>C	ENST00000370360.3	-	18	1715	c.1634A>G	c.(1633-1635)gAg>gGg	p.E545G	GLMN_ENST00000534881.1_Missense_Mutation_p.E531G	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	545					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		ATTAGGGATCTCTTCTCCACT	0.368									Multiple Glomus Tumors (of the Skin), Familial																												p.E545G		Atlas-SNP	.											GLMN,NS,carcinoma,0,1	GLMN	37	.	0			c.A1634G						.						138.0	145.0	142.0					1																	92712653		2203	4300	6503	SO:0001583	missense	11146	exon18	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	GGGATCTCTTCTC	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"""venous malformation with glomus cells"""	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1634A>G	chr1.hg19:g.92712653T>C	ENSP00000359385:p.Glu545Gly	47.0	0.0		24.0	2.0	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823688	0.50739	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.46451	0.87;0.87	6.17	5.03	0.67393	.	0.175572	0.64402	D	0.000012	T	0.21145	0.0509	L	0.36672	1.1	0.36542	D	0.871352	B;B	0.24317	0.101;0.081	B;B	0.28465	0.09;0.061	T	0.07328	-1.0778	10	0.62326	D	0.03	-3.7276	12.8097	0.57634	0.1226:0.0:0.0:0.8774	.	531;545	B4DJ85;Q92990	.;GLMN_HUMAN	G	545;531	ENSP00000359385:E545G;ENSP00000440156:E531G	ENSP00000359385:E545G	E	-	2	0	GLMN	92485241	1.000000	0.71417	0.984000	0.44739	0.703000	0.40648	5.467000	0.66737	1.111000	0.41721	0.533000	0.62120	GAG	.	.		0.368	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070	
CCDC18	343099	hgsc.bcm.edu	37	1	93677670	93677670	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:93677670A>G	ENST00000343253.7	+	11	1849	c.1347A>G	c.(1345-1347)gcA>gcG	p.A449A	CCDC18_ENST00000401026.3_Silent_p.A449A|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000338949.4_Silent_p.A248A|CCDC18_ENST00000557479.1_Silent_p.A567A			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	449										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TTAAGCTTGCAATAAAAGAGG	0.313																																					p.A449A		Atlas-SNP	.											.	CCDC18	93	.	0			c.A1347G						.						101.0	99.0	99.0					1																	93677670		1803	4063	5866	SO:0001819	synonymous_variant	343099	exon11			GCTTGCAATAAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1347A>G	chr1.hg19:g.93677670A>G		142.0	0.0		98.0	4.0	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	hg19		.	.	.	.	.	.	.	.	.	.	A	10.04	1.242781	0.22796	.	.	ENSG00000122483	ENST00000370276	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	T	0.64216	0.2578	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64689	-0.6348	4	.	.	.	.	15.8222	0.78662	1.0:0.0:0.0:0.0	.	.	.	.	R	503	.	.	Q	+	2	0	CCDC18	93450258	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.267000	0.58877	2.123000	0.65237	0.460000	0.39030	CAA	.	.		0.313	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
ABCA4	24	hgsc.bcm.edu	37	1	94520858	94520858	+	Missense_Mutation	SNP	G	G	T	rs542919944|rs281865399		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:94520858G>T	ENST00000370225.3	-	16	2482	c.2396C>A	c.(2395-2397)cCg>cAg	p.P799Q	ABCA4_ENST00000535735.1_Missense_Mutation_p.P725Q	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	799					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AAATGCCACCGGAGACAGTAA	0.567																																					p.P799Q		Atlas-SNP	.											.	ABCA4	275	.	0			c.C2396A						.						62.0	57.0	59.0					1																	94520858		2203	4300	6503	SO:0001583	missense	24	exon16			GCCACCGGAGACA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2396C>A	chr1.hg19:g.94520858G>T	ENSP00000359245:p.Pro799Gln	69.0	0.0		64.0	4.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.385296	0.25031	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;T	0.87256	-2.23;-0.57	5.55	5.55	0.83447	.	0.263117	0.38164	N	0.001788	T	0.72503	0.3468	N	0.26092	0.79	0.35233	D	0.777139	B;B	0.23591	0.088;0.001	B;B	0.21917	0.037;0.016	T	0.71879	-0.4459	10	0.46703	T	0.11	.	15.0531	0.71891	0.0:0.0:0.8574:0.1426	.	725;799	F5H6E5;P78363	.;ABCA4_HUMAN	Q	799;725	ENSP00000359245:P799Q;ENSP00000437682:P725Q	ENSP00000359245:P799Q	P	-	2	0	ABCA4	94293446	1.000000	0.71417	0.996000	0.52242	0.239000	0.25481	2.783000	0.47766	2.626000	0.88956	0.650000	0.86243	CCG	.	.		0.567	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
PLPPR5	163404	hgsc.bcm.edu	37	1	99418828	99418828	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:99418828C>A	ENST00000263177.4	-	3	640	c.419G>T	c.(418-420)gGa>gTa	p.G140V	LPPR5_ENST00000370188.3_Missense_Mutation_p.G140V	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		140						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										GACTACTTGTCCAGCATTTAC	0.403																																					p.G140V		Atlas-SNP	.											.	.	.	.	0			c.G419T						.						79.0	78.0	79.0					1																	99418828		2203	4300	6503	SO:0001583	missense	0	exon3			ACTTGTCCAGCAT																												ENST00000263177.4:c.419G>T	chr1.hg19:g.99418828C>A	ENSP00000263177:p.Gly140Val	91.0	0.0		79.0	4.0	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156654	0.57259	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.74209	-0.82;-0.82	4.9	4.9	0.64082	.	0.158353	0.56097	D	0.000028	T	0.73590	0.3606	L	0.49778	1.585	0.80722	D	1	D;D	0.65815	0.994;0.995	P;D	0.64595	0.88;0.927	T	0.69781	-0.5052	10	0.10111	T	0.7	.	17.4358	0.87552	0.0:1.0:0.0:0.0	.	140;140	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	V	140	ENSP00000359207:G140V;ENSP00000263177:G140V	ENSP00000263177:G140V	G	-	2	0	AL161744.1	99191416	1.000000	0.71417	0.991000	0.47740	0.736000	0.42039	7.442000	0.80503	2.407000	0.81776	0.655000	0.94253	GGA	.	.		0.403	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1		
PALMD	54873	hgsc.bcm.edu	37	1	100154877	100154877	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:100154877C>A	ENST00000263174.4	+	7	1436	c.1061C>A	c.(1060-1062)tCg>tAg	p.S354*	PALMD_ENST00000605497.1_Nonsense_Mutation_p.S354*	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	354					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		TGGGAAGAATCGAATGTCATG	0.493																																					p.S354X		Atlas-SNP	.											.	PALMD	64	.	0			c.C1061A						.						59.0	55.0	56.0					1																	100154877		2203	4300	6503	SO:0001587	stop_gained	54873	exon7			AAGAATCGAATGT	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1061C>A	chr1.hg19:g.100154877C>A	ENSP00000263174:p.Ser354*	92.0	0.0		91.0	5.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Nonsense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.043021	0.93685	.	.	ENSG00000099260	ENST00000263174	.	.	.	5.93	5.93	0.95920	.	1.348970	0.04374	N	0.359659	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0E-4	14.0993	0.65044	0.0:0.8066:0.1934:0.0	.	.	.	.	X	354	.	ENSP00000263174:S354X	S	+	2	0	PALMD	99927465	0.003000	0.15002	0.015000	0.15790	0.012000	0.07955	1.649000	0.37281	2.802000	0.96397	0.563000	0.77884	TCG	.	.		0.493	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	
ATXN7L2	127002	hgsc.bcm.edu	37	1	110032963	110032963	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:110032963G>T	ENST00000369870.3	+	9	1322	c.1307G>T	c.(1306-1308)tGc>tTc	p.C436F		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	436										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GACCGGTTCTGCTCAGCACTC	0.552											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C436F		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.G1307T						.						82.0	76.0	78.0					1																	110032963		2203	4300	6503	SO:0001583	missense	127002	exon9			GGTTCTGCTCAGC	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1307G>T	chr1.hg19:g.110032963G>T	ENSP00000358886:p.Cys436Phe	75.0	0.0	1424	70.0	4.0	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199607	0.58126	.	.	ENSG00000162650	ENST00000369870;ENST00000541125;ENST00000369869	T	0.41065	1.01	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000001	T	0.50394	0.1613	L	0.47716	1.5	0.52099	D	0.999944	D	0.67145	0.996	D	0.67725	0.953	T	0.45366	-0.9266	10	0.56958	D	0.05	-12.0532	17.3447	0.87307	0.0:0.0:1.0:0.0	.	436	Q5T6C5	AT7L2_HUMAN	F	436;436;63	ENSP00000358886:C436F	ENSP00000358885:C63F	C	+	2	0	ATXN7L2	109834486	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.622000	0.90953	2.837000	0.97791	0.655000	0.94253	TGC	.	.		0.552	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340	
KCNA10	3744	hgsc.bcm.edu	37	1	111061042	111061042	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111061042T>C	ENST00000369771.2	-	1	755	c.368A>G	c.(367-369)gAc>gGc	p.D123G		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	123					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TCTCATGGAGTCAAAGAACTG	0.468																																					p.D123G		Atlas-SNP	.											.	KCNA10	92	.	0			c.A368G						.						68.0	72.0	70.0					1																	111061042		2203	4300	6503	SO:0001583	missense	3744	exon1			ATGGAGTCAAAGA	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.368A>G	chr1.hg19:g.111061042T>C	ENSP00000358786:p.Asp123Gly	42.0	0.0		29.0	5.0	NM_005549		Missense_Mutation	SNP	ENST00000369771.2	hg19	CCDS826.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743242	0.69418	.	.	ENSG00000143105	ENST00000369771	T	0.78126	-1.15	5.72	5.72	0.89469	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.92198	0.7526	H	0.98883	4.36	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.95141	0.8264	10	0.87932	D	0	.	14.8223	0.70082	0.0:0.0:0.0:1.0	.	123	Q16322	KCA10_HUMAN	G	123	ENSP00000358786:D123G	ENSP00000358786:D123G	D	-	2	0	KCNA10	110862565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.171000	0.68590	0.533000	0.62120	GAC	.	.		0.468	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549	
CHI3L2	1117	hgsc.bcm.edu	37	1	111773369	111773369	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111773369G>A	ENST00000445067.2	+	5	847	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	CHI3L2_ENST00000369744.2_Missense_Mutation_p.A16T|CHI3L2_ENST00000524472.1_5'UTR|CHI3L2_ENST00000369748.4_Missense_Mutation_p.A26T|CHI3L2_ENST00000466741.1_5'UTR			Q15782	CH3L2_HUMAN	chitinase 3-like 2	26					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		TCCAGGATCTGCCTACAAACT	0.488																																					p.A26T		Atlas-SNP	.											.	CHI3L2	38	.	0			c.G76A						.						72.0	68.0	69.0					1																	111773369		2203	4300	6503	SO:0001583	missense	1117	exon3			GGATCTGCCTACA	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.76G>A	chr1.hg19:g.111773369G>A	ENSP00000437082:p.Ala26Thr	77.0	0.0		60.0	4.0	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	hg19	CCDS30802.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738828	0.49045	.	.	ENSG00000064886	ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304	T;T;T;T;T	0.15139	3.3;2.49;2.45;3.3;3.3	4.09	2.22	0.28083	.	0.000000	0.40554	N	0.001067	T	0.07458	0.0188	L	0.43757	1.38	0.21184	N	0.999761	D;D	0.54397	0.966;0.966	P;P	0.48227	0.571;0.571	T	0.18650	-1.0330	10	0.36615	T	0.2	-2.6827	8.0089	0.30342	0.2034:0.0:0.7966:0.0	.	16;26	A6NNY3;Q15782	.;CH3L2_HUMAN	T	26;26;26;16;26;26	ENSP00000437082:A26T;ENSP00000436077:A26T;ENSP00000431968:A26T;ENSP00000358759:A16T;ENSP00000358763:A26T	ENSP00000358759:A16T	A	+	1	0	CHI3L2	111574892	0.931000	0.31567	0.645000	0.29479	0.962000	0.63368	0.718000	0.25866	0.371000	0.24564	0.655000	0.94253	GCC	.	.		0.488	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
CHIA	27159	hgsc.bcm.edu	37	1	111857977	111857977	+	Missense_Mutation	SNP	G	G	T	rs551479392		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111857977G>T	ENST00000369740.1	+	6	503	c.400G>T	c.(400-402)Ggg>Tgg	p.G134W	CHIA_ENST00000343320.6_Missense_Mutation_p.G134W|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000430615.1_Missense_Mutation_p.G26W|CHIA_ENST00000353665.6_Intron|RP5-1125M8.2_ENST00000426321.1_RNA	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	134					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGAGTTTGACGGGCTGGACTT	0.547																																					p.G134W		Atlas-SNP	.											.	CHIA	115	.	0			c.G400T						.						96.0	91.0	93.0					1																	111857977		2203	4300	6503	SO:0001583	missense	27159	exon6			TTTGACGGGCTGG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.400G>T	chr1.hg19:g.111857977G>T	ENSP00000358755:p.Gly134Trp	133.0	0.0		91.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.654769	0.67472	.	.	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320;ENST00000430615	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	4.72	3.8	0.43715	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000003	T	0.73953	0.3653	H	0.99752	4.75	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.83514	0.0082	10	0.87932	D	0	-8.8093	11.22	0.48848	0.0925:0.0:0.9075:0.0	.	134	Q9BZP6	CHIA_HUMAN	W	78;134;134;26	ENSP00000387671:G78W;ENSP00000358755:G134W;ENSP00000341828:G134W;ENSP00000391132:G26W	ENSP00000341828:G134W	G	+	1	0	CHIA	111659500	1.000000	0.71417	0.840000	0.33206	0.817000	0.46193	5.612000	0.67681	1.096000	0.41439	0.655000	0.94253	GGG	.	.		0.547	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
HIPK1	204851	hgsc.bcm.edu	37	1	114499248	114499248	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:114499248G>T	ENST00000369558.1	+	6	1639		c.e6-1		HIPK1_ENST00000369554.2_Splice_Site|HIPK1_ENST00000369553.1_Splice_Site|HIPK1_ENST00000406344.1_Splice_Site|HIPK1_ENST00000369561.4_Splice_Site|HIPK1_ENST00000369555.2_Splice_Site|HIPK1_ENST00000369559.4_Splice_Site|HIPK1_ENST00000340480.4_Splice_Site|HIPK1_ENST00000426820.2_Splice_Site			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1						anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCTTTGGAAGGTGAATATGT	0.388																																					.		Atlas-SNP	.											.	HIPK1	195	.	0			c.1408-1G>T						.						66.0	63.0	64.0					1																	114499248		2203	4300	6503	SO:0001630	splice_region_variant	204851	exon6			TTGGAAGGTGAAT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1408-1G>T	chr1.hg19:g.114499248G>T		95.0	0.0		60.0	4.0	NM_152696	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Splice_Site	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967471	0.74131	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480;ENST00000369553;ENST00000406344	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6579	0.91460	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HIPK1	114300771	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.657000	0.98554	2.646000	0.89796	0.650000	0.86243	.	.	.		0.388	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	Intron
ATP1A1	476	hgsc.bcm.edu	37	1	116942136	116942136	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:116942136G>T	ENST00000295598.5	+	18	2795	c.2543G>T	c.(2542-2544)cGg>cTg	p.R848L	ATP1A1_ENST00000537345.1_Missense_Mutation_p.R848L|ATP1A1_ENST00000369496.4_Missense_Mutation_p.R817L	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	848					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GTGAATGAGCGGCTGATCAGC	0.532																																					p.R848L		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G2543T						.						88.0	78.0	81.0					1																	116942136		2203	4300	6503	SO:0001583	missense	476	exon18			ATGAGCGGCTGAT	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2543G>T	chr1.hg19:g.116942136G>T	ENSP00000295598:p.Arg848Leu	116.0	0.0		92.0	4.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	33	5.280459	0.95489	.	.	ENSG00000163399	ENST00000295598;ENST00000445896;ENST00000537345;ENST00000369496;ENST00000440951	D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89	5.04	5.04	0.67666	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.98588	0.9528	H	0.97103	3.94	0.80722	D	1	D;D	0.64830	0.993;0.994	D;D	0.71870	0.958;0.975	D	0.99624	1.0984	10	0.87932	D	0	.	18.5698	0.91130	0.0:0.0:1.0:0.0	.	848;848	F5H3A1;P05023	.;AT1A1_HUMAN	L	848;17;848;817;15	ENSP00000295598:R848L;ENSP00000445306:R848L;ENSP00000358508:R817L;ENSP00000396236:R15L	ENSP00000295598:R848L	R	+	2	0	ATP1A1	116743659	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.823000	0.86660	2.611000	0.88343	0.655000	0.94253	CGG	.	.		0.532	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
VTCN1	79679	hgsc.bcm.edu	37	1	117690333	117690333	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:117690333A>G	ENST00000369458.3	-	5	874	c.796T>C	c.(796-798)Ttt>Ctt	p.F266L	VTCN1_ENST00000328189.3_Missense_Mutation_p.F150L|VTCN1_ENST00000539893.1_Missense_Mutation_p.F171L|VTCN1_ENST00000359008.4_Missense_Mutation_p.F269L	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1									p.F265fs*14(1)		large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		CTGATGGCAAAGAAAGAAGAG	0.458																																					p.F266L		Atlas-SNP	.											.	VTCN1	26	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T796C						.						114.0	108.0	110.0					1																	117690333		2203	4300	6503	SO:0001583	missense	79679	exon5			TGGCAAAGAAAGA	BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28873	protein-coding gene	gene with protein product	"""B7 family member, H4"", ""B7 superfamily member 1"""	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.796T>C	chr1.hg19:g.117690333A>G	ENSP00000358470:p.Phe266Leu	94.0	0.0		58.0	4.0	NM_024626		Missense_Mutation	SNP	ENST00000369458.3	hg19	CCDS894.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-2.005974	0.00426	.	.	ENSG00000134258	ENST00000369458;ENST00000359008;ENST00000328189;ENST00000539893	T;T;T;T	0.20332	3.54;3.53;2.08;3.77	5.49	-0.842	0.10748	.	0.988038	0.08242	N	0.975883	T	0.03053	0.0090	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46331	-0.9199	10	0.23891	T	0.37	-15.0185	6.6871	0.23152	0.5635:0.1474:0.2891:0.0	.	150;266	Q7Z7D3-2;Q7Z7D3	.;VTCN1_HUMAN	L	266;269;150;171	ENSP00000358470:F266L;ENSP00000351899:F269L;ENSP00000328168:F150L;ENSP00000444724:F171L	ENSP00000328168:F150L	F	-	1	0	VTCN1	117491856	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.344000	0.07780	-0.609000	0.05724	-2.096000	0.00365	TTT	.	.		0.458	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626	
VPS72	6944	hgsc.bcm.edu	37	1	151150609	151150609	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:151150609C>A	ENST00000354473.4	-	5	611	c.575G>T	c.(574-576)cGg>cTg	p.R192L	VPS72_ENST00000496809.1_5'UTR|TMOD4_ENST00000416280.2_5'Flank|TMOD4_ENST00000601585.1_5'Flank			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	192					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGCCTCGAGCCGCTCATATGT	0.478																																					p.R192L	Pancreas(109;1131 2287 3209 24201)	Atlas-SNP	.											.	VPS72	31	.	0			c.G575T						.						68.0	65.0	66.0					1																	151150609		2203	4300	6503	SO:0001583	missense	6944	exon5			TCGAGCCGCTCAT	D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"""transcription factor-like 1"", ""vacuolar protein sorting 72 (yeast)"""	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.575G>T	chr1.hg19:g.151150609C>A	ENSP00000346464:p.Arg192Leu	71.0	0.0		78.0	4.0	NM_001271087	A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Missense_Mutation	SNP	ENST00000354473.4	hg19	CCDS59201.1	.	.	.	.	.	.	.	.	.	.	.	24.0	4.483923	0.84854	.	.	ENSG00000163159	ENST00000368892;ENST00000354473	.	.	.	5.18	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.60650	0.2285	L	0.56769	1.78	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	T	0.64305	-0.6439	9	0.51188	T	0.08	-6.3222	12.1919	0.54277	0.171:0.829:0.0:0.0	.	192	Q15906	VPS72_HUMAN	L	192	.	ENSP00000346464:R192L	R	-	2	0	VPS72	149417233	1.000000	0.71417	0.218000	0.23776	0.990000	0.78478	7.188000	0.77739	1.388000	0.46506	0.655000	0.94253	CGG	.	.		0.478	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997	
RORC	6097	hgsc.bcm.edu	37	1	151779983	151779983	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:151779983T>C	ENST00000318247.6	-	11	1629	c.1522A>G	c.(1522-1524)Act>Gct	p.T508A	LINGO4_ENST00000368820.3_5'Flank|RORC_ENST00000356728.6_Missense_Mutation_p.T487A|RORC_ENST00000480719.1_5'UTR|RORC_ENST00000392697.3_Missense_Mutation_p.T562A	NM_005060.3	NP_005051.2	P51449	RORG_HUMAN	RAR-related orphan receptor C	508	Ligand-binding.				adipose tissue development (GO:0060612)|cellular response to sterol (GO:0036315)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lymph node development (GO:0048535)|negative regulation of thymocyte apoptotic process (GO:0070244)|Peyer's patch development (GO:0048541)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of fat cell differentiation (GO:0045598)|regulation of gamma-delta T cell differentiation (GO:0045586)|regulation of glucose metabolic process (GO:0010906)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|T cell differentiation in thymus (GO:0033077)|T-helper 17 cell differentiation (GO:0072539)|T-helper cell differentiation (GO:0042093)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCGGTTTCAGTGCTGAAGAGC	0.602																																					p.T508A		Atlas-SNP	.											.	RORC	70	.	0			c.A1522G						.						110.0	99.0	103.0					1																	151779983		2203	4300	6503	SO:0001583	missense	6097	exon11			TTTCAGTGCTGAA	U16997	CCDS1004.1, CCDS30856.1	1q21	2013-01-16			ENSG00000143365	ENSG00000143365		"""Nuclear hormone receptors"""	10260	protein-coding gene	gene with protein product		602943				7811290	Standard	NM_005060		Approved	RZRG, RORG, NR1F3, TOR	uc001ezh.3	P51449	OTTHUMG00000013053	ENST00000318247.6:c.1522A>G	chr1.hg19:g.151779983T>C	ENSP00000327025:p.Thr508Ala	73.0	0.0		76.0	4.0	NM_005060	Q5SZR9|Q8N5V7|Q8NCY8	Missense_Mutation	SNP	ENST00000318247.6	hg19	CCDS1004.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.103716	0.56291	.	.	ENSG00000143365	ENST00000356728;ENST00000392697;ENST00000318247	D;D;D	0.94046	-3.31;-3.34;-3.32	5.5	4.38	0.52667	Nuclear hormone receptor, ligand-binding (2);	0.314066	0.26159	U	0.025996	T	0.81749	0.4888	L	0.54323	1.7	0.29163	N	0.877634	B;B;B;B	0.28998	0.112;0.23;0.057;0.1	B;B;B;B	0.26864	0.05;0.05;0.05;0.074	T	0.71334	-0.4624	10	0.28530	T	0.3	.	4.3785	0.11283	0.1745:0.0903:0.0:0.7352	.	496;562;508;487	B6ZGS6;B4DPR1;P51449;F1D8P6	.;.;RORG_HUMAN;.	A	487;562;508	ENSP00000349164:T487A;ENSP00000376461:T562A;ENSP00000327025:T508A	ENSP00000327025:T508A	T	-	1	0	RORC	150046607	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.453000	0.35167	2.085000	0.62840	0.533000	0.62120	ACT	.	.		0.602	RORC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036626.1		
SPRR2A	6700	hgsc.bcm.edu	37	1	153029108	153029108	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:153029108G>T	ENST00000392653.2	-	2	189	c.104C>A	c.(103-105)cCc>cAc	p.P35H		NM_005988.2	NP_005979.1	P35326	SPR2A_HUMAN	small proline-rich protein 2A	35	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(2)|ovary(1)	3	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGGTGGGCAGGGCTCAGGGCA	0.607																																					p.P35H		Atlas-SNP	.											.	SPRR2A	9	.	0			c.C104A						.						68.0	65.0	66.0					1																	153029108		2202	4278	6480	SO:0001583	missense	6700	exon2			GGGCAGGGCTCAG	X53064	CCDS1034.1	1q21-q22	2008-02-05			ENSG00000241794	ENSG00000241794			11261	protein-coding gene	gene with protein product		182267				8325635	Standard	NM_005988		Approved		uc001fbd.3	P35326	OTTHUMG00000014395	ENST00000392653.2:c.104C>A	chr1.hg19:g.153029108G>T	ENSP00000376423:p.Pro35His	183.0	0.0		183.0	34.0	NM_005988	B2R4T3|D3DV35|Q5T529	Missense_Mutation	SNP	ENST00000392653.2	hg19	CCDS1034.1	.	.	.	.	.	.	.	.	.	.	G	9.563	1.118924	0.20877	.	.	ENSG00000241794	ENST00000392653	T	0.53857	0.6	2.79	2.79	0.32731	.	0.000000	0.32671	N	0.005794	T	0.56717	0.2004	.	.	.	0.18873	N	0.999981	D	0.89917	1.0	D	0.87578	0.998	T	0.44065	-0.9352	9	0.87932	D	0	.	9.1956	0.37226	0.0:0.0:1.0:0.0	.	35	P35326	SPR2A_HUMAN	H	35	ENSP00000376423:P35H	ENSP00000376423:P35H	P	-	2	0	SPRR2A	151295732	1.000000	0.71417	0.419000	0.26584	0.386000	0.30323	4.127000	0.57944	1.551000	0.49450	0.400000	0.26472	CCC	.	.		0.607	SPRR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040049.1	NM_005988	
DENND4B	9909	hgsc.bcm.edu	37	1	153903278	153903278	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:153903278C>A	ENST00000361217.4	-	26	4588	c.4170G>T	c.(4168-4170)ttG>ttT	p.L1390F	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1390					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCAACAGTGCCAAACTAAGGG	0.597																																					p.L1390F		Atlas-SNP	.											.	DENND4B	210	.	0			c.G4170T						.						22.0	23.0	23.0					1																	153903278		2001	4185	6186	SO:0001583	missense	9909	exon26			CAGTGCCAAACTA	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.4170G>T	chr1.hg19:g.153903278C>A	ENSP00000354597:p.Leu1390Phe	49.0	0.0		100.0	4.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	C	9.859	1.195729	0.22037	.	.	ENSG00000198837	ENST00000361217	T	0.07567	3.18	5.14	1.93	0.25924	.	0.184794	0.26400	N	0.024593	T	0.02767	0.0083	L	0.36672	1.1	0.38547	D	0.949367	P	0.41748	0.761	B	0.41571	0.36	T	0.46162	-0.9211	10	0.56958	D	0.05	-1.5912	4.6914	0.12783	0.2682:0.531:0.1205:0.0803	.	1390	O75064	DEN4B_HUMAN	F	1390	ENSP00000354597:L1390F	ENSP00000354597:L1390F	L	-	3	2	DENND4B	152169902	0.906000	0.30813	0.263000	0.24496	0.779000	0.44077	1.166000	0.31834	0.708000	0.31955	0.563000	0.77884	TTG	.	.		0.597	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
FDPS	2224	hgsc.bcm.edu	37	1	155289468	155289468	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:155289468T>C	ENST00000356657.6	+	9	1075	c.913T>C	c.(913-915)Ttt>Ctt	p.F305L	RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368354.3_5'Flank|FDPS_ENST00000447866.1_Missense_Mutation_p.F239L|FDPS_ENST00000368356.4_Missense_Mutation_p.F305L|RUSC1_ENST00000368352.5_5'Flank|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	305					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	GGGGGAGTTCTTTCAGATTCA	0.547																																					p.F305L		Atlas-SNP	.											.	FDPS	41	.	0			c.T913C						.						79.0	80.0	80.0					1																	155289468		2203	4300	6503	SO:0001583	missense	2224	exon9			GAGTTCTTTCAGA	J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"""farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"""	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.913T>C	chr1.hg19:g.155289468T>C	ENSP00000349078:p.Phe305Leu	118.0	0.0		88.0	4.0	NM_001135821	D3DV91|E9PCI9|Q96G29	Missense_Mutation	SNP	ENST00000356657.6	hg19	CCDS1110.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.876048	0.91664	.	.	ENSG00000160752	ENST00000447866;ENST00000368356;ENST00000356657	D;D;D	0.82526	-1.62;-1.62;-1.62	4.06	4.06	0.47325	Terpenoid synthase (2);	0.000000	0.45126	D	0.000394	D	0.91188	0.7224	M	0.93594	3.435	0.80722	D	1	D	0.61080	0.989	D	0.66979	0.948	D	0.93060	0.6473	10	0.87932	D	0	-16.4506	12.9405	0.58340	0.0:0.0:0.0:1.0	.	305	P14324	FPPS_HUMAN	L	239;305;305	ENSP00000391755:F239L;ENSP00000357340:F305L;ENSP00000349078:F305L	ENSP00000349078:F305L	F	+	1	0	FDPS	153556092	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.711000	0.84669	2.066000	0.61787	0.459000	0.35465	TTT	.	.		0.547	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004	
CCT3	7203	hgsc.bcm.edu	37	1	156280946	156280946	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:156280946C>T	ENST00000295688.3	-	12	1476	c.1196G>A	c.(1195-1197)cGc>cAc	p.R399H	CCT3_ENST00000472765.2_Missense_Mutation_p.R354H|CCT3_ENST00000368259.2_Missense_Mutation_p.R361H|CCT3_ENST00000368261.3_Missense_Mutation_p.R354H	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	399					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GAGAACATTGCGACACACTTG	0.537																																					p.R399H		Atlas-SNP	.											.	CCT3	61	.	0			c.G1196A						.						76.0	73.0	74.0					1																	156280946		2203	4300	6503	SO:0001583	missense	7203	exon12			ACATTGCGACACA	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"""Heat Shock Proteins / Chaperonins"""	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.1196G>A	chr1.hg19:g.156280946C>T	ENSP00000295688:p.Arg399His	141.0	0.0		157.0	23.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	33	5.252956	0.95336	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.92740	0.7692	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.73708	0.96;0.981;0.972	D	0.94427	0.7646	10	0.72032	D	0.01	-9.7785	17.4945	0.87713	0.0:1.0:0.0:0.0	.	361;398;399	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	H	399;361;354;354	ENSP00000295688:R399H;ENSP00000357242:R361H;ENSP00000357244:R354H;ENSP00000431543:R354H	ENSP00000295688:R399H	R	-	2	0	CCT3	154547570	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.441000	0.80485	2.726000	0.93360	0.650000	0.86243	CGC	.	.		0.537	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
RRNAD1	51093	hgsc.bcm.edu	37	1	156703277	156703277	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:156703277C>T	ENST00000368216.4	+	5	1231	c.601C>T	c.(601-603)Cag>Tag	p.Q201*	RRNAD1_ENST00000368218.4_Nonsense_Mutation_p.Q201*|RRNAD1_ENST00000476229.1_Nonsense_Mutation_p.Q78*	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	201						integral component of membrane (GO:0016021)	rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9						GGAGCTTCTGCAGGCTCTGGA	0.607																																					p.Q201X		Atlas-SNP	.											.	RRNAD1	39	.	0			c.C601T						.						72.0	83.0	79.0					1																	156703277		2203	4300	6503	SO:0001587	stop_gained	51093	exon5			CTTCTGCAGGCTC	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303			24273	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 66"""	C1orf66		10810093, 310876	Standard	NM_015997		Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.601C>T	chr1.hg19:g.156703277C>T	ENSP00000357199:p.Gln201*	77.0	0.0		75.0	4.0	NM_015997	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	Nonsense_Mutation	SNP	ENST00000368216.4	hg19	CCDS1154.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148138	0.57151	.	.	ENSG00000143303	ENST00000368218;ENST00000368216;ENST00000519086;ENST00000484742;ENST00000476229	.	.	.	4.75	2.68	0.31781	.	0.580363	0.19514	N	0.112445	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3672	7.1541	0.25626	0.3157:0.5962:0.0:0.0881	.	.	.	.	X	201;201;180;99;78	.	ENSP00000357199:Q201X	Q	+	1	0	RRNAD1	154969901	0.550000	0.26489	1.000000	0.80357	0.974000	0.67602	0.677000	0.25262	1.213000	0.43380	0.555000	0.69702	CAG	.	.		0.607	RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	NM_015997	
SPTA1	6708	hgsc.bcm.edu	37	1	158641151	158641151	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:158641151G>T	ENST00000368147.4	-	12	1761	c.1581C>A	c.(1579-1581)gcC>gcA	p.A527A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	527					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTCTTCCTGGGCAGTAAAGG	0.468																																					p.A527A		Atlas-SNP	.											.	SPTA1	720	.	0			c.C1581A						.						103.0	98.0	99.0					1																	158641151		1849	4092	5941	SO:0001819	synonymous_variant	6708	exon12			TTCCTGGGCAGTA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1581C>A	chr1.hg19:g.158641151G>T		141.0	0.0		203.0	9.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.468	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
APCS	325	hgsc.bcm.edu	37	1	159558025	159558025	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:159558025A>T	ENST00000255040.2	+	2	296	c.199A>T	c.(199-201)Agc>Tgc	p.S67C		NM_001639.3	NP_001630.1	P02743	SAMP_HUMAN	amyloid P component, serum	67	Pentaxin.				acute-phase response (GO:0006953)|chaperone-mediated protein complex assembly (GO:0051131)|innate immune response (GO:0045087)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral process (GO:0048525)|negative regulation of wound healing (GO:0061045)|protein folding (GO:0006457)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_hematologic(112;0.0429)					TCGTGCCTACAGCCTCTTCTC	0.413																																					p.S67C		Atlas-SNP	.											.	APCS	48	.	0			c.A199T						.						116.0	115.0	115.0					1																	159558025		2203	4300	6503	SO:0001583	missense	325	exon2			GCCTACAGCCTCT		CCDS1186.1	1q21-q23	2012-10-02			ENSG00000132703	ENSG00000132703			584	protein-coding gene	gene with protein product	"""pentaxin-related"", ""9.5S alpha-1-glycoprotein"""	104770				2987268	Standard	NM_001639		Approved	SAP, PTX2, MGC88159	uc001ftv.3	P02743	OTTHUMG00000022741	ENST00000255040.2:c.199A>T	chr1.hg19:g.159558025A>T	ENSP00000255040:p.Ser67Cys	90.0	0.0		179.0	14.0	NM_001639		Missense_Mutation	SNP	ENST00000255040.2	hg19	CCDS1186.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358230	0.41801	.	.	ENSG00000132703	ENST00000255040	T	0.09817	2.94	4.45	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.268199	0.41294	D	0.000916	T	0.27384	0.0672	M	0.91300	3.195	0.41910	D	0.990463	D	0.89917	1.0	D	0.91635	0.999	T	0.12941	-1.0528	10	0.87932	D	0	-18.5039	7.5418	0.27742	0.8092:0.0:0.0:0.1908	.	67	P02743	SAMP_HUMAN	C	67	ENSP00000255040:S67C	ENSP00000255040:S67C	S	+	1	0	APCS	157824649	0.957000	0.32711	0.895000	0.35142	0.023000	0.10783	2.214000	0.42853	1.984000	0.57885	0.533000	0.62120	AGC	.	.		0.413	APCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059024.2	NM_001639	
CD84	8832	hgsc.bcm.edu	37	1	160519720	160519720	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:160519720T>C	ENST00000311224.4	-	7	1025	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	CD84_ENST00000368051.3_Silent_p.A270A|CD84_ENST00000534968.1_Missense_Mutation_p.Q189R|CD84_ENST00000368048.3_Missense_Mutation_p.Q314R|RP11-528G1.2_ENST00000446952.1_RNA|CD84_ENST00000368054.3_Missense_Mutation_p.Q303R	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	320					blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.Q303L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ATCAGCAAACTGCACTTCGGA	0.512																																					p.Q320R		Atlas-SNP	.											CD84_ENST00000311224,NS,carcinoma,0,2	CD84	71	.	1	Substitution - Missense(1)	lung(1)	c.A959G						.						127.0	115.0	119.0					1																	160519720		2203	4300	6503	SO:0001583	missense	8832	exon7			GCAAACTGCACTT	AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1704	protein-coding gene	gene with protein product		604513	"""CD84 antigen (leukocyte antigen)"", ""CD84 molecule """			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.959A>G	chr1.hg19:g.160519720T>C	ENSP00000312367:p.Gln320Arg	90.0	0.0		69.0	3.0	NM_001184879	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	hg19	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.343616	0.41498	.	.	ENSG00000066294	ENST00000534968;ENST00000368054;ENST00000368048;ENST00000311224	T;T;T;T	0.63913	2.11;-0.07;-0.02;0.01	4.51	3.38	0.38709	.	0.349704	0.25549	N	0.029904	T	0.33498	0.0865	.	.	.	0.31601	N	0.652746	B;P;P;P	0.45474	0.202;0.779;0.859;0.859	B;B;B;B	0.41571	0.111;0.197;0.36;0.36	T	0.14117	-1.0484	9	0.39692	T	0.17	-2.9994	6.8508	0.24014	0.0:0.1056:0.0:0.8944	.	189;320;314;303	Q9UIB8-7;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;SLAF5_HUMAN;.;.	R	189;303;314;320	ENSP00000442845:Q189R;ENSP00000357033:Q303R;ENSP00000357027:Q314R;ENSP00000312367:Q320R	ENSP00000312367:Q320R	Q	-	2	0	CD84	158786344	0.987000	0.35691	0.684000	0.30055	0.020000	0.10135	1.959000	0.40412	0.864000	0.35578	0.460000	0.39030	CAG	.	.		0.512	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874	
CD48	962	hgsc.bcm.edu	37	1	160648872	160648872	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:160648872C>T	ENST00000368046.3	-	4	789	c.702G>A	c.(700-702)gtG>gtA	p.V234V	RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|RP11-404F10.2_ENST00000598917.2_RNA	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	234					blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAATGGTGGGCACCGTGACCA	0.453																																					p.V234V		Atlas-SNP	.											.	CD48	31	.	0			c.G702A						.						120.0	112.0	115.0					1																	160648872		2203	4300	6503	SO:0001819	synonymous_variant	962	exon4			GGTGGGCACCGTG	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.702G>A	chr1.hg19:g.160648872C>T		134.0	0.0		136.0	44.0	NM_001778	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	hg19	CCDS1208.1																																																																																			.	.		0.453	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
PPOX	5498	hgsc.bcm.edu	37	1	161138329	161138329	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:161138329C>A	ENST00000367999.4	+	6	845	c.579C>A	c.(577-579)acC>acA	p.T193T	PPOX_ENST00000495483.1_3'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000544598.1_Intron|PPOX_ENST00000352210.5_Silent_p.T193T	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	193					heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CTGAGCAAACCCATCGTTCCA	0.547																																					p.T193T		Atlas-SNP	.											.	PPOX	34	.	0			c.C579A						.						100.0	87.0	91.0					1																	161138329		2203	4300	6503	SO:0001819	synonymous_variant	5498	exon6			GCAAACCCATCGT	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"""variegate porphyria"""	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.579C>A	chr1.hg19:g.161138329C>A		106.0	0.0		94.0	4.0	NM_000309	D3DVG0|Q5VTW8	Silent	SNP	ENST00000367999.4	hg19	CCDS1221.1	.	.	.	.	.	.	.	.	.	.	C	9.098	1.003320	0.19121	.	.	ENSG00000143224	ENST00000537523	.	.	.	5.23	-0.285	0.12866	.	.	.	.	.	T	0.36331	0.0963	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.26087	-1.0113	4	.	.	.	-24.08	6.4416	0.21853	0.6146:0.2279:0.0:0.1574	.	.	.	.	H	6	.	.	P	+	2	0	PPOX	159404953	0.000000	0.05858	0.985000	0.45067	0.987000	0.75469	-0.749000	0.04813	0.067000	0.16545	-0.188000	0.12872	CCC	.	.		0.547	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	
DDR2	4921	hgsc.bcm.edu	37	1	162743270	162743270	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:162743270T>C	ENST00000367922.3	+	15	2178	c.1740T>C	c.(1738-1740)tgT>tgC	p.C580C	DDR2_ENST00000367921.3_Silent_p.C580C	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	580	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TTCATCTCTGTGAAGTGGAGG	0.448																																					p.C580C	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.T1740C						.						114.0	109.0	111.0					1																	162743270		2203	4300	6503	SO:0001819	synonymous_variant	4921	exon15			TCTCTGTGAAGTG	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.1740T>C	chr1.hg19:g.162743270T>C		112.0	0.0		117.0	5.0	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	hg19	CCDS1241.1																																																																																			.	.		0.448	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
ALDH9A1	223	hgsc.bcm.edu	37	1	165664622	165664622	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:165664622G>T	ENST00000354775.4	-	2	498	c.194C>A	c.(193-195)gCt>gAt	p.A65D	ALDH9A1_ENST00000538148.1_5'UTR|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	41					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TGTGAAAGTAGCTATCACTCG	0.343																																					p.A65D	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.C194A						.						92.0	92.0	92.0					1																	165664622		2203	4300	6503	SO:0001583	missense	223	exon2			AAAGTAGCTATCA	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.194C>A	chr1.hg19:g.165664622G>T	ENSP00000346827:p.Ala65Asp	98.0	0.0		96.0	4.0	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	hg19	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437233	0.62955	.	.	ENSG00000143149	ENST00000354775	T	0.79247	-1.25	5.44	4.52	0.55395	.	0.149162	0.64402	D	0.000010	T	0.78824	0.4344	M	0.76170	2.325	0.33790	D	0.625315	D;D	0.56035	0.974;0.974	P;P	0.53809	0.645;0.735	T	0.82948	-0.0204	9	0.72032	D	0.01	.	13.8734	0.63634	0.0:0.1542:0.8458:0.0	.	55;65	B4DX14;B9EKV4	.;.	D	65	ENSP00000346827:A65D	ENSP00000346827:A65D	A	-	2	0	ALDH9A1	163931246	0.511000	0.26179	0.961000	0.40146	0.730000	0.41778	1.493000	0.35605	1.256000	0.44068	0.655000	0.94253	GCT	.	.		0.343	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
DPT	1805	hgsc.bcm.edu	37	1	168670334	168670334	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:168670334C>A	ENST00000367817.3	-	3	549	c.460G>T	c.(460-462)Ggt>Tgt	p.G154C		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	154	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					ATTTCCTCACCATAGTGACCT	0.418																																					p.G154C		Atlas-SNP	.											.	DPT	29	.	0			c.G460T						.						197.0	186.0	190.0					1																	168670334		2203	4300	6503	SO:0001583	missense	1805	exon3			CCTCACCATAGTG	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.460G>T	chr1.hg19:g.168670334C>A	ENSP00000356791:p.Gly154Cys	98.0	0.0		94.0	5.0	NM_001937	A8K981|Q8N4R2|Q9UIX8	Missense_Mutation	SNP	ENST00000367817.3	hg19	CCDS1275.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166262	0.78339	.	.	ENSG00000143196	ENST00000367817	T	0.46819	0.86	5.72	5.72	0.89469	.	0.099859	0.64402	D	0.000002	T	0.54303	0.1850	L	0.51422	1.61	0.43199	D	0.995045	D	0.71674	0.998	D	0.64237	0.923	T	0.45160	-0.9280	9	0.36615	T	0.2	-18.1772	18.7179	0.91682	0.0:1.0:0.0:0.0	.	154	Q07507	DERM_HUMAN	C	154	ENSP00000356791:G154C	ENSP00000356791:G154C	G	-	1	0	DPT	166936958	1.000000	0.71417	0.982000	0.44146	0.999000	0.98932	4.649000	0.61433	2.697000	0.92050	0.644000	0.83932	GGT	.	.		0.418	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937	
C1orf112	55732	hgsc.bcm.edu	37	1	169806089	169806089	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:169806089T>C	ENST00000286031.6	+	17	2261	c.1561T>C	c.(1561-1563)Tcc>Ccc	p.S521P	C1orf112_ENST00000359326.4_Missense_Mutation_p.S521P|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	521										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCAGAAATTTTCCCCAAAAGA	0.398																																					p.S521P		Atlas-SNP	.											.,1	C1orf112	74	.	0			c.T1561C						.						49.0	49.0	49.0					1																	169806089		2203	4300	6503	SO:0001583	missense	55732	exon17			AAATTTTCCCCAA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1561T>C	chr1.hg19:g.169806089T>C	ENSP00000286031:p.Ser521Pro	34.0	0.0		36.0	2.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	hg19	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.122968	0.37436	.	.	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.47528	0.84;0.84	6.03	-4.92	0.03075	.	0.250031	0.47852	N	0.000209	T	0.06188	0.0160	N	0.05351	-0.065	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.37549	-0.9701	10	0.02654	T	1	-0.5306	9.9667	0.41730	0.0:0.5133:0.1127:0.374	.	463;521	B4DGF2;Q9NSG2	.;CA112_HUMAN	P	521	ENSP00000352276:S521P;ENSP00000286031:S521P	ENSP00000286031:S521P	S	+	1	0	C1orf112	168072713	0.031000	0.19500	0.800000	0.32199	0.962000	0.63368	-0.984000	0.03755	-0.669000	0.05289	0.533000	0.62120	TCC	.	.		0.398	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
FMO3	2328	hgsc.bcm.edu	37	1	171076816	171076816	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:171076816A>G	ENST00000367755.4	+	4	433	c.322A>G	c.(322-324)Aca>Gca	p.T108A	FMO3_ENST00000392085.2_Splice_Site_p.T108A|FMO3_ENST00000542847.1_Splice_Site_p.T88A|FMO3_ENST00000538429.1_Splice_Site_p.T45A	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	108					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	TTTCTCTTAGACATTTGTATC	0.348																																					p.T108A		Atlas-SNP	.											.	FMO3	73	.	0			c.A322G						.						78.0	78.0	78.0					1																	171076816		2203	4300	6503	SO:0001630	splice_region_variant	2328	exon4			TCTTAGACATTTG	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.322-1A>G	chr1.hg19:g.171076816A>G		156.0	0.0		143.0	6.0	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	hg19	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	A	19.75	3.885920	0.72410	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.61392	0.11;0.11;0.11;0.11	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.71945	0.3400	M	0.88640	2.97	0.58432	D	0.999994	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.985;0.996	T	0.77539	-0.2550	9	.	.	.	-13.2412	10.0866	0.42421	0.8497:0.0:0.0:0.1503	.	45;88;108	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	A	108;108;88;45	ENSP00000356729:T108A;ENSP00000375935:T108A;ENSP00000444073:T88A;ENSP00000439500:T45A	.	T	+	1	0	FMO3	169343440	1.000000	0.71417	0.998000	0.56505	0.895000	0.52256	7.079000	0.76829	1.787000	0.52448	0.482000	0.46254	ACA	.	.		0.348	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	Missense_Mutation
CACNA1E	777	hgsc.bcm.edu	37	1	181684513	181684513	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:181684513C>T	ENST00000367573.2	+	9	1211	c.1211C>T	c.(1210-1212)aCa>aTa	p.T404I	CACNA1E_ENST00000358338.5_Missense_Mutation_p.T355I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.T404I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.T404I|CACNA1E_ENST00000367567.4_Missense_Mutation_p.T11I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.T404I|CACNA1E_ENST00000357570.5_Missense_Mutation_p.T355I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	404					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AATGCTGGAACATCCGCCTTA	0.378																																					p.T404I		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C1211T						.						56.0	54.0	55.0					1																	181684513		1850	4114	5964	SO:0001583	missense	777	exon9			CTGGAACATCCGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1211C>T	chr1.hg19:g.181684513C>T	ENSP00000356545:p.Thr404Ile	67.0	0.0		96.0	5.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227589	0.79576	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D;D	0.96265	-3.21;-3.21;-3.21;-3.21;-3.21;-3.96;-3.21;-3.21	5.36	5.36	0.76844	.	0.861229	0.10542	N	0.662567	D	0.94637	0.8271	N	0.17474	0.49	0.42244	D	0.991947	D;D	0.53745	0.962;0.962	P;P	0.49276	0.605;0.605	D	0.93198	0.6589	10	0.46703	T	0.11	.	19.0518	0.93050	0.0:1.0:0.0:0.0	.	404;404	Q15878-2;Q15878-3	.;.	I	404;404;404;355;355;11;404;404	ENSP00000432038:T404I;ENSP00000356542:T404I;ENSP00000434814:T404I;ENSP00000350183:T355I;ENSP00000351101:T355I;ENSP00000356539:T11I;ENSP00000353222:T404I;ENSP00000356545:T404I	ENSP00000350183:T355I	T	+	2	0	CACNA1E	179951136	0.880000	0.30214	0.253000	0.24343	0.823000	0.46562	2.290000	0.43531	2.673000	0.90976	0.650000	0.86243	ACA	.	.		0.378	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
LAMC1	3915	hgsc.bcm.edu	37	1	183086467	183086467	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:183086467G>T	ENST00000258341.4	+	9	1834	c.1577G>T	c.(1576-1578)tGg>tTg	p.W526L		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	526	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GAGGATGGGTGGCGTGCGGAA	0.473																																					p.W526L		Atlas-SNP	.											.	LAMC1	176	.	0			c.G1577T						.						134.0	116.0	122.0					1																	183086467		2203	4300	6503	SO:0001583	missense	3915	exon9			ATGGGTGGCGTGC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1577G>T	chr1.hg19:g.183086467G>T	ENSP00000258341:p.Trp526Leu	93.0	0.0		87.0	5.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982234	0.93044	.	.	ENSG00000135862	ENST00000258341	T	0.32753	1.44	5.04	5.04	0.67666	Laminin B type IV (1);	0.117057	0.64402	D	0.000007	T	0.61664	0.2365	M	0.91140	3.18	0.80722	D	1	D	0.69078	0.997	P	0.59643	0.861	T	0.72404	-0.4304	10	0.62326	D	0.03	.	18.3933	0.90490	0.0:0.0:1.0:0.0	.	526	P11047	LAMC1_HUMAN	L	526	ENSP00000258341:W526L	ENSP00000258341:W526L	W	+	2	0	LAMC1	181353090	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.013000	0.93629	2.338000	0.79540	0.591000	0.81541	TGG	.	.		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
CAMSAP2	23271	hgsc.bcm.edu	37	1	200708967	200708967	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:200708967T>C	ENST00000236925.4	+	1	61	c.12T>C	c.(10-12)gcT>gcC	p.A4A	CAMSAP2_ENST00000413307.2_Silent_p.A4A|CAMSAP2_ENST00000358823.2_Silent_p.A4A			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	4					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										TGGGGGATGCTGCAGACCCCA	0.592																																					p.A4A		Atlas-SNP	.											.	.	.	.	0			c.T12C						.						91.0	74.0	80.0					1																	200708967		2203	4300	6503	SO:0001819	synonymous_variant	23271	exon1			GGATGCTGCAGAC	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.12T>C	chr1.hg19:g.200708967T>C		175.0	0.0		184.0	8.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.592	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
CAMSAP2	23271	hgsc.bcm.edu	37	1	200817629	200817629	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:200817629T>C	ENST00000236925.4	+	12	1814	c.1765T>C	c.(1765-1767)Tta>Cta	p.L589L	CAMSAP2_ENST00000413307.2_Silent_p.L562L|CAMSAP2_ENST00000358823.2_Silent_p.L578L			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	589					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AATGAGTATCTTAAATTCAAA	0.348																																					p.L578L		Atlas-SNP	.											.	.	.	.	0			c.T1732C						.						44.0	45.0	45.0					1																	200817629		2202	4298	6500	SO:0001819	synonymous_variant	23271	exon11			AGTATCTTAAATT	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1765T>C	chr1.hg19:g.200817629T>C		103.0	0.0		100.0	4.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.348	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
DYRK3	8444	hgsc.bcm.edu	37	1	206822049	206822049	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:206822049T>C	ENST00000367109.2	+	3	1674	c.1506T>C	c.(1504-1506)tgT>tgC	p.C502C	DYRK3_ENST00000367106.1_Silent_p.C482C|DYRK3_ENST00000367108.3_Silent_p.C482C|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	502	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TGAAAAGGTGTCTTCACTGGG	0.532																																					p.C502C	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.T1506C						.						56.0	57.0	57.0					1																	206822049		2203	4300	6503	SO:0001819	synonymous_variant	8444	exon3			AAGGTGTCTTCAC	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"""regulatory erythroid kinase"", ""dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5"", ""protein kinase Dyrk3"""	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1506T>C	chr1.hg19:g.206822049T>C		138.0	0.0		111.0	5.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Silent	SNP	ENST00000367109.2	hg19	CCDS30999.1																																																																																			.	.		0.532	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582	
C1orf116	79098	hgsc.bcm.edu	37	1	207195943	207195943	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:207195943C>A	ENST00000359470.5	-	4	1415	c.1166G>T	c.(1165-1167)gGt>gTt	p.G389V	C1orf116_ENST00000461135.2_Missense_Mutation_p.G143V	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	389	Ala-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.G389A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					ctgagccagacctggagctgg	0.622																																					p.G389V		Atlas-SNP	.											C1orf116,NS,carcinoma,0,1	C1orf116	64	.	1	Substitution - Missense(1)	lung(1)	c.G1166T						.						50.0	56.0	54.0					1																	207195943		2201	4300	6501	SO:0001583	missense	79098	exon4			GCCAGACCTGGAG		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"""specifically androgen-regulated gene"""	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.1166G>T	chr1.hg19:g.207195943C>A	ENSP00000352447:p.Gly389Val	49.0	0.0		40.0	2.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	C	5.692	0.312305	0.10789	.	.	ENSG00000182795	ENST00000359470;ENST00000461135	T;T	0.16897	3.17;2.31	4.95	0.726	0.18248	.	1.401590	0.04545	N	0.388796	T	0.10852	0.0265	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34329	-0.9833	10	0.22109	T	0.4	2.5361	8.4468	0.32847	0.0:0.1417:0.3254:0.533	.	389	Q9BW04	SARG_HUMAN	V	389;143	ENSP00000352447:G389V;ENSP00000436862:G143V	ENSP00000352447:G389V	G	-	2	0	C1orf116	205262566	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.643000	0.24750	0.172000	0.19760	-3.036000	0.00072	GGT	.	.		0.622	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115	
IRF6	3664	hgsc.bcm.edu	37	1	209974642	209974642	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:209974642G>A	ENST00000367021.3	-	3	289	c.117C>T	c.(115-117)ccC>ccT	p.P39P	IRF6_ENST00000542854.1_Intron	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	39			P -> A (in VWS1). {ECO:0000269|PubMed:12219090}.		cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CATGTTTCCAGGGAATCTGGA	0.502										HNSCC(57;0.16)																											p.P39P		Atlas-SNP	.											.	IRF6	65	.	0			c.C117T						.						88.0	94.0	92.0					1																	209974642		2203	4300	6503	SO:0001819	synonymous_variant	3664	exon3			TTTCCAGGGAATC	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"""Van der Woude syndrome"""	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.117C>T	chr1.hg19:g.209974642G>A		101.0	0.0		79.0	4.0	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Silent	SNP	ENST00000367021.3	hg19	CCDS1492.1																																																																																			.	.		0.502	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147	
RPS6KC1	26750	hgsc.bcm.edu	37	1	213349823	213349823	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:213349823G>T	ENST00000366960.3	+	8	1182	c.1032G>T	c.(1030-1032)ggG>ggT	p.G344G	RPS6KC1_ENST00000366959.3_Silent_p.G332G|RPS6KC1_ENST00000543354.1_Silent_p.G47G|RPS6KC1_ENST00000543470.1_Intron|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	344	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAGTCCTTGGGGTGATTGACA	0.453																																					p.G344G		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.G1032T						.						126.0	121.0	123.0					1																	213349823		2203	4300	6503	SO:0001819	synonymous_variant	26750	exon8			CCTTGGGGTGATT	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1032G>T	chr1.hg19:g.213349823G>T		111.0	0.0		123.0	5.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Silent	SNP	ENST00000366960.3	hg19	CCDS1513.1																																																																																			.	.		0.453	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
HHIPL2	79802	hgsc.bcm.edu	37	1	222717113	222717113	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:222717113T>C	ENST00000343410.6	-	2	798	c.740A>G	c.(739-741)gAt>gGt	p.D247G		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	247					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCGACTCCCATCAGGGAGGTA	0.592																																					p.D247G		Atlas-SNP	.											.	HHIPL2	122	.	0			c.A740G						.						85.0	79.0	81.0					1																	222717113		2203	4300	6503	SO:0001583	missense	79802	exon2			CTCCCATCAGGGA	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.740A>G	chr1.hg19:g.222717113T>C	ENSP00000342118:p.Asp247Gly	101.0	0.0		87.0	4.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223114	0.39300	.	.	ENSG00000143512	ENST00000343410	T	0.15256	2.44	5.31	4.18	0.49190	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.099910	0.64402	N	0.000004	T	0.27832	0.0685	L	0.58669	1.825	0.49483	D	0.999797	P	0.46142	0.873	P	0.51945	0.685	T	0.01111	-1.1448	10	0.59425	D	0.04	-18.5314	10.4995	0.44798	0.0:0.0772:0.0:0.9228	.	247	Q6UWX4	HIPL2_HUMAN	G	247	ENSP00000342118:D247G	ENSP00000342118:D247G	D	-	2	0	HHIPL2	220783736	1.000000	0.71417	0.919000	0.36401	0.578000	0.36192	3.916000	0.56416	0.850000	0.35239	0.383000	0.25322	GAT	.	.		0.592	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
NVL	4931	hgsc.bcm.edu	37	1	224475675	224475675	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:224475675C>A	ENST00000281701.6	-	14	1855	c.1596G>T	c.(1594-1596)ctG>ctT	p.L532L	NVL_ENST00000361463.3_Silent_p.L426L|NVL_ENST00000340871.4_Silent_p.L343L|NVL_ENST00000482491.1_Silent_p.L256L|NVL_ENST00000391875.2_Silent_p.L426L|NVL_ENST00000469075.1_Silent_p.L441L	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	532						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		TTAGCAACCCCAGCAGCCTTT	0.408																																					p.L532L		Atlas-SNP	.											.	NVL	74	.	0			c.G1596T						.						61.0	61.0	61.0					1																	224475675		2203	4300	6503	SO:0001819	synonymous_variant	4931	exon14			CAACCCCAGCAGC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"""ATPases / AAA-type"""	8070	protein-coding gene	gene with protein product	"""Nuclear valosin-containing protein-like"", ""nuclear VCP-like protein"""	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1596G>T	chr1.hg19:g.224475675C>A		66.0	0.0		70.0	4.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Silent	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	C	6.827	0.521689	0.13005	.	.	ENSG00000143748	ENST00000469968	.	.	.	5.58	3.38	0.38709	.	.	.	.	.	T	0.59004	0.2162	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55976	-0.8055	4	.	.	.	-9.0371	9.1489	0.36951	0.0:0.6816:0.1209:0.1976	.	.	.	.	W	415	.	.	G	-	1	0	NVL	222542298	0.950000	0.32346	0.830000	0.32933	0.843000	0.47879	2.100000	0.41777	1.358000	0.45922	-0.150000	0.13652	GGG	.	.		0.408	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533	
DNAH14	127602	hgsc.bcm.edu	37	1	225440023	225440023	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:225440023G>A	ENST00000445597.2	+	31	5488	c.5488G>A	c.(5488-5490)Gaa>Aaa	p.E1830K	DNAH14_ENST00000430092.1_Missense_Mutation_p.E2251K|DNAH14_ENST00000439375.2_Missense_Mutation_p.E2251K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1830					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						ACCAACTGGTGAATGTTCCAT	0.353																																					p.E2251K		Atlas-SNP	.											.	DNAH14	300	.	0			c.G6751A						.						281.0	234.0	248.0					1																	225440023		692	1591	2283	SO:0001583	missense	127602	exon44			ACTGGTGAATGTT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.5488G>A	chr1.hg19:g.225440023G>A	ENSP00000409472:p.Glu1830Lys	485.0	2.0		460.0	209.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	hg19		.	.	.	.	.	.	.	.	.	.	g	15.12	2.738464	0.49045	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.29397	2.54;1.57;1.57	4.74	1.29	0.21616	.	.	.	.	.	T	0.14570	0.0352	N	0.14661	0.345	0.31076	N	0.712465	B	0.15930	0.015	B	0.16722	0.016	T	0.38023	-0.9680	9	0.06625	T	0.88	.	8.8703	0.35311	0.2323:0.0:0.7677:0.0	.	2251	Q0VDD8-4	.	K	1830;2251;2251	ENSP00000409472:E1830K;ENSP00000414402:E2251K;ENSP00000392061:E2251K	ENSP00000414402:E2251K	E	+	1	0	DNAH14	223506646	0.189000	0.23263	0.029000	0.17559	0.282000	0.26991	0.072000	0.14617	0.030000	0.15379	0.598000	0.82781	GAA	.	.		0.353	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
EPHX1	2052	hgsc.bcm.edu	37	1	226027000	226027000	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:226027000G>T	ENST00000366837.4	+	5	871	c.675G>T	c.(673-675)ggG>ggT	p.G225G	EPHX1_ENST00000272167.5_Silent_p.G225G|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	225					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TTCAAGGAGGGGACTGGGGGT	0.567																																					p.G225G		Atlas-SNP	.											.	EPHX1	57	.	0			c.G675T						.						75.0	83.0	80.0					1																	226027000		2203	4300	6503	SO:0001819	synonymous_variant	2052	exon5			AGGAGGGGACTGG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.675G>T	chr1.hg19:g.226027000G>T		151.0	0.0		133.0	6.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	hg19	CCDS1547.1																																																																																			.	.		0.567	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
CNST	163882	hgsc.bcm.edu	37	1	246784775	246784775	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:246784775C>T	ENST00000366513.4	+	3	693	c.424C>T	c.(424-426)Cta>Tta	p.L142L	CNST_ENST00000366512.3_Silent_p.L142L|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	142					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AGAAAAAGTACTAAGCGCAGT	0.398																																					p.L142L		Atlas-SNP	.											.	CNST	73	.	0			c.C424T						.						201.0	207.0	205.0					1																	246784775		2203	4300	6503	SO:0001819	synonymous_variant	163882	exon3			AAAGTACTAAGCG	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.424C>T	chr1.hg19:g.246784775C>T		68.0	0.0		92.0	4.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Silent	SNP	ENST00000366513.4	hg19	CCDS1628.1																																																																																			.	.		0.398	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
OR6F1	343169	hgsc.bcm.edu	37	1	247875382	247875382	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:247875382G>T	ENST00000302084.2	-	1	723	c.676C>A	c.(676-678)Ctc>Atc	p.L226I	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GGGATCCTGAGGATGGTGCTG	0.522																																					p.L226I		Atlas-SNP	.											.	OR6F1	88	.	0			c.C676A						.						126.0	113.0	117.0					1																	247875382		2203	4300	6503	SO:0001583	missense	343169	exon1			TCCTGAGGATGGT	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"""GPCR / Class A : Olfactory receptors"""	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.676C>A	chr1.hg19:g.247875382G>T	ENSP00000305640:p.Leu226Ile	95.0	0.0		97.0	4.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061550	0.08339	.	.	ENSG00000169214	ENST00000302084	T	0.00302	8.2	3.72	-2.46	0.06461	GPCR, rhodopsin-like superfamily (1);	0.428415	0.17142	N	0.185383	T	0.00178	0.0005	L	0.58510	1.815	0.20703	N	0.999865	B	0.12630	0.006	B	0.16722	0.016	T	0.45440	-0.9261	10	0.54805	T	0.06	-23.7073	2.7977	0.05406	0.1689:0.253:0.4493:0.1288	.	226	Q8NGZ6	OR6F1_HUMAN	I	226	ENSP00000305640:L226I	ENSP00000305640:L226I	L	-	1	0	OR6F1	245942005	0.000000	0.05858	0.006000	0.13384	0.023000	0.10783	-2.281000	0.01157	-0.241000	0.09681	0.591000	0.81541	CTC	.	.		0.522	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
KIDINS220	57498	hgsc.bcm.edu	37	2	8919191	8919191	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:8919191G>T	ENST00000256707.3	-	19	2630	c.2449C>A	c.(2449-2451)Cag>Aag	p.Q817K	KIDINS220_ENST00000427284.1_Missense_Mutation_p.Q817K|KIDINS220_ENST00000319688.5_Missense_Mutation_p.Q818K|KIDINS220_ENST00000473731.1_Missense_Mutation_p.Q817K|KIDINS220_ENST00000418530.1_Missense_Mutation_p.Q775K	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	817	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTGAGGTTCTGGTTAATTGCC	0.418																																					p.Q817K		Atlas-SNP	.											.	KIDINS220	136	.	0			c.C2449A						.						210.0	189.0	195.0					2																	8919191		1858	4111	5969	SO:0001583	missense	57498	exon19			GGTTCTGGTTAAT	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2449C>A	chr2.hg19:g.8919191G>T	ENSP00000256707:p.Gln817Lys	137.0	0.0		81.0	4.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939734	0.92526	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63;1.63	5.64	5.64	0.86602	KAP P-loop (1);	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.69078	0.985;0.971;0.997;0.996	D;P;D;D	0.83275	0.981;0.796;0.992;0.996	T	0.32771	-0.9894	10	0.33940	T	0.23	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	818;818;775;817	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	K	564;501;817;817;775;817;818;818	ENSP00000420364:Q564K;ENSP00000256707:Q817K;ENSP00000411849:Q817K;ENSP00000414923:Q775K;ENSP00000418974:Q817K;ENSP00000419964:Q818K;ENSP00000319947:Q818K	ENSP00000256707:Q817K	Q	-	1	0	KIDINS220	8836642	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.506000	0.97992	2.820000	0.97059	0.650000	0.86243	CAG	.	.		0.418	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
WDR35	57539	hgsc.bcm.edu	37	2	20133274	20133274	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:20133274T>C	ENST00000345530.3	-	23	2696		c.e23-2		WDR35_ENST00000416055.2_Intron|WDR35_ENST00000281405.4_Splice_Site	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35						cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTATTTCCTGTACAAACAA	0.343																																					.		Atlas-SNP	.											.	WDR35	92	.	0			c.2548-2A>G						.						99.0	86.0	91.0					2																	20133274		2203	4300	6503	SO:0001630	splice_region_variant	57539	exon23			ATTTCCTGTACAA	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2581-2A>G	chr2.hg19:g.20133274T>C		63.0	0.0		91.0	4.0	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Splice_Site	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	19.98	3.926318	0.73327	.	.	ENSG00000118965	ENST00000345530;ENST00000281405	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3615	0.66773	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR35	19996755	1.000000	0.71417	0.997000	0.53966	0.857000	0.48899	7.661000	0.83786	2.049000	0.60858	0.460000	0.39030	.	.	.		0.343	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	Intron
C2orf44	80304	hgsc.bcm.edu	37	2	24261602	24261602	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:24261602C>A	ENST00000295148.4	-	2	820	c.763G>T	c.(763-765)Ggt>Tgt	p.G255C	C2orf44_ENST00000406895.3_Missense_Mutation_p.G255C	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	255									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTACTTCACCAATAACTGGT	0.378			T	ALK	NSCLC																																p.G255C		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.G763T						.						84.0	83.0	84.0					2																	24261602		2203	4300	6503	SO:0001583	missense	80304	exon2			CTTCACCAATAAC	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.763G>T	chr2.hg19:g.24261602C>A	ENSP00000295148:p.Gly255Cys	121.0	0.0		112.0	5.0	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	hg19	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.387681	0.25031	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.48201	0.82;0.82	5.51	1.67	0.24075	WD40/YVTN repeat-like-containing domain (1);	0.820821	0.11399	N	0.568010	T	0.38453	0.1041	N	0.08118	0	0.09310	N	1	D;D	0.63046	0.992;0.992	P;P	0.53360	0.724;0.724	T	0.33599	-0.9862	10	0.62326	D	0.03	-0.0589	10.773	0.46334	0.0:0.7279:0.0:0.2721	.	255;255	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	C	255	ENSP00000295148:G255C;ENSP00000385816:G255C	ENSP00000295148:G255C	G	-	1	0	C2orf44	24115106	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	1.518000	0.35877	0.394000	0.25230	-0.136000	0.14681	GGT	.	.		0.378	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
HADHA	3030	hgsc.bcm.edu	37	2	26453120	26453120	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:26453120T>C	ENST00000380649.3	-	7	745	c.616A>G	c.(616-618)Agc>Ggc	p.S206G	HADHA_ENST00000461025.1_5'Flank|HADHA_ENST00000457468.2_Missense_Mutation_p.S119G	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	206				S -> N (in Ref. 2; AAA56664). {ECO:0000305}.	cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACGAATGCTTCTACCAGTC	0.458																																					p.S206G		Atlas-SNP	.											.	HADHA	87	.	0			c.A616G						.						192.0	173.0	179.0					2																	26453120		2203	4300	6503	SO:0001583	missense	3030	exon7			GAATGCTTCTACC	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.616A>G	chr2.hg19:g.26453120T>C	ENSP00000370023:p.Ser206Gly	108.0	0.0		82.0	4.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928614	0.52759	.	.	ENSG00000084754	ENST00000380649;ENST00000457468	T;T	0.69306	-0.39;-0.39	5.94	3.42	0.39159	Crotonase, core (1);	0.216560	0.53938	N	0.000041	T	0.56761	0.2007	L	0.46885	1.475	0.19775	N	0.999953	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.0;0.0	T	0.51988	-0.8635	10	0.49607	T	0.09	-28.0796	9.0929	0.36621	0.0:0.1646:0.0:0.8354	.	119;206;206	B4DYP2;E9KL44;P40939	.;.;ECHA_HUMAN	G	206;119	ENSP00000370023:S206G;ENSP00000405344:S119G	ENSP00000370023:S206G	S	-	1	0	HADHA	26306624	1.000000	0.71417	0.983000	0.44433	0.985000	0.73830	3.037000	0.49775	0.998000	0.38996	0.455000	0.32223	AGC	.	.		0.458	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
DRC1	92749	hgsc.bcm.edu	37	2	26624926	26624926	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:26624926C>T	ENST00000288710.2	+	1	143	c.69C>T	c.(67-69)ctC>ctT	p.L23L		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	23					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											CCCAGATTCTCGCGCCCTCGG	0.697																																					p.L23L		Atlas-SNP	.											.	CCDC164	84	.	0			c.C69T						.						35.0	31.0	32.0					2																	26624926		2203	4300	6503	SO:0001819	synonymous_variant	92749	exon1			GATTCTCGCGCCC	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.69C>T	chr2.hg19:g.26624926C>T		122.0	0.0		64.0	4.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Silent	SNP	ENST00000288710.2	hg19	CCDS1723.1																																																																																			.	.		0.697	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
TMEM214	54867	hgsc.bcm.edu	37	2	27258128	27258128	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27258128A>G	ENST00000238788.9	+	3	539	c.477A>G	c.(475-477)gaA>gaG	p.E159E	TMEM214_ENST00000404032.3_Silent_p.E159E	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	159					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTCTAAGTGAACCCACGCTGA	0.468																																					p.E159E		Atlas-SNP	.											.	TMEM214	41	.	0			c.A477G						.						85.0	84.0	84.0					2																	27258128		1975	4168	6143	SO:0001819	synonymous_variant	54867	exon3			AAGTGAACCCACG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.477A>G	chr2.hg19:g.27258128A>G		150.0	0.0		96.0	4.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Silent	SNP	ENST00000238788.9	hg19	CCDS42664.1																																																																																			.	.		0.468	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
CAD	790	hgsc.bcm.edu	37	2	27465209	27465209	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27465209G>T	ENST00000403525.1	+	39	6091	c.5947G>T	c.(5947-5949)Ggg>Tgg	p.G1983W	CAD_ENST00000264705.4_Missense_Mutation_p.G2046W			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATCAATGCTGGGGATGGGGT	0.617																																					p.G2046W		Atlas-SNP	.											.	CAD	199	.	0			c.G6136T						.						33.0	36.0	35.0					2																	27465209		2203	4300	6503	SO:0001583	missense	790	exon40			AATGCTGGGGATG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5947G>T	chr2.hg19:g.27465209G>T	ENSP00000384510:p.Gly1983Trp	91.0	0.0		60.0	4.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.3	4.623149	0.87460	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.99220	-5.58;-5.58	4.88	4.88	0.63580	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.99800	4.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96579	0.9429	10	0.87932	D	0	-11.1868	16.5999	0.84810	0.0:0.0:1.0:0.0	.	1983;2046	F8VPD4;P27708	.;PYR1_HUMAN	W	2046;1983	ENSP00000264705:G2046W;ENSP00000384510:G1983W	ENSP00000264705:G2046W	G	+	1	0	CAD	27318713	1.000000	0.71417	0.836000	0.33094	0.947000	0.59692	9.106000	0.94253	2.239000	0.73571	0.491000	0.48974	GGG	.	.		0.617	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
GTF3C2	2976	hgsc.bcm.edu	37	2	27551011	27551011	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27551011C>A	ENST00000359541.2	-	17	2731	c.2302G>T	c.(2302-2304)Ggt>Tgt	p.G768C	GTF3C2_ENST00000264720.3_Missense_Mutation_p.G768C|MPV17_ENST00000357186.6_5'Flank			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	768					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTCTGGACCTTCAGGACTG	0.433																																					p.P768S		Atlas-SNP	.											.	GTF3C2	73	.	0			c.C2302T						.						93.0	89.0	90.0					2																	27551011		2203	4300	6503	SO:0001583	missense	2976	exon18			CTGGACCTTCAGG	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2302G>T	chr2.hg19:g.27551011C>A	ENSP00000352536:p.Gly768Cys	98.0	0.0		100.0	4.0	NM_001521	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.46|18.46|18.46	3.628299|3.628299|3.628299	0.67015|0.67015|0.67015	.|.|.	.|.|.	ENSG00000115207|ENSG00000115207|ENSG00000115207	ENST00000359541;ENST00000264720|ENST00000454704;ENST00000415683|ENST00000457098	T;T|.|.	0.72942|.|.	-0.7;-0.7|.|.	5.16|5.16|5.16	5.16|5.16|5.16	0.70880|0.70880|0.70880	WD40 repeat-like-containing domain (1);|.|.	1.082350|.|.	0.06921|.|.	N|.|.	0.809368|.|.	T|T|T	0.32852|0.32852|0.32852	0.0843|0.0843|0.0843	N|N|N	0.08118|0.08118|0.08118	0|0|0	0.32594|0.32594|0.32594	N|N|N	0.526821|0.526821|0.526821	P|.|.	0.51791|.|.	0.948|.|.	B|.|.	0.43155|.|.	0.41|.|.	T|T|T	0.40887|0.40887|0.40887	-0.9539|-0.9539|-0.9539	10|5|5	0.56958|.|.	D|.|.	0.05|.|.	0.0308|0.0308|0.0308	14.1451|14.1451|14.1451	0.65347|0.65347|0.65347	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	768|.|.	Q8WUA4|.|.	TF3C2_HUMAN|.|.	C|N|M	768|276;190|61	ENSP00000352536:G768C;ENSP00000264720:G768C|.|.	ENSP00000264720:G768C|.|.	G|K|R	-|-|-	1|3|2	0|2|0	GTF3C2|GTF3C2|GTF3C2	27404515|27404515|27404515	0.676000|0.676000|0.676000	0.27567|0.27567|0.27567	0.961000|0.961000|0.961000	0.40146|0.40146|0.40146	0.956000|0.956000|0.956000	0.61745|0.61745|0.61745	3.374000|3.374000|3.374000	0.52402|0.52402|0.52402	2.399000|2.399000|2.399000	0.81585|0.81585|0.81585	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GGT|AAG|AGG	.	.		0.433	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
SNX17	9784	hgsc.bcm.edu	37	2	27597622	27597622	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27597622T>C	ENST00000233575.2	+	8	900	c.678T>C	c.(676-678)gcT>gcC	p.A226A	ZNF513_ENST00000491924.1_5'Flank|SNX17_ENST00000542478.1_Silent_p.A12A|SNX17_ENST00000543024.1_Silent_p.A12A|SNX17_ENST00000537606.1_Silent_p.A201A	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	226	FERM-like.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTTATGCTCAGGTGAGCT	0.517																																					p.A226A		Atlas-SNP	.											.	SNX17	40	.	0			c.T678C						.						152.0	138.0	143.0					2																	27597622		2203	4300	6503	SO:0001819	synonymous_variant	9784	exon8			TTATGCTCAGGTG	D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"""Sorting nexins"""	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.678T>C	chr2.hg19:g.27597622T>C		110.0	0.0		89.0	4.0	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Silent	SNP	ENST00000233575.2	hg19	CCDS1750.1																																																																																			.	.		0.517	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748	
IFT172	26160	hgsc.bcm.edu	37	2	27679376	27679376	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27679376A>G	ENST00000260570.3	-	30	3475		c.e30+1			NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172						bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TTGGGGCCTCACCAATTGTCT	0.512																																					.		Atlas-SNP	.											.	IFT172	119	.	0			c.3371+2T>C						.						90.0	88.0	89.0					2																	27679376		2203	4300	6503	SO:0001630	splice_region_variant	26160	exon31			GGCCTCACCAATT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.3371+1T>C	chr2.hg19:g.27679376A>G		120.0	0.0		106.0	5.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Splice_Site	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.110658	0.37242	.	.	ENSG00000138002	ENST00000260570	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2885	0.73849	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IFT172	27532880	1.000000	0.71417	1.000000	0.80357	0.047000	0.14425	8.841000	0.92131	2.292000	0.77174	0.533000	0.62120	.	.	.		0.512	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	Intron
IFT172	26160	hgsc.bcm.edu	37	2	27703934	27703934	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27703934A>G	ENST00000260570.3	-	8	867	c.764T>C	c.(763-765)gTt>gCt	p.V255A	IFT172_ENST00000416524.2_Missense_Mutation_p.V234A|IFT172_ENST00000359466.6_Missense_Mutation_p.V255A	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	255					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TCCTAGCACAACAGACTGGCC	0.468																																					p.V255A		Atlas-SNP	.											.	IFT172	119	.	0			c.T764C						.						70.0	63.0	66.0					2																	27703934		2203	4300	6503	SO:0001583	missense	26160	exon8			AGCACAACAGACT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.764T>C	chr2.hg19:g.27703934A>G	ENSP00000260570:p.Val255Ala	117.0	0.0		83.0	4.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	A	31	5.084199	0.94100	.	.	ENSG00000138002	ENST00000260570;ENST00000359466;ENST00000416524	T;T;T	0.69306	-0.39;-0.39;1.38	5.85	5.85	0.93711	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.174068	0.50627	D	0.000118	T	0.81969	0.4935	M	0.87900	2.915	0.58432	D	0.999995	D;D;D;D	0.57899	0.969;0.967;0.969;0.981	P;P;P;P	0.61070	0.766;0.883;0.766;0.851	D	0.83873	0.0275	10	0.46703	T	0.11	-14.9757	15.0355	0.71744	1.0:0.0:0.0:0.0	.	255;255;255;255	A5PKZ0;Q9UG01-2;E7EP25;Q9UG01	.;.;.;IF172_HUMAN	A	255;255;234	ENSP00000260570:V255A;ENSP00000352443:V255A;ENSP00000407408:V234A	ENSP00000260570:V255A	V	-	2	0	IFT172	27557438	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	8.581000	0.90788	2.227000	0.72691	0.455000	0.32223	GTT	.	.		0.468	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
CCDC121	79635	hgsc.bcm.edu	37	2	27852779	27852779	+	5'Flank	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27852779G>T	ENST00000324364.3	-	0	0				GPN1_ENST00000458167.2_5'UTR|RP11-158I13.2_ENST00000505973.1_RNA|CCDC121_ENST00000394775.3_5'Flank|GPN1_ENST00000264718.3_Silent_p.L69L|ZNF512_ENST00000556601.1_3'UTR|GPN1_ENST00000503738.1_5'UTR|GPN1_ENST00000515877.1_5'UTR|GPN1_ENST00000407583.3_Silent_p.L43L|GPN1_ENST00000424214.1_5'UTR|GPN1_ENST00000610189.1_Silent_p.L55L|GPN1_ENST00000461249.1_3'UTR	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					TGATCAACCTGGATCCAGCAG	0.493																																					p.L69L		Atlas-SNP	.											.	GPN1	28	.	0			c.G207T						.						143.0	115.0	124.0					2																	27852779		2203	4300	6503	SO:0001631	upstream_gene_variant	11321	exon2			CAACCTGGATCCA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427		chr2.hg19:g.27852779G>T	Exception_encountered	148.0	0.0		121.0	5.0	NM_007266	B3KW66|J3KQZ8|Q9H8G6	Silent	SNP	ENST00000324364.3	hg19	CCDS1759.1																																																																																			.	.		0.493	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584	
BIRC6	57448	hgsc.bcm.edu	37	2	32678911	32678911	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:32678911G>T	ENST00000421745.2	+	23	4788	c.4654G>T	c.(4654-4656)Ggt>Tgt	p.G1552C		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1552					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGCTGCTGAGGGTAGTTTCAC	0.388																																					p.G1552C	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G4654T						.						205.0	190.0	195.0					2																	32678911		2203	4300	6503	SO:0001583	missense	57448	exon23			GCTGAGGGTAGTT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4654G>T	chr2.hg19:g.32678911G>T	ENSP00000393596:p.Gly1552Cys	176.0	0.0		152.0	8.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	20.8	4.045012	0.75846	.	.	ENSG00000115760	ENST00000421745	T	0.74947	-0.89	5.51	5.51	0.81932	.	0.063521	0.64402	D	0.000009	T	0.80633	0.4660	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.68765	0.96	T	0.80251	-0.1460	10	0.45353	T	0.12	.	19.4105	0.94670	0.0:0.0:1.0:0.0	.	1552	Q9NR09	BIRC6_HUMAN	C	1552	ENSP00000393596:G1552C	ENSP00000393596:G1552C	G	+	1	0	BIRC6	32532415	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.987000	0.88182	2.593000	0.87608	0.585000	0.79938	GGT	.	.		0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LTBP1	4052	hgsc.bcm.edu	37	2	33526595	33526595	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:33526595A>G	ENST00000404816.2	+	22	3718	c.3365A>G	c.(3364-3366)gAt>gGt	p.D1122G	LTBP1_ENST00000390003.4_Missense_Mutation_p.D797G|LTBP1_ENST00000402934.1_Missense_Mutation_p.D743G|LTBP1_ENST00000407925.1_Missense_Mutation_p.D796G|LTBP1_ENST00000418533.2_Missense_Mutation_p.D796G|LTBP1_ENST00000272273.5_Missense_Mutation_p.D62G|LTBP1_ENST00000354476.3_Missense_Mutation_p.D1123G|LTBP1_ENST00000404525.1_Missense_Mutation_p.D743G|LTBP1_ENST00000498013.1_3'UTR			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1122	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ATAGACATTGATGAATGCCAG	0.438																																					p.D1122G		Atlas-SNP	.											.	LTBP1	317	.	0			c.A3365G						.						154.0	147.0	149.0					2																	33526595		2203	4300	6503	SO:0001583	missense	4052	exon22			ACATTGATGAATG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3365A>G	chr2.hg19:g.33526595A>G	ENSP00000386043:p.Asp1122Gly	118.0	0.0		94.0	4.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.26|12.26	1.885121|1.885121	0.33255|0.33255	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273|ENST00000415140	D;D;D;D;D;D;D;D|.	0.95588|.	-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75|.	5.36|5.36	5.36|5.36	0.76844|0.76844	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);|.	.|.	.|.	.|.	.|.	D|D	0.86760|0.86760	0.6010|0.6010	H|H	0.95437|0.95437	3.67|3.67	0.46564|0.46564	D|D	0.999104|0.999104	P;B;P;P;B;B;B|.	0.49090|.	0.778;0.438;0.587;0.919;0.239;0.15;0.384|.	P;P;B;P;B;B;B|.	0.54238|.	0.484;0.559;0.336;0.746;0.304;0.226;0.423|.	D|D	0.90634|0.90634	0.4569|0.4569	9|5	0.72032|.	D|.	0.01|.	.|.	14.3408|14.3408	0.66624|0.66624	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	62;1122;796;743;796;797;1123|.	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4|.	.;LTBP1_HUMAN;.;.;.;.;.|.	G|V	1122;1123;797;796;743;743;796;62|84	ENSP00000386043:D1122G;ENSP00000346467:D1123G;ENSP00000374653:D797G;ENSP00000393057:D796G;ENSP00000384373:D743G;ENSP00000385359:D743G;ENSP00000384091:D796G;ENSP00000272273:D62G|.	ENSP00000272273:D62G|.	D|M	+|+	2|1	0|0	LTBP1|LTBP1	33380099|33380099	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.092000|0.092000	0.18411|0.18411	7.408000|7.408000	0.80041|0.80041	2.029000|2.029000	0.59856|0.59856	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.438	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
RMDN2	151393	hgsc.bcm.edu	37	2	38178622	38178622	+	Intron	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:38178622T>A	ENST00000406384.1	+	2	646				RMDN2_ENST00000417700.2_Intron|RMDN2_ENST00000234195.3_Silent_p.A88A|RMDN2_ENST00000407257.1_Silent_p.A88A|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000354545.2_Intron|RMDN2_ENST00000402091.3_Silent_p.A88A	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											AAAGAAATGCTTCCCCTTACT	0.353																																					p.A88A		Atlas-SNP	.											.	.	.	.	0			c.T264A						.						83.0	87.0	86.0					2																	38178622		2203	4300	6503	SO:0001627	intron_variant	151393	exon2			AAATGCTTCCCCT	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"""family with sequence similarity 82, member A1"""	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.452+21750T>A	chr2.hg19:g.38178622T>A		76.0	0.0		54.0	4.0	NM_144713	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Silent	SNP	ENST00000406384.1	hg19	CCDS54351.1																																																																																			.	.		0.353	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713	
EPAS1	2034	hgsc.bcm.edu	37	2	46605102	46605102	+	Missense_Mutation	SNP	C	C	A	rs540130771	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:46605102C>A	ENST00000263734.3	+	10	1829	c.1319C>A	c.(1318-1320)aCg>aAg	p.T440K		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	440					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CCATGGGCCACGGAGTTGAGG	0.672																																					p.T440K		Atlas-SNP	.											.	EPAS1	83	.	0			c.C1319A						.						20.0	18.0	19.0					2																	46605102		2177	4261	6438	SO:0001583	missense	2034	exon10			GGGCCACGGAGTT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1319C>A	chr2.hg19:g.46605102C>A	ENSP00000263734:p.Thr440Lys	141.0	0.0		100.0	4.0	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.747677	0.00669	.	.	ENSG00000116016	ENST00000263734	T	0.45276	0.9	5.58	-1.3	0.09259	.	4.242400	0.00166	N	0.000006	T	0.16257	0.0391	N	0.04203	-0.255	0.09310	N	1	B	0.17038	0.02	B	0.13407	0.009	T	0.20672	-1.0268	10	0.02654	T	1	.	1.6473	0.02764	0.2761:0.3684:0.197:0.1585	.	440	Q99814	EPAS1_HUMAN	K	440	ENSP00000263734:T440K	ENSP00000263734:T440K	T	+	2	0	EPAS1	46458606	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.372000	0.07504	-0.082000	0.12640	0.655000	0.94253	ACG	.	.		0.672	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430	
MSH2	4436	hgsc.bcm.edu	37	2	47703706	47703706	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:47703706C>A	ENST00000233146.2	+	13	2429	c.2206C>A	c.(2206-2208)Ctc>Atc	p.L736I	MSH2_ENST00000543555.1_Missense_Mutation_p.L670I|MSH2_ENST00000406134.1_Missense_Mutation_p.L736I	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	736					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCTTCTATCCTCAGGTAAGT	0.438			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.L736I		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	MSH2,NS,carcinoma,0,1	MSH2	198	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C2206A						.						129.0	117.0	121.0					2																	47703706		2203	4300	6503	SO:0001583	missense	4436	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTATCCTCAGGT	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.2206C>A	chr2.hg19:g.47703706C>A	ENSP00000233146:p.Leu736Ile	64.0	0.0		42.0	2.0	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	hg19	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352194	0.82132	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000413880	D;D;D	0.91068	-2.78;-2.78;-2.78	6.17	6.17	0.99709	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.95796	0.8632	M	0.81341	2.54	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.95	D;D;P	0.91635	0.999;0.999;0.823	D	0.94587	0.7784	10	0.49607	T	0.09	-10.741	20.8794	0.99867	0.0:1.0:0.0:0.0	.	670;736;736	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	I	736;670;736;736;522	ENSP00000233146:L736I;ENSP00000442697:L670I;ENSP00000384199:L736I	ENSP00000233146:L736I	L	+	1	0	MSH2	47557210	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	4.626000	0.61269	2.941000	0.99782	0.655000	0.94253	CTC	.	.		0.438	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
FAM161A	84140	hgsc.bcm.edu	37	2	62067708	62067708	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:62067708G>A	ENST00000405894.3	-	3	532	c.431C>T	c.(430-432)tCa>tTa	p.S144L	FAM161A_ENST00000404929.1_Missense_Mutation_p.S144L	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	144					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GTTCTTTTCTGATACAGATCT	0.343																																					p.S144L		Atlas-SNP	.											.	FAM161A	200	.	0			c.C431T						.						67.0	59.0	61.0					2																	62067708		1833	4086	5919	SO:0001583	missense	84140	exon3			TTTTCTGATACAG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.431C>T	chr2.hg19:g.62067708G>A	ENSP00000385893:p.Ser144Leu	200.0	0.0		159.0	76.0	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	G	13.01	2.110039	0.37242	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.25250	2.62;1.81	4.66	1.63	0.23807	.	0.372310	0.26453	N	0.024295	T	0.21921	0.0528	L	0.56769	1.78	0.09310	N	1	P;B	0.50156	0.932;0.274	B;B	0.44278	0.445;0.084	T	0.13019	-1.0525	9	.	.	.	-9.5961	2.1742	0.03858	0.1828:0.2952:0.3944:0.1276	.	144;144	Q3B820;Q3B820-3	F161A_HUMAN;.	L	144	ENSP00000385158:S144L;ENSP00000385893:S144L	.	S	-	2	0	FAM161A	61921212	0.997000	0.39634	0.163000	0.22734	0.918000	0.54935	1.814000	0.38972	0.513000	0.28278	0.563000	0.77884	TCA	.	.		0.343	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
EHBP1	23301	hgsc.bcm.edu	37	2	62998523	62998523	+	Missense_Mutation	SNP	A	A	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:62998523A>C	ENST00000263991.5	+	5	790	c.308A>C	c.(307-309)gAa>gCa	p.E103A	EHBP1_ENST00000354487.3_Missense_Mutation_p.E103A|EHBP1_ENST00000405289.1_Missense_Mutation_p.E103A|EHBP1_ENST00000431489.1_Missense_Mutation_p.E103A|EHBP1_ENST00000405015.3_Missense_Mutation_p.E103A	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	103						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TTTGTCATAGAAAATGTAAGC	0.333																																					p.E103A		Atlas-SNP	.											.	EHBP1	127	.	0			c.A308C						.						114.0	113.0	113.0					2																	62998523		2203	4296	6499	SO:0001583	missense	23301	exon5			TCATAGAAAATGT	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.308A>C	chr2.hg19:g.62998523A>C	ENSP00000263991:p.Glu103Ala	152.0	0.0		145.0	26.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.618486	0.87359	.	.	ENSG00000115504	ENST00000405015;ENST00000413434;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.06	5.06	0.68205	.	0.122342	0.56097	D	0.000023	T	0.68513	0.3009	M	0.87180	2.865	0.80722	D	1	P;D;D;P	0.71674	0.726;0.979;0.998;0.689	P;D;D;P	0.81914	0.525;0.973;0.995;0.73	T	0.75539	-0.3282	10	0.87932	D	0	.	14.5025	0.67732	1.0:0.0:0.0:0.0	.	103;103;103;103	Q8NDI1-2;A8K930;Q8NDI1-3;Q8NDI1	.;.;.;EHBP1_HUMAN	A	103;71;103;103;103;103;103	ENSP00000384143:E103A;ENSP00000392192:E71A;ENSP00000384829:E103A;ENSP00000403783:E103A;ENSP00000263991:E103A;ENSP00000346482:E103A;ENSP00000385524:E103A	ENSP00000263991:E103A	E	+	2	0	EHBP1	62852027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.964000	0.93389	1.909000	0.55274	0.528000	0.53228	GAA	.	.		0.333	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
PLEK	5341	hgsc.bcm.edu	37	2	68607861	68607861	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:68607861T>C	ENST00000234313.7	+	3	384	c.205T>C	c.(205-207)Ttt>Ctt	p.F69L		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	69	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		TCAGTTTGTGTTTAAGATCAC	0.478																																					p.F69L		Atlas-SNP	.											.	PLEK	64	.	0			c.T205C						.						116.0	115.0	115.0					2																	68607861		2203	4300	6503	SO:0001583	missense	5341	exon3			TTTGTGTTTAAGA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.205T>C	chr2.hg19:g.68607861T>C	ENSP00000234313:p.Phe69Leu	111.0	0.0		95.0	5.0	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	hg19	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.445498	0.63178	.	.	ENSG00000115956	ENST00000234313	T	0.35236	1.32	5.79	5.79	0.91817	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.042653	0.85682	N	0.000000	T	0.42988	0.1227	M	0.74258	2.255	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.17433	0.018;0.015	T	0.30679	-0.9970	10	0.46703	T	0.11	.	16.1338	0.81465	0.0:0.0:0.0:1.0	.	87;69	Q59GZ2;P08567	.;PLEK_HUMAN	L	69	ENSP00000234313:F69L	ENSP00000234313:F69L	F	+	1	0	PLEK	68461365	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.676000	0.84012	2.216000	0.71823	0.528000	0.53228	TTT	.	.		0.478	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
SFXN5	94097	hgsc.bcm.edu	37	2	73247367	73247367	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:73247367C>T	ENST00000272433.2	-	6	488		c.e6+1		SFXN5_ENST00000474528.1_Splice_Site|SFXN5_ENST00000410065.1_Splice_Site	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						GTAACACTTACAATTGGCGTC	0.383																																					.		Atlas-SNP	.											.	SFXN5	31	.	0			c.357+1G>A						.						87.0	86.0	86.0					2																	73247367		2203	4300	6503	SO:0001630	splice_region_variant	94097	exon7			CACTTACAATTGG	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"""Sideroflexins"""	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.357+1G>A	chr2.hg19:g.73247367C>T		126.0	0.0		89.0	4.0	NM_144579	A8K116|Q494Y3|Q53T29	Splice_Site	SNP	ENST00000272433.2	hg19	CCDS1922.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547892	0.65311	.	.	ENSG00000144040	ENST00000272433;ENST00000411783;ENST00000410065;ENST00000442582	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8549	0.63519	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SFXN5	73100875	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.640000	0.61368	2.726000	0.93360	0.655000	0.94253	.	.	.		0.383	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579	Intron
FBXO41	150726	hgsc.bcm.edu	37	2	73496418	73496418	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:73496418G>A	ENST00000521871.1	-	2	756	c.341C>T	c.(340-342)cCc>cTc	p.P114L	FBXO41_ENST00000520186.1_5'Flank|FBXO41_ENST00000520530.2_Missense_Mutation_p.P114L|FBXO41_ENST00000295133.5_Missense_Mutation_p.P175L			Q8TF61	FBX41_HUMAN	F-box protein 41	114										breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						GTGGGCGAGGGGAGCGTGGTG	0.726																																					p.P114L		Atlas-SNP	.											.	FBXO41	82	.	0			c.C341T						.						1.0	2.0	2.0					2																	73496418		1163	2298	3461	SO:0001583	missense	150726	exon1			GCGAGGGGAGCGT	AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013		"""F-boxes /  ""other"""""	29409	protein-coding gene	gene with protein product		609108				11853319	Standard	NM_001080410		Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.341C>T	chr2.hg19:g.73496418G>A	ENSP00000428646:p.Pro114Leu	129.0	0.0		60.0	4.0	NM_001080410	G3V0Z7|Q2M1V8	Missense_Mutation	SNP	ENST00000521871.1	hg19	CCDS46337.2	.	.	.	.	.	.	.	.	.	.	G	15.39	2.820856	0.50633	.	.	ENSG00000163013	ENST00000295133;ENST00000521871;ENST00000520530	.	.	.	4.4	4.4	0.53042	.	0.144200	0.32503	N	0.006007	T	0.37265	0.0997	N	0.08118	0	0.41524	D	0.988414	B	0.15141	0.012	B	0.09377	0.004	T	0.33650	-0.9860	9	0.66056	D	0.02	-14.6849	12.6472	0.56742	0.0:0.0:1.0:0.0	.	114	Q8TF61	FBX41_HUMAN	L	175;114;175	.	ENSP00000295133:P175L	P	-	2	0	FBXO41	73349926	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	-0.033000	0.12246	2.428000	0.82296	0.462000	0.41574	CCC	.	.		0.726	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1		
DNAH6	1768	hgsc.bcm.edu	37	2	84822786	84822786	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:84822786T>C	ENST00000237449.6	+	17	2749	c.2741T>C	c.(2740-2742)cTg>cCg	p.L914P	DNAH6_ENST00000389394.3_Missense_Mutation_p.L914P|DNAH6_ENST00000398278.2_Missense_Mutation_p.L914P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	914	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTGATTGCCTGGATCCAGAA	0.333																																					p.L914P		Atlas-SNP	.											.	DNAH6	194	.	0			c.T2741C						.						57.0	48.0	51.0					2																	84822786		692	1591	2283	SO:0001583	missense	1768	exon18			ATTGCCTGGATCC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2741T>C	chr2.hg19:g.84822786T>C	ENSP00000237449:p.Leu914Pro	54.0	0.0		93.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896152	0.72639	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.66460	-0.21;-0.21;-0.21	5.82	5.82	0.92795	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.86548	0.5959	H	0.94183	3.505	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.90224	0.4274	9	0.87932	D	0	.	15.159	0.72767	0.0:0.0:0.0:1.0	.	914	Q9C0G6	DYH6_HUMAN	P	914	ENSP00000374045:L914P;ENSP00000381326:L914P;ENSP00000237449:L914P	ENSP00000237449:L914P	L	+	2	0	DNAH6	84676297	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.206000	0.72154	2.215000	0.71742	0.528000	0.53228	CTG	.	.		0.333	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
DNAH6	1768	hgsc.bcm.edu	37	2	84955003	84955003	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:84955003C>A	ENST00000237449.6	+	60	10191	c.10183C>A	c.(10183-10185)Cga>Aga	p.R3395R	DNAH6_ENST00000389394.3_Silent_p.R3395R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3395					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTCTTTCTCCGAGGTTCTGC	0.413																																					p.R3395R		Atlas-SNP	.											.	DNAH6	194	.	0			c.C10183A						.						102.0	83.0	89.0					2																	84955003		692	1591	2283	SO:0001819	synonymous_variant	1768	exon61			TTTCTCCGAGGTT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.10183C>A	chr2.hg19:g.84955003C>A		103.0	0.0		91.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.413	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
GNLY	10578	hgsc.bcm.edu	37	2	85922521	85922521	+	Missense_Mutation	SNP	C	C	T	rs573832985		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:85922521C>T	ENST00000263863.4	+	2	259	c.131C>T	c.(130-132)cCg>cTg	p.P44L	GNLY_ENST00000533041.1_3'UTR|GNLY_ENST00000409696.3_Missense_Mutation_p.P29L|GNLY_ENST00000524600.1_Missense_Mutation_p.P71L	NM_006433.3	NP_006424.2	P22749	GNLY_HUMAN	granulysin	44					cellular defense response (GO:0006968)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular space (GO:0005615)				endometrium(4)|kidney(10)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	19						AAATCCTGCCCGTGCCTGGCC	0.622													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18397	0.0		0.0	False		,,,				2504	0.0				p.P44L		Atlas-SNP	.											.	GNLY	29	.	0			c.C131T						.						77.0	64.0	69.0					2																	85922521		2203	4300	6503	SO:0001583	missense	10578	exon2			CCTGCCCGTGCCT	X54101	CCDS1984.1, CCDS46354.1	2p12-q11	2008-02-05			ENSG00000115523	ENSG00000115523			4414	protein-coding gene	gene with protein product	"""T-lymphocyte activation gene 519"""	188855		LAG2		2212946, 2434598	Standard	NM_012483		Approved	NKG5, LAG-2, D2S69E, TLA519	uc002sql.4	P22749	OTTHUMG00000130179	ENST00000263863.4:c.131C>T	chr2.hg19:g.85922521C>T	ENSP00000263863:p.Pro44Leu	78.0	0.0		84.0	4.0	NM_006433	P09325|Q6GU08	Missense_Mutation	SNP	ENST00000263863.4	hg19	CCDS1984.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.649|8.649	0.897716|0.897716	0.17686|0.17686	.|.	.|.	ENSG00000115523|ENSG00000115523	ENST00000263863;ENST00000524600;ENST00000409696|ENST00000526018	T;T;T|.	0.48201|.	0.87;0.82;0.87|.	1.64|1.64	-3.28|-3.28	0.05033|0.05033	.|.	2.881540|.	0.01470|.	U|.	0.016250|.	T|T	0.17280|0.17280	0.0415|0.0415	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	P;P|.	0.46512|.	0.879;0.879|.	B;B|.	0.26517|.	0.07;0.07|.	T|T	0.23226|0.23226	-1.0194|-1.0194	10|5	0.33141|.	T|.	0.24|.	.|.	5.7405|5.7405	0.18092|0.18092	0.2475:0.5939:0.1586:0.0|0.2475:0.5939:0.1586:0.0	.|.	71;44|.	B4E3H9;P22749|.	.;GNLY_HUMAN|.	L|C	44;71;29|11	ENSP00000263863:P44L;ENSP00000436423:P71L;ENSP00000387116:P29L|.	ENSP00000263863:P44L|.	P|R	+|+	2|1	0|0	GNLY|GNLY	85776032|85776032	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.125000|0.125000	0.20455|0.20455	-0.562000|-0.562000	0.05950|0.05950	-1.619000|-1.619000	0.01566|0.01566	0.306000|0.306000	0.20318|0.20318	CCG|CGT	.	.		0.622	GNLY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252497.1	NM_006433	
MRPS5	64969	hgsc.bcm.edu	37	2	95756225	95756225	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:95756225C>T	ENST00000272418.2	-	11	1182	c.974G>A	c.(973-975)cGg>cAg	p.R325Q		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	325					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						GCCAATGAGCCGGCAGATGGT	0.572																																					p.R325Q		Atlas-SNP	.											.	MRPS5	52	.	0			c.G974A						.						99.0	100.0	100.0					2																	95756225		2203	4300	6503	SO:0001583	missense	64969	exon11			ATGAGCCGGCAGA	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.974G>A	chr2.hg19:g.95756225C>T	ENSP00000272418:p.Arg325Gln	122.0	0.0		87.0	24.0	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652325	0.47362	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.09	4.0	0.46444	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5, C-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.122060	0.51477	D	0.000094	T	0.26521	0.0648	N	0.25144	0.715	0.26531	N	0.974258	B	0.20261	0.043	B	0.15484	0.013	T	0.11203	-1.0597	9	0.52906	T	0.07	-10.0992	7.817	0.29265	0.0:0.8007:0.0:0.1993	.	325	P82675	RT05_HUMAN	Q	325	.	ENSP00000272418:R325Q	R	-	2	0	MRPS5	95119952	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	2.213000	0.42844	2.360000	0.80028	0.591000	0.81541	CGG	.	.		0.572	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	
FAHD2A	51011	hgsc.bcm.edu	37	2	96078508	96078508	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:96078508T>C	ENST00000233379.4	+	7	1031	c.878T>C	c.(877-879)cTc>cCc	p.L293P	FAHD2A_ENST00000447036.1_Missense_Mutation_p.L293P	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	293							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						CCTGTCTTTCTCAAGGTAGGT	0.517																																					p.L293P		Atlas-SNP	.											.	FAHD2A	25	.	0			c.T878C						.						37.0	37.0	37.0					2																	96078508		2203	4300	6503	SO:0001583	missense	51011	exon7			TCTTTCTCAAGGT	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.878T>C	chr2.hg19:g.96078508T>C	ENSP00000233379:p.Leu293Pro	105.0	0.0		98.0	4.0	NM_016044	Q9Y3B0	Missense_Mutation	SNP	ENST00000233379.4	hg19	CCDS2014.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816199	0.70912	.	.	ENSG00000115042	ENST00000447036;ENST00000233379	D;D	0.98633	-5.04;-5.04	3.38	3.38	0.38709	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99429	0.9798	H	0.98996	4.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98190	1.0462	10	0.87932	D	0	.	10.0306	0.42099	0.0:0.0:0.0:1.0	.	293	Q96GK7	FAH2A_HUMAN	P	293	ENSP00000406424:L293P;ENSP00000233379:L293P	ENSP00000233379:L293P	L	+	2	0	FAHD2A	95442235	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.987000	0.76206	1.527000	0.49086	0.402000	0.26972	CTC	.	.		0.517	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044	
KANSL3	55683	hgsc.bcm.edu	37	2	97302719	97302719	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:97302719T>C	ENST00000431828.1	-	2	230	c.154A>G	c.(154-156)Agt>Ggt	p.S52G	KANSL3_ENST00000435669.1_5'UTR|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000599854.1_5'UTR|KANSL3_ENST00000441706.2_5'UTR|KANSL3_ENST00000440133.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	52					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGGGCACTACTGGCATCTGGG	0.582																																					p.S52G		Atlas-SNP	.											.	.	.	.	0			c.A154G						.						54.0	47.0	49.0					2																	97302719		692	1591	2283	SO:0001583	missense	55683	exon2			CACTACTGGCATC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"""KIAA1310"""	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.154A>G	chr2.hg19:g.97302719T>C	ENSP00000396749:p.Ser52Gly	161.0	0.0		101.0	5.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295076	0.60086	.	.	ENSG00000114982	ENST00000431828	T	0.69561	-0.41	4.73	4.73	0.59995	.	.	.	.	.	T	0.64713	0.2623	L	0.58101	1.795	0.80722	D	1	B	0.23128	0.08	B	0.29440	0.102	T	0.66551	-0.5895	9	0.87932	D	0	.	12.218	0.54416	0.0:0.0:0.0:1.0	.	52	Q9P2N6-3	.	G	52	ENSP00000396749:S52G	ENSP00000410775:S52G	S	-	1	0	KIAA1310	96666446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.087000	0.76893	1.982000	0.57802	0.460000	0.39030	AGT	.	.		0.582	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991	
ZAP70	7535	hgsc.bcm.edu	37	2	98349776	98349776	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:98349776A>G	ENST00000264972.5	+	7	1022	c.807A>G	c.(805-807)acA>acG	p.T269T	ZAP70_ENST00000442208.1_Silent_p.T143T|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000451498.2_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	269	Interdomain B.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CTGCTCCCACACTCCCAGCCC	0.706																																					p.T269T		Atlas-SNP	.											.	ZAP70	77	.	0			c.A807G						.						18.0	18.0	18.0					2																	98349776		2203	4297	6500	SO:0001819	synonymous_variant	7535	exon7			TCCCACACTCCCA	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.807A>G	chr2.hg19:g.98349776A>G		191.0	0.0		124.0	6.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	hg19	CCDS33254.1																																																																																			.	.		0.706	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
LYG2	254773	hgsc.bcm.edu	37	2	99870712	99870712	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:99870712G>T	ENST00000409238.1	-	1	32	c.12C>A	c.(10-12)tcC>tcA	p.S4S	LYG2_ENST00000409679.1_Silent_p.S4S|LYG2_ENST00000423800.1_Silent_p.S4S|LYG2_ENST00000333017.2_Silent_p.S4S			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	4					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						AAAACACCACGGAGGATAACA	0.398																																					p.S4S		Atlas-SNP	.											.	LYG2	26	.	0			c.C12A						.						119.0	109.0	112.0					2																	99870712		2203	4300	6503	SO:0001819	synonymous_variant	254773	exon2			CACCACGGAGGAT	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.12C>A	chr2.hg19:g.99870712G>T		73.0	0.0		57.0	5.0	NM_175735	Q496G2|Q53RW0	Silent	SNP	ENST00000409238.1	hg19	CCDS2042.1																																																																																			.	.		0.398	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735	
AFF3	3899	hgsc.bcm.edu	37	2	100185316	100185316	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:100185316T>C	ENST00000409236.2	-	17	3092	c.2980A>G	c.(2980-2982)Atg>Gtg	p.M994V	AFF3_ENST00000317233.4_Missense_Mutation_p.M994V|AFF3_ENST00000409579.1_Missense_Mutation_p.M1019V|AFF3_ENST00000356421.2_Missense_Mutation_p.M1019V			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	994					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.M1019V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GGTCTCACCATTGCATCTGCT	0.383																																					p.M1019V		Atlas-SNP	.											AFF3,NS,carcinoma,0,1	AFF3	164	.	1	Substitution - Missense(1)	breast(1)	c.A3055G						.						208.0	190.0	197.0					2																	100185316		2203	4300	6503	SO:0001583	missense	3899	exon18			TCACCATTGCATC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2980A>G	chr2.hg19:g.100185316T>C	ENSP00000387207:p.Met994Val	125.0	0.0		121.0	6.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	T	18.71	3.681634	0.68042	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000445815	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.71492	0.3346	M	0.63428	1.95	0.50813	D	0.999892	B;P	0.51147	0.237;0.942	B;P	0.53649	0.387;0.731	T	0.72704	-0.4213	10	0.49607	T	0.09	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	994;1019	P51826;P51826-2	AFF3_HUMAN;.	V	994;1019;1019;994;36	ENSP00000317421:M994V;ENSP00000348793:M1019V;ENSP00000386834:M1019V;ENSP00000387207:M994V;ENSP00000416685:M36V	ENSP00000317421:M994V	M	-	1	0	AFF3	99551748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.842000	0.62831	2.326000	0.78906	0.533000	0.62120	ATG	.	.		0.383	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
RFX8	731220	hgsc.bcm.edu	37	2	102031354	102031354	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:102031354T>C	ENST00000376826.2	-	10	861	c.862A>G	c.(862-864)Aga>Gga	p.R288G	RFX8_ENST00000428343.1_Missense_Mutation_p.R175G			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	288					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|stomach(1)	3						CTTCTTAGTCTTTTGACAAAT	0.428																																					p.R175G		Atlas-SNP	.											.	RFX8	16	.	0			c.A523G						.						204.0	157.0	172.0					2																	102031354		692	1591	2283	SO:0001583	missense	731220	exon7			TTAGTCTTTTGAC	AK124976	CCDS46376.1	2q11.2	2012-11-15	2012-11-15		ENSG00000196460	ENSG00000196460			37253	protein-coding gene	gene with protein product			"""regulatory factor X, 8"", ""RFX gene family member 8, lacking RFX DNA binding domain"""				Standard	NM_001145664		Approved	FLJ42986	uc010yvx.1	Q6ZV50	OTTHUMG00000130693	ENST00000376826.2:c.862A>G	chr2.hg19:g.102031354T>C	ENSP00000366022:p.Arg288Gly	115.0	0.0		76.0	4.0	NM_001145664	B4DQ32	Missense_Mutation	SNP	ENST00000376826.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.83	3.485641	0.63962	.	.	ENSG00000196460	ENST00000376826;ENST00000428343	T;T	0.76968	-1.06;0.91	5.08	5.08	0.68730	.	.	.	.	.	T	0.81569	0.4850	L	0.40543	1.245	0.32727	N	0.509538	D	0.76494	0.999	D	0.83275	0.996	T	0.81852	-0.0742	9	0.29301	T	0.29	.	11.2069	0.48775	0.0:0.0:0.0:1.0	.	175	Q6ZV50-3	.	G	288;175	ENSP00000366022:R288G;ENSP00000401536:R175G	ENSP00000366022:R288G	R	-	1	2	RFX8	101397786	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	3.845000	0.55880	2.153000	0.67306	0.454000	0.30748	AGA	.	.		0.428	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
IL1R1	3554	hgsc.bcm.edu	37	2	102791944	102791944	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:102791944A>G	ENST00000410023.1	+	11	1460	c.1142A>G	c.(1141-1143)gAt>gGt	p.D381G	IL1R1_ENST00000409929.1_Intron|IL1R1_ENST00000424272.1_Missense_Mutation_p.D381G|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409329.1_Missense_Mutation_p.D381G|IL1R1_ENST00000233946.3_Missense_Mutation_p.D381G|IL1R1_ENST00000409288.1_Missense_Mutation_p.D381G|IL1R1_ENST00000409589.1_Intron			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	381					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TTAGCTTCAGATGGAAAGACC	0.348																																					p.D381G		Atlas-SNP	.											.	IL1R1	52	.	0			c.A1142G						.						228.0	214.0	219.0					2																	102791944		2203	4300	6503	SO:0001583	missense	3554	exon10			CTTCAGATGGAAA	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1142A>G	chr2.hg19:g.102791944A>G	ENSP00000386380:p.Asp381Gly	555.0	0.0		557.0	109.0	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079933	0.76528	.	.	ENSG00000115594	ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T	0.02606	4.23;4.23;4.23;4.23;4.23;4.23	5.23	5.23	0.72850	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.155915	0.56097	D	0.000030	T	0.19406	0.0466	M	0.88450	2.955	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.01245	-1.1407	10	0.87932	D	0	.	15.4254	0.75045	1.0:0.0:0.0:0.0	.	381;381	P14778;B8ZZ73	IL1R1_HUMAN;.	G	381;381;237;381;381;381	ENSP00000415366:D381G;ENSP00000387131:D381G;ENSP00000410461:D237G;ENSP00000386478:D381G;ENSP00000386380:D381G;ENSP00000233946:D381G	ENSP00000233946:D381G	D	+	2	0	IL1R1	102158376	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.777000	0.62361	2.104000	0.64026	0.456000	0.33151	GAT	.	.		0.348	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
NCK2	8440	hgsc.bcm.edu	37	2	106498261	106498261	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:106498261G>A	ENST00000233154.4	+	4	1146	c.704G>A	c.(703-705)tGg>tAg	p.W235*	NCK2_ENST00000522586.1_Intron|NCK2_ENST00000393349.2_Nonsense_Mutation_p.W235*|NCK2_ENST00000451463.2_Intron	NM_003581.4	NP_003572.2	O43639	NCK2_HUMAN	NCK adaptor protein 2	235	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|lamellipodium assembly (GO:0030032)|negative regulation of cell proliferation (GO:0008285)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of translation (GO:0006417)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|lung(3)|ovary(1)	5						CCCGAGTGGTGGAAATGCAAA	0.622																																					p.W235X		Atlas-SNP	.											.	NCK2	75	.	0			c.G704A						.						73.0	81.0	78.0					2																	106498261		2203	4300	6503	SO:0001587	stop_gained	8440	exon3			AGTGGTGGAAATG	AF043119	CCDS33266.1	2q12	2013-02-14			ENSG00000071051	ENSG00000071051		"""SH2 domain containing"""	7665	protein-coding gene	gene with protein product		604930				9737977, 16752908	Standard	NM_001004720		Approved	NCKbeta	uc002tdi.3	O43639	OTTHUMG00000153116	ENST00000233154.4:c.704G>A	chr2.hg19:g.106498261G>A	ENSP00000233154:p.Trp235*	118.0	0.0		91.0	5.0	NM_001004720	D3DVK1|Q9BWN9|Q9UIC3	Nonsense_Mutation	SNP	ENST00000233154.4	hg19	CCDS33266.1	.	.	.	.	.	.	.	.	.	.	G	40	8.081717	0.98643	.	.	ENSG00000071051	ENST00000233154;ENST00000393349	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6619	19.782	0.96420	0.0:0.0:1.0:0.0	.	.	.	.	X	235	.	ENSP00000233154:W235X	W	+	2	0	NCK2	105864693	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.354000	0.97083	2.757000	0.94681	0.462000	0.41574	TGG	.	.		0.622	NCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329634.1	NM_003581	
TFCP2L1	29842	hgsc.bcm.edu	37	2	121991665	121991665	+	Splice_Site	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:121991665A>T	ENST00000263707.5	-	12	1296		c.e12+1			NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1						cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CCCACAACTCACCAGACAGGT	0.577																																					.		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.1198+2T>A						.						95.0	87.0	90.0					2																	121991665		2203	4300	6503	SO:0001630	splice_region_variant	29842	exon13			CAACTCACCAGAC	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1198+1T>A	chr2.hg19:g.121991665A>T		61.0	0.0		56.0	4.0	NM_014553	Q4ZG43	Splice_Site	SNP	ENST00000263707.5	hg19	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303855	0.23736	.	.	ENSG00000115112	ENST00000263707	.	.	.	5.53	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2086	0.48784	0.9282:0.0:0.0718:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TFCP2L1	121708135	1.000000	0.71417	0.994000	0.49952	0.064000	0.16182	4.675000	0.61619	0.955000	0.37878	0.448000	0.29417	.	.	.		0.577	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553	Intron
PROC	5624	hgsc.bcm.edu	37	2	128186178	128186178	+	Silent	SNP	C	C	A	rs121918141		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:128186178C>A	ENST00000234071.3	+	9	1129	c.1042C>A	c.(1042-1044)Cga>Aga	p.R348R	PROC_ENST00000409048.1_Silent_p.R382R|PROC_ENST00000422777.3_Silent_p.R348R|PROC_ENST00000453608.2_Silent_p.R403R	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	348	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCACAGCAGCCGAGAGAAGGA	0.612																																					p.R348R		Atlas-SNP	.											.	PROC	31	.	0			c.C1042A	GRCh37	CM870018	PROC	M	rs121918141	.						101.0	116.0	111.0					2																	128186178		2203	4300	6503	SO:0001819	synonymous_variant	5624	exon9			AGCAGCCGAGAGA	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"""Endogenous ligands"""	9451	protein-coding gene	gene with protein product	"""prepro-protein C"""	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.1042C>A	chr2.hg19:g.128186178C>A		131.0	0.0		67.0	4.0	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	hg19	CCDS2145.1																																																																																			.	.		0.612	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
LRP1B	53353	hgsc.bcm.edu	37	2	141773444	141773444	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:141773444C>A	ENST00000389484.3	-	13	2982	c.2011G>T	c.(2011-2013)Gac>Tac	p.D671Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	671					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCCACGCTGTCATCTATTTCA	0.408										TSP Lung(27;0.18)																											p.D671Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G2011T						.						156.0	152.0	154.0					2																	141773444		2203	4300	6503	SO:0001583	missense	53353	exon13			CGCTGTCATCTAT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2011G>T	chr2.hg19:g.141773444C>A	ENSP00000374135:p.Asp671Tyr	322.0	0.0		238.0	72.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031998	0.75504	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90197	-2.63	5.75	5.75	0.90469	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	U	0.000000	D	0.93148	0.7818	L	0.50333	1.59	0.52099	D	0.999946	P	0.50066	0.931	P	0.57152	0.814	D	0.92568	0.6064	10	0.54805	T	0.06	.	20.312	0.98644	0.0:1.0:0.0:0.0	.	671	Q9NZR2	LRP1B_HUMAN	Y	671;609	ENSP00000374135:D671Y	ENSP00000374135:D671Y	D	-	1	0	LRP1B	141489914	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.951000	0.56684	2.866000	0.98385	0.650000	0.86243	GAC	.	.		0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LRP1B	53353	hgsc.bcm.edu	37	2	141777526	141777526	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:141777526A>G	ENST00000389484.3	-	12	2906	c.1935T>C	c.(1933-1935)tcT>tcC	p.S645S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	645					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTCTGGGATGAGACATTTCAC	0.373										TSP Lung(27;0.18)																											p.S645S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T1935C						.						92.0	93.0	93.0					2																	141777526		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon12			GGGATGAGACATT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1935T>C	chr2.hg19:g.141777526A>G		100.0	0.0		84.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
XIRP2	129446	hgsc.bcm.edu	37	2	168107554	168107554	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:168107554C>T	ENST00000409195.1	+	9	9741	c.9652C>T	c.(9652-9654)Cct>Tct	p.P3218S	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.P2996S|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.P3218S|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3043					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CATCATGTCTCCTGCAACACT	0.448																																					p.P3218S		Atlas-SNP	.											.	XIRP2	914	.	0			c.C9652T						.						70.0	69.0	69.0					2																	168107554		1927	4131	6058	SO:0001583	missense	129446	exon9			ATGTCTCCTGCAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9652C>T	chr2.hg19:g.168107554C>T	ENSP00000386840:p.Pro3218Ser	140.0	0.0		101.0	5.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346807	0.82022	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02763	4.18;4.18;4.17	5.45	5.45	0.79879	.	0.369002	0.30840	N	0.008776	T	0.15565	0.0375	M	0.72894	2.215	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.993	T	0.00026	-1.2309	10	0.66056	D	0.02	-15.7534	18.4306	0.90624	0.0:1.0:0.0:0.0	.	3043;3043;2996	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	3218;3218;2996;632	ENSP00000386840:P3218S;ENSP00000295237:P3218S;ENSP00000387255:P2996S	ENSP00000295237:P3218S	P	+	1	0	XIRP2	167815800	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.782000	0.75073	2.729000	0.93468	0.460000	0.39030	CCT	.	.		0.448	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
LRP2	4036	hgsc.bcm.edu	37	2	170044602	170044602	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:170044602T>A	ENST00000263816.3	-	49	9491	c.9206A>T	c.(9205-9207)cAc>cTc	p.H3069L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3069	LDL-receptor class A 24. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TTCTGGGGTGTGGCACAGGTG	0.512																																					p.H3069L		Atlas-SNP	.											.	LRP2	751	.	0			c.A9206T						.						162.0	136.0	145.0					2																	170044602		2203	4300	6503	SO:0001583	missense	4036	exon49			GGGGTGTGGCACA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.9206A>T	chr2.hg19:g.170044602T>A	ENSP00000263816:p.His3069Leu	318.0	0.0		196.0	49.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	3.858	-0.030439	0.07543	.	.	ENSG00000081479	ENST00000263816	D	0.90444	-2.67	5.68	0.456	0.16655	.	0.717713	0.14809	N	0.297148	T	0.80665	0.4666	L	0.37630	1.12	0.09310	N	1	B	0.28552	0.215	B	0.25614	0.062	T	0.65705	-0.6103	10	0.27785	T	0.31	.	1.9714	0.03406	0.1242:0.3487:0.254:0.2731	.	3069	P98164	LRP2_HUMAN	L	3069	ENSP00000263816:H3069L	ENSP00000263816:H3069L	H	-	2	0	LRP2	169752848	0.000000	0.05858	0.143000	0.22291	0.045000	0.14185	-0.678000	0.05209	0.408000	0.25621	0.528000	0.53228	CAC	.	.		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
TTN	7273	hgsc.bcm.edu	37	2	179577619	179577619	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:179577619T>C	ENST00000591111.1	-	92	26406	c.26182A>G	c.(26182-26184)Aca>Gca	p.T8728A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T7801A|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.T9045A|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12884	Ig-like 70.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAGGAGGTGTTCCTTTTACG	0.423																																					p.T9045A		Atlas-SNP	.											.	TTN	18412	.	0			c.A27133G						.						59.0	54.0	55.0					2																	179577619		1925	4121	6046	SO:0001583	missense	7273	exon94			GAGGTGTTCCTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.26182A>G	chr2.hg19:g.179577619T>C	ENSP00000465570:p.Thr8728Ala	59.0	0.0		84.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.08	1.533562	0.27387	.	.	ENSG00000155657	ENST00000342992	T	0.66995	-0.24	5.48	4.3	0.51218	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60077	0.2241	L	0.52266	1.64	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.58381	-0.7646	9	0.87932	D	0	.	10.4484	0.44507	0.3117:0.0:0.0:0.6883	.	8728	Q8WZ42	TITIN_HUMAN	A	7801	ENSP00000343764:T7801A	ENSP00000343764:T7801A	T	-	1	0	TTN	179285864	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.774000	0.47694	0.973000	0.38340	0.533000	0.62120	ACA	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HECW2	57520	hgsc.bcm.edu	37	2	197172805	197172805	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:197172805C>T	ENST00000260983.3	-	11	2621	c.2439G>A	c.(2437-2439)tgG>tgA	p.W813*	HECW2_ENST00000409111.1_Nonsense_Mutation_p.W457*	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	813	Interaction with TP73.|WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TGCGTGCCTCCCAGTCTAAAT	0.527																																					p.W813X		Atlas-SNP	.											.	HECW2	239	.	0			c.G2439A						.						44.0	42.0	43.0					2																	197172805		2203	4300	6503	SO:0001587	stop_gained	57520	exon11			TGCCTCCCAGTCT	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2439G>A	chr2.hg19:g.197172805C>T	ENSP00000260983:p.Trp813*	68.0	0.0		89.0	4.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Nonsense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	43	9.939275	0.99300	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8496	0.92222	0.0:1.0:0.0:0.0	.	.	.	.	X	457;813	.	ENSP00000260983:W813X	W	-	3	0	HECW2	196881050	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.320000	0.79064	2.692000	0.91855	0.555000	0.69702	TGG	.	.		0.527	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
PARD3B	117583	hgsc.bcm.edu	37	2	205912377	205912377	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:205912377A>G	ENST00000406610.2	+	4	675	c.468A>G	c.(466-468)tcA>tcG	p.S156S	PARD3B_ENST00000462231.1_Silent_p.S156S|PARD3B_ENST00000351153.1_Silent_p.S156S|PARD3B_ENST00000358768.2_Silent_p.S156S|PARD3B_ENST00000349953.3_Silent_p.S156S	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	156					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CAAGCGCTTCACACCCTGGTG	0.532																																					p.S156S		Atlas-SNP	.											.	PARD3B	314	.	0			c.A468G						.						37.0	41.0	40.0					2																	205912377		1907	3991	5898	SO:0001819	synonymous_variant	117583	exon4			CGCTTCACACCCT	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.468A>G	chr2.hg19:g.205912377A>G		130.0	0.0		75.0	4.0	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	hg19																																																																																				.	.		0.532	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
GPR1	2825	hgsc.bcm.edu	37	2	207041152	207041152	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:207041152G>T	ENST00000407325.2	-	3	1182	c.820C>A	c.(820-822)Cac>Aac	p.H274N	GPR1_ENST00000437420.1_Missense_Mutation_p.H274N	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	274					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TAGCTATTGTGGTGAATGGTG	0.478																																					p.H274N		Atlas-SNP	.											.	GPR1	38	.	0			c.C820A						.						107.0	101.0	103.0					2																	207041152		2203	4300	6503	SO:0001583	missense	2825	exon3			TATTGTGGTGAAT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.820C>A	chr2.hg19:g.207041152G>T	ENSP00000384345:p.His274Asn	127.0	0.0		83.0	4.0	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	hg19	CCDS2368.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.091780	0.55968	.	.	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.71341	-0.56;-0.56	5.7	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.118678	0.56097	D	0.000023	T	0.72463	0.3463	L	0.31526	0.94	0.47094	D	0.999318	D	0.57257	0.979	P	0.57846	0.828	T	0.74763	-0.3555	10	0.52906	T	0.07	.	14.7805	0.69764	0.0693:0.0:0.9307:0.0	.	274	P46091	GPR1_HUMAN	N	274	ENSP00000384345:H274N;ENSP00000397535:H274N	ENSP00000384345:H274N	H	-	1	0	GPR1	206749397	1.000000	0.71417	0.997000	0.53966	0.652000	0.38707	3.569000	0.53827	1.415000	0.47037	0.655000	0.94253	CAC	.	.		0.478	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217303199	217303199	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:217303199G>T	ENST00000357276.4	+	10	2031	c.1701G>T	c.(1699-1701)ccG>ccT	p.P567P	SMARCAL1_ENST00000358207.5_Silent_p.P567P	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	567	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CAGCTATGCCGGTCCTAAAGG	0.488									Schimke Immuno-Osseous Dysplasia																												p.P567P		Atlas-SNP	.											SMARCAL1,colon,carcinoma,0,1	SMARCAL1	93	.	0			c.G1701T						.						76.0	68.0	71.0					2																	217303199		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon10	Familial Cancer Database	SIOD	TATGCCGGTCCTA	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.1701G>T	chr2.hg19:g.217303199G>T		56.0	0.0		40.0	2.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	5.189	0.220328	0.09863	.	.	ENSG00000138375	ENST00000445153	.	.	.	4.69	1.8	0.24995	.	.	.	.	.	T	0.54078	0.1836	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42766	-0.9432	4	.	.	.	-24.6343	6.5006	0.22166	0.0:0.3516:0.4695:0.1789	.	.	.	.	L	125	.	.	R	+	2	0	SMARCAL1	217011444	0.993000	0.37304	0.891000	0.34965	0.552000	0.35366	0.451000	0.21779	0.258000	0.21686	-0.311000	0.09066	CGG	.	.		0.488	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
GPBAR1	151306	hgsc.bcm.edu	37	2	219127770	219127770	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:219127770G>T	ENST00000522678.1	+	2	1191	c.323G>T	c.(322-324)gGg>gTg	p.G108V	GPBAR1_ENST00000479077.1_Missense_Mutation_p.G108V|GPBAR1_ENST00000521462.1_Missense_Mutation_p.G108V|GPBAR1_ENST00000519574.1_Missense_Mutation_p.G108V	NM_001077191.1	NP_001070659.1	Q8TDU6	GPBAR_HUMAN	G protein-coupled bile acid receptor 1	108					cell surface bile acid receptor signaling pathway (GO:0038184)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid receptor activity (GO:0038181)|G-protein coupled bile acid receptor activity (GO:0038182)			cervix(1)|kidney(1)|large_intestine(1)|ovary(1)	4		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGTGCACGGGGAGCGCTAC	0.637																																					p.G108V		Atlas-SNP	.											.	GPBAR1	22	.	0			c.G323T						.						60.0	65.0	63.0					2																	219127770		2146	4247	6393	SO:0001583	missense	151306	exon2			TGCACGGGGAGCG	AB086170	CCDS46515.1	2q35	2012-08-08			ENSG00000179921	ENSG00000179921			19680	protein-coding gene	gene with protein product		610147				12419312	Standard	NM_170699		Approved	BG37, GPCR, TGR5, M-BAR, GPCR19, GPR131, MGC40597	uc010zjw.1	Q8TDU6	OTTHUMG00000155203	ENST00000522678.1:c.323G>T	chr2.hg19:g.219127770G>T	ENSP00000430886:p.Gly108Val	109.0	0.0		122.0	21.0	NM_170699	B3KV35	Missense_Mutation	SNP	ENST00000522678.1	hg19	CCDS46515.1	.	.	.	.	.	.	.	.	.	.	G	9.043	0.990248	0.18966	.	.	ENSG00000179921	ENST00000479077;ENST00000522678;ENST00000519574;ENST00000521462	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.15	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.301296	0.27549	U	0.018864	T	0.14700	0.0355	N	0.11064	0.09	0.53005	D	0.99996	B	0.31611	0.331	B	0.39503	0.301	T	0.18304	-1.0341	10	0.02654	T	1	-4.988	5.0789	0.14646	0.1654:0.1846:0.65:0.0	.	108	Q8TDU6	GPBAR_HUMAN	V	108	ENSP00000430698:G108V;ENSP00000430886:G108V;ENSP00000430202:G108V;ENSP00000428824:G108V	ENSP00000430698:G108V	G	+	2	0	GPBAR1	218836014	1.000000	0.71417	0.873000	0.34254	0.503000	0.33858	3.713000	0.54882	1.348000	0.45733	0.561000	0.74099	GGG	.	.		0.637	GPBAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338767.3	NM_001077191	
CATIP	375307	hgsc.bcm.edu	37	2	219222293	219222293	+	Missense_Mutation	SNP	C	C	T	rs369378162		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:219222293C>T	ENST00000289388.3	+	3	184	c.155C>T	c.(154-156)aCg>aTg	p.T52M	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		52					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCTCTGAGACGCTGGCCATG	0.577																																					p.T52M		Atlas-SNP	.											.	C2orf62	28	.	0			c.C155T						.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	43.0	40.0	41.0		155	4.3	0.9	2		41	0,8600		0,0,4300	no	missense	C2orf62	NM_198559.1	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	52/388	219222293	1,13005	2203	4300	6503	SO:0001583	missense	375307	exon3			CTGAGACGCTGGC																												ENST00000289388.3:c.155C>T	chr2.hg19:g.219222293C>T	ENSP00000289388:p.Thr52Met	111.0	0.0		109.0	13.0	NM_198559		Missense_Mutation	SNP	ENST00000289388.3	hg19	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378286	0.42207	2.27E-4	0.0	ENSG00000158428	ENST00000289388	.	.	.	4.32	4.32	0.51571	.	0.058136	0.64402	D	0.000001	T	0.68650	0.3024	M	0.67953	2.075	0.33075	D	0.535836	D	0.89917	1.0	D	0.91635	0.999	T	0.77571	-0.2538	9	0.87932	D	0	-18.5541	12.4741	0.55803	0.0:1.0:0.0:0.0	.	52	Q7Z7H3	CB062_HUMAN	M	52	.	ENSP00000289388:T52M	T	+	2	0	C2orf62	218930537	0.953000	0.32496	0.900000	0.35374	0.025000	0.11179	2.350000	0.44063	2.398000	0.81561	0.462000	0.41574	ACG	.	.		0.577	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1		
CRYBA2	1412	hgsc.bcm.edu	37	2	219856962	219856962	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:219856962C>A	ENST00000295728.2	-	2	401	c.165G>T	c.(163-165)tgG>tgT	p.W55C	CRYBA2_ENST00000487181.1_5'Flank|CRYBA2_ENST00000392096.2_Missense_Mutation_p.W55C	NM_057093.1	NP_476434.1	P53672	CRBA2_HUMAN	crystallin, beta A2	55	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)		structural constituent of eye lens (GO:0005212)			endometrium(1)|lung(3)|prostate(1)	5		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAAAGGCCACCCAACTGGAAA	0.582																																					p.W55C		Atlas-SNP	.											.	CRYBA2	13	.	0			c.G165T						.						40.0	42.0	41.0					2																	219856962		2203	4300	6503	SO:0001583	missense	1412	exon3			GGCCACCCAACTG		CCDS2429.1	2q35	2013-02-14			ENSG00000163499	ENSG00000163499			2395	protein-coding gene	gene with protein product		600836				7490092, 12907171	Standard	NM_057093		Approved		uc002vjj.1	P53672	OTTHUMG00000133084	ENST00000295728.2:c.165G>T	chr2.hg19:g.219856962C>A	ENSP00000295728:p.Trp55Cys	87.0	0.0		84.0	4.0	NM_057094	Q4ZFX0|Q9Y562	Missense_Mutation	SNP	ENST00000295728.2	hg19	CCDS2429.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052241	0.75960	.	.	ENSG00000163499	ENST00000392096;ENST00000295728;ENST00000453769	D;D;D	0.85702	-2.02;-2.02;-2.02	4.46	4.46	0.54185	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.94398	0.8198	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95841	0.8866	10	0.87932	D	0	.	16.4349	0.83872	0.0:1.0:0.0:0.0	.	55	P53672	CRBA2_HUMAN	C	55	ENSP00000375946:W55C;ENSP00000295728:W55C;ENSP00000395120:W55C	ENSP00000295728:W55C	W	-	3	0	CRYBA2	219565206	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.373000	0.79623	2.476000	0.83614	0.655000	0.94253	TGG	.	.		0.582	CRYBA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336424.1	NM_057093	
ATG9A	79065	hgsc.bcm.edu	37	2	220089453	220089453	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220089453G>T	ENST00000409618.1	-	8	1079	c.640C>A	c.(640-642)Cgt>Agt	p.R214S	ATG9A_ENST00000396761.2_Missense_Mutation_p.R214S|ATG9A_ENST00000409422.1_Missense_Mutation_p.R153S|ATG9A_ENST00000361242.4_Missense_Mutation_p.R214S|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000488833.1_5'Flank			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	214					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCTGGAAACGGAGGATGCGG	0.577																																					p.R214S		Atlas-SNP	.											.	ATG9A	50	.	0			c.C640A						.						115.0	118.0	117.0					2																	220089453		2134	4241	6375	SO:0001583	missense	79065	exon8			GGAAACGGAGGAT	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.640C>A	chr2.hg19:g.220089453G>T	ENSP00000386710:p.Arg214Ser	165.0	0.0		98.0	4.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178098	0.78564	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000431715	T;T;T;T	0.62364	0.47;0.47;0.47;0.03	5.28	5.28	0.74379	.	0.157884	0.56097	D	0.000021	T	0.73473	0.3591	H	0.95260	3.645	0.80722	D	1	P	0.39282	0.666	B	0.33521	0.165	T	0.82723	-0.0316	10	0.87932	D	0	.	18.5131	0.90925	0.0:0.0:1.0:0.0	.	214	Q7Z3C6	ATG9A_HUMAN	S	214;214;214;153;118	ENSP00000379983:R214S;ENSP00000386710:R214S;ENSP00000355173:R214S;ENSP00000386535:R153S	ENSP00000355173:R214S	R	-	1	0	ATG9A	219797697	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.819000	0.99357	2.449000	0.82847	0.655000	0.94253	CGT	.	.		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
GMPPA	29926	hgsc.bcm.edu	37	2	220366718	220366718	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220366718C>T	ENST00000358215.3	+	5	757	c.388C>T	c.(388-390)Cac>Tac	p.H130Y	GMPPA_ENST00000373908.1_Missense_Mutation_p.H130Y|GMPPA_ENST00000313597.5_Missense_Mutation_p.H130Y|GMPPA_ENST00000341142.3_Missense_Mutation_p.H130Y|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373917.3_Missense_Mutation_p.H130Y	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	130					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GTTGGAAGCCCACCGACGCCA	0.587																																					p.H130Y		Atlas-SNP	.											.	GMPPA	50	.	0			c.C388T						.						185.0	168.0	174.0					2																	220366718		2203	4300	6503	SO:0001583	missense	29926	exon5			GAAGCCCACCGAC	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.388C>T	chr2.hg19:g.220366718C>T	ENSP00000350949:p.His130Tyr	115.0	0.0		65.0	6.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961313	0.53400	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000455657;ENST00000435316;ENST00000341142;ENST00000373924	D;D;D;D;T;T;D	0.94862	-3.54;-3.54;-3.54;-3.54;-0.93;-0.93;-3.54	4.89	3.98	0.46160	Nucleotidyl transferase (1);	0.119716	0.56097	N	0.000021	D	0.94145	0.8122	M	0.71036	2.16	0.42599	D	0.993274	B;B	0.31227	0.011;0.314	B;B	0.39935	0.029;0.314	D	0.92724	0.6194	10	0.51188	T	0.08	-24.9987	12.0301	0.53394	0.0:0.9114:0.0:0.0886	.	130;130	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	Y	130;130;130;130;130;95;130;60	ENSP00000315925:H130Y;ENSP00000363027:H130Y;ENSP00000350949:H130Y;ENSP00000363016:H130Y;ENSP00000392465:H130Y;ENSP00000411060:H95Y;ENSP00000340760:H130Y	ENSP00000315925:H130Y	H	+	1	0	GMPPA	220074962	0.999000	0.42202	0.996000	0.52242	0.809000	0.45718	2.616000	0.46376	0.999000	0.39023	0.561000	0.74099	CAC	.	.		0.587	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
OBSL1	23363	hgsc.bcm.edu	37	2	220422083	220422083	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220422083A>G	ENST00000404537.1	-	12	4104	c.4048T>C	c.(4048-4050)Ttc>Ctc	p.F1350L	OBSL1_ENST00000265318.4_Missense_Mutation_p.F1258L|OBSL1_ENST00000373876.1_Intron|OBSL1_ENST00000265317.5_Intron|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000603926.1_Missense_Mutation_p.F1350L	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1350	Ig-like 11.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CTGACAAGGAAGATGCGGCTG	0.667																																					p.F1350L		Atlas-SNP	.											.	OBSL1	120	.	0			c.T4048C						.						17.0	21.0	20.0					2																	220422083		2175	4243	6418	SO:0001583	missense	23363	exon12			CAAGGAAGATGCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4048T>C	chr2.hg19:g.220422083A>G	ENSP00000385636:p.Phe1350Leu	54.0	0.0		38.0	4.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	a	21.6	4.169419	0.78452	.	.	ENSG00000124006	ENST00000265318;ENST00000404537	T;T	0.04603	3.59;3.59	3.89	3.89	0.44902	Immunoglobulin subtype (1);	.	.	.	.	T	0.19967	0.0480	M	0.82132	2.575	0.48975	D	0.999734	D;D	0.61080	0.989;0.979	D;D	0.74348	0.983;0.983	T	0.01488	-1.1342	9	0.35671	T	0.21	.	12.9034	0.58139	1.0:0.0:0.0:0.0	.	1351;1350	A4KVA4;O75147	.;OBSL1_HUMAN	L	1258;1350	ENSP00000265318:F1258L;ENSP00000385636:F1350L	ENSP00000265318:F1258L	F	-	1	0	OBSL1	220130327	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.183000	0.58317	1.643000	0.50594	0.375000	0.23000	TTC	.	.		0.667	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
PAX3	5077	hgsc.bcm.edu	37	2	223066865	223066865	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:223066865G>T	ENST00000350526.4	-	8	1354	c.1218C>A	c.(1216-1218)ccC>ccA	p.P406P	PAX3_ENST00000336840.6_Intron|PAX3_ENST00000392070.2_Silent_p.P406P|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000392069.2_Silent_p.P406P|PAX3_ENST00000409551.3_Silent_p.P405P|PAX3_ENST00000344493.4_Intron	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	406					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AATCAGTCTGGGGCTGATGAG	0.542			T	"""FOXO1A, NCOA1"""	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.P406P		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.C1218A						.						64.0	63.0	63.0					2																	223066865		2203	4300	6503	SO:0001819	synonymous_variant	5077	exon8			AGTCTGGGGCTGA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"""Paired boxes"", ""Homeoboxes / PRD class"""	8617	protein-coding gene	gene with protein product		606597	"""Waardenburg syndrome 1"", ""paired box gene 3 (Waardenburg syndrome 1)"""	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1218C>A	chr2.hg19:g.223066865G>T		115.0	0.0		81.0	4.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	hg19	CCDS42826.1																																																																																			.	.		0.542	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1		
CUL3	8452	hgsc.bcm.edu	37	2	225376256	225376256	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225376256T>C	ENST00000264414.4	-	6	1036	c.698A>G	c.(697-699)tAt>tGt	p.Y233C	CUL3_ENST00000409777.1_Missense_Mutation_p.Y209C|CUL3_ENST00000409096.1_Missense_Mutation_p.Y209C|CUL3_ENST00000432260.2_5'Flank|CUL3_ENST00000344951.4_Missense_Mutation_p.Y167C	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	233					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTTCTTTATATATACTGAAGC	0.308																																					p.Y239C		Atlas-SNP	.											.	CUL3	96	.	0			c.A716G						.						117.0	118.0	118.0					2																	225376256		2202	4299	6501	SO:0001583	missense	8452	exon6			TTTATATATACTG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.698A>G	chr2.hg19:g.225376256T>C	ENSP00000264414:p.Tyr233Cys	110.0	0.0		118.0	5.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395818	0.83011	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.64	5.64	0.86602	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83741	0.5320	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89060	0.3462	10	0.87932	D	0	.	16.1486	0.81594	0.0:0.0:0.0:1.0	.	167;211;233	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	C	233;167;209;209	ENSP00000264414:Y233C;ENSP00000343601:Y167C;ENSP00000387200:Y209C;ENSP00000386525:Y209C	ENSP00000264414:Y233C	Y	-	2	0	CUL3	225084500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.265000	0.75225	0.482000	0.46254	TAT	.	.		0.308	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
DOCK10	55619	hgsc.bcm.edu	37	2	225751231	225751231	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225751231T>C	ENST00000258390.7	-	5	501	c.434A>G	c.(433-435)gAg>gGg	p.E145G	DOCK10_ENST00000409592.3_Missense_Mutation_p.E139G	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	145					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AGGAAGCTTCTCTGGTTTGTA	0.328																																					p.E145G		Atlas-SNP	.											.	DOCK10	308	.	0			c.A434G						.						91.0	85.0	87.0					2																	225751231		1836	4073	5909	SO:0001583	missense	55619	exon5			AGCTTCTCTGGTT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.434A>G	chr2.hg19:g.225751231T>C	ENSP00000258390:p.Glu145Gly	95.0	0.0		73.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.532934	0.85812	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.48201	0.82;0.82	5.69	5.69	0.88448	.	0.106120	0.64402	D	0.000006	T	0.68366	0.2993	M	0.70842	2.15	0.52501	D	0.999958	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.71020	-0.4713	10	0.59425	D	0.04	.	15.9476	0.79806	0.0:0.0:0.0:1.0	.	145;145;139	Q96BY6;Q96BY6-2;B3FL70	DOC10_HUMAN;.;.	G	139;145	ENSP00000386694:E139G;ENSP00000258390:E145G	ENSP00000258390:E145G	E	-	2	0	DOCK10	225459475	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.173000	0.68751	0.533000	0.62120	GAG	.	.		0.328	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
DOCK10	55619	hgsc.bcm.edu	37	2	225796364	225796364	+	Nonsense_Mutation	SNP	C	C	A	rs186136248	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225796364C>A	ENST00000258390.7	-	2	212	c.145G>T	c.(145-147)Gag>Tag	p.E49*	DOCK10_ENST00000474102.1_5'UTR|DOCK10_ENST00000409592.3_Nonsense_Mutation_p.E43*	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	49					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCCAAAGGCTCGAGAAGCCTA	0.398																																					p.E49X		Atlas-SNP	.											.	DOCK10	308	.	0			c.G145T						.						88.0	85.0	86.0					2																	225796364		1860	4104	5964	SO:0001587	stop_gained	55619	exon2			AAGGCTCGAGAAG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.145G>T	chr2.hg19:g.225796364C>A	ENSP00000258390:p.Glu49*	81.0	0.0		50.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Nonsense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174291	0.94807	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	.	.	.	5.59	4.71	0.59529	.	0.148988	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.6234	0.84935	0.0:0.8698:0.1302:0.0	.	.	.	.	X	43;49	.	ENSP00000258390:E49X	E	-	1	0	DOCK10	225504608	0.993000	0.37304	0.864000	0.33941	0.695000	0.40330	3.186000	0.50942	1.499000	0.48617	0.563000	0.77884	GAG	.	C|0.999;T|0.001		0.398	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
NYAP2	57624	hgsc.bcm.edu	37	2	226378371	226378371	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:226378371C>T	ENST00000272907.6	+	3	919	c.506C>T	c.(505-507)aCc>aTc	p.T169I	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	169					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGCGGGAAAACCCCTGAGAGG	0.542																																					p.T169I		Atlas-SNP	.											.	.	.	.	0			c.C506T						.						60.0	73.0	69.0					2																	226378371		2051	4207	6258	SO:0001583	missense	57624	exon3			GGAAAACCCCTGA	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.506C>T	chr2.hg19:g.226378371C>T	ENSP00000272907:p.Thr169Ile	86.0	0.0		67.0	14.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799329	0.50208	.	.	ENSG00000144460	ENST00000272907	T	0.42900	0.96	5.46	-3.88	0.04205	.	1.155810	0.06302	N	0.701107	T	0.25865	0.0630	N	0.22421	0.69	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.25745	-1.0123	10	0.34782	T	0.22	0.1231	7.788	0.29103	0.0:0.128:0.5199:0.3521	.	169	Q9P242	K1486_HUMAN	I	169	ENSP00000272907:T169I	ENSP00000272907:T169I	T	+	2	0	KIAA1486	226086615	0.000000	0.05858	0.000000	0.03702	0.969000	0.65631	0.510000	0.22723	-0.592000	0.05851	0.563000	0.77884	ACC	.	.		0.542	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
NYAP2	57624	hgsc.bcm.edu	37	2	226447056	226447056	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:226447056A>G	ENST00000272907.6	+	4	1336	c.923A>G	c.(922-924)aAg>aGg	p.K308R	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	308					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GACTTCGCCAAGGCCTCAGTG	0.597																																					p.K308R		Atlas-SNP	.											.	.	.	.	0			c.A923G						.						64.0	67.0	66.0					2																	226447056		2069	4190	6259	SO:0001583	missense	57624	exon4			TCGCCAAGGCCTC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.923A>G	chr2.hg19:g.226447056A>G	ENSP00000272907:p.Lys308Arg	114.0	0.0		117.0	27.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.615003	0.28712	.	.	ENSG00000144460	ENST00000272907	T	0.44482	0.92	5.84	3.49	0.39957	.	0.212320	0.41294	N	0.000920	T	0.31606	0.0802	L	0.45137	1.4	0.80722	D	1	B	0.15930	0.015	B	0.15870	0.014	T	0.06917	-1.0800	10	0.15499	T	0.54	-20.2547	10.2151	0.43164	0.8774:0.0:0.1226:0.0	.	308	Q9P242	K1486_HUMAN	R	308	ENSP00000272907:K308R	ENSP00000272907:K308R	K	+	2	0	KIAA1486	226155300	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.141000	0.42168	0.487000	0.27698	0.528000	0.53228	AAG	.	.		0.597	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
TRIP12	9320	hgsc.bcm.edu	37	2	230643664	230643664	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:230643664C>T	ENST00000283943.5	-	34	5090	c.4912G>A	c.(4912-4914)Gta>Ata	p.V1638I	TRIP12_ENST00000389044.4_Missense_Mutation_p.V1686I|TRIP12_ENST00000389045.3_Missense_Mutation_p.V1368I	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1638					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TCCTGAGATACAAGCGCATAA	0.398																																					p.V1638I		Atlas-SNP	.											.	TRIP12	207	.	0			c.G4912A						.						168.0	167.0	167.0					2																	230643664		2203	4300	6503	SO:0001583	missense	9320	exon34			GAGATACAAGCGC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4912G>A	chr2.hg19:g.230643664C>T	ENSP00000283943:p.Val1638Ile	106.0	0.0		82.0	4.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	34	5.393726	0.96009	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.43294	0.95;0.95;0.95	6.03	6.03	0.97812	HECT (4);	0.000000	0.85682	D	0.000000	T	0.62648	0.2445	L	0.54965	1.715	0.80722	D	1	P;D;P	0.54601	0.92;0.967;0.92	D;D;D	0.70716	0.956;0.97;0.956	T	0.58399	-0.7643	10	0.52906	T	0.07	.	20.1617	0.98138	0.0:1.0:0.0:0.0	.	1368;1686;1638	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	I	1638;1368;1686	ENSP00000283943:V1638I;ENSP00000373697:V1368I;ENSP00000373696:V1686I	ENSP00000283943:V1638I	V	-	1	0	TRIP12	230351908	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.405000	0.80007	2.854000	0.98071	0.655000	0.94253	GTA	.	.		0.398	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
DIS3L2	129563	hgsc.bcm.edu	37	2	232880358	232880358	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:232880358T>C	ENST00000409307.1	+	2	187	c.187T>C	c.(187-189)Ttg>Ctg	p.L63L	DIS3L2_ENST00000273009.6_Silent_p.L63L|DIS3L2_ENST00000360410.4_Silent_p.L63L|DIS3L2_ENST00000409401.3_Silent_p.L63L|AC105461.1_ENST00000413841.1_RNA|DIS3L2_ENST00000325385.7_Silent_p.L63L					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TTCAGAAGGCTTGAAGAGAGG	0.403																																					p.L63L		Atlas-SNP	.											.	DIS3L2	77	.	0			c.T187C						.						114.0	102.0	106.0					2																	232880358		1885	4121	6006	SO:0001819	synonymous_variant	129563	exon3			GAAGGCTTGAAGA	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.187T>C	chr2.hg19:g.232880358T>C		128.0	0.0		102.0	5.0	NM_001257282		Silent	SNP	ENST00000409307.1	hg19	CCDS42834.1																																																																																			.	.		0.403	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
AGXT	189	hgsc.bcm.edu	37	2	241813425	241813425	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:241813425A>G	ENST00000307503.3	+	6	1013	c.626A>G	c.(625-627)aAg>aGg	p.K209R		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	209					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GGCTCCCAGAAGGCCCTGAAC	0.632																																					p.K209R		Atlas-SNP	.											.	AGXT	50	.	0			c.A626G						.						108.0	95.0	100.0					2																	241813425		2203	4300	6503	SO:0001583	missense	189	exon6			CCCAGAAGGCCCT	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"""oxalosis I"", ""primary hyperoxaluria type 1"", ""L-alanine: glyoxylate aminotransferase 1"", ""serine:pyruvate aminotransferase"", ""glycolicaciduria"""	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.626A>G	chr2.hg19:g.241813425A>G	ENSP00000302620:p.Lys209Arg	74.0	0.0		52.0	4.0	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145225	0.57044	.	.	ENSG00000172482	ENST00000307503	D	0.99474	-5.97	4.1	4.1	0.47936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.095585	0.64402	D	0.000001	D	0.99687	0.9882	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97383	0.9984	10	0.87932	D	0	-39.91	13.3954	0.60849	1.0:0.0:0.0:0.0	.	209	P21549	SPYA_HUMAN	R	209	ENSP00000302620:K209R	ENSP00000302620:K209R	K	+	2	0	AGXT	241462098	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.335000	0.65929	1.634000	0.50500	0.472000	0.43445	AAG	.	.		0.632	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030	
ITPR1	3708	hgsc.bcm.edu	37	3	4730230	4730230	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4730230C>T	ENST00000443694.2	+	28	3709	c.3709C>T	c.(3709-3711)Cag>Tag	p.Q1237*	ITPR1_ENST00000357086.4_Nonsense_Mutation_p.Q1243*|ITPR1_ENST00000423119.2_Nonsense_Mutation_p.Q1243*|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Nonsense_Mutation_p.Q1252*|ITPR1_ENST00000302640.8_Nonsense_Mutation_p.Q1237*|ITPR1_ENST00000456211.2_Nonsense_Mutation_p.Q1228*			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1252					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TGAATTTTTGCAGAATTTCTG	0.468																																					p.Q1243X		Atlas-SNP	.											.	ITPR1	659	.	0			c.C3727T						.						120.0	118.0	119.0					3																	4730230		1904	4124	6028	SO:0001587	stop_gained	3708	exon31			TTTTTGCAGAATT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3709C>T	chr3.hg19:g.4730230C>T	ENSP00000401671:p.Gln1237*	139.0	0.0		97.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Nonsense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	44	10.686949	0.99450	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.1808	0.93622	0.0:1.0:0.0:0.0	.	.	.	.	X	1252;1237;1252;1243;1243;1228;1237	.	ENSP00000306253:Q1237X	Q	+	1	0	ITPR1	4705230	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.673000	0.83973	2.518000	0.84900	0.655000	0.94253	CAG	.	.		0.468	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
ITPR1	3708	hgsc.bcm.edu	37	3	4735176	4735176	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4735176G>T	ENST00000443694.2	+	30	3987	c.3987G>T	c.(3985-3987)ctG>ctT	p.L1329L	ITPR1_ENST00000357086.4_Silent_p.L1335L|ITPR1_ENST00000423119.2_Silent_p.L1335L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Silent_p.L1344L|ITPR1_ENST00000302640.8_Silent_p.L1329L|ITPR1_ENST00000456211.2_Silent_p.L1320L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1344					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTATGTAGCTGGTCAATTCGG	0.483																																					p.L1335L		Atlas-SNP	.											.	ITPR1	659	.	0			c.G4005T						.						267.0	246.0	253.0					3																	4735176		1908	4138	6046	SO:0001819	synonymous_variant	3708	exon33			GTAGCTGGTCAAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3987G>T	chr3.hg19:g.4735176G>T		122.0	0.0		98.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	hg19	CCDS54551.1																																																																																			.	.		0.483	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
ITPR1	3708	hgsc.bcm.edu	37	3	4747895	4747895	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4747895G>A	ENST00000443694.2	+	34	4657	c.4657G>A	c.(4657-4659)Gtc>Atc	p.V1553I	ITPR1_ENST00000357086.4_Missense_Mutation_p.V1559I|ITPR1_ENST00000423119.2_Missense_Mutation_p.V1559I|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.V1568I|ITPR1_ENST00000302640.8_Missense_Mutation_p.V1553I|ITPR1_ENST00000456211.2_Missense_Mutation_p.V1544I			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1568					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GGACAGCCAAGTCAACAACCT	0.562																																					p.V1559I		Atlas-SNP	.											.	ITPR1	659	.	0			c.G4675A						.						62.0	65.0	64.0					3																	4747895		2008	4163	6171	SO:0001583	missense	3708	exon37			AGCCAAGTCAACA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.4657G>A	chr3.hg19:g.4747895G>A	ENSP00000401671:p.Val1553Ile	135.0	0.0		86.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.986143|3.986143	0.74589|0.74589	.|.	.|.	ENSG00000150995|ENSG00000150995	ENST00000426160|ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.|T;T;T;T;T;T	.|0.63255	.|-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54431|0.54431	0.1858|0.1858	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	.|P;B	.|0.40909	.|0.732;0.065	.|B;B	.|0.33254	.|0.16;0.03	T|T	0.54009|0.54009	-0.8357|-0.8357	6|10	0.72032|0.18276	D|T	0.01|0.48	.|.	19.4633|19.4633	0.94927|0.94927	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1568;1559	.|Q14643;G5E9P1	.|ITPR1_HUMAN;.	N|I	15|1568;1553;1568;1559;1559;1544;1553	.|ENSP00000306253:V1553I;ENSP00000346595:V1568I;ENSP00000405934:V1559I;ENSP00000349597:V1559I;ENSP00000397885:V1544I;ENSP00000401671:V1553I	ENSP00000409258:S15N|ENSP00000306253:V1553I	S|V	+|+	2|1	0|0	ITPR1|ITPR1	4722895|4722895	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.994000|0.994000	0.84299|0.84299	9.571000|9.571000	0.98176|0.98176	2.666000|2.666000	0.90696|0.90696	0.655000|0.655000	0.94253|0.94253	AGT|GTC	.	.		0.562	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
ITPR1	3708	hgsc.bcm.edu	37	3	4774886	4774886	+	Missense_Mutation	SNP	G	G	T	rs369108656		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4774886G>T	ENST00000443694.2	+	40	5290	c.5290G>T	c.(5290-5292)Ggc>Tgc	p.G1764C	ITPR1_ENST00000357086.4_Missense_Mutation_p.G1731C|ITPR1_ENST00000423119.2_Missense_Mutation_p.G1731C|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.G1764C|ITPR1_ENST00000302640.8_Missense_Mutation_p.G1764C|ITPR1_ENST00000456211.2_Missense_Mutation_p.G1716C			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1779					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGGAGGACCCGGCAAGCCCGG	0.522																																					p.G1764C		Atlas-SNP	.											.	ITPR1	659	.	0			c.G5290T						.						63.0	70.0	67.0					3																	4774886		1985	4142	6127	SO:0001583	missense	3708	exon42			GGACCCGGCAAGC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.5290G>T	chr3.hg19:g.4774886G>T	ENSP00000401671:p.Gly1764Cys	59.0	0.0		52.0	4.0	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465638	0.63513	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91945	-2.94;-2.82;-2.88;-2.88;-2.88;-2.94	5.56	3.15	0.36227	.	0.213424	0.49916	D	0.000133	D	0.89760	0.6808	N	0.19112	0.55	0.80722	D	1	D;D	0.61080	0.989;0.971	P;P	0.58077	0.832;0.753	D	0.87355	0.2340	10	0.54805	T	0.06	.	9.5	0.39011	0.6366:0.0:0.3634:0.0	.	1779;1731	Q14643;G5E9P1	ITPR1_HUMAN;.	C	1779;1764;1764;1731;225;1731;1716;1764	ENSP00000306253:G1764C;ENSP00000346595:G1764C;ENSP00000405934:G1731C;ENSP00000349597:G1731C;ENSP00000397885:G1716C;ENSP00000401671:G1764C	ENSP00000306253:G1764C	G	+	1	0	ITPR1	4749886	0.234000	0.23783	1.000000	0.80357	0.973000	0.67179	0.394000	0.20834	0.137000	0.18759	-0.332000	0.08345	GGC	.	.		0.522	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
HRH1	3269	hgsc.bcm.edu	37	3	11302057	11302057	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:11302057G>T	ENST00000397056.1	+	3	1525	c.1334G>T	c.(1333-1335)tGc>tTc	p.C445F	HRH1_ENST00000438284.2_Missense_Mutation_p.C445F|HRH1_ENST00000431010.2_Missense_Mutation_p.C445F	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	445					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	AAGAACTGTTGCAATGAACAT	0.468																																					p.C445F		Atlas-SNP	.											HRH1,NS,carcinoma,0,1	HRH1	58	.	0			c.G1334T						.						240.0	246.0	244.0					3																	11302057		2203	4300	6503	SO:0001583	missense	3269	exon3			ACTGTTGCAATGA		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"""GPCR / Class A : Histamine receptors"""	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.1334G>T	chr3.hg19:g.11302057G>T	ENSP00000380247:p.Cys445Phe	70.0	0.0		54.0	3.0	NM_000861	A8K047|Q6P9E5	Missense_Mutation	SNP	ENST00000397056.1	hg19	CCDS2604.1	.	.	.	.	.	.	.	.	.	.	G	1.722	-0.496430	0.04291	.	.	ENSG00000196639	ENST00000438284;ENST00000431010;ENST00000397056	T;T;T	0.71103	-0.54;-0.54;-0.54	6.08	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.264594	0.38492	N	0.001674	T	0.58836	0.2150	L	0.50333	1.59	0.40591	D	0.981485	B	0.13145	0.007	B	0.12837	0.008	T	0.52419	-0.8578	10	0.41790	T	0.15	-14.0251	4.0971	0.09996	0.0858:0.2332:0.4409:0.24	.	445	P35367	HRH1_HUMAN	F	445	ENSP00000406705:C445F;ENSP00000397028:C445F;ENSP00000380247:C445F	ENSP00000380247:C445F	C	+	2	0	HRH1	11277057	0.000000	0.05858	0.438000	0.26821	0.200000	0.23975	-0.089000	0.11180	0.424000	0.26061	0.655000	0.94253	TGC	.	.		0.468	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2		
NUP210	23225	hgsc.bcm.edu	37	3	13413453	13413453	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13413453G>A	ENST00000254508.5	-	13	1749	c.1667C>T	c.(1666-1668)cCc>cTc	p.P556L		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	556					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GATCCTCAGGGGCAGCTCCAG	0.647																																					p.P556L		Atlas-SNP	.											.	NUP210	182	.	0			c.C1667T						.						25.0	21.0	23.0					3																	13413453		2202	4299	6501	SO:0001583	missense	23225	exon13			CTCAGGGGCAGCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.1667C>T	chr3.hg19:g.13413453G>A	ENSP00000254508:p.Pro556Leu	130.0	0.0		94.0	5.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324811	0.95708	.	.	ENSG00000132182	ENST00000254508	T	0.05447	3.44	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.00611	-1.1645	10	0.59425	D	0.04	-30.4294	20.1865	0.98220	0.0:0.0:1.0:0.0	.	556;556	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	L	556	ENSP00000254508:P556L	ENSP00000254508:P556L	P	-	2	0	NUP210	13388453	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	9.837000	0.99465	2.775000	0.95449	0.655000	0.94253	CCC	.	.		0.647	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
NUP210	23225	hgsc.bcm.edu	37	3	13429809	13429809	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13429809G>T	ENST00000254508.5	-	5	760	c.678C>A	c.(676-678)gtC>gtA	p.V226V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	226					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CCACCTTGTAGACAGCCTCCT	0.592																																					p.V226V		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	.	0			c.C678A						.						82.0	80.0	81.0					3																	13429809		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon5			CTTGTAGACAGCC	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.678C>A	chr3.hg19:g.13429809G>T		77.0	0.0		44.0	2.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	hg19	CCDS33704.1																																																																																			.	.		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
WNT7A	7476	hgsc.bcm.edu	37	3	13860913	13860913	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13860913T>C	ENST00000285018.4	-	4	882	c.578A>G	c.(577-579)gAg>gGg	p.E193G		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	193					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CATGTTCTCCTCCAGGATCTG	0.657																																					p.E193G		Atlas-SNP	.											.	WNT7A	70	.	0			c.A578G						.						88.0	85.0	86.0					3																	13860913		2203	4300	6503	SO:0001583	missense	7476	exon4			TTCTCCTCCAGGA	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.578A>G	chr3.hg19:g.13860913T>C	ENSP00000285018:p.Glu193Gly	62.0	0.0		59.0	4.0	NM_004625	Q96H90|Q9Y560	Missense_Mutation	SNP	ENST00000285018.4	hg19	CCDS2616.1	.	.	.	.	.	.	.	.	.	.	t	18.65	3.670592	0.67814	.	.	ENSG00000154764	ENST00000285018	T	0.76578	-1.03	4.29	4.29	0.51040	.	0.170785	0.49916	D	0.000132	T	0.78685	0.4322	M	0.77820	2.39	0.80722	D	1	B	0.30973	0.302	B	0.36186	0.219	T	0.76397	-0.2974	10	0.27082	T	0.32	.	13.7615	0.62968	0.0:0.0:0.0:1.0	.	193	O00755	WNT7A_HUMAN	G	193	ENSP00000285018:E193G	ENSP00000285018:E193G	E	-	2	0	WNT7A	13835914	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	8.032000	0.88838	1.724000	0.51502	0.456000	0.33151	GAG	.	.		0.657	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
SLC6A6	6533	hgsc.bcm.edu	37	3	14526411	14526411	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:14526411C>T	ENST00000454876.2	+	15	2088	c.1759C>T	c.(1759-1761)Cgc>Tgc	p.R587C	SLC6A6_ENST00000360861.3_Missense_Mutation_p.R587C			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	587					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						GGAACCCAACCGCTGGGCTGT	0.607																																					p.R587C		Atlas-SNP	.											.	SLC6A6	58	.	0			c.C1759T						.						56.0	48.0	50.0					3																	14526411		2203	4300	6503	SO:0001583	missense	6533	exon15			CCCAACCGCTGGG		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.1759C>T	chr3.hg19:g.14526411C>T	ENSP00000398063:p.Arg587Cys	117.0	0.0		68.0	4.0	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	hg19	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.899168	0.72754	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.73047	-0.71;-0.71	5.17	2.17	0.27698	.	0.626892	0.16013	N	0.233707	T	0.59676	0.2211	N	0.24115	0.695	0.45852	D	0.998718	D	0.62365	0.991	P	0.45660	0.489	T	0.63287	-0.6671	10	0.54805	T	0.06	.	12.4998	0.55950	0.1125:0.5636:0.3239:0.0	.	587	P31641	SC6A6_HUMAN	C	587	ENSP00000398063:R587C;ENSP00000354107:R587C	ENSP00000354107:R587C	R	+	1	0	SLC6A6	14501415	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	0.702000	0.25631	1.132000	0.42129	0.313000	0.20887	CGC	.	.		0.607	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
FGD5	152273	hgsc.bcm.edu	37	3	14958766	14958766	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:14958766T>C	ENST00000285046.5	+	12	3526	c.3416T>C	c.(3415-3417)gTg>gCg	p.V1139A	FGD5_ENST00000543601.1_Missense_Mutation_p.V898A|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1139	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						ATGAACGATGTGCTCCTGTAC	0.567																																					p.V1139A		Atlas-SNP	.											.	FGD5	248	.	0			c.T3416C						.						60.0	60.0	60.0					3																	14958766		1921	4125	6046	SO:0001583	missense	152273	exon12			ACGATGTGCTCCT	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3416T>C	chr3.hg19:g.14958766T>C	ENSP00000285046:p.Val1139Ala	121.0	0.0		84.0	4.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	11.81	1.750753	0.31046	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76316	-1.01;-1.01	4.42	3.26	0.37387	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.614817	0.14306	N	0.327976	T	0.78868	0.4351	L	0.54908	1.71	0.23003	N	0.998443	P;P	0.44877	0.845;0.845	P;P	0.53360	0.724;0.724	T	0.65352	-0.6189	10	0.33141	T	0.24	-5.6493	7.4459	0.27211	0.0:0.1039:0.0:0.8961	.	898;1139	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	A	1139;898	ENSP00000285046:V1139A;ENSP00000445949:V898A	ENSP00000285046:V1139A	V	+	2	0	FGD5	14933770	0.994000	0.37717	0.400000	0.26346	0.772000	0.43724	2.551000	0.45820	0.589000	0.29677	0.482000	0.46254	GTG	.	.		0.567	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
TBC1D5	9779	hgsc.bcm.edu	37	3	17333464	17333464	+	Missense_Mutation	SNP	C	C	A	rs143029277		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:17333464C>A	ENST00000253692.7	-	15	2832	c.1168G>T	c.(1168-1170)Ggc>Tgc	p.G390C	TBC1D5_ENST00000446818.2_Missense_Mutation_p.G390C|TBC1D5_ENST00000429383.4_Missense_Mutation_p.G390C|TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429924.2_Missense_Mutation_p.G342C	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	390						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						ATCAGAAGGCCGAGACAGGTC	0.383																																					p.G390C		Atlas-SNP	.											.	TBC1D5	69	.	0			c.G1168T						.						89.0	87.0	88.0					3																	17333464		2203	4300	6503	SO:0001583	missense	9779	exon15			GAAGGCCGAGACA	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1168G>T	chr3.hg19:g.17333464C>A	ENSP00000253692:p.Gly390Cys	103.0	0.0		72.0	4.0	NM_014744	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	hg19	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.962192	0.74016	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	6.03	6.03	0.97812	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.34687	0.0906	M	0.61703	1.905	0.80722	D	1	B;P;P	0.44241	0.345;0.801;0.829	B;P;P	0.46253	0.2;0.509;0.509	T	0.02081	-1.1217	10	0.62326	D	0.03	-19.4637	20.1672	0.98154	0.0:1.0:0.0:0.0	.	342;390;390	C9J3F6;C9JP52;Q92609	.;.;TBCD5_HUMAN	C	390;390;390;342	ENSP00000253692:G390C;ENSP00000398127:G390C;ENSP00000402935:G390C;ENSP00000411925:G342C	ENSP00000253692:G390C	G	-	1	0	TBC1D5	17308468	1.000000	0.71417	0.976000	0.42696	0.993000	0.82548	7.284000	0.78650	2.861000	0.98227	0.655000	0.94253	GGC	.	C|1.000;T|0.000		0.383	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
SATB1	6304	hgsc.bcm.edu	37	3	18393620	18393620	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:18393620T>C	ENST00000338745.6	-	10	3377	c.1643A>G	c.(1642-1644)aAc>aGc	p.N548S	SATB1_ENST00000417717.2_Missense_Mutation_p.N548S|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.N548S	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	548					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CATGGAGAGGTTCTCCCACAG	0.517																																					p.N548S		Atlas-SNP	.											.	SATB1	96	.	0			c.A1643G						.						103.0	96.0	98.0					3																	18393620		2203	4300	6503	SO:0001583	missense	6304	exon10			GAGAGGTTCTCCC		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1643A>G	chr3.hg19:g.18393620T>C	ENSP00000341024:p.Asn548Ser	220.0	0.0		146.0	6.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.870657	0.91587	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.63255	-0.01;-0.01;-0.03	5.52	5.52	0.82312	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.81457	-0.0924	10	0.66056	D	0.02	-19.5847	15.6295	0.76893	0.0:0.0:0.0:1.0	.	548;548	Q01826-2;Q01826	.;SATB1_HUMAN	S	548	ENSP00000341024:N548S;ENSP00000399708:N548S;ENSP00000399518:N548S	ENSP00000341024:N548S	N	-	2	0	SATB1	18368624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.013000	0.88655	2.091000	0.63221	0.533000	0.62120	AAC	.	.		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
KAT2B	8850	hgsc.bcm.edu	37	3	20153102	20153102	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:20153102G>A	ENST00000263754.4	+	6	1321	c.866G>A	c.(865-867)tGc>tAc	p.C289Y		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	289					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CTGTGTTACTGCAACGTGCCA	0.458																																					p.C289Y		Atlas-SNP	.											.	KAT2B	73	.	0			c.G866A						.						137.0	118.0	125.0					3																	20153102		2203	4300	6503	SO:0001583	missense	8850	exon6			GTTACTGCAACGT	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"""Chromatin-modifying enzymes / K-acetyltransferases"""	8638	protein-coding gene	gene with protein product		602303	"""p300/CBP-associated factor"""	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.866G>A	chr3.hg19:g.20153102G>A	ENSP00000263754:p.Cys289Tyr	86.0	0.0		73.0	4.0	NM_003884	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	hg19	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856854	0.91433	.	.	ENSG00000114166	ENST00000263754	T	0.39787	1.06	5.7	5.7	0.88788	PCAF, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73544	-0.3949	10	0.87932	D	0	-18.9628	19.8232	0.96605	0.0:0.0:1.0:0.0	.	289	Q92831	KAT2B_HUMAN	Y	289	ENSP00000263754:C289Y	ENSP00000263754:C289Y	C	+	2	0	KAT2B	20128106	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.734000	0.98822	2.684000	0.91462	0.650000	0.86243	TGC	.	.		0.458	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884	
NGLY1	55768	hgsc.bcm.edu	37	3	25778936	25778936	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:25778936G>T	ENST00000280700.5	-	6	1052	c.892C>A	c.(892-894)Cct>Act	p.P298T	NGLY1_ENST00000396649.3_Missense_Mutation_p.P298T|NGLY1_ENST00000428257.1_Missense_Mutation_p.P298T|NGLY1_ENST00000417874.2_Missense_Mutation_p.P256T|NGLY1_ENST00000422724.2_Silent_p.T146T	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	298					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						AGTTTCTCAGGGTTATTATAT	0.353																																					p.P298T		Atlas-SNP	.											.	NGLY1	57	.	0			c.C892A						.						65.0	65.0	65.0					3																	25778936		2203	4300	6503	SO:0001583	missense	55768	exon6			TCTCAGGGTTATT	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.892C>A	chr3.hg19:g.25778936G>T	ENSP00000280700:p.Pro298Thr	52.0	0.0		45.0	4.0	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Missense_Mutation	SNP	ENST00000280700.5	hg19	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681043	0.88542	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000396649;ENST00000308710;ENST00000417874	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.48	5.48	0.80851	Transglutaminase-like (1);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	0.979;0.987;0.987;1.0	D;P;D;D	0.87578	0.938;0.905;0.929;0.998	T	0.55958	-0.8058	9	.	.	.	-17.0907	19.7098	0.96094	0.0:0.0:1.0:0.0	.	256;298;298;298	B4DJE9;Q96IV0-2;Q96IV0-3;Q96IV0	.;.;.;NGLY1_HUMAN	T	298;298;298;295;256	ENSP00000387430:P298T;ENSP00000280700:P298T;ENSP00000379886:P298T;ENSP00000307980:P295T;ENSP00000389888:P256T	.	P	-	1	0	NGLY1	25753940	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.524000	0.98036	2.713000	0.92767	0.655000	0.94253	CCT	.	.		0.353	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2		
AZI2	64343	hgsc.bcm.edu	37	3	28368437	28368437	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:28368437T>C	ENST00000479665.1	-	7	1183	c.652A>G	c.(652-654)Aat>Gat	p.N218D	AZI2_ENST00000295748.3_5'UTR	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	218	Interaction with TBK1 and IKBKE.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						TGCTGCATATTATCACTGAAA	0.318																																					p.N218D		Atlas-SNP	.											.	AZI2	33	.	0			c.A652G						.						82.0	77.0	79.0					3																	28368437		2203	4299	6502	SO:0001583	missense	64343	exon7			GCATATTATCACT	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.652A>G	chr3.hg19:g.28368437T>C	ENSP00000419371:p.Asn218Asp	105.0	0.0		92.0	4.0	NM_022461	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Missense_Mutation	SNP	ENST00000479665.1	hg19	CCDS2647.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.157028	0.38119	.	.	ENSG00000163512	ENST00000479665	.	.	.	5.83	2.15	0.27550	Tbk1/Ikki binding domain (1);	0.240399	0.46145	N	0.000306	T	0.41903	0.1179	L	0.35723	1.085	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.17289	-1.0374	9	0.36615	T	0.2	-12.0707	6.3789	0.21523	0.0:0.1408:0.134:0.7252	.	218	Q9H6S1	AZI2_HUMAN	D	218	.	ENSP00000419371:N218D	N	-	1	0	AZI2	28343441	0.999000	0.42202	0.921000	0.36526	0.977000	0.68977	1.856000	0.39389	0.444000	0.26612	0.528000	0.53228	AAT	.	.		0.318	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37107332	37107332	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:37107332C>A	ENST00000336686.4	-	23	1748	c.1668G>T	c.(1666-1668)caG>caT	p.Q556H	LRRFIP2_ENST00000440230.1_Missense_Mutation_p.Q259H|LRRFIP2_ENST00000354379.4_Missense_Mutation_p.Q235H|MLH1_ENST00000536378.1_3'UTR|LRRFIP2_ENST00000421276.2_Missense_Mutation_p.Q259H|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.Q556H|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.Q338H			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	556					Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						ACTCCAAGACCTGAGCAGCTT	0.463																																					p.Q556H		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.G1668T						.						103.0	102.0	102.0					3																	37107332		2203	4300	6503	SO:0001583	missense	9209	exon24			CAAGACCTGAGCA	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1668G>T	chr3.hg19:g.37107332C>A	ENSP00000338727:p.Gln556His	167.0	0.0		137.0	6.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	hg19	CCDS2664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.48|14.48	2.547956|2.547956	0.45383|0.45383	.|.	.|.	ENSG00000093167|ENSG00000093167	ENST00000440742|ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230	.|T;T;T;T;T;T	.|0.46451	.|0.87;0.87;0.87;0.87;0.87;0.87	6.17|6.17	3.3|3.3	0.37823|0.37823	.|.	.|0.099259	.|0.64402	.|D	.|0.000001	T|T	0.24198|0.24198	0.0586|0.0586	N|N	0.21583|0.21583	0.68|0.68	0.52099|0.52099	D|D	0.999946|0.999946	.|B;B;B;B	.|0.14805	.|0.005;0.001;0.0;0.011	.|B;B;B;B	.|0.20384	.|0.029;0.005;0.008;0.029	T|T	0.10154|0.10154	-1.0642|-1.0642	5|10	.|0.45353	.|T	.|0.12	-14.5176|-14.5176	2.4894|2.4894	0.04607|0.04607	0.1332:0.5163:0.1293:0.2213|0.1332:0.5163:0.1293:0.2213	.|.	.|338;235;259;556	.|A8MXR0;Q9Y608-2;Q9Y608-4;Q9Y608	.|.;.;.;LRRF2_HUMAN	C|H	138|556;235;556;259;338;259	.|ENSP00000392217:Q556H;ENSP00000346349:Q235H;ENSP00000338727:Q556H;ENSP00000416364:Q259H;ENSP00000379705:Q338H;ENSP00000405480:Q259H	.|ENSP00000338727:Q556H	G|Q	-|-	1|3	0|2	LRRFIP2|LRRFIP2	37082336|37082336	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	0.667000|0.667000	0.25112|0.25112	0.938000|0.938000	0.37419|0.37419	0.655000|0.655000	0.94253|0.94253	GGT|CAG	.	.		0.463	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
VILL	50853	hgsc.bcm.edu	37	3	38044030	38044030	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:38044030G>T	ENST00000283713.6	+	14	1889	c.1623G>T	c.(1621-1623)ctG>ctT	p.L541L	VILL_ENST00000383759.2_Silent_p.L541L|VILL_ENST00000465644.1_Silent_p.L259L			O15195	VILL_HUMAN	villin-like	541					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCTTCTTGCTGGTCACAGCCA	0.577																																					p.L541L		Atlas-SNP	.											.	VILL	61	.	0			c.G1623T						.						153.0	118.0	130.0					3																	38044030		2203	4300	6503	SO:0001819	synonymous_variant	50853	exon13			CTTGCTGGTCACA		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1623G>T	chr3.hg19:g.38044030G>T		87.0	0.0		119.0	7.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	hg19	CCDS2670.2																																																																																			.	.		0.577	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
CSRNP1	64651	hgsc.bcm.edu	37	3	39184971	39184971	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39184971A>G	ENST00000273153.5	-	5	1522	c.1345T>C	c.(1345-1347)Ttc>Ctc	p.F449L	CSRNP1_ENST00000514182.1_Missense_Mutation_p.F449L	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	449					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CCTGATGTGAAGCTACAGCCA	0.567																																					p.F449L		Atlas-SNP	.											.	CSRNP1	59	.	0			c.T1345C						.						64.0	62.0	63.0					3																	39184971		2203	4300	6503	SO:0001583	missense	64651	exon5			ATGTGAAGCTACA	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.1345T>C	chr3.hg19:g.39184971A>G	ENSP00000273153:p.Phe449Leu	124.0	0.0		88.0	5.0	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	hg19	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.793807	0.00623	.	.	ENSG00000144655	ENST00000273153;ENST00000514182;ENST00000318290	T;T	0.39406	1.08;1.08	4.52	-0.818	0.10833	.	1.069230	0.07196	N	0.856677	T	0.10594	0.0259	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29518	-1.0009	10	0.10636	T	0.68	-16.6951	6.468	0.21993	0.3045:0.1212:0.5743:0.0	.	449	Q96S65	CSRN1_HUMAN	L	449;449;107	ENSP00000273153:F449L;ENSP00000422532:F449L	ENSP00000273153:F449L	F	-	1	0	CSRNP1	39159975	0.989000	0.36119	0.014000	0.15608	0.327000	0.28475	0.309000	0.19332	0.001000	0.14605	-0.242000	0.12053	TTC	.	.		0.567	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
CSRNP1	64651	hgsc.bcm.edu	37	3	39185786	39185786	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39185786G>T	ENST00000273153.5	-	4	799	c.622C>A	c.(622-624)Cga>Aga	p.R208R	CSRNP1_ENST00000514182.1_Silent_p.R208R	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	208					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						AGCAGAGCTCGACGTCGCCGG	0.627																																					p.R208R		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C622A						.						76.0	72.0	73.0					3																	39185786		2203	4300	6503	SO:0001819	synonymous_variant	64651	exon4			GAGCTCGACGTCG	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.622C>A	chr3.hg19:g.39185786G>T		146.0	0.0		90.0	6.0	NM_033027	Q69YY5	Silent	SNP	ENST00000273153.5	hg19	CCDS2682.1																																																																																			.	.		0.627	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
XIRP1	165904	hgsc.bcm.edu	37	3	39229162	39229162	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39229162T>C	ENST00000340369.3	-	2	2003	c.1775A>G	c.(1774-1776)cAg>cGg	p.Q592R	XIRP1_ENST00000396251.1_Missense_Mutation_p.Q592R|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	592	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCGGATGGTCTGCACATCGCC	0.587																																					p.Q592R		Atlas-SNP	.											.	XIRP1	173	.	0			c.A1775G						.						74.0	63.0	67.0					3																	39229162		2203	4300	6503	SO:0001583	missense	165904	exon2			ATGGTCTGCACAT	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1775A>G	chr3.hg19:g.39229162T>C	ENSP00000343140:p.Gln592Arg	189.0	0.0		134.0	8.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629289	0.46944	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.36520	1.25;1.25	4.8	-1.23	0.09465	.	0.246709	0.38005	N	0.001842	T	0.30916	0.0780	L	0.55103	1.725	0.80722	D	1	B;D	0.57899	0.012;0.981	B;P	0.48454	0.018;0.578	T	0.13656	-1.0501	10	0.56958	D	0.05	.	2.4487	0.04512	0.1401:0.0845:0.2887:0.4867	.	592;592	Q702N8;Q702N8-2	XIRP1_HUMAN;.	R	592	ENSP00000379550:Q592R;ENSP00000343140:Q592R	ENSP00000343140:Q592R	Q	-	2	0	XIRP1	39204166	1.000000	0.71417	0.986000	0.45419	0.622000	0.37654	3.934000	0.56553	-0.037000	0.13646	0.379000	0.24179	CAG	.	.		0.587	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
ZNF620	253639	hgsc.bcm.edu	37	3	40558019	40558019	+	Nonsense_Mutation	SNP	G	G	T	rs377575762		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:40558019G>T	ENST00000314529.6	+	5	1083	c.934G>T	c.(934-936)Gaa>Taa	p.E312*	ZNF620_ENST00000418905.1_Nonsense_Mutation_p.E198*	NM_175888.3	NP_787084.1	Q6ZNG0	ZN620_HUMAN	zinc finger protein 620	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(1)|urinary_tract(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		TGAATGTAACGAATGTTGGAA	0.473																																					p.E312X		Atlas-SNP	.											ZNF620,NS,carcinoma,0,1	ZNF620	38	.	0			c.G934T						.						60.0	61.0	60.0					3																	40558019		2203	4300	6503	SO:0001587	stop_gained	253639	exon5			TGTAACGAATGTT	AK093599	CCDS33740.1, CCDS58825.1	3p21.33	2013-01-08			ENSG00000177842	ENSG00000177842		"""Zinc fingers, C2H2-type"", ""-"""	28742	protein-coding gene	gene with protein product						12477932	Standard	NM_175888		Approved	MGC50836	uc003ckk.4	Q6ZNG0	OTTHUMG00000156044	ENST00000314529.6:c.934G>T	chr3.hg19:g.40558019G>T	ENSP00000322265:p.Glu312*	27.0	0.0		40.0	2.0	NM_175888	Q8N223	Nonsense_Mutation	SNP	ENST00000314529.6	hg19	CCDS33740.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.938329	0.34189	.	.	ENSG00000177842	ENST00000314529;ENST00000418905	.	.	.	2.65	1.72	0.24424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.1546	0.06500	0.1502:0.0:0.5563:0.2934	.	.	.	.	X	312;198	.	.	E	+	1	0	ZNF620	40533023	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.244000	0.18124	0.395000	0.25257	0.591000	0.81541	GAA	.	.		0.473	ZNF620-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342824.1	XM_171060	
CTNNB1	1499	hgsc.bcm.edu	37	3	41275034	41275034	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:41275034T>C	ENST00000349496.5	+	9	1480	c.1200T>C	c.(1198-1200)ggT>ggC	p.G400G	CTNNB1_ENST00000453024.1_Silent_p.G393G|CTNNB1_ENST00000396183.3_Silent_p.G400G|CTNNB1_ENST00000396185.3_Silent_p.G400G|CTNNB1_ENST00000405570.1_Silent_p.G400G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	400					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGATGGAAGGTCTCCTTGGGA	0.413		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.G400G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	.	CTNNB1	4904	.	0			c.T1200C						.						142.0	135.0	137.0					3																	41275034		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon9	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GGAAGGTCTCCTT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1200T>C	chr3.hg19:g.41275034T>C		107.0	0.0		97.0	5.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.413	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
TRAK1	22906	hgsc.bcm.edu	37	3	42244317	42244317	+	Intron	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:42244317A>G	ENST00000327628.5	+	13	2144				TRAK1_ENST00000449246.1_Missense_Mutation_p.K532R|TRAK1_ENST00000341421.3_Intron|TRAK1_ENST00000396175.1_Intron|TRAK1_ENST00000487159.1_Intron	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CACCTGCGGAAGGCGGGGCAC	0.642																																					p.K532R	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.A1595G						.																																			SO:0001627	intron_variant	22906	exon12			TGCGGAAGGCGGG		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1744+73A>G	chr3.hg19:g.42244317A>G		107.0	0.0		66.0	4.0	NM_001265610	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	hg19	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.558139	0.27827	.	.	ENSG00000182606	ENST00000449246	T	0.09538	2.97	5.64	1.89	0.25635	.	.	.	.	.	T	0.06554	0.0168	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43718	-0.9374	7	.	.	.	.	7.6486	0.28336	0.6404:0.2885:0.0711:0.0	.	532	E9PDS2	.	R	532	ENSP00000410717:K532R	.	K	+	2	0	TRAK1	42219321	0.004000	0.15560	0.000000	0.03702	0.262000	0.26303	1.861000	0.39438	0.080000	0.16959	0.528000	0.53228	AAG	.	.		0.642	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
CCDC13	152206	hgsc.bcm.edu	37	3	42754719	42754719	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:42754719T>C	ENST00000310232.6	-	14	1891	c.1808A>G	c.(1807-1809)gAg>gGg	p.E603G		NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	603										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GCGTATCTTCTCCAGATGTTG	0.607																																					p.E603G		Atlas-SNP	.											.	CCDC13	71	.	0			c.A1808G						.						123.0	111.0	115.0					3																	42754719		2203	4300	6503	SO:0001583	missense	152206	exon14			ATCTTCTCCAGAT	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1808A>G	chr3.hg19:g.42754719T>C	ENSP00000309836:p.Glu603Gly	122.0	0.0		80.0	5.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455851	0.43634	.	.	ENSG00000244607	ENST00000310232	T	0.12569	2.67	4.99	3.84	0.44239	.	0.057010	0.64402	N	0.000003	T	0.29321	0.0730	M	0.79475	2.455	0.37976	D	0.933447	D	0.57257	0.979	P	0.56563	0.801	T	0.12502	-1.0545	10	0.52906	T	0.07	.	9.5852	0.39512	0.0:0.085:0.0:0.915	.	603	Q8IYE1	CCD13_HUMAN	G	603	ENSP00000309836:E603G	ENSP00000309836:E603G	E	-	2	0	CCDC13	42729723	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.739000	0.38217	0.762000	0.33152	0.482000	0.46254	GAG	.	.		0.607	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
ANO10	55129	hgsc.bcm.edu	37	3	43621859	43621859	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:43621859T>C	ENST00000292246.3	-	5	748	c.578A>G	c.(577-579)aAg>aGg	p.K193R	ANO10_ENST00000396091.3_Missense_Mutation_p.K127R|ANO10_ENST00000350459.4_Missense_Mutation_p.K193R|ANO10_ENST00000414522.2_Missense_Mutation_p.K193R|ANO10_ENST00000451430.2_Missense_Mutation_p.K82R	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	193					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						GGGCTGATACTTCAAAGCAAA	0.483																																					p.K193R		Atlas-SNP	.											ANO10,NS,carcinoma,0,1	ANO10	70	.	0			c.A578G						.						213.0	176.0	188.0					3																	43621859		2203	4300	6503	SO:0001583	missense	55129	exon5			TGATACTTCAAAG	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25519	protein-coding gene	gene with protein product		613726	"""transmembrane protein 16K"""	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.578A>G	chr3.hg19:g.43621859T>C	ENSP00000292246:p.Lys193Arg	38.0	0.0		30.0	4.0	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	hg19	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	T	8.029	0.761378	0.15914	.	.	ENSG00000160746	ENST00000292246;ENST00000350459;ENST00000396091;ENST00000414522;ENST00000451430;ENST00000428472	T;T;T;T;T;T	0.67865	-0.01;-0.09;0.0;0.03;-0.17;-0.29	5.98	4.82	0.62117	.	0.289920	0.39615	N	0.001311	T	0.59459	0.2195	L	0.58101	1.795	0.09310	N	1	B;B;B;B;B	0.21452	0.004;0.001;0.056;0.001;0.0	B;B;B;B;B	0.30251	0.005;0.002;0.113;0.005;0.001	T	0.53056	-0.8492	10	0.35671	T	0.21	.	4.3114	0.10972	0.0:0.1996:0.1707:0.6297	.	82;193;193;127;193	Q9NW15-4;C9JHS1;Q9NW15-2;Q9NW15-3;Q9NW15	.;.;.;.;ANO10_HUMAN	R	193;193;127;193;82;82	ENSP00000292246:K193R;ENSP00000327767:K193R;ENSP00000379398:K127R;ENSP00000396990:K193R;ENSP00000394119:K82R;ENSP00000416266:K82R	ENSP00000292246:K193R	K	-	2	0	ANO10	43596863	0.906000	0.30813	0.099000	0.21106	0.625000	0.37756	2.544000	0.45761	1.091000	0.41335	0.482000	0.46254	AAG	.	.		0.483	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075	
CCR9	10803	hgsc.bcm.edu	37	3	45942794	45942794	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:45942794A>G	ENST00000357632.2	+	3	694	c.514A>G	c.(514-516)Atc>Gtc	p.I172V	LZTFL1_ENST00000536047.1_Intron|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000395963.2_Missense_Mutation_p.I160V|CCR9_ENST00000422395.1_3'UTR|CCR9_ENST00000355983.2_Missense_Mutation_p.I160V|Y_RNA_ENST00000364765.1_RNA	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	172					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TTGCTTTACCATCTGGGTATT	0.488																																					p.I172V		Atlas-SNP	.											CCR9,NS,carcinoma,0,1	CCR9	45	.	0			c.A514G						.						77.0	78.0	78.0					3																	45942794		2203	4300	6503	SO:0001583	missense	10803	exon3			TTTACCATCTGGG	AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.514A>G	chr3.hg19:g.45942794A>G	ENSP00000350256:p.Ile172Val	106.0	0.0		72.0	20.0	NM_031200	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	hg19	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.737593	0.00681	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.70282	-0.47;-0.47;-0.47	4.96	-1.93	0.07594	GPCR, rhodopsin-like superfamily (1);	0.392917	0.25860	N	0.027824	T	0.41743	0.1172	N	0.10664	0.02	0.21355	N	0.999711	B	0.02656	0.0	B	0.12156	0.007	T	0.35500	-0.9786	10	0.02654	T	1	.	12.8268	0.57725	0.3575:0.0:0.6425:0.0	.	172	P51686	CCR9_HUMAN	V	172;160;160	ENSP00000350256:I172V;ENSP00000379292:I160V;ENSP00000348260:I160V	ENSP00000348260:I160V	I	+	1	0	CCR9	45917798	0.726000	0.28059	0.013000	0.15412	0.503000	0.33858	1.040000	0.30278	-0.630000	0.05567	-0.376000	0.06991	ATC	.	.		0.488	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2		
NBEAL2	23218	hgsc.bcm.edu	37	3	47046023	47046023	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:47046023G>T	ENST00000450053.3	+	38	6416	c.6237G>T	c.(6235-6237)ttG>ttT	p.L2079F	NBEAL2_ENST00000292309.5_Missense_Mutation_p.L1895F|NBEAL2_ENST00000383740.2_Missense_Mutation_p.L358F	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2079	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TCGAGTACTTGATGCAACTCA	0.582																																					p.L2079F		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G6237T						.						100.0	111.0	107.0					3																	47046023		2099	4220	6319	SO:0001583	missense	23218	exon38			GTACTTGATGCAA	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6237G>T	chr3.hg19:g.47046023G>T	ENSP00000415034:p.Leu2079Phe	139.0	0.0		74.0	4.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.40|19.40|19.40	3.820435|3.820435|3.820435	0.71028|0.71028|0.71028	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550|ENST00000416683	.|D;D;D|.	.|0.88201|.	.|-2.35;-2.35;-2.35|.	4.96|4.96|4.96	4.08|4.08|4.08	0.47627|0.47627|0.47627	.|BEACH domain (4);|.	.|0.147291|.	.|0.45606|.	.|D|.	.|0.000344|.	D|D|.	0.88991|0.88991|.	0.6588|0.6588|.	H|H|H	0.99286|0.99286|0.99286	4.5|4.5|4.5	0.58432|0.58432|0.58432	D|D|D	0.999996|0.999996|0.999996	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.97110|.	.|0.999;1.0|.	D|D|.	0.92912|0.92912|.	0.6348|0.6348|.	5|10|.	.|0.87932|.	.|D|.	.|0|.	.|.|.	13.6862|13.6862|13.6862	0.62517|0.62517|0.62517	0.0:0.2934:0.7065:0.0|0.0:0.2934:0.7065:0.0|0.0:0.2934:0.7065:0.0	.|.|.	.|1895;2079|.	.|Q6ZNJ1-2;Q6ZNJ1|.	.|.;NBEL2_HUMAN|.	Y|F|L	448|1895;358;2079;22|1367	.|ENSP00000292309:L1895F;ENSP00000373246:L358F;ENSP00000415034:L2079F|.	.|ENSP00000292309:L1895F|.	D|L|X	+|+|+	1|3|2	0|2|2	NBEAL2|NBEAL2|NBEAL2	47021027|47021027|47021027	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	2.988000|2.988000|2.988000	0.49386|0.49386|0.49386	1.296000|1.296000|1.296000	0.44742|0.44742|0.44742	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAT|TTG|TGA	.	.		0.582	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
PLXNB1	5364	hgsc.bcm.edu	37	3	48465517	48465517	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:48465517C>T	ENST00000358536.4	-	3	773	c.504G>A	c.(502-504)gtG>gtA	p.V168V	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.V168V|PLXNB1_ENST00000456774.1_Silent_p.V168V|PLXNB1_ENST00000296440.6_Silent_p.V168V	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	168	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ATCCTCGCCCCACAAACAGGA	0.662																																					p.V168V		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G504A						.						9.0	12.0	11.0					3																	48465517		2175	4250	6425	SO:0001819	synonymous_variant	5364	exon3			TCGCCCCACAAAC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.504G>A	chr3.hg19:g.48465517C>T		91.0	0.0		88.0	4.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
SLC26A6	65010	hgsc.bcm.edu	37	3	48669737	48669737	+	Nonsense_Mutation	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:48669737T>A	ENST00000395550.2	-	5	573	c.526A>T	c.(526-528)Aga>Tga	p.R176*	SLC26A6_ENST00000455886.2_Intron|SLC26A6_ENST00000337000.8_Intron|SLC26A6_ENST00000482282.1_5'UTR|SLC26A6_ENST00000383733.3_Nonsense_Mutation_p.R176*|SLC26A6_ENST00000358747.6_Nonsense_Mutation_p.R155*|SLC26A6_ENST00000420764.2_Nonsense_Mutation_p.R176*			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	176					angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		GCAGCATCTCTGGCTGTCTCA	0.582																																					p.R176X	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.A526T						.						63.0	70.0	68.0					3																	48669737		2132	4239	6371	SO:0001587	stop_gained	65010	exon5			CATCTCTGGCTGT	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"""Solute carriers"""	14472	protein-coding gene	gene with protein product	"""pendrin-like protein 1"", ""pendrin L1"", ""sulfate anion transporter"", ""anion transporter 1"""	610068	"""solute carrier family 26, member 6"""			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.526A>T	chr3.hg19:g.48669737T>A	ENSP00000378920:p.Arg176*	340.0	0.0		262.0	109.0	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Nonsense_Mutation	SNP	ENST00000395550.2	hg19	CCDS43087.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.136113	0.37728	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000447978;ENST00000358747;ENST00000421649	.	.	.	3.87	0.197	0.15164	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0949	0.14727	0.0:0.2673:0.1592:0.5734	.	.	.	.	X	176;176;176;189;155;22	.	ENSP00000351597:R155X	R	-	1	2	SLC26A6	48644741	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.144000	0.16135	-0.123000	0.11745	0.455000	0.32223	AGA	.	.		0.582	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	
WDR6	11180	hgsc.bcm.edu	37	3	49049708	49049708	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49049708G>T	ENST00000608424.1	+	2	780	c.741G>T	c.(739-741)cgG>cgT	p.R247R	WDR6_ENST00000415265.2_Intron|WDR6_ENST00000395474.3_Silent_p.R277R|WDR6_ENST00000448293.1_Silent_p.R196R|WDR6_ENST00000489684.1_3'UTR			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	247					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CTGGGGGTCGGGTGCAGAATA	0.552																																					p.R277R		Atlas-SNP	.											.	WDR6	79	.	0			c.G831T						.						92.0	96.0	95.0					3																	49049708		2203	4300	6503	SO:0001819	synonymous_variant	11180	exon2			GGGTCGGGTGCAG	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.741G>T	chr3.hg19:g.49049708G>T		147.0	0.0		117.0	5.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Silent	SNP	ENST00000608424.1	hg19																																																																																				.	.		0.552	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
WDR6	11180	hgsc.bcm.edu	37	3	49051271	49051271	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49051271A>G	ENST00000608424.1	+	2	2343	c.2304A>G	c.(2302-2304)acA>acG	p.T768T	WDR6_ENST00000415265.2_Silent_p.T216T|WDR6_ENST00000395474.3_Silent_p.T798T|WDR6_ENST00000448293.1_Silent_p.T717T			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	768					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		ACGCACTCACAGCTGTTTGTA	0.577											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T798T		Atlas-SNP	.											.	WDR6	79	.	0			c.A2394G						.						86.0	80.0	82.0					3																	49051271		2203	4300	6503	SO:0001819	synonymous_variant	11180	exon2			ACTCACAGCTGTT	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2304A>G	chr3.hg19:g.49051271A>G		99.0	0.0	959	84.0	4.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Silent	SNP	ENST00000608424.1	hg19																																																																																				.	.		0.577	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
CCDC36	339834	hgsc.bcm.edu	37	3	49293752	49293752	+	Silent	SNP	G	G	T	rs143925037	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49293752G>T	ENST00000438782.1	+	8	1058	c.822G>T	c.(820-822)tcG>tcT	p.S274S	CCDC36_ENST00000296449.5_Silent_p.S274S|CCDC36_ENST00000452691.2_Silent_p.S274S			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	274										endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		CTCAGACGTCGCCACCTTTGG	0.542																																					p.S274S		Atlas-SNP	.											CCDC36_ENST00000438782,NS,carcinoma,0,2	CCDC36	77	.	0			c.G822T						.						65.0	63.0	64.0					3																	49293752		2203	4300	6503	SO:0001819	synonymous_variant	339834	exon8			GACGTCGCCACCT	AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"""cancer/testis antigen 74"""						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.822G>T	chr3.hg19:g.49293752G>T		42.0	0.0		47.0	2.0	NM_001135197	C9JJL0|Q05DG9|Q96LP7	Silent	SNP	ENST00000438782.1	hg19	CCDS33755.2																																																																																			.	G|1.000;A|0.000		0.542	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173	
UBA7	7318	hgsc.bcm.edu	37	3	49841899	49841899	+	IGR	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49841899C>T	ENST00000333486.3	-	0	3299				FAM212A_ENST00000333323.4_Nonsense_Mutation_p.Q115*|MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCCTGTATCCCAGCGCCCAGC	0.647																																					p.Q115X		Atlas-SNP	.											.	.	.	.	0			c.C343T						.						96.0	92.0	93.0					3																	49841899		2203	4300	6503	SO:0001628	intergenic_variant	389119	exon2			GTATCCCAGCGCC	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		chr3.hg19:g.49841899C>T		124.0	0.0		83.0	4.0	NM_203370	Q9BRB2	Nonsense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	8.961	0.970684	0.18659	.	.	ENSG00000185614	ENST00000333323	.	.	.	4.9	4.9	0.64082	.	0.717703	0.12099	N	0.499647	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	7.9022	0.29742	0.0:0.8223:0.0:0.1777	.	.	.	.	X	115	.	ENSP00000329735:Q115X	Q	+	1	0	C3orf54	49816903	0.706000	0.27856	0.052000	0.19188	0.021000	0.10359	2.036000	0.41165	2.430000	0.82344	0.561000	0.74099	CAG	.	.		0.647	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335	
CYB561D2	11068	hgsc.bcm.edu	37	3	50390719	50390719	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:50390719T>C	ENST00000418577.1	+	3	789	c.213T>C	c.(211-213)agT>agC	p.S71S	CYB561D2_ENST00000425346.1_Silent_p.S71S|CYB561D2_ENST00000419046.1_3'UTR|CYB561D2_ENST00000424512.1_Silent_p.S71S|XXcos-LUCA11.5_ENST00000606589.1_Intron|CYB561D2_ENST00000232508.5_Silent_p.S71S|NPRL2_ENST00000232501.3_5'Flank			O14569	C56D2_HUMAN	cytochrome b561 family, member D2	71	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCCTGAGAGTTCGCTGCTGC	0.607																																					p.S71S		Atlas-SNP	.											.	CYB561D2	13	.	0			c.T213C						.						110.0	107.0	108.0					3																	50390719		2203	4300	6503	SO:0001819	synonymous_variant	11068	exon4			TGAGAGTTCGCTG	AF040704	CCDS2827.1	3p21.3	2013-03-14	2013-03-14		ENSG00000114395	ENSG00000114395		"""Cytochrome b genes"""	30253	protein-coding gene	gene with protein product	"""putative tumor suppressor 101F6"""	607068	"""cytochrome b-561 domain containing 2"""			9122200, 11085536, 23249217	Standard	XM_005264832		Approved	101F6, TSP10	uc003dal.3	O14569	OTTHUMG00000156813	ENST00000418577.1:c.213T>C	chr3.hg19:g.50390719T>C		86.0	0.0		91.0	4.0	NM_007022	A8K552	Silent	SNP	ENST00000418577.1	hg19	CCDS2827.1																																																																																			.	.		0.607	CYB561D2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345973.1	NM_007022	
DOCK3	1795	hgsc.bcm.edu	37	3	51376393	51376393	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:51376393G>A	ENST00000266037.9	+	37	3723	c.3700G>A	c.(3700-3702)Gaa>Aaa	p.E1234K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1234	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GATTAACAAGGAAGAAATGTA	0.448																																					p.E1234K		Atlas-SNP	.											.	DOCK3	397	.	0			c.G3700A						.						48.0	47.0	47.0					3																	51376393		1909	4140	6049	SO:0001583	missense	1795	exon37			AACAAGGAAGAAA	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3700G>A	chr3.hg19:g.51376393G>A	ENSP00000266037:p.Glu1234Lys	108.0	0.0		98.0	4.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.817569	0.70912	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	T	0.56776	0.44	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	L	0.37800	1.135	0.80722	D	1	B	0.24675	0.109	B	0.26614	0.071	T	0.31530	-0.9940	10	0.12103	T	0.63	.	18.4995	0.90876	0.0:0.0:1.0:0.0	.	1234	Q8IZD9	DOCK3_HUMAN	K	1234;30	ENSP00000266037:E1234K	ENSP00000266037:E1234K	E	+	1	0	DOCK3	51351433	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	2.606000	0.88127	0.650000	0.86243	GAA	.	.		0.448	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
VPRBP	9730	hgsc.bcm.edu	37	3	51505002	51505002	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:51505002T>C	ENST00000335891.5	-	2	139	c.130A>G	c.(130-132)Aaa>Gaa	p.K44E				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	44					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TCAGTTTCTTTTTCAATCAAT	0.393																																					p.K44E		Atlas-SNP	.											.	VPRBP	107	.	0			c.A130G						.						105.0	94.0	97.0					3																	51505002		1850	4100	5950	SO:0001583	missense	9730	exon4			TTTCTTTTTCAAT	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.130A>G	chr3.hg19:g.51505002T>C	ENSP00000338857:p.Lys44Glu	119.0	0.0		99.0	4.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	T	14.84	2.655051	0.47467	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.55413	0.52;0.9	4.93	4.93	0.64822	.	0.103596	0.64402	D	0.000005	T	0.40839	0.1133	N	0.26042	0.785	0.25380	N	0.98862	P	0.35714	0.517	B	0.37239	0.244	T	0.30238	-0.9985	10	0.28530	T	0.3	-2.9551	13.6041	0.62037	0.0:0.0:0.0:1.0	.	44	Q9Y4B6	VPRBP_HUMAN	E	44	ENSP00000338857:K44E;ENSP00000421724:K44E	ENSP00000338857:K44E	K	-	1	0	VPRBP	51480042	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.300000	0.65721	1.849000	0.53698	0.369000	0.22263	AAA	.	.		0.393	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
GLT8D1	55830	hgsc.bcm.edu	37	3	52730329	52730329	+	Silent	SNP	G	G	T	rs371584519		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:52730329G>T	ENST00000407584.3	-	7	1303	c.453C>A	c.(451-453)acC>acA	p.T151T	GLT8D1_ENST00000463827.1_5'UTR|GLT8D1_ENST00000491606.1_Silent_p.T151T|GLT8D1_ENST00000478968.2_Silent_p.T151T|GLT8D1_ENST00000266014.5_Silent_p.T151T|GLT8D1_ENST00000394783.3_Silent_p.T151T	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	151						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ACCTTGCAAAGGTTAACTGGA	0.408																																					p.T151T		Atlas-SNP	.											.	GLT8D1	28	.	0			c.C453A						.						84.0	77.0	79.0					3																	52730329		2203	4300	6503	SO:0001819	synonymous_variant	55830	exon6			TGCAAAGGTTAAC	AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"""Glycosyltransferase family 8 domain containing"""	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.453C>A	chr3.hg19:g.52730329G>T		128.0	0.0		90.0	4.0	NM_152932	Q7Z4D1|Q8N2J6|Q9P0I5	Silent	SNP	ENST00000407584.3	hg19	CCDS2862.1																																																																																			.	.		0.408	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932	
TMEM110	375346	hgsc.bcm.edu	37	3	52874604	52874604	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:52874604T>C	ENST00000355083.5	-	8	936	c.791A>G	c.(790-792)gAg>gGg	p.E264G	TMEM110-MUSTN1_ENST00000504329.1_Missense_Mutation_p.E264G|TMEM110_ENST00000464769.1_5'UTR	NM_198563.2	NP_940965.1	Q86TL2	TM110_HUMAN	transmembrane protein 110	264						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)	4				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)		CTCCTCCATCTCATCATCCGC	0.592																																					p.E264G		Atlas-SNP	.											.	.	.	.	0			c.A791G						.						87.0	92.0	90.0					3																	52874604		2203	4300	6503	SO:0001583	missense	100526772	exon8			TCCATCTCATCAT	BC047015	CCDS2866.1	3p21.1	2010-08-13			ENSG00000213533	ENSG00000213533			30526	protein-coding gene	gene with protein product						12477932	Standard	NM_198563		Approved	MGC52022		Q86TL2	OTTHUMG00000150346	ENST00000355083.5:c.791A>G	chr3.hg19:g.52874604T>C	ENSP00000347195:p.Glu264Gly	66.0	0.0		55.0	4.0	NM_001198974		Missense_Mutation	SNP	ENST00000355083.5	hg19	CCDS2866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.027780|4.027780	0.75390|0.75390	.|.	.|.	ENSG00000248592;ENSG00000213533;ENSG00000213533|ENSG00000248592	ENST00000504329;ENST00000482155;ENST00000355083|ENST00000514466	.|.	.|.	.|.	5.58|5.58	4.4|4.4	0.53042|0.53042	.|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.51449|0.51449	0.1675|0.1675	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.99;0.996|.	P;P|.	0.60012|.	0.815;0.867|.	T|T	0.42413|0.42413	-0.9453|-0.9453	9|5	0.38643|.	T|.	0.18|.	-11.2934|-11.2934	11.9796|11.9796	0.53113|0.53113	0.13:0.0:0.0:0.87|0.13:0.0:0.0:0.87	.|.	264;264|.	Q86TL2;A8MSY1|.	TM110_HUMAN;.|.	G|G	264;7;264|54	.|.	ENSP00000347195:E264G|.	E|R	-|-	2|1	0|2	TMEM110-MUSTN1;TMEM110|TMEM110-MUSTN1	52849644|52849644	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.597000|0.597000	0.36814|0.36814	7.441000|7.441000	0.80485|0.80485	0.932000|0.932000	0.37266|0.37266	0.496000|0.496000	0.49642|0.49642	GAG|AGA	.	.		0.592	TMEM110-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352949.2	NM_198563	
TKT	7086	hgsc.bcm.edu	37	3	53289863	53289863	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:53289863C>T	ENST00000462138.1	-	1	184	c.96G>A	c.(94-96)gcG>gcA	p.A32A	TKT_ENST00000423525.2_Silent_p.A32A|TKT_ENST00000296289.6_5'UTR|TKT_ENST00000423516.1_Silent_p.A32A			P29401	TKT_HUMAN	transketolase	32					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		CAGAGCCCGCCGCAGTGGTGG	0.731																																					p.A32A	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.G96A						.						35.0	32.0	33.0					3																	53289863		2202	4300	6502	SO:0001819	synonymous_variant	7086	exon1			GCCCGCCGCAGTG		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.96G>A	chr3.hg19:g.53289863C>T		148.0	0.0		80.0	4.0	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	hg19	CCDS2871.1																																																																																			.	.		0.731	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
CACNA1D	776	hgsc.bcm.edu	37	3	53815596	53815596	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:53815596A>G	ENST00000350061.5	+	39	5205	c.4694A>G	c.(4693-4695)aAc>aGc	p.N1565S	CACNA1D_ENST00000422281.2_Missense_Mutation_p.N1550S|CACNA1D_ENST00000540742.1_Missense_Mutation_p.N457S|CACNA1D_ENST00000288139.4_Missense_Mutation_p.N1585S	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1565					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AATCCAGGGAACCTGGAGCAA	0.473																																					p.N1585S		Atlas-SNP	.											.	CACNA1D	324	.	0			c.A4754G						.						79.0	82.0	81.0					3																	53815596		2203	4300	6503	SO:0001583	missense	776	exon40			CAGGGAACCTGGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.4694A>G	chr3.hg19:g.53815596A>G	ENSP00000288133:p.Asn1565Ser	176.0	0.0		117.0	5.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.070312	0.55539	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000540742	D;D;D;T;T	0.96427	-3.97;-4.01;-4.01;3.03;3.03	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.92912	0.7745	N	0.25890	0.77	0.80722	D	1	B;B;P;B;B	0.41188	0.031;0.004;0.741;0.007;0.234	B;B;B;B;B	0.39419	0.017;0.012;0.299;0.009;0.272	D	0.93357	0.6723	10	0.49607	T	0.09	.	15.7098	0.77615	1.0:0.0:0.0:0.0	.	1550;457;1258;1565;1585	B0FYA3;F5H313;Q59GD8;Q01668;Q01668-2	.;.;.;CAC1D_HUMAN;.	S	1565;1585;1550;1258;457	ENSP00000288133:N1565S;ENSP00000288139:N1585S;ENSP00000409174:N1550S;ENSP00000418014:N1258S;ENSP00000438229:N457S	ENSP00000288139:N1585S	N	+	2	0	CACNA1D	53790636	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.241000	0.95402	2.179000	0.69175	0.528000	0.53228	AAC	.	.		0.473	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
ROBO2	6092	hgsc.bcm.edu	37	3	77617564	77617564	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:77617564C>A	ENST00000461745.1	+	13	2850	c.1950C>A	c.(1948-1950)acC>acA	p.T650T	ROBO2_ENST00000332191.8_Silent_p.T650T|ROBO2_ENST00000487694.3_Silent_p.T666T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	650	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TGACTCCCACCACGGTTCAGG	0.458																																					p.T650T		Atlas-SNP	.											.	ROBO2	527	.	0			c.C1950A						.						108.0	106.0	107.0					3																	77617564		2075	4212	6287	SO:0001819	synonymous_variant	6092	exon13			TCCCACCACGGTT	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1950C>A	chr3.hg19:g.77617564C>A		108.0	0.0		95.0	4.0	NM_002942	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	hg19	CCDS43109.1																																																																																			.	.		0.458	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
STX19	415117	hgsc.bcm.edu	37	3	93733245	93733245	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:93733245C>T	ENST00000315099.2	-	2	1125	c.869G>A	c.(868-870)tGc>tAc	p.C290Y	ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000303097.7_Intron|ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000535334.1_Intron|ARL13B_ENST00000486562.1_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	290	Cys-rich.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						TGAGCTACAGCATGGACAGCA	0.318																																					p.C290Y		Atlas-SNP	.											.	STX19	19	.	0			c.G869A						.						46.0	43.0	44.0					3																	93733245		2203	4298	6501	SO:0001583	missense	415117	exon2			CTACAGCATGGAC	AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.869G>A	chr3.hg19:g.93733245C>T	ENSP00000320679:p.Cys290Tyr	99.0	0.0		84.0	5.0	NM_001001850		Missense_Mutation	SNP	ENST00000315099.2	hg19	CCDS33793.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.453435	0.43531	.	.	ENSG00000178750	ENST00000315099	T	0.50548	0.74	5.2	5.2	0.72013	.	0.103138	0.64402	D	0.000002	T	0.49321	0.1550	M	0.69358	2.11	0.39259	D	0.964184	B	0.31054	0.306	B	0.27500	0.08	T	0.54964	-0.8214	10	0.54805	T	0.06	-5.212	18.6137	0.91295	0.0:1.0:0.0:0.0	.	290	Q8N4C7	STX19_HUMAN	Y	290	ENSP00000320679:C290Y	ENSP00000320679:C290Y	C	-	2	0	STX19	95215935	0.677000	0.27577	0.959000	0.39883	0.983000	0.72400	1.587000	0.36622	2.805000	0.96524	0.655000	0.94253	TGC	.	.		0.318	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850	
DHFRL1	200895	hgsc.bcm.edu	37	3	93779792	93779792	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:93779792T>C	ENST00000394221.2	-	2	1013	c.564A>G	c.(562-564)taA>taG	p.*188*	DHFRL1_ENST00000314636.2_Silent_p.*188*|DHFRL1_ENST00000481631.1_Intron|NSUN3_ENST00000314622.4_5'Flank	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	0					glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)			kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						CACCTTCATATTAATCATCCT	0.378																																					p.X188X		Atlas-SNP	.											.	DHFRL1	25	.	0			c.A564G						.						88.0	83.0	84.0					3																	93779792		2203	4300	6503	SO:0001819	synonymous_variant	200895	exon2			TTCATATTAATCA	AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"""dihydrofolate reductase pseudogene 4"""	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.564A>G	chr3.hg19:g.93779792T>C		122.0	0.0		125.0	5.0	NM_001195643	D3DN30|Q6P4I9	Silent	SNP	ENST00000394221.2	hg19	CCDS2926.1																																																																																			.	.		0.378	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815	
TRMT10C	54931	hgsc.bcm.edu	37	3	101284095	101284095	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:101284095G>T	ENST00000309922.6	+	2	624	c.470G>T	c.(469-471)aGg>aTg	p.R157M		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	157					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GCAGCAGCAAGGGAAGAAGCA	0.308																																					p.R157M		Atlas-SNP	.											.	.	.	.	0			c.G470T						.						44.0	43.0	43.0					3																	101284095		1809	4076	5885	SO:0001583	missense	54931	exon2			CAGCAAGGGAAGA	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 1"""	615423	"""RNA (guanine-9-) methyltransferase domain containing 1"""	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.470G>T	chr3.hg19:g.101284095G>T	ENSP00000312356:p.Arg157Met	69.0	0.0		50.0	4.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	hg19	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	G	8.347	0.830109	0.16749	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.47528	0.84;0.84	5.74	-6.52	0.01872	.	1.047670	0.07392	N	0.889222	T	0.33789	0.0875	L	0.36672	1.1	0.28829	N	0.897279	B	0.27229	0.172	B	0.25140	0.058	T	0.34304	-0.9834	10	0.41790	T	0.15	-11.2128	11.4372	0.50074	0.1091:0.0:0.7029:0.1879	.	157	Q7L0Y3	MRRP1_HUMAN	M	157	ENSP00000312356:R157M;ENSP00000419389:R157M	ENSP00000312356:R157M	R	+	2	0	RG9MTD1	102766785	0.041000	0.20044	0.325000	0.25375	0.388000	0.30384	-0.434000	0.06939	-0.877000	0.04012	0.655000	0.94253	AGG	.	.		0.308	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819	
PLCXD2	257068	hgsc.bcm.edu	37	3	111432801	111432801	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:111432801C>A	ENST00000477665.1	+	3	1016	c.692C>A	c.(691-693)cCa>cAa	p.P231Q	PLCXD2_ENST00000393934.3_Missense_Mutation_p.P231Q|PLCXD2_ENST00000472215.1_3'UTR	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	231					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						AAGAAGATTCCAGCGCCCTGG	0.498																																					p.P231Q		Atlas-SNP	.											.	PLCXD2	36	.	0			c.C692A						.						79.0	80.0	80.0					3																	111432801		2203	4300	6503	SO:0001583	missense	257068	exon3			AGATTCCAGCGCC	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.692C>A	chr3.hg19:g.111432801C>A	ENSP00000420686:p.Pro231Gln	98.0	0.0		52.0	4.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.441884	0.83993	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.39	5.39	0.77823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.79100	0.4389	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.75903	-0.3153	8	0.14656	T	0.56	-9.4779	16.6677	0.85257	0.0:1.0:0.0:0.0	.	231;231	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	Q	231	.	ENSP00000377511:P231Q	P	+	2	0	PLCXD2	112915491	1.000000	0.71417	0.985000	0.45067	0.955000	0.61496	7.376000	0.79658	2.512000	0.84698	0.563000	0.77884	CCA	.	.		0.498	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268	
BOC	91653	hgsc.bcm.edu	37	3	112987288	112987288	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:112987288C>T	ENST00000495514.1	+	5	1223	c.519C>T	c.(517-519)tcC>tcT	p.S173S	BOC_ENST00000273395.4_Silent_p.S173S|BOC_ENST00000355385.3_Silent_p.S173S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	173	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGAGGCCTCCAGAGGTGAGT	0.622																																					p.S173S		Atlas-SNP	.											.	BOC	139	.	0			c.C519T						.						51.0	47.0	48.0					3																	112987288		2203	4300	6503	SO:0001819	synonymous_variant	91653	exon5			GGCCTCCAGAGGT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.519C>T	chr3.hg19:g.112987288C>T		65.0	0.0		68.0	16.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	hg19	CCDS2971.1																																																																																			.	.		0.622	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
KIAA1407	57577	hgsc.bcm.edu	37	3	113737567	113737567	+	Missense_Mutation	SNP	C	C	A	rs76418892	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:113737567C>A	ENST00000295878.3	-	8	1267	c.1121G>T	c.(1120-1122)cGg>cTg	p.R374L	KIAA1407_ENST00000545063.1_Missense_Mutation_p.R205L	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	374			R -> W (in dbSNP:rs17603649).							endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTGAGTCTCCCGCTCCAACTT	0.448																																					p.R374L		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G1121T						.						172.0	186.0	182.0					3																	113737567		2203	4300	6503	SO:0001583	missense	57577	exon8			GTCTCCCGCTCCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1121G>T	chr3.hg19:g.113737567C>A	ENSP00000295878:p.Arg374Leu	93.0	0.0		81.0	4.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427362	0.62733	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.59502	0.98;0.26;0.48	5.76	3.98	0.46160	.	0.292319	0.33199	N	0.005167	T	0.67306	0.2879	M	0.71581	2.175	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.997	P;P;P	0.58172	0.706;0.834;0.773	T	0.68439	-0.5408	10	0.72032	D	0.01	.	8.7673	0.34711	0.0:0.7174:0.0:0.2826	.	361;250;374	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	L	374;205;361	ENSP00000295878:R374L;ENSP00000446381:R205L;ENSP00000418099:R361L	ENSP00000295878:R374L	R	-	2	0	KIAA1407	115220257	0.996000	0.38824	0.966000	0.40874	0.818000	0.46254	1.382000	0.34374	0.797000	0.33971	-0.140000	0.14226	CGG	.	C|0.991;T|0.009		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
QTRTD1	79691	hgsc.bcm.edu	37	3	113789666	113789666	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:113789666G>T	ENST00000493014.1	+	2	277	c.209G>T	c.(208-210)cGg>cTg	p.R70L	QTRTD1_ENST00000479882.1_Missense_Mutation_p.R53L|QTRTD1_ENST00000281273.4_Missense_Mutation_p.R176L|QTRTD1_ENST00000485050.1_Missense_Mutation_p.R188L	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						AACTGTCTGCGGCTGCAGGAA	0.458																																					p.R188L		Atlas-SNP	.											.	QTRTD1	29	.	0			c.G563T						.						72.0	70.0	71.0					3																	113789666		2203	4300	6503	SO:0001583	missense	79691	exon5			GTCTGCGGCTGCA	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.209G>T	chr3.hg19:g.113789666G>T	ENSP00000419169:p.Arg70Leu	57.0	0.0		93.0	4.0	NM_001256835		Missense_Mutation	SNP	ENST00000493014.1	hg19	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	G	8.134	0.783777	0.16189	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	5.5	-0.545	0.11843	.	0.756596	0.12397	N	0.472504	T	0.14485	0.0350	N	0.08118	0	0.25024	N	0.99132	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.26916	-1.0089	8	.	.	.	-0.1312	4.6807	0.12734	0.6221:0.0:0.2063:0.1716	.	70;53;176	B7Z472;B7Z5R2;Q9H974	.;.;QTRD1_HUMAN	L	188;176;53;70	.	.	R	+	2	0	QTRTD1	115272356	0.883000	0.30277	0.889000	0.34880	0.277000	0.26821	1.041000	0.30291	-0.008000	0.14320	0.561000	0.74099	CGG	.	.		0.458	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638	
POPDC2	64091	hgsc.bcm.edu	37	3	119378819	119378819	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:119378819T>C	ENST00000264231.3	-	1	618	c.452A>G	c.(451-453)gAg>gGg	p.E151G	POPDC2_ENST00000468801.1_Missense_Mutation_p.E151G|POPDC2_ENST00000474523.1_5'UTR|POPDC2_ENST00000538678.1_Missense_Mutation_p.E151G|POPDC2_ENST00000493094.1_Missense_Mutation_p.E151G	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	151					regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		GATGGGTGTCTCACCCTCCAC	0.542																																					p.E151G		Atlas-SNP	.											.	POPDC2	36	.	0			c.A452G						.						134.0	132.0	133.0					3																	119378819		2203	4300	6503	SO:0001583	missense	64091	exon1			GGTGTCTCACCCT	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.452A>G	chr3.hg19:g.119378819T>C	ENSP00000264231:p.Glu151Gly	96.0	0.0		76.0	5.0	NM_022135	Q86UE7	Missense_Mutation	SNP	ENST00000264231.3	hg19	CCDS2992.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903812	0.92035	.	.	ENSG00000121577	ENST00000264231;ENST00000493094;ENST00000468801;ENST00000538678	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.69	5.69	0.88448	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.046397	0.85682	D	0.000000	T	0.42314	0.1197	L	0.34521	1.04	0.80722	D	1	D;D	0.67145	0.996;0.986	P;P	0.62813	0.857;0.907	T	0.15607	-1.0431	10	0.35671	T	0.21	.	15.9315	0.79663	0.0:0.0:0.0:1.0	.	151;151	Q9HBU9-2;Q9HBU9	.;POPD2_HUMAN	G	151	ENSP00000264231:E151G;ENSP00000417250:E151G;ENSP00000420715:E151G;ENSP00000438271:E151G	ENSP00000264231:E151G	E	-	2	0	POPDC2	120861509	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.136000	0.71703	2.162000	0.67917	0.533000	0.62120	GAG	.	.		0.542	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135	
PARP14	54625	hgsc.bcm.edu	37	3	122419215	122419215	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:122419215A>G	ENST00000474629.2	+	6	2080	c.1814A>G	c.(1813-1815)aAc>aGc	p.N605S		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GAAGTTGAGAACAAAGAAGTT	0.388																																					p.N605S		Atlas-SNP	.											.	PARP14	242	.	0			c.A1814G						.						37.0	36.0	36.0					3																	122419215		1869	4091	5960	SO:0001583	missense	54625	exon6			TTGAGAACAAAGA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1814A>G	chr3.hg19:g.122419215A>G	ENSP00000418194:p.Asn605Ser	92.0	0.0		79.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.209543	0.39003	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.08370	3.1	5.22	2.88	0.33553	.	0.342378	0.27056	N	0.021143	T	0.05547	0.0146	N	0.22421	0.69	0.25439	N	0.98811	B;B	0.29716	0.005;0.255	B;B	0.22152	0.004;0.038	T	0.30937	-0.9961	10	0.72032	D	0.01	.	8.4903	0.33095	0.8411:0.0:0.1589:0.0	.	605;605	Q460N5-4;Q460N5	.;PAR14_HUMAN	S	605;524	ENSP00000418194:N605S	ENSP00000381228:N524S	N	+	2	0	PARP14	123901905	1.000000	0.71417	0.122000	0.21767	0.004000	0.04260	5.648000	0.67930	0.465000	0.27167	-0.376000	0.06991	AAC	.	.		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
CCDC14	64770	hgsc.bcm.edu	37	3	123634090	123634090	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:123634090G>T	ENST00000488653.2	-	13	2488	c.2398C>A	c.(2398-2400)Cag>Aag	p.Q800K	CCDC14_ENST00000310351.4_Missense_Mutation_p.Q640K|CCDC14_ENST00000489746.1_Missense_Mutation_p.Q600K|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000433542.2_Missense_Mutation_p.Q759K|CCDC14_ENST00000485727.1_Missense_Mutation_p.Q600K			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	800					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		ATTTGTGGCTGAGGGGATAGT	0.388																																					p.Q759K		Atlas-SNP	.											.	CCDC14	97	.	0			c.C2275A						.						74.0	75.0	74.0					3																	123634090		2203	4300	6503	SO:0001583	missense	64770	exon12			GTGGCTGAGGGGA	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2398C>A	chr3.hg19:g.123634090G>T	ENSP00000420180:p.Gln800Lys	109.0	0.0		76.0	4.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.053	-1.243834	0.01481	.	.	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000419247	T;T;T;T;T;T;T	0.44482	0.95;0.95;0.95;0.95;0.95;0.95;0.92	5.05	4.09	0.47781	.	0.121048	0.36854	N	0.002369	T	0.47135	0.1429	L	0.56769	1.78	0.09310	N	1	D;D;D	0.56035	0.974;0.974;0.974	P;P;P	0.53861	0.736;0.736;0.736	T	0.30851	-0.9964	10	0.24483	T	0.36	.	9.7046	0.40207	0.0839:0.0:0.7706:0.1455	.	800;759;641	Q49A88;Q49A88-6;Q49A88-5	CCD14_HUMAN;.;.	K	800;640;600;600;759;781;298	ENSP00000420180:Q800K;ENSP00000312031:Q640K;ENSP00000418002:Q600K;ENSP00000418403:Q600K;ENSP00000395706:Q759K;ENSP00000386866:Q781K;ENSP00000400957:Q298K	ENSP00000312031:Q640K	Q	-	1	0	CCDC14	125116780	0.249000	0.23941	0.435000	0.26784	0.035000	0.12851	1.936000	0.40183	2.623000	0.88846	0.591000	0.81541	CAG	.	.		0.388	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
HEG1	57493	hgsc.bcm.edu	37	3	124732817	124732817	+	Missense_Mutation	SNP	C	C	A	rs574836585		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:124732817C>A	ENST00000311127.4	-	6	1673	c.1606G>T	c.(1606-1608)Ggt>Tgt	p.G536C	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	536	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.G536C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						CGCACTTGACCGTAGCTAATC	0.443																																					p.G536C		Atlas-SNP	.											HEG1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HEG1	109	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1606T						.						91.0	84.0	86.0					3																	124732817		1934	4143	6077	SO:0001583	missense	57493	exon6			CTTGACCGTAGCT	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1606G>T	chr3.hg19:g.124732817C>A	ENSP00000311502:p.Gly536Cys	44.0	1.0		46.0	3.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662490	0.67700	.	.	ENSG00000173706	ENST00000311127	D	0.88277	-2.36	5.54	0.0224	0.14133	.	.	.	.	.	D	0.86260	0.5890	N	0.22421	0.69	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.60682	0.878;0.758	T	0.75522	-0.3288	9	0.66056	D	0.02	.	5.0469	0.14488	0.0:0.3339:0.2895:0.3766	.	536;536	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	C	536	ENSP00000311502:G536C	ENSP00000311502:G536C	G	-	1	0	HEG1	126215507	0.000000	0.05858	0.000000	0.03702	0.512000	0.34134	-0.074000	0.11450	-0.195000	0.10382	-0.150000	0.13652	GGT	.	.		0.443	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
IFT122	55764	hgsc.bcm.edu	37	3	129238004	129238004	+	Missense_Mutation	SNP	C	C	A	rs373326394		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:129238004C>A	ENST00000348417.2	+	28	3523	c.3446C>A	c.(3445-3447)cCg>cAg	p.P1149Q	IFT122_ENST00000504021.1_Missense_Mutation_p.P1026Q|IFT122_ENST00000296266.3_Missense_Mutation_p.P1200Q|IFT122_ENST00000347300.2_Missense_Mutation_p.P1090Q|IFT122_ENST00000431818.2_Missense_Mutation_p.P999Q|IFT122_ENST00000440957.2_Missense_Mutation_p.P940Q|IFT122_ENST00000349441.2_Missense_Mutation_p.P1039Q|IFT122_ENST00000507564.1_Missense_Mutation_p.P1142Q	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1149					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.P1200Q(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GATGAGGACCCGTTCACAGCT	0.587																																					p.P1200Q		Atlas-SNP	.											.	IFT122	117	.	1	Substitution - Missense(1)	lung(1)	c.C3599A						.						120.0	111.0	114.0					3																	129238004		2203	4300	6503	SO:0001583	missense	55764	exon29			AGGACCCGTTCAC	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3446C>A	chr3.hg19:g.129238004C>A	ENSP00000324005:p.Pro1149Gln	145.0	0.0		93.0	5.0	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998072	0.74818	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957	T;T;T;T;T;T;T;T	0.62498	0.66;0.02;0.14;0.19;0.81;0.8;0.64;0.22	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.72898	0.3518	L	0.34521	1.04	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.988;1.0;1.0;0.997;1.0;1.0	D;D;D;D;P;D;D;D;D;D	0.91635	0.999;0.999;0.997;0.996;0.708;0.995;0.991;0.932;0.999;0.999	T	0.72690	-0.4217	10	0.52906	T	0.07	-15.0043	20.1054	0.97890	0.0:1.0:0.0:0.0	.	940;475;1142;537;1026;991;1039;1090;1149;1200	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	Q	1090;1200;1142;999;1026;1039;1149;991;940	ENSP00000323973:P1090Q;ENSP00000296266:P1200Q;ENSP00000425536:P1142Q;ENSP00000410946:P999Q;ENSP00000422179:P1026Q;ENSP00000324165:P1039Q;ENSP00000324005:P1149Q;ENSP00000401569:P940Q	ENSP00000296266:P1200Q	P	+	2	0	IFT122	130720694	1.000000	0.71417	0.965000	0.40720	0.359000	0.29487	7.025000	0.76449	2.757000	0.94681	0.655000	0.94253	CCG	.	.		0.587	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
PLXND1	23129	hgsc.bcm.edu	37	3	129279245	129279245	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:129279245C>G	ENST00000324093.4	-	31	5239	c.5061G>C	c.(5059-5061)aaG>aaC	p.K1687N	PLXND1_ENST00000393239.1_Missense_Mutation_p.K1687N	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1687					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						GGTGAGACTTCTTGGGCTCCG	0.667																																					p.K1687N	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G5061C						.						70.0	58.0	62.0					3																	129279245		2203	4299	6502	SO:0001583	missense	23129	exon31			AGACTTCTTGGGC	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.5061G>C	chr3.hg19:g.129279245C>G	ENSP00000317128:p.Lys1687Asn	197.0	0.0		117.0	5.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.62|12.62	1.993734|1.993734	0.35131|0.35131	.|.	.|.	ENSG00000004399|ENSG00000004399	ENST00000506979|ENST00000324093;ENST00000393239	.|T;T	.|0.12774	.|2.65;2.65	5.0|5.0	3.17|3.17	0.36434|0.36434	.|Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	.|0.348813	.|0.29814	.|N	.|0.011130	T|T	0.13157|0.13157	0.0319|0.0319	N|N	0.05280|0.05280	-0.08|-0.08	0.50813|0.50813	D|D	0.999894|0.999894	.|B;D	.|0.64830	.|0.322;0.994	.|B;P	.|0.61003	.|0.126;0.882	T|T	0.13150|0.13150	-1.0520|-1.0520	5|10	.|0.87932	.|D	.|0	.|.	8.321|8.321	0.32130|0.32130	0.0:0.6927:0.0:0.3073|0.0:0.6927:0.0:0.3073	.|.	.|282;1687	.|B4DRU3;Q9Y4D7	.|.;PLXD1_HUMAN	Q|N	31|1687	.|ENSP00000317128:K1687N;ENSP00000376931:K1687N	.|ENSP00000317128:K1687N	E|K	-|-	1|3	0|2	PLXND1|PLXND1	130761935|130761935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	2.562000|2.562000	0.45914|0.45914	1.107000|1.107000	0.41642|0.41642	0.462000|0.462000	0.41574|0.41574	GAA|AAG	.	.		0.667	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
DNAJC13	23317	hgsc.bcm.edu	37	3	132193831	132193831	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:132193831G>T	ENST00000260818.6	+	22	2595	c.2347G>T	c.(2347-2349)Gaa>Taa	p.E783*		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	783					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AACACGAGAAGAACTGAAAGA	0.383																																					p.E783X		Atlas-SNP	.											.	DNAJC13	253	.	0			c.G2347T						.						107.0	112.0	110.0					3																	132193831		2203	4300	6503	SO:0001587	stop_gained	23317	exon22			CGAGAAGAACTGA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2347G>T	chr3.hg19:g.132193831G>T	ENSP00000260818:p.Glu783*	102.0	0.0		86.0	4.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Nonsense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	G	43	10.191783	0.99355	.	.	ENSG00000138246	ENST00000260818	.	.	.	5.68	4.81	0.61882	.	0.121103	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.1936	0.65654	0.0712:0.0:0.9288:0.0	.	.	.	.	X	783	.	ENSP00000260818:E783X	E	+	1	0	DNAJC13	133676521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.623000	0.98386	1.413000	0.46997	0.650000	0.86243	GAA	.	.		0.383	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
CEP63	80254	hgsc.bcm.edu	37	3	134264444	134264444	+	Missense_Mutation	SNP	G	G	T	rs529386244		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:134264444G>T	ENST00000337090.3	+	7	745	c.572G>T	c.(571-573)cGg>cTg	p.R191L	CEP63_ENST00000332047.5_Missense_Mutation_p.R191L|CEP63_ENST00000513612.2_Missense_Mutation_p.R191L|CEP63_ENST00000606977.1_Missense_Mutation_p.R191L|CEP63_ENST00000354446.3_Missense_Mutation_p.R191L|CEP63_ENST00000383229.3_Missense_Mutation_p.R191L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	191					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CTTGTCAATCGGAAACAGAAA	0.353																																					p.R191L		Atlas-SNP	.											.	CEP63	56	.	0			c.G572T						.						79.0	75.0	76.0					3																	134264444		2203	4300	6503	SO:0001583	missense	80254	exon7			TCAATCGGAAACA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.572G>T	chr3.hg19:g.134264444G>T	ENSP00000336524:p.Arg191Leu	105.0	0.0		78.0	4.0	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.811746|4.811746	0.90707|0.90707	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000508778|ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612	.|T;T;T;T;T	.|0.36157	.|1.93;1.66;1.92;1.27;1.92	6.1|6.1	6.1|6.1	0.99115|0.99115	.|.	.|0.068772	.|0.64402	.|D	.|0.000016	.|T	.|0.60431	.|0.2268	M|M	0.68952|0.68952	2.095|2.095	0.53688|0.53688	D|D	0.999977|0.999977	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.997	.|D;D;D;P	.|0.91635	.|0.999;0.985;0.985;0.898	.|T	.|0.47275	.|-0.9130	.|10	.|0.23891	.|T	.|0.37	-13.8266|-13.8266	20.7146|20.7146	0.99709|0.99709	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191;191;191;191	.|Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	.|CEP63_HUMAN;.;.;.	X|L	97|191	.|ENSP00000328382:R191L;ENSP00000346432:R191L;ENSP00000336524:R191L;ENSP00000372716:R191L;ENSP00000426129:R191L	.|ENSP00000328382:R191L	G|R	+|+	1|2	0|0	CEP63|CEP63	135747134|135747134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	6.717000|6.717000	0.74707|0.74707	2.902000|2.902000	0.99343|0.99343	0.650000|0.650000	0.86243|0.86243	GGA|CGG	.	.		0.353	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
CLSTN2	64084	hgsc.bcm.edu	37	3	140251313	140251313	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:140251313G>T	ENST00000458420.3	+	9	1682	c.1492G>T	c.(1492-1494)Ggc>Tgc	p.G498C		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	498					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACTCACAGTCGGCGCTTGTTG	0.443										HNSCC(16;0.037)																											p.G498C	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G1492T						.						136.0	113.0	121.0					3																	140251313		2203	4300	6503	SO:0001583	missense	64084	exon9			ACAGTCGGCGCTT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1492G>T	chr3.hg19:g.140251313G>T	ENSP00000402460:p.Gly498Cys	122.0	0.0		91.0	5.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.499134	0.85069	.	.	ENSG00000158258	ENST00000458420	D	0.89270	-2.49	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94871	0.8030	9	.	.	.	-12.4934	17.2644	0.87081	0.0:0.0:1.0:0.0	.	498	Q9H4D0	CSTN2_HUMAN	C	498	ENSP00000402460:G498C	.	G	+	1	0	CLSTN2	141734003	1.000000	0.71417	0.971000	0.41717	0.880000	0.50808	9.869000	0.99810	2.697000	0.92050	0.655000	0.94253	GGC	.	.		0.443	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
EIF2A	83939	hgsc.bcm.edu	37	3	150285799	150285799	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:150285799G>A	ENST00000460851.1	+	8	769	c.660G>A	c.(658-660)aaG>aaA	p.K220K	EIF2A_ENST00000487799.1_Silent_p.K195K|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Silent_p.K215K|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000383043.3_Splice_Site|EIF2A_ENST00000406576.3_Silent_p.K159K			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	220					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GTTTCTTTAAGGCAGATAAAG	0.338																																					p.K220K		Atlas-SNP	.											.	EIF2A	59	.	0			c.G660A						.						65.0	61.0	62.0					3																	150285799		1824	4087	5911	SO:0001819	synonymous_variant	83939	exon8			CTTTAAGGCAGAT	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.660G>A	chr3.hg19:g.150285799G>A		61.0	0.0		61.0	19.0	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	hg19	CCDS46935.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.822993	0.50739	.	.	ENSG00000144895	ENST00000383043	.	.	.	6.07	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1513	0.20313	0.5938:0.0:0.4062:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF2A	151768489	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.664000	0.46783	0.796000	0.33947	0.655000	0.94253	.	.	.		0.338	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153840716	153840716	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:153840716T>C	ENST00000356448.4	+	2	1219	c.935T>C	c.(934-936)tTg>tCg	p.L312S	ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.L312S|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.L312S|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	312					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CGGAGAGGCTTGCGGTCCACG	0.577																																					p.L312S	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.T935C						.						44.0	61.0	55.0					3																	153840716		2035	4194	6229	SO:0001583	missense	26084	exon2			GAGGCTTGCGGTC	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.935T>C	chr3.hg19:g.153840716T>C	ENSP00000348828:p.Leu312Ser	160.0	0.0		95.0	4.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761436	0.89932	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.63417	-0.04;-0.04;1.39	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000001	T	0.77471	0.4135	M	0.65498	2.005	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80118	-0.1516	10	0.72032	D	0.01	-11.9824	15.2386	0.73450	0.0:0.0:0.0:1.0	.	312;312	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	S	312	ENSP00000348828:L312S;ENSP00000423418:L312S;ENSP00000423295:L312S	ENSP00000348828:L312S	L	+	2	0	ARHGEF26	155323406	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	6.967000	0.76079	2.005000	0.58758	0.454000	0.30748	TTG	.	.		0.577	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
GPR149	344758	hgsc.bcm.edu	37	3	154145382	154145382	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:154145382C>T	ENST00000389740.2	-	2	1196	c.1097G>A	c.(1096-1098)cGc>cAc	p.R366H		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	366					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GTGGGTCCAGCGTTTGGACAA	0.527																																					p.R366H		Atlas-SNP	.											GPR149,NS,carcinoma,0,1	GPR149	134	.	0			c.G1097A						.						71.0	75.0	74.0					3																	154145382		2024	4194	6218	SO:0001583	missense	344758	exon2			GTCCAGCGTTTGG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1097G>A	chr3.hg19:g.154145382C>T	ENSP00000374390:p.Arg366His	116.0	0.0		71.0	3.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366027	0.41902	.	.	ENSG00000174948	ENST00000389740	.	.	.	6.03	2.79	0.32731	.	0.203131	0.53938	N	0.000058	T	0.38026	0.1025	L	0.27053	0.805	0.44956	D	0.99797	B	0.19445	0.036	B	0.10450	0.005	T	0.08932	-1.0698	9	0.18276	T	0.48	-12.0261	7.941	0.29959	0.0:0.5739:0.0:0.4261	.	366	Q86SP6	GP149_HUMAN	H	366	.	ENSP00000374390:R366H	R	-	2	0	GPR149	155628076	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	0.448000	0.21726	0.605000	0.29947	0.655000	0.94253	CGC	.	.		0.527	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
KCNAB1	7881	hgsc.bcm.edu	37	3	155838515	155838515	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:155838515T>C	ENST00000490337.1	+	1	179	c.115T>C	c.(115-117)Tca>Cca	p.S39P	KCNAB1_ENST00000389636.5_Missense_Mutation_p.S39P	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	39					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CAAGAAAGCCTCAGAAAACGC	0.542																																					p.S39P		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T115C						.						76.0	80.0	79.0					3																	155838515		2203	4300	6503	SO:0001583	missense	7881	exon1			AAAGCCTCAGAAA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.115T>C	chr3.hg19:g.155838515T>C	ENSP00000419952:p.Ser39Pro	197.0	0.0		137.0	6.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.070024	0.36566	.	.	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.11821	3.16;2.74	5.47	-3.34	0.04943	.	.	.	.	.	T	0.04815	0.0130	N	0.08118	0	0.41283	D	0.986929	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33266	-0.9875	9	0.35671	T	0.21	-7.1239	2.5176	0.04672	0.1268:0.3006:0.3317:0.241	.	39;39	B7Z8E5;Q14722	.;KCAB1_HUMAN	P	39	ENSP00000419952:S39P;ENSP00000374287:S39P	ENSP00000374287:S39P	S	+	1	0	KCNAB1	157321209	0.000000	0.05858	0.656000	0.29637	0.979000	0.70002	-1.078000	0.03413	-0.474000	0.06862	0.455000	0.32223	TCA	.	.		0.542	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
TRIM59	286827	hgsc.bcm.edu	37	3	160155954	160155954	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:160155954C>G	ENST00000309784.4	-	3	1203	c.1018G>C	c.(1018-1020)Gta>Cta	p.V340L	RP11-432B6.3_ENST00000483754.1_Intron|TRIM59_ENST00000543469.1_Intron	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	340					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ATCAGTATTACTGAAATTAAT	0.308																																					p.V340L		Atlas-SNP	.											.	TRIM59	42	.	0			c.G1018C						.						59.0	62.0	61.0					3																	160155954		2201	4297	6498	SO:0001583	missense	286827	exon3			GTATTACTGAAAT	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	30834	protein-coding gene	gene with protein product			"""tripartite motif-containing 57"", ""tripartite motif-containing 59"""	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.1018G>C	chr3.hg19:g.160155954C>G	ENSP00000311219:p.Val340Leu	299.0	0.0		271.0	85.0	NM_173084	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	hg19	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	C	6.199	0.404851	0.11754	.	.	ENSG00000213186	ENST00000309784	T	0.22539	1.95	5.77	1.75	0.24633	.	0.507764	0.20377	N	0.093523	T	0.12732	0.0309	L	0.40543	1.245	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.22730	-1.0208	9	.	.	.	-1.2124	2.1154	0.03713	0.2416:0.3814:0.2378:0.1392	.	340	Q8IWR1	TRI59_HUMAN	L	340	ENSP00000311219:V340L	.	V	-	1	0	TRIM59	161638648	0.000000	0.05858	0.724000	0.30704	0.843000	0.47879	0.012000	0.13287	0.334000	0.23590	0.561000	0.74099	GTA	.	.		0.308	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084	
SPATA16	83893	hgsc.bcm.edu	37	3	172835323	172835323	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:172835323T>C	ENST00000351008.3	-	2	382	c.199A>G	c.(199-201)Aag>Gag	p.K67E		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	67					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TTGATGCCCTTTGTCATTTTT	0.388																																					p.K67E		Atlas-SNP	.											.	SPATA16	111	.	0			c.A199G						.						340.0	323.0	329.0					3																	172835323		2203	4300	6503	SO:0001583	missense	83893	exon2			TGCCCTTTGTCAT	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.199A>G	chr3.hg19:g.172835323T>C	ENSP00000341765:p.Lys67Glu	696.0	0.0		1219.0	190.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.710873	0.48517	.	.	ENSG00000144962	ENST00000351008	T	0.16196	2.36	5.27	5.27	0.74061	.	0.107922	0.41396	D	0.000884	T	0.09862	0.0242	N	0.17082	0.46	0.32811	D	0.501493	B	0.31318	0.319	B	0.26416	0.069	T	0.13388	-1.0511	10	0.38643	T	0.18	-15.4234	9.0924	0.36619	0.0:0.0845:0.0:0.9155	.	67	Q9BXB7	SPT16_HUMAN	E	67	ENSP00000341765:K67E	ENSP00000341765:K67E	K	-	1	0	SPATA16	174318017	0.897000	0.30589	1.000000	0.80357	0.976000	0.68499	1.652000	0.37313	1.985000	0.57927	0.528000	0.53228	AAG	.	.		0.388	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
YEATS2	55689	hgsc.bcm.edu	37	3	183521785	183521785	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:183521785C>A	ENST00000305135.5	+	27	3788	c.3593C>A	c.(3592-3594)gCa>gAa	p.A1198E	YEATS2-AS1_ENST00000425008.3_RNA|AC131160.1_ENST00000401347.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1198					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TGGCAAAGAGCAATGACAATG	0.408																																					p.A1198E		Atlas-SNP	.											.	YEATS2	111	.	0			c.C3593A						.						58.0	57.0	57.0					3																	183521785		1889	4122	6011	SO:0001583	missense	55689	exon27			AAAGAGCAATGAC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3593C>A	chr3.hg19:g.183521785C>A	ENSP00000306983:p.Ala1198Glu	129.0	0.0		111.0	5.0	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	hg19	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	C	31	5.101983	0.94245	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	D	0.86627	-2.15	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000001	D	0.93667	0.7977	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94294	0.7531	10	0.87932	D	0	-20.758	18.8616	0.92275	0.0:1.0:0.0:0.0	.	1198	Q9ULM3	YETS2_HUMAN	E	1198	ENSP00000306983:A1198E	ENSP00000306983:A1198E	A	+	2	0	YEATS2	185004479	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.065000	0.76727	2.444000	0.82710	0.655000	0.94253	GCA	.	.		0.408	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
EIF4G1	1981	hgsc.bcm.edu	37	3	184049840	184049840	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:184049840C>A	ENST00000346169.2	+	32	4855	c.4584C>A	c.(4582-4584)ctC>ctA	p.L1528L	EIF4G1_ENST00000382330.3_Silent_p.L1535L|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000352767.3_Silent_p.L1535L|EIF4G1_ENST00000441154.1_Silent_p.L1365L|EIF4G1_ENST00000392537.2_Silent_p.L1441L|EIF4G1_ENST00000427845.1_Silent_p.L1442L|EIF4G1_ENST00000342981.4_Silent_p.L1529L|EIF4G1_ENST00000434061.2_Silent_p.L1333L|EIF4G1_ENST00000319274.6_Silent_p.L1528L|EIF4G1_ENST00000350481.5_Silent_p.L1364L|EIF4G1_ENST00000414031.1_Silent_p.L1488L|EIF4G1_ENST00000411531.1_Silent_p.L1489L|EIF4G1_ENST00000424196.1_Silent_p.L1535L|EIF4G1_ENST00000435046.2_Silent_p.L1332L	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1528	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTACGCCCTCCAGGCCCTTG	0.612																																					p.L1535L		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4605A						.						54.0	51.0	52.0					3																	184049840		2203	4300	6503	SO:0001819	synonymous_variant	1981	exon33			CGCCCTCCAGGCC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4584C>A	chr3.hg19:g.184049840C>A		86.0	0.0		78.0	4.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.612	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
SENP2	59343	hgsc.bcm.edu	37	3	185316214	185316214	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:185316214C>A	ENST00000296257.5	+	3	412	c.172C>A	c.(172-174)Caa>Aaa	p.Q58K	SENP2_ENST00000465201.1_3'UTR|SENP2_ENST00000545472.1_Missense_Mutation_p.Q48K|SENP2_ENST00000427465.2_5'UTR	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	58					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTTTATTCACCAAGTGAAAAA	0.368																																					p.Q58K		Atlas-SNP	.											.	SENP2	88	.	0			c.C172A						.						64.0	63.0	63.0					3																	185316214		2203	4300	6503	SO:0001583	missense	59343	exon3			ATTCACCAAGTGA	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"""SUMO1/sentrin/SMT3 specific protease 2"""			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.172C>A	chr3.hg19:g.185316214C>A	ENSP00000296257:p.Gln58Lys	186.0	0.0		175.0	7.0	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	ENST00000296257.5	hg19	CCDS33902.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.914001	0.72983	.	.	ENSG00000163904	ENST00000430355;ENST00000545472;ENST00000296257;ENST00000437107	T;T	0.22945	1.93;1.94	4.98	4.98	0.66077	.	0.177411	0.27636	N	0.018485	T	0.15696	0.0378	N	0.14661	0.345	0.80722	D	1	B;B	0.23316	0.083;0.034	B;B	0.22601	0.04;0.025	T	0.08764	-1.0706	10	0.21014	T	0.42	-5.4854	13.9415	0.64057	0.0:1.0:0.0:0.0	.	48;58	B4DQ42;Q9HC62	.;SENP2_HUMAN	K	112;48;58;58	ENSP00000439653:Q48K;ENSP00000296257:Q58K	ENSP00000296257:Q58K	Q	+	1	0	SENP2	186798908	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.109000	0.41863	2.739000	0.93911	0.650000	0.86243	CAA	.	.		0.368	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627	
LPP	4026	hgsc.bcm.edu	37	3	188327323	188327323	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:188327323G>T	ENST00000312675.4	+	6	1050	c.804G>T	c.(802-804)cgG>cgT	p.R268R	LPP_ENST00000448637.1_Silent_p.R268R|LPP_ENST00000543006.1_Silent_p.R268R|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	268	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTTCAACACGGGGAGGCATGG	0.557			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""																																p.R268R		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.G804T						.						77.0	68.0	71.0					3																	188327323		2203	4300	6503	SO:0001819	synonymous_variant	4026	exon6			AACACGGGGAGGC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.804G>T	chr3.hg19:g.188327323G>T		119.0	0.0		89.0	4.0	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	hg19	CCDS3291.1																																																																																			.	.		0.557	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
LPP	4026	hgsc.bcm.edu	37	3	188592145	188592145	+	Missense_Mutation	SNP	G	G	T	rs9830664	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:188592145G>T	ENST00000312675.4	+	11	1963	c.1717G>T	c.(1717-1719)Ggt>Tgt	p.G573C	LPP_ENST00000543006.1_Missense_Mutation_p.G573C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	573	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTAGGATTGCGGTGGTCTCCT	0.488			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""																																p.G573C		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.G1717T						.						187.0	165.0	172.0					3																	188592145		2203	4300	6503	SO:0001583	missense	4026	exon11			GATTGCGGTGGTC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1717G>T	chr3.hg19:g.188592145G>T	ENSP00000318089:p.Gly573Cys	67.0	0.0		79.0	4.0	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	hg19	CCDS3291.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149572	0.78001	.	.	ENSG00000145012	ENST00000312675;ENST00000543006	D;D	0.88354	-2.37;-2.37	5.79	5.79	0.91817	Zinc finger, LIM-type (4);	0.045098	0.85682	D	0.000000	D	0.96185	0.8756	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.987;0.999	D	0.96557	0.9412	10	0.66056	D	0.02	.	19.0299	0.92952	0.0:0.0:1.0:0.0	.	426;573	B7Z8W0;Q93052	.;LPP_HUMAN	C	573	ENSP00000318089:G573C;ENSP00000438891:G573C	ENSP00000318089:G573C	G	+	1	0	LPP	190074839	1.000000	0.71417	0.996000	0.52242	0.611000	0.37282	9.750000	0.98875	2.736000	0.93811	0.655000	0.94253	GGT	.	G|0.998;A|0.002		0.488	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
CPN2	1370	hgsc.bcm.edu	37	3	194062557	194062557	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:194062557A>G	ENST00000323830.3	-	2	964	c.875T>C	c.(874-876)gTt>gCt	p.V292A	CPN2_ENST00000429275.1_Missense_Mutation_p.V292A	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	292					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		AGACAGGCCAACCAGGCACGG	0.577																																					p.V292A		Atlas-SNP	.											.	CPN2	56	.	0			c.T875C						.						51.0	49.0	50.0					3																	194062557		2203	4300	6503	SO:0001583	missense	1370	exon2			AGGCCAACCAGGC	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.875T>C	chr3.hg19:g.194062557A>G	ENSP00000319464:p.Val292Ala	146.0	0.0		97.0	4.0	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	hg19	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	A	0.524	-0.860978	0.02610	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.24723	1.84;1.84	5.01	-0.324	0.12706	.	0.530450	0.14094	N	0.341800	T	0.13713	0.0332	L	0.37850	1.14	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.33317	-0.9873	10	0.09084	T	0.74	.	3.8831	0.09086	0.5414:0.0:0.2233:0.2352	.	292	P22792	CPN2_HUMAN	A	292	ENSP00000319464:V292A;ENSP00000402232:V292A	ENSP00000319464:V292A	V	-	2	0	CPN2	195544252	0.000000	0.05858	0.021000	0.16686	0.111000	0.19643	-1.910000	0.01584	0.319000	0.23209	0.459000	0.35465	GTT	.	.		0.577	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
SLC51A	200931	hgsc.bcm.edu	37	3	195944788	195944788	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:195944788A>G	ENST00000296327.5	+	2	323	c.114A>G	c.(112-114)acA>acG	p.T38T		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	38					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	AGCCTCCCACAGCAGCCCAAC	0.607																																					p.T38T		Atlas-SNP	.											.	.	.	.	0			c.A114G						.						51.0	46.0	48.0					3																	195944788		2203	4300	6503	SO:0001819	synonymous_variant	200931	exon2			TCCCACAGCAGCC		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"""Solute carriers"""	29955	protein-coding gene	gene with protein product	"""organic solute transporter, alpha subunit"""	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.114A>G	chr3.hg19:g.195944788A>G		85.0	0.0		43.0	5.0	NM_152672	Q6ZMC7	Silent	SNP	ENST00000296327.5	hg19	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	A	4.040	0.005065	0.07866	.	.	ENSG00000163959	ENST00000428985	.	.	.	5.89	-11.8	0.00035	.	.	.	.	.	T	0.30510	0.0767	.	.	.	0.53005	D	0.999965	.	.	.	.	.	.	T	0.38824	-0.9643	4	.	.	.	.	1.3954	0.02260	0.4026:0.1863:0.2685:0.1426	.	.	.	.	R	9	.	.	Q	+	2	0	AC069257.9	197429185	0.000000	0.05858	0.326000	0.25389	0.519000	0.34347	-4.969000	0.00165	-2.420000	0.00564	-0.908000	0.02827	CAG	.	.		0.607	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672	
MFSD7	84179	hgsc.bcm.edu	37	4	678289	678289	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:678289C>T	ENST00000404286.2	-	6	841	c.826G>A	c.(826-828)Gca>Aca	p.A276T	MFSD7_ENST00000347950.5_Missense_Mutation_p.A157T|MFSD7_ENST00000515118.1_Missense_Mutation_p.A179T|MFSD7_ENST00000322224.4_Missense_Mutation_p.A275T|MFSD7_ENST00000513740.1_5'Flank|MFSD7_ENST00000503156.1_Missense_Mutation_p.A211T	NM_032219.2	NP_115595.2	Q6UXD7	MFSD7_HUMAN	major facilitator superfamily domain containing 7	276					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				cervix(1)|kidney(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	11						TGGCCGCTTGCACAGAGGATC	0.637											OREG0016025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A275T		Atlas-SNP	.											.	MFSD7	50	.	0			c.G823A						.						77.0	80.0	79.0					4																	678289		2203	4300	6503	SO:0001583	missense	84179	exon6			CGCTTGCACAGAG	AK025922	CCDS3338.1, CCDS75086.1	4p16.3	2013-05-22			ENSG00000169026	ENSG00000169026		"""Solute carriers"""	26177	protein-coding gene	gene with protein product						12975309	Standard	XM_005272295		Approved	FLJ22269, LP2561	uc003gax.3	Q6UXD7	OTTHUMG00000119001	ENST00000404286.2:c.826G>A	chr4.hg19:g.678289C>T	ENSP00000384616:p.Ala276Thr	125.0	0.0	590	79.0	4.0	NM_032219	A8K7J5|Q6XYD4|Q8N6H1|Q9H6H6	Missense_Mutation	SNP	ENST00000404286.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.70	1.423382	0.25639	.	.	ENSG00000169026	ENST00000347950;ENST00000322224;ENST00000404286;ENST00000515118;ENST00000503156;ENST00000507165	T;T;T;T;T;T	0.80480	0.33;0.33;0.33;0.33;0.33;-1.38	4.73	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);	0.520933	0.18640	N	0.135310	T	0.67998	0.2953	N	0.11927	0.2	0.26626	N	0.972569	B;P;P;B;P	0.45672	0.1;0.864;0.864;0.157;0.726	B;B;B;B;B	0.43867	0.063;0.434;0.434;0.105;0.146	T	0.61739	-0.7001	10	0.31617	T	0.26	-15.0889	13.1096	0.59267	0.0:1.0:0.0:0.0	.	211;179;157;276;275	D6RIZ6;D6R9R0;Q6UXD7-3;Q6UXD7;Q6UXD7-2	.;.;.;MFSD7_HUMAN;.	T	157;275;276;179;211;212	ENSP00000307545:A157T;ENSP00000320234:A275T;ENSP00000384616:A276T;ENSP00000423204:A179T;ENSP00000425753:A211T;ENSP00000424556:A212T	ENSP00000320234:A275T	A	-	1	0	MFSD7	668289	0.030000	0.19436	0.275000	0.24674	0.012000	0.07955	2.116000	0.41930	2.460000	0.83146	0.460000	0.39030	GCA	.	.		0.637	MFSD7-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358585.1	NM_032219	
GAK	2580	hgsc.bcm.edu	37	4	843758	843758	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:843758C>T	ENST00000314167.4	-	27	3866	c.3756G>A	c.(3754-3756)gtG>gtA	p.V1252V	GAK_ENST00000511163.1_Silent_p.V1173V|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1252	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CGGCCATGCCCACGGGCGTCC	0.677																																					p.V1252V		Atlas-SNP	.											.	GAK	104	.	0			c.G3756A						.						24.0	24.0	24.0					4																	843758		2202	4298	6500	SO:0001819	synonymous_variant	2580	exon27			CATGCCCACGGGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3756G>A	chr4.hg19:g.843758C>T		94.0	0.0		84.0	4.0	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	C	1.760	-0.486963	0.04352	.	.	ENSG00000178950	ENST00000511980	.	.	.	4.77	3.78	0.43462	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.3922	6.7194	0.23323	0.2491:0.5863:0.1646:0.0	.	.	.	.	X	408	.	.	W	-	2	0	GAK	833758	0.998000	0.40836	0.994000	0.49952	0.016000	0.09150	0.661000	0.25023	2.338000	0.79540	0.637000	0.83480	TGG	.	.		0.677	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
SLC26A1	10861	hgsc.bcm.edu	37	4	984946	984946	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:984946G>T	ENST00000361661.2	-	3	923	c.546C>A	c.(544-546)acC>acA	p.T182T	IDUA_ENST00000453894.1_Intron|SLC26A1_ENST00000398520.2_Silent_p.T182T|SLC26A1_ENST00000513138.1_5'UTR|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Silent_p.T182T	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	182					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCGTGAGGGCGGTGGCGACAC	0.687																																					p.T182T		Atlas-SNP	.											.	SLC26A1	44	.	0			c.C546A						.						31.0	33.0	32.0					4																	984946		2201	4293	6494	SO:0001819	synonymous_variant	10861	exon2			GAGGGCGGTGGCG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.546C>A	chr4.hg19:g.984946G>T		156.0	0.0		121.0	5.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	hg19	CCDS33934.1																																																																																			.	.		0.687	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425	
HTT	3064	hgsc.bcm.edu	37	4	3131704	3131704	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3131704G>T	ENST00000355072.5	+	13	1942	c.1797G>T	c.(1795-1797)caG>caT	p.Q599H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	599					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GACAGCCCCAGGATGAAGATG	0.507																																					p.Q599H		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	.	0			c.G1797T						.						89.0	88.0	88.0					4																	3131704		1897	4136	6033	SO:0001583	missense	3064	exon13			GCCCCAGGATGAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1797G>T	chr4.hg19:g.3131704G>T	ENSP00000347184:p.Gln599His	100.0	0.0		99.0	6.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.194400	0.38806	.	.	ENSG00000197386	ENST00000355072	T	0.06371	3.31	4.5	3.64	0.41730	Armadillo-type fold (1);	0.244527	0.42964	D	0.000623	T	0.06325	0.0163	L	0.38175	1.15	0.52099	D	0.999946	P	0.39326	0.668	B	0.41088	0.347	T	0.31280	-0.9949	10	0.66056	D	0.02	.	5.4243	0.16417	0.1627:0.0:0.672:0.1652	.	599	P42858	HD_HUMAN	H	599	ENSP00000347184:Q599H	ENSP00000347184:Q599H	Q	+	3	2	HTT	3101502	1.000000	0.71417	0.702000	0.30337	0.041000	0.13682	1.226000	0.32563	1.003000	0.39130	-0.314000	0.08810	CAG	.	.		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HTT	3064	hgsc.bcm.edu	37	4	3225849	3225849	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3225849G>T	ENST00000355072.5	+	56	7901	c.7756G>T	c.(7756-7758)Gct>Tct	p.A2586S		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2586					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TCTGTCTCCGGCTACTACAGG	0.507																																					p.A2586S		Atlas-SNP	.											.	HTT	221	.	0			c.G7756T						.						130.0	144.0	139.0					4																	3225849		2141	4261	6402	SO:0001583	missense	3064	exon56			TCTCCGGCTACTA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7756G>T	chr4.hg19:g.3225849G>T	ENSP00000347184:p.Ala2586Ser	98.0	0.0		98.0	35.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	6.407	0.443274	0.12164	.	.	ENSG00000197386	ENST00000355072	T	0.05447	3.44	5.53	4.64	0.57946	.	0.202412	0.43747	D	0.000527	T	0.05227	0.0139	L	0.29908	0.895	0.31287	N	0.689856	B	0.19331	0.035	B	0.14023	0.01	T	0.07616	-1.0763	10	0.28530	T	0.3	.	9.8937	0.41304	0.0:0.1293:0.6232:0.2475	.	2586	P42858	HD_HUMAN	S	2586	ENSP00000347184:A2586S	ENSP00000347184:A2586S	A	+	1	0	HTT	3195647	1.000000	0.71417	0.429000	0.26710	0.156000	0.22039	3.703000	0.54808	2.611000	0.88343	0.650000	0.86243	GCT	.	.		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HTT	3064	hgsc.bcm.edu	37	4	3241606	3241606	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3241606G>T	ENST00000355072.5	+	67	9394	c.9249G>T	c.(9247-9249)ctG>ctT	p.L3083L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3083					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGGGCAAGCTGGAGCAGGTGG	0.582																																					p.L3083L		Atlas-SNP	.											.	HTT	221	.	0			c.G9249T						.						29.0	31.0	30.0					4																	3241606		2151	4240	6391	SO:0001819	synonymous_variant	3064	exon67			CAAGCTGGAGCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9249G>T	chr4.hg19:g.3241606G>T		91.0	0.0		92.0	4.0	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.582	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
RGS12	6002	hgsc.bcm.edu	37	4	3424105	3424105	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3424105G>T	ENST00000344733.5	+	11	3745	c.2841G>T	c.(2839-2841)tcG>tcT	p.S947S	RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Silent_p.S947S|RGS12_ENST00000306648.7_Silent_p.S345S|RGS12_ENST00000382788.3_Silent_p.S947S|RGS12_ENST00000338806.4_Silent_p.S299S|RGS12_ENST00000538395.1_Silent_p.S289S	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	947					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTCCCCAGTCGGAGGCCTGCA	0.667																																					p.S947S		Atlas-SNP	.											.	RGS12	128	.	0			c.G2841T						.						43.0	38.0	40.0					4																	3424105		2198	4297	6495	SO:0001819	synonymous_variant	6002	exon11			CCAGTCGGAGGCC	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.2841G>T	chr4.hg19:g.3424105G>T		141.0	0.0		122.0	5.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Silent	SNP	ENST00000344733.5	hg19	CCDS3366.1																																																																																			.	.		0.667	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
HGFAC	3083	hgsc.bcm.edu	37	4	3443800	3443800	+	Silent	SNP	G	G	C	rs372137428		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3443800G>C	ENST00000382774.3	+	1	187	c.72G>C	c.(70-72)ctG>ctC	p.L24L	HGFAC_ENST00000511533.1_Silent_p.L24L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	24					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTGCTGCTGCTGC	0.716													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13355	0.0		0.0	False		,,,				2504	0.0				p.L24L		Atlas-SNP	.											.	HGFAC	69	.	0			c.G72C						.	G		5,3433		0,5,1714	13.0	16.0	15.0		72	0.1	1.0	4		15	0,7164		0,0,3582	no	coding-synonymous	HGFAC	NM_001528.2		0,5,5296	CC,CG,GG		0.0,0.1454,0.0472		24/656	3443800	5,10597	1719	3582	5301	SO:0001819	synonymous_variant	3083	exon1			CCTCCTGCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.72G>C	chr4.hg19:g.3443800G>C		27.0	0.0		22.0	4.0	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
STK32B	55351	hgsc.bcm.edu	37	4	5399971	5399971	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:5399971G>T	ENST00000282908.5	+	5	894	c.472G>T	c.(472-474)Gga>Tga	p.G158*	STK32B_ENST00000510398.1_Splice_Site_p.G111*|STK32B_ENST00000512636.1_Splice_Site_p.A111S	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GGATGAACACGGTAAGCCTGC	0.488																																					p.G158X		Atlas-SNP	.											STK32B,NS,carcinoma,0,1	STK32B	87	.	0			c.G472T						.						134.0	126.0	129.0					4																	5399971		2203	4300	6503	SO:0001630	splice_region_variant	55351	exon5			GAACACGGTAAGC	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.472+1G>T	chr4.hg19:g.5399971G>T		146.0	0.0		96.0	4.0	NM_018401		Nonsense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.808128|5.808128	0.96967|0.96967	.|.	.|.	ENSG00000152953|ENSG00000152953	ENST00000512636|ENST00000282908;ENST00000510398	T|.	0.46063|.	0.88|.	4.4|4.4	4.4|4.4	0.53042|0.53042	.|.	.|0.000000	.|0.39475	.|U	.|0.001358	T|.	0.67429|.	0.2892|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.77822|.	-0.2445|.	5|.	0.87932|0.87932	D|D	0|0	.|.	12.6557|12.6557	0.56786|0.56786	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|X	111|158;111	ENSP00000423209:A111S|.	ENSP00000423209:A111S|ENSP00000282908:G158X	A|G	+|+	1|1	0|0	STK32B|STK32B	5450872|5450872	0.997000|0.997000	0.39634|0.39634	0.988000|0.988000	0.46212|0.46212	0.563000|0.563000	0.35712|0.35712	3.880000|3.880000	0.56145|0.56145	2.440000|2.440000	0.82611|0.82611	0.655000|0.655000	0.94253|0.94253	GCT|GGA	.	.		0.488	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	Nonsense_Mutation
SORCS2	57537	hgsc.bcm.edu	37	4	7735080	7735080	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:7735080C>T	ENST00000507866.2	+	24	3249	c.3140C>T	c.(3139-3141)gCa>gTa	p.A1047V	SORCS2_ENST00000329016.9_Missense_Mutation_p.A875V	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1047					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GTGCTGAACGCACAGAAGATC	0.652																																					p.A1047V		Atlas-SNP	.											.	SORCS2	98	.	0			c.C3140T						.						14.0	18.0	17.0					4																	7735080		2019	4143	6162	SO:0001583	missense	57537	exon24			TGAACGCACAGAA	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.3140C>T	chr4.hg19:g.7735080C>T	ENSP00000422185:p.Ala1047Val	117.0	0.0		107.0	5.0	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	5.234	0.228737	0.09916	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.14893	2.47;2.48	3.97	2.19	0.27852	.	0.625527	0.14631	N	0.307817	T	0.13756	0.0333	L	0.46157	1.445	0.09310	N	1	B;B	0.33583	0.418;0.363	B;B	0.32533	0.147;0.118	T	0.21042	-1.0257	10	0.66056	D	0.02	.	4.6175	0.12433	0.215:0.6683:0.0:0.1167	.	875;1047	B5MED8;Q96PQ0	.;SORC2_HUMAN	V	1047;875	ENSP00000422185:A1047V;ENSP00000329124:A875V	ENSP00000329124:A875V	A	+	2	0	SORCS2	7785980	0.004000	0.15560	0.008000	0.14137	0.006000	0.05464	0.390000	0.20768	0.323000	0.23307	-0.357000	0.07601	GCA	.	.		0.652	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
WDR1	9948	hgsc.bcm.edu	37	4	10100740	10100740	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:10100740A>G	ENST00000499869.2	-	4	446	c.253T>C	c.(253-255)Tgg>Cgg	p.W85R	WDR1_ENST00000382451.2_Intron|WDR1_ENST00000382452.2_Missense_Mutation_p.W85R|WDR1_ENST00000502702.1_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	85					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		GTGGTATCCCAGATCCTCAGC	0.592																																					p.W85R		Atlas-SNP	.											.	WDR1	93	.	0			c.T253C						.						79.0	77.0	78.0					4																	10100740		1936	4128	6064	SO:0001583	missense	9948	exon4			TATCCCAGATCCT	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.253T>C	chr4.hg19:g.10100740A>G	ENSP00000427687:p.Trp85Arg	173.0	0.0		99.0	4.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	hg19	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.967437	0.92855	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000508079	D;D;D	0.83506	-1.73;-1.73;-1.73	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.95043	0.8395	H	0.99811	4.8	0.80722	D	1	P	0.44260	0.83	P	0.57502	0.822	D	0.96868	0.9637	10	0.87932	D	0	-5.8267	15.1289	0.72503	1.0:0.0:0.0:0.0	.	85	O75083	WDR1_HUMAN	R	85;85;89	ENSP00000427687:W85R;ENSP00000371890:W85R;ENSP00000425481:W89R	ENSP00000371890:W85R	W	-	1	0	WDR1	9709838	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.836000	0.92105	2.169000	0.68431	0.533000	0.62120	TGG	.	.		0.592	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
BOD1L1	259282	hgsc.bcm.edu	37	4	13603749	13603749	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:13603749C>T	ENST00000040738.5	-	10	4910	c.4775G>A	c.(4774-4776)gGt>gAt	p.G1592D		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1592						nucleus (GO:0005634)	DNA binding (GO:0003677)										AACAGCCCCACCTTCTTCAGC	0.483																																					p.G1592D		Atlas-SNP	.											.	.	.	.	0			c.G4775A						.						52.0	50.0	51.0					4																	13603749		2203	4300	6503	SO:0001583	missense	259282	exon10			GCCCCACCTTCTT	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4775G>A	chr4.hg19:g.13603749C>T	ENSP00000040738:p.Gly1592Asp	123.0	0.0		95.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	16.68	3.191206	0.58017	.	.	ENSG00000038219	ENST00000040738	T	0.13420	2.59	5.23	5.23	0.72850	.	0.000000	0.56097	D	0.000033	T	0.29458	0.0734	L	0.36672	1.1	0.44668	D	0.997655	D	0.89917	1.0	D	0.87578	0.998	T	0.01583	-1.1319	10	0.66056	D	0.02	-10.5684	16.9701	0.86296	0.0:1.0:0.0:0.0	.	1592	Q8NFC6	BOD1L_HUMAN	D	1592	ENSP00000040738:G1592D	ENSP00000040738:G1592D	G	-	2	0	BOD1L	13212847	0.996000	0.38824	0.823000	0.32752	0.382000	0.30200	3.261000	0.51530	2.429000	0.82318	0.650000	0.86243	GGT	.	.		0.483	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
KCNIP4	80333	hgsc.bcm.edu	37	4	20852249	20852249	+	Missense_Mutation	SNP	G	G	A	rs548454366		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:20852249G>A	ENST00000382152.2	-	3	372	c.205C>T	c.(205-207)Cgg>Tgg	p.R69W	KCNIP4_ENST00000382150.4_Missense_Mutation_p.R48W|KCNIP4_ENST00000447367.2_Missense_Mutation_p.R35W|KCNIP4_ENST00000359001.5_Missense_Mutation_p.R7W|KCNIP4_ENST00000509207.1_Missense_Mutation_p.R7W|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382148.3_Missense_Mutation_p.R44W	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	69	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				GCTTCAGGCCGATGCCTGACG	0.468													G|||	1	0.000199681	0.0	0.0	5008	,	,		18121	0.0		0.0	False		,,,				2504	0.001				p.R49W		Atlas-SNP	.											KCNIP4_ENST00000447367,NS,carcinoma,+1,4	KCNIP4	85	.	0			c.C145T						.						70.0	69.0	69.0					4																	20852249		2203	4300	6503	SO:0001583	missense	80333	exon2			CAGGCCGATGCCT	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"""EF-hand domain containing"""	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.205C>T	chr4.hg19:g.20852249G>A	ENSP00000371587:p.Arg69Trp	57.0	0.0		43.0	2.0	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Missense_Mutation	SNP	ENST00000382152.2	hg19	CCDS43216.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241883	0.79912	.	.	ENSG00000185774	ENST00000382148;ENST00000447367;ENST00000382150;ENST00000413487;ENST00000382152;ENST00000509207;ENST00000359001	T;T;T;T;T;T	0.68479	-0.33;1.93;-0.33;1.93;-0.33;-0.33	5.42	5.42	0.78866	.	0.228508	0.44688	D	0.000434	D	0.82595	0.5071	M	0.84326	2.69	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;D;D	0.75484	0.934;0.871;0.934;0.986	D	0.85146	0.0983	10	0.87932	D	0	.	14.9878	0.71362	0.0:0.0:0.8486:0.1514	.	44;48;52;69	Q3YAB9;Q3YAC0;Q3YAB7;Q6PIL6	.;.;.;KCIP4_HUMAN	W	44;35;48;7;69;7;7	ENSP00000371583:R44W;ENSP00000399080:R35W;ENSP00000371585:R48W;ENSP00000371587:R69W;ENSP00000423257:R7W;ENSP00000351892:R7W	ENSP00000351892:R7W	R	-	1	2	KCNIP4	20461347	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.259000	0.65485	2.521000	0.84997	0.655000	0.94253	CGG	.	.		0.468	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221	
LGI2	55203	hgsc.bcm.edu	37	4	25005815	25005815	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:25005815C>A	ENST00000382114.4	-	8	1081	c.896G>T	c.(895-897)gGc>gTc	p.G299V		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	299						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				AATGTGAGAGCCACCGAAGAG	0.473																																					p.G299V		Atlas-SNP	.											.	LGI2	62	.	0			c.G896T						.						177.0	180.0	179.0					4																	25005815		2203	4300	6503	SO:0001583	missense	55203	exon8			TGAGAGCCACCGA	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.896G>T	chr4.hg19:g.25005815C>A	ENSP00000371548:p.Gly299Val	152.0	0.0		89.0	4.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551812	0.86127	.	.	ENSG00000153012	ENST00000382114	D	0.81499	-1.5	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.89413	0.6708	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89676	0.3887	10	0.87932	D	0	-37.1251	19.8769	0.96880	0.0:1.0:0.0:0.0	.	299	Q8N0V4	LGI2_HUMAN	V	299	ENSP00000371548:G299V	ENSP00000371548:G299V	G	-	2	0	LGI2	24614913	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.776000	0.85560	2.767000	0.95098	0.557000	0.71058	GGC	.	.		0.473	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
SLAIN2	57606	hgsc.bcm.edu	37	4	48422205	48422205	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:48422205T>C	ENST00000264313.6	+	7	1842	c.1424T>C	c.(1423-1425)gTg>gCg	p.V475A	SLAIN2_ENST00000512093.1_Missense_Mutation_p.V308A	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	475					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						CGGCAACCAGTGAAAGCATTT	0.498																																					p.V475A		Atlas-SNP	.											.	SLAIN2	31	.	0			c.T1424C						.						99.0	95.0	96.0					4																	48422205		1996	4163	6159	SO:0001583	missense	57606	exon7			AACCAGTGAAAGC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"""KIAA1458"""	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1424T>C	chr4.hg19:g.48422205T>C	ENSP00000264313:p.Val475Ala	178.0	0.0		96.0	4.0	NM_020846	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	hg19	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930569	0.52866	.	.	ENSG00000109171	ENST00000264313;ENST00000512093	.	.	.	5.02	5.02	0.67125	.	0.389109	0.28425	N	0.015390	T	0.53965	0.1829	L	0.43152	1.355	0.49130	D	0.999756	P	0.41450	0.75	B	0.41917	0.37	T	0.59506	-0.7442	9	0.62326	D	0.03	-3.3571	14.7394	0.69442	0.0:0.0:0.0:1.0	.	475	Q9P270	SLAI2_HUMAN	A	475;308	.	ENSP00000264313:V475A	V	+	2	0	SLAIN2	48116962	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	6.610000	0.74178	1.901000	0.55032	0.455000	0.32223	GTG	.	.		0.498	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846	
TMPRSS11BNL	401136	hgsc.bcm.edu	37	4	69078095	69078095	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:69078095G>T	ENST00000432593.3	-	2	275	c.109C>A	c.(109-111)Cat>Aat	p.H37N	FTLP10_ENST00000503647.1_RNA|RP11-646E20.6_ENST00000510782.1_RNA					TMPRSS11B N-terminal like, pseudogene											autonomic_ganglia(1)	1						GCCAGAAAATGAACAAGGAGA	0.328																																					p.H37N		Atlas-SNP	.											.	TMPRSS11BNL	4	.	0			c.C109A						.						126.0	95.0	105.0					4																	69078095		692	1591	2283	SO:0001583	missense	401136	exon2			GAAAATGAACAAG			4q13.2	2014-05-09	2014-05-08		ENSG00000226894	ENSG00000250026			37262	pseudogene	pseudogene			"""TMPRSS11B N terminal-like"", ""TMPRSS11B N-terminal like"""				Standard	NR_104048		Approved	FLJ41562	uc003hdv.1		OTTHUMG00000160802	ENST00000432593.3:c.109C>A	chr4.hg19:g.69078095G>T	ENSP00000391149:p.His37Asn	438.0	1.0		306.0	89.0	NM_001129907		Missense_Mutation	SNP	ENST00000432593.3	hg19	CCDS47066.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461041	0.43736	.	.	ENSG00000226894	ENST00000432593	T	0.34667	1.35	5.16	5.16	0.70880	.	.	.	.	.	T	0.60470	0.2271	M	0.74647	2.275	0.24997	N	0.991495	D	0.67145	0.996	D	0.79784	0.993	T	0.53968	-0.8363	9	0.72032	D	0.01	.	14.0064	0.64465	0.0:0.0:1.0:0.0	.	37	B3KVV0	TM11L_HUMAN	N	37	ENSP00000391149:H37N	ENSP00000391149:H37N	H	-	1	0	TMPRSS11BNL	68760690	1.000000	0.71417	1.000000	0.80357	0.203000	0.24098	2.684000	0.46951	2.697000	0.92050	0.650000	0.86243	CAT	.	.		0.328	TMPRSS11BNL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001129907	
ANKRD17	26057	hgsc.bcm.edu	37	4	74005966	74005966	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:74005966T>C	ENST00000358602.4	-	15	2483	c.2367A>G	c.(2365-2367)ccA>ccG	p.P789P	ANKRD17_ENST00000330838.6_Intron|ANKRD17_ENST00000509867.2_Silent_p.P676P|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	789					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GGCTGTTTGCTGGCAAATGGC	0.453																																					p.P789P		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A2367G						.						65.0	65.0	65.0					4																	74005966		2203	4300	6503	SO:0001819	synonymous_variant	26057	exon15			GTTTGCTGGCAAA	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2367A>G	chr4.hg19:g.74005966T>C		89.0	0.0		84.0	4.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.453	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
G3BP2	9908	hgsc.bcm.edu	37	4	76573877	76573877	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:76573877G>A	ENST00000359707.4	-	9	1659	c.874C>T	c.(874-876)Cgt>Tgt	p.R292C	G3BP2_ENST00000357854.3_Missense_Mutation_p.R259C|G3BP2_ENST00000395719.3_Missense_Mutation_p.R292C	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	292					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CGTTGTTCACGCACACGAGGT	0.408																																					p.R292C		Atlas-SNP	.											.	G3BP2	52	.	0			c.C874T						.						102.0	92.0	96.0					4																	76573877		2203	4300	6503	SO:0001583	missense	9908	exon9			GTTCACGCACACG	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"""RNA binding motif (RRM) containing"""	30291	protein-coding gene	gene with protein product	"""Ras-GTPase activating protein SH3 domain-binding protein 2"""					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.874C>T	chr4.hg19:g.76573877G>A	ENSP00000352738:p.Arg292Cys	34.0	0.0		35.0	4.0	NM_012297	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	hg19	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.077733	0.55753	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.78707	-1.19;-1.19;-1.2	5.96	5.96	0.96718	.	0.050014	0.85682	D	0.000000	D	0.86053	0.5841	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.74023	0.489;0.982	D	0.86364	0.1719	10	0.66056	D	0.02	.	15.1472	0.72667	0.0:0.0:0.8588:0.1412	.	259;292	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	C	292;292;259	ENSP00000379069:R292C;ENSP00000352738:R292C;ENSP00000350518:R259C	ENSP00000350518:R259C	R	-	1	0	G3BP2	76792901	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	4.978000	0.63799	2.813000	0.96785	0.655000	0.94253	CGT	.	.		0.408	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297	
SCD5	79966	hgsc.bcm.edu	37	4	83582036	83582036	+	Intron	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:83582036A>G	ENST00000319540.4	-	3	889				SCD5_ENST00000273908.4_Missense_Mutation_p.V255A	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5						fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCTTCAGAATACCTCCAGGGA	0.463																																					p.V255A		Atlas-SNP	.											.	SCD5	58	.	0			c.T764C						.						120.0	116.0	117.0					4																	83582036		2203	4300	6503	SO:0001627	intron_variant	79966	exon4			CAGAATACCTCCA	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.569+19823T>C	chr4.hg19:g.83582036A>G		114.0	0.0		99.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	A	7.564	0.665249	0.14710	.	.	ENSG00000145284	ENST00000273908	.	.	.	3.92	1.46	0.22682	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.29274	-1.0017	7	0.87932	D	0	.	3.1377	0.06444	0.6794:0.0:0.1128:0.2079	.	255	Q86SK9-2	.	A	255	.	ENSP00000273908:V255A	V	-	2	0	SCD5	83801060	0.000000	0.05858	0.003000	0.11579	0.050000	0.14768	-0.029000	0.12329	0.338000	0.23692	0.477000	0.44152	GTA	.	.		0.463	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906	
PTPN13	5783	hgsc.bcm.edu	37	4	87690933	87690933	+	Nonsense_Mutation	SNP	G	G	T	rs549399227		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:87690933G>T	ENST00000411767.2	+	29	4564	c.4501G>T	c.(4501-4503)Gag>Tag	p.E1501*	PTPN13_ENST00000316707.6_Nonsense_Mutation_p.E1310*|PTPN13_ENST00000427191.2_Nonsense_Mutation_p.E1482*|PTPN13_ENST00000511467.1_Nonsense_Mutation_p.E1506*|PTPN13_ENST00000436978.1_Nonsense_Mutation_p.E1506*			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1501	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAATACATTTGAGGTAAAATT	0.284																																					p.E1506X		Atlas-SNP	.											.	PTPN13	203	.	0			c.G4516T						.						21.0	21.0	21.0					4																	87690933		1779	4047	5826	SO:0001587	stop_gained	5783	exon29			ACATTTGAGGTAA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4501G>T	chr4.hg19:g.87690933G>T	ENSP00000407249:p.Glu1501*	81.0	0.0		93.0	4.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Nonsense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	48	14.498267	0.99798	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	.	.	.	5.74	5.74	0.90152	.	0.000000	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.9357	0.97140	0.0:0.0:1.0:0.0	.	.	.	.	X	1482;1506;1310;1501;1506;1450	.	ENSP00000322675:E1310X	E	+	1	0	PTPN13	87909957	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.188000	0.94921	2.715000	0.92844	0.655000	0.94253	GAG	.	.		0.284	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
HERC6	55008	hgsc.bcm.edu	37	4	89356960	89356960	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:89356960T>C	ENST00000264346.7	+	18	2393	c.2334T>C	c.(2332-2334)ccT>ccC	p.P778P	HERC6_ENST00000380265.5_Silent_p.P742P	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	778	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		CTAACCTTCCTTTCCCACTGG	0.368																																					p.P778P		Atlas-SNP	.											.	HERC6	104	.	0			c.T2334C						.						60.0	56.0	57.0					4																	89356960		1910	4180	6090	SO:0001819	synonymous_variant	55008	exon18			CCTTCCTTTCCCA	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.2334T>C	chr4.hg19:g.89356960T>C		129.0	0.0		104.0	5.0	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Silent	SNP	ENST00000264346.7	hg19	CCDS47098.1																																																																																			.	.		0.368	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
UNC5C	8633	hgsc.bcm.edu	37	4	96104119	96104119	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:96104119C>T	ENST00000453304.1	-	14	2728	c.2380G>A	c.(2380-2382)Gtt>Att	p.V794I		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	794					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		AGTTTGCAAACCAGCTCCACT	0.488																																					p.V794I		Atlas-SNP	.											.	UNC5C	141	.	0			c.G2380A						.						155.0	132.0	140.0					4																	96104119		2203	4300	6503	SO:0001583	missense	8633	exon14			TGCAAACCAGCTC	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.2380G>A	chr4.hg19:g.96104119C>T	ENSP00000406022:p.Val794Ile	155.0	0.0		98.0	4.0	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	hg19	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326783	0.60743	.	.	ENSG00000182168	ENST00000453304;ENST00000331502	T	0.47869	0.83	5.83	5.83	0.93111	.	0.233837	0.40469	N	0.001086	T	0.41880	0.1178	L	0.36672	1.1	0.80722	D	1	B	0.29716	0.255	B	0.19148	0.024	T	0.31475	-0.9942	10	0.66056	D	0.02	.	20.1338	0.98010	0.0:1.0:0.0:0.0	.	794	O95185	UNC5C_HUMAN	I	794;753	ENSP00000406022:V794I	ENSP00000328673:V753I	V	-	1	0	UNC5C	96323142	0.984000	0.35163	1.000000	0.80357	0.985000	0.73830	1.925000	0.40074	2.770000	0.95276	0.655000	0.94253	GTT	.	.		0.488	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
TET2	54790	hgsc.bcm.edu	37	4	106155605	106155605	+	Missense_Mutation	SNP	A	A	T	rs545616524		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:106155605A>T	ENST00000540549.1	+	3	1366	c.506A>T	c.(505-507)cAt>cTt	p.H169L	TET2_ENST00000380013.4_Missense_Mutation_p.H169L|TET2_ENST00000545826.1_Missense_Mutation_p.H169L|TET2_ENST00000305737.2_Missense_Mutation_p.H169L|TET2_ENST00000513237.1_Missense_Mutation_p.H190L|TET2_ENST00000394764.1_Missense_Mutation_p.H169L|TET2_ENST00000413648.2_Missense_Mutation_p.H169L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	169					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTTTCAACACATAACTGCAGT	0.388			"""Mis N, F"""		MDS																																p.H169L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.A506T						.						44.0	42.0	43.0					4																	106155605		2203	4300	6503	SO:0001583	missense	54790	exon3			CAACACATAACTG	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.506A>T	chr4.hg19:g.106155605A>T	ENSP00000442788:p.His169Leu	220.0	0.0		149.0	43.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	hg19	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	A	7.287	0.610195	0.14066	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.03717	3.83;4.5;3.83;4.5;4.5;3.83;3.84	5.28	-3.22	0.05125	.	14.800100	0.00728	N	0.000920	T	0.03348	0.0097	N	0.19112	0.55	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.46938	-0.9155	10	0.56958	D	0.05	.	8.0142	0.30372	0.3563:0.0:0.5205:0.1233	.	190;169;169	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	L	169;169;169;190;169;169;169;169	ENSP00000306705:H169L;ENSP00000442788:H169L;ENSP00000442867:H169L;ENSP00000425443:H190L;ENSP00000369351:H169L;ENSP00000378245:H169L;ENSP00000391448:H169L	ENSP00000265149:H169L	H	+	2	0	TET2	106375054	0.000000	0.05858	0.002000	0.10522	0.219000	0.24729	-0.261000	0.08694	-0.319000	0.08652	0.533000	0.62120	CAT	.	.		0.388	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
SGMS2	166929	hgsc.bcm.edu	37	4	108824505	108824505	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:108824505G>T	ENST00000394684.4	+	5	1247	c.690G>T	c.(688-690)acG>acT	p.T230T	RP11-286E11.1_ENST00000513071.1_RNA|RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000359079.4_Silent_p.T230T|SGMS2_ENST00000394686.3_Silent_p.T230T	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	230					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		GCGGTCACACGGTTACGCTGA	0.453																																					p.T230T		Atlas-SNP	.											.	SGMS2	39	.	0			c.G690T						.						149.0	137.0	141.0					4																	108824505		2203	4300	6503	SO:0001819	synonymous_variant	166929	exon4			TCACACGGTTACG	BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.690G>T	chr4.hg19:g.108824505G>T		92.0	0.0		98.0	4.0	NM_001136257	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	hg19	CCDS3677.1																																																																																			.	.		0.453	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621	
ELOVL6	79071	hgsc.bcm.edu	37	4	111119423	111119423	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:111119423G>A	ENST00000394607.3	-	2	232	c.69C>T	c.(67-69)atC>atT	p.I23I	ELOVL6_ENST00000302274.3_Silent_p.I23I|ELOVL6_ENST00000506461.1_5'UTR			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	23					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		GCATCCATTGGATGGCTTCAT	0.493																																					p.I23I		Atlas-SNP	.											.	ELOVL6	27	.	0			c.C69T						.						236.0	200.0	213.0					4																	111119423		2203	4300	6503	SO:0001819	synonymous_variant	79071	exon2			CCATTGGATGGCT	AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"""ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"""			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.69C>T	chr4.hg19:g.111119423G>A		140.0	0.0		78.0	5.0	NM_001130721	Q4W5L0|Q8NCD1	Silent	SNP	ENST00000394607.3	hg19	CCDS3690.1																																																																																			.	.		0.493	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090	
ANXA5	308	hgsc.bcm.edu	37	4	122607464	122607464	+	Silent	SNP	G	G	T	rs370872365		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:122607464G>T	ENST00000296511.5	-	3	358	c.73C>A	c.(73-75)Cgg>Agg	p.R25R	ANXA5_ENST00000509016.1_5'UTR|ANXA5_ENST00000501272.2_Intron|ANXA5_ENST00000515017.1_Silent_p.R25R	NM_001154.3	NP_001145.1	P08758	ANXA5_HUMAN	annexin A5	25					blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543)			NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)	15						ATAGCCTTCCGAAGAGTTTCT	0.378																																					p.R25R	Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188)	Atlas-SNP	.											.	ANXA5	29	.	0			c.C73A						.						95.0	93.0	94.0					4																	122607464		2203	4300	6503	SO:0001819	synonymous_variant	308	exon3			CCTTCCGAAGAGT	U05770	CCDS3720.1	4q27	2008-02-05			ENSG00000164111	ENSG00000164111		"""Annexins"""	543	protein-coding gene	gene with protein product		131230		ENX2, ANX5		2960376	Standard	NM_001154		Approved		uc003idv.4	P08758	OTTHUMG00000133034	ENST00000296511.5:c.73C>A	chr4.hg19:g.122607464G>T		124.0	0.0		80.0	4.0	NM_001154	D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9	Silent	SNP	ENST00000296511.5	hg19	CCDS3720.1																																																																																			.	.		0.378	ANXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256636.2	NM_001154	
KIAA1109	84162	hgsc.bcm.edu	37	4	123274969	123274969	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:123274969G>T	ENST00000264501.4	+	82	14475	c.14102G>T	c.(14101-14103)gGc>gTc	p.G4701V	KIAA1109_ENST00000388738.3_Splice_Site_p.G4701V			Q2LD37	K1109_HUMAN	KIAA1109	4701					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTTGTTGTAGGCTCCAGTGAT	0.318																																					p.G4701V		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G14102T						.						61.0	56.0	58.0					4																	123274969		1800	4073	5873	SO:0001630	splice_region_variant	84162	exon80			TTGTAGGCTCCAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14102-1G>T	chr4.hg19:g.123274969G>T		132.0	0.0		87.0	4.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.55|14.55	2.568440|2.568440	0.45798|0.45798	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	.|T;T;T	.|0.31247	.|2.48;2.48;1.5	5.47|5.47	5.47|5.47	0.80525|0.80525	.|Fragile site-associated protein, C-terminal (1);	.|0.164157	.|0.53938	.|D	.|0.000047	T|T	0.50667|0.50667	0.1629|0.1629	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.77557	.|0.964;0.99	T|T	0.30387|0.30387	-0.9980|-0.9980	5|9	.|.	.|.	.|.	.|.	19.7313|19.7313	0.96182|0.96182	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|4700;4701	.|Q2LD37-4;Q2LD37	.|.;K1109_HUMAN	S|V	1077|4701;4701;1370;302	.|ENSP00000264501:G4701V;ENSP00000373390:G4701V;ENSP00000410874:G1370V	.|.	A|G	+|+	1|2	0|0	KIAA1109|KIAA1109	123494419|123494419	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.653000|0.653000	0.38743|0.38743	6.746000|6.746000	0.74866|0.74866	2.761000|2.761000	0.94854|0.94854	0.650000|0.650000	0.86243|0.86243	GCT|GGC	.	.		0.318	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	Missense_Mutation
GAB1	2549	hgsc.bcm.edu	37	4	144378898	144378898	+	Intron	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:144378898G>T	ENST00000262994.4	+	7	1887				GAB1_ENST00000505913.1_Intron|GAB1_ENST00000262995.4_Missense_Mutation_p.G551C	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1						activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					ACAAACCATAGGTGACTTTGC	0.338																																					p.G551C		Atlas-SNP	.											.	GAB1	80	.	0			c.G1651T						.						58.0	53.0	55.0					4																	144378898		2203	4298	6501	SO:0001627	intron_variant	2549	exon7			ACCATAGGTGACT	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"""Pleckstrin homology (PH) domain containing"""	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1586-1640G>T	chr4.hg19:g.144378898G>T		112.0	0.0		87.0	4.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.906295	0.72868	.	.	ENSG00000109458	ENST00000262995	T	0.15603	2.41	5.18	4.33	0.51752	.	0.075533	0.50627	D	0.000105	T	0.27419	0.0673	N	0.22421	0.69	0.80722	D	1	D	0.69078	0.997	D	0.65874	0.939	T	0.07635	-1.0762	10	0.87932	D	0	-5.757	15.6984	0.77517	0.0:0.1372:0.8628:0.0	.	551	Q13480-2	.	C	551	ENSP00000262995:G551C	ENSP00000262995:G551C	G	+	1	0	GAB1	144598348	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.356000	0.79445	1.162000	0.42619	0.655000	0.94253	GGT	.	.		0.338	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039	
DCHS2	54798	hgsc.bcm.edu	37	4	155244428	155244428	+	Intron	SNP	T	T	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:155244428T>G	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Missense_Mutation_p.K1358Q	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tttgtttgttttttgCACGAC	0.383																																					p.K1358Q		Atlas-SNP	.											DCHS2_ENST00000339452,NS,carcinoma,0,1	DCHS2	594	.	0			c.A4072C						.						86.0	65.0	71.0					4																	155244428		692	1591	2283	SO:0001627	intron_variant	54798	exon8			TTTGTTTTTTGCA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2654-788A>C	chr4.hg19:g.155244428T>G		53.0	1.0		81.0	5.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	5.448	0.267684	0.10294	.	.	ENSG00000197410	ENST00000339452	T	0.59083	0.29	1.19	-2.19	0.07015	.	.	.	.	.	T	0.29321	0.0730	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.16867	-1.0388	9	0.13470	T	0.59	.	2.2509	0.04043	0.0:0.2273:0.3135:0.4592	.	1358	E9PC11	.	Q	1358	ENSP00000345062:K1358Q	ENSP00000345062:K1358Q	K	-	1	0	DCHS2	155463878	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.498000	0.02287	-0.611000	0.05709	-0.579000	0.04138	AAA	.	.		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
ANXA10	11199	hgsc.bcm.edu	37	4	169060641	169060641	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:169060641T>C	ENST00000359299.3	+	3	291	c.105T>C	c.(103-105)tgT>tgC	p.C35C		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	35						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		TTCCAGACTGTGACAAAGACA	0.413																																					p.C35C		Atlas-SNP	.											.	ANXA10	44	.	0			c.T105C						.						89.0	87.0	88.0					4																	169060641		2203	4300	6503	SO:0001819	synonymous_variant	11199	exon3			AGACTGTGACAAA	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"""Annexins"""	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.105T>C	chr4.hg19:g.169060641T>C		146.0	0.0		100.0	4.0	NM_007193	Q96IQ5|Q9UJV4	Silent	SNP	ENST00000359299.3	hg19	CCDS34096.1																																																																																			.	.		0.413	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	
CBR4	84869	hgsc.bcm.edu	37	4	169931172	169931172	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:169931172G>T	ENST00000306193.3	-	1	237	c.69C>A	c.(67-69)gcC>gcA	p.A23A	CBR4_ENST00000504480.1_Silent_p.A23A|RP11-483A20.3_ENST00000506933.1_RNA	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4	23					daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)			kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		AGCCTTTCCGGGCCATTAACT	0.582											OREG0016397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A23A		Atlas-SNP	.											.	CBR4	15	.	0			c.C69A						.						39.0	43.0	42.0					4																	169931172		2203	4300	6503	SO:0001819	synonymous_variant	84869	exon1			TTTCCGGGCCATT	BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	25891	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 45C, member 1"""					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.69C>A	chr4.hg19:g.169931172G>T		116.0	0.0	1881	93.0	4.0	NM_032783	Q8WTW8|Q96K93	Silent	SNP	ENST00000306193.3	hg19	CCDS3812.1																																																																																			.	.		0.582	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783	
GALNTL6	442117	hgsc.bcm.edu	37	4	173730515	173730515	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:173730515A>G	ENST00000506823.1	+	6	1214	c.557A>G	c.(556-558)cAc>cGc	p.H186R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.H169R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	186	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TACCTAGAACACCTGAAGGAT	0.433																																					p.H186R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A557G						.						91.0	88.0	89.0					4																	173730515		2203	4300	6503	SO:0001583	missense	442117	exon6			TAGAACACCTGAA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.557A>G	chr4.hg19:g.173730515A>G	ENSP00000423313:p.His186Arg	138.0	0.0		94.0	4.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220922	0.39201	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.58940	0.3;0.3	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000003	T	0.72358	0.3450	L	0.58510	1.815	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.74191	-0.3745	10	0.56958	D	0.05	.	15.7979	0.78424	1.0:0.0:0.0:0.0	.	186	Q49A17	GLTL6_HUMAN	R	186;186;169	ENSP00000423313:H186R;ENSP00000423827:H169R	ENSP00000385382:H186R	H	+	2	0	GALNTL6	173967090	1.000000	0.71417	0.999000	0.59377	0.013000	0.08279	9.287000	0.95975	2.196000	0.70406	0.402000	0.26972	CAC	.	.		0.433	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
STOX2	56977	hgsc.bcm.edu	37	4	184930350	184930350	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:184930350T>C	ENST00000308497.4	+	3	1794	c.359T>C	c.(358-360)cTg>cCg	p.L120P	STOX2_ENST00000438269.1_Missense_Mutation_p.L120P	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	120					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CGGCACACGCTGAACACGCTG	0.443																																					p.L120P		Atlas-SNP	.											.	STOX2	142	.	0			c.T359C						.						53.0	48.0	50.0					4																	184930350		1920	4156	6076	SO:0001583	missense	56977	exon3			ACACGCTGAACAC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.359T>C	chr4.hg19:g.184930350T>C	ENSP00000311257:p.Leu120Pro	91.0	0.0		86.0	5.0	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	hg19	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803740	0.90623	.	.	ENSG00000173320	ENST00000308497;ENST00000438269;ENST00000512520	D;D;D	0.88586	-2.4;-2.4;-2.4	5.55	5.55	0.83447	Storkhead-box protein, winged-helix domain (1);	0.000000	0.64402	D	0.000001	D	0.93858	0.8035	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94443	0.7660	10	0.87932	D	0	-13.753	15.8615	0.79026	0.0:0.0:0.0:1.0	.	120	Q9P2F5	STOX2_HUMAN	P	120;120;58	ENSP00000311257:L120P;ENSP00000390127:L120P;ENSP00000425388:L58P	ENSP00000311257:L120P	L	+	2	0	STOX2	185167344	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.868000	0.87116	2.333000	0.79357	0.533000	0.62120	CTG	.	.		0.443	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
PDZD2	23037	hgsc.bcm.edu	37	5	32098708	32098708	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:32098708C>A	ENST00000438447.1	+	23	8574	c.8186C>A	c.(8185-8187)tCc>tAc	p.S2729Y	PDZD2_ENST00000282493.3_Missense_Mutation_p.S2729Y			O15018	PDZD2_HUMAN	PDZ domain containing 2	2729					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGTTTGCTGTCCAGAAAGACC	0.547																																					p.S2729Y		Atlas-SNP	.											.	PDZD2	306	.	0			c.C8186A						.						46.0	44.0	44.0					5																	32098708		2203	4300	6503	SO:0001583	missense	23037	exon22			TGCTGTCCAGAAA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.8186C>A	chr5.hg19:g.32098708C>A	ENSP00000402033:p.Ser2729Tyr	67.0	0.0		65.0	4.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088140	0.76642	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.08102	3.13;3.13	5.22	4.34	0.51931	.	0.253674	0.28521	N	0.015043	T	0.12944	0.0314	L	0.32530	0.975	0.27874	N	0.939914	D	0.56521	0.976	P	0.53450	0.726	T	0.02288	-1.1182	10	0.66056	D	0.02	.	11.9527	0.52964	0.0:0.8256:0.1744:0.0	.	2729	O15018	PDZD2_HUMAN	Y	2729;2530;2729	ENSP00000402033:S2729Y;ENSP00000282493:S2729Y	ENSP00000282493:S2729Y	S	+	2	0	PDZD2	32134465	0.869000	0.29996	0.591000	0.28745	0.683000	0.39861	1.531000	0.36018	1.152000	0.42452	0.655000	0.94253	TCC	.	.		0.547	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
NADK2	133686	hgsc.bcm.edu	37	5	36217963	36217963	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:36217963C>A	ENST00000381937.4	-	6	667	c.668G>T	c.(667-669)aGg>aTg	p.R223M	NADK2_ENST00000514504.1_Missense_Mutation_p.R223M|NADK2_ENST00000282512.3_Missense_Mutation_p.R60M|NADK2_ENST00000506945.1_Missense_Mutation_p.R60M|NADK2_ENST00000397338.1_Missense_Mutation_p.R60M	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	223					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										AAGGTATAACCTGATTCTCTG	0.368																																					p.R223M		Atlas-SNP	.											.	NADKD1	47	.	0			c.G668T						.						120.0	106.0	111.0					5																	36217963		2203	4300	6503	SO:0001583	missense	133686	exon6			TATAACCTGATTC	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"""mitochondrial NAD kinase"""	615787	"""chromosome 5 open reading frame 33"", ""NAD kinase domain containing 1"""	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.668G>T	chr5.hg19:g.36217963C>A	ENSP00000371362:p.Arg223Met	164.0	0.0		103.0	5.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781693	0.90282	.	.	ENSG00000152620	ENST00000397338;ENST00000282512;ENST00000381937;ENST00000506945;ENST00000514504;ENST00000511088	T;T;T;T;T;T	0.45668	0.89;0.89;0.94;0.89;0.89;0.89	6.08	5.22	0.72569	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	T	0.73754	-0.3883	10	0.87932	D	0	-10.8315	15.1343	0.72552	0.0:0.932:0.0:0.068	.	60;223;223	B7Z8V7;Q4G0N4-2;Q4G0N4	.;.;NAKD1_HUMAN	M	60;60;223;60;223;60	ENSP00000380499:R60M;ENSP00000282512:R60M;ENSP00000371362:R223M;ENSP00000422250:R60M;ENSP00000421029:R223M;ENSP00000426084:R60M	ENSP00000282512:R60M	R	-	2	0	NADKD1	36253720	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.938000	0.75904	1.595000	0.50050	0.591000	0.81541	AGG	.	.		0.368	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013	
MAST4	375449	hgsc.bcm.edu	37	5	66459398	66459398	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:66459398G>A	ENST00000403625.2	+	29	4686	c.4391G>A	c.(4390-4392)cGc>cAc	p.R1464H	MAST4_ENST00000261569.7_Missense_Mutation_p.R1270H|MAST4_ENST00000405643.1_Missense_Mutation_p.R1285H|MAST4_ENST00000403666.1_Missense_Mutation_p.R1275H|MAST4_ENST00000404260.3_Missense_Mutation_p.R1467H	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1467						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTGTGCTCCCGCAAGCACAGC	0.667																																					p.R1464H		Atlas-SNP	.											.	MAST4	218	.	0			c.G4391A						.						13.0	18.0	16.0					5																	66459398		2090	4194	6284	SO:0001583	missense	375449	exon29			GCTCCCGCAAGCA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.4391G>A	chr5.hg19:g.66459398G>A	ENSP00000385727:p.Arg1464His	88.0	0.0		62.0	4.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	33	5.194465	0.94960	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	T;T;T;T;T	0.72394	-0.63;-0.63;-0.65;-0.65;-0.62	5.92	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.84506	0.5487	M	0.83953	2.67	0.39097	D	0.96121	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.86817	0.2002	10	0.66056	D	0.02	-21.9289	14.5277	0.67900	0.0697:0.0:0.9303:0.0	.	1467;1275	O15021;O15021-3	MAST4_HUMAN;.	H	1467;1464;1275;1285;1285;1270	ENSP00000385048:R1467H;ENSP00000385727:R1464H;ENSP00000384313:R1275H;ENSP00000384099:R1285H;ENSP00000261569:R1270H	ENSP00000261569:R1270H	R	+	2	0	MAST4	66495154	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.643000	0.98464	2.818000	0.97014	0.655000	0.94253	CGC	.	.		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
CARTPT	9607	hgsc.bcm.edu	37	5	71015234	71015234	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:71015234G>T	ENST00000296777.4	+	1	245	c.114G>T	c.(112-114)ctG>ctT	p.L38L		NM_004291.3	NP_004282.1	Q16568	CART_HUMAN	CART prepropeptide	38					activation of MAPKK activity (GO:0000186)|adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|circadian regulation of gene expression (GO:0032922)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of appetite (GO:0032099)|negative regulation of bone resorption (GO:0045779)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of osteoclast differentiation (GO:0045671)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of epinephrine secretion (GO:0032812)|positive regulation of transmission of nerve impulse (GO:0051971)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|somatostatin secretion (GO:0070253)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|secretory granule (GO:0030141)				large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(167;0.00153)|Ovarian(174;0.0175)|Prostate(74;0.11)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;8.4e-56)	Amphetamine(DB00182)	CCCGAGCCCTGGACATCTACT	0.652																																					p.L38L		Atlas-SNP	.											.	CARTPT	10	.	0			c.G114T						.						72.0	70.0	70.0					5																	71015234		2203	4300	6503	SO:0001819	synonymous_variant	9607	exon1			AGCCCTGGACATC	U16826	CCDS4011.1	5q13.2	2008-02-05			ENSG00000164326	ENSG00000164326			24323	protein-coding gene	gene with protein product	"""cocaine and amphetamine regulated transcript"""	602606				9590691, 8647455	Standard	NM_004291		Approved	CART	uc003kbv.2	Q16568	OTTHUMG00000131261	ENST00000296777.4:c.114G>T	chr5.hg19:g.71015234G>T		104.0	0.0		95.0	4.0	NM_004291	Q6FG92	Silent	SNP	ENST00000296777.4	hg19	CCDS4011.1																																																																																			.	.		0.652	CARTPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254029.2	NM_004291	
ENC1	8507	hgsc.bcm.edu	37	5	73930624	73930624	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:73930624C>A	ENST00000302351.4	-	2	2817	c.1687G>T	c.(1687-1689)Gac>Tac	p.D563Y	ENC1_ENST00000510316.1_Missense_Mutation_p.D490Y|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Missense_Mutation_p.D563Y	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	563				YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532). {ECO:0000305}.	multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		TTCCACACGTCTAATGTTGGA	0.478																																					p.D563Y		Atlas-SNP	.											.	ENC1	56	.	0			c.G1687T						.						116.0	88.0	97.0					5																	73930624		2203	4300	6503	SO:0001583	missense	8507	exon2			ACACGTCTAATGT	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1687G>T	chr5.hg19:g.73930624C>A	ENSP00000306356:p.Asp563Tyr	150.0	0.0		100.0	4.0	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	hg19	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630395	0.67015	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.80304	-1.36;-1.36;-1.36	5.75	5.75	0.90469	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.92629	0.7658	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93679	0.6997	10	0.87932	D	0	.	19.9421	0.97168	0.0:1.0:0.0:0.0	.	563	O14682	ENC1_HUMAN	Y	563;490;563	ENSP00000306356:D563Y;ENSP00000423804:D490Y;ENSP00000446289:D563Y	ENSP00000306356:D563Y	D	-	1	0	ENC1	73966380	1.000000	0.71417	0.229000	0.23960	0.898000	0.52572	7.818000	0.86416	2.714000	0.92807	0.561000	0.74099	GAC	.	.		0.478	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
GFM2	84340	hgsc.bcm.edu	37	5	74028915	74028915	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:74028915G>T	ENST00000296805.3	-	16	1976	c.1519C>A	c.(1519-1521)Cat>Aat	p.H507N	GFM2_ENST00000509430.1_Missense_Mutation_p.H507N|GFM2_ENST00000345239.2_Missense_Mutation_p.H460N|GFM2_ENST00000515125.1_5'UTR	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TTCAACGCATGTTCCAAATCT	0.343																																					p.H507N		Atlas-SNP	.											.	GFM2	38	.	0			c.C1519A						.						117.0	110.0	112.0					5																	74028915		2203	4300	6503	SO:0001583	missense	84340	exon16			ACGCATGTTCCAA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1519C>A	chr5.hg19:g.74028915G>T	ENSP00000296805:p.His507Asn	108.0	0.0		84.0	4.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417379	0.11870	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.70749	-0.51;-0.51;-0.51	5.07	4.17	0.49024	Elongation factor G/III/V (1);	0.246709	0.38663	N	0.001603	T	0.47040	0.1424	N	0.10874	0.06	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.31971	-0.9924	10	0.31617	T	0.26	-8.6912	6.5471	0.22412	0.0955:0.0:0.6032:0.3013	.	507;460;507	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	N	507;460;507;507	ENSP00000296805:H507N;ENSP00000296804:H460N;ENSP00000427004:H507N	ENSP00000296805:H507N	H	-	1	0	GFM2	74064671	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.058000	0.49939	1.067000	0.40740	0.557000	0.71058	CAT	.	.		0.343	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
JMY	133746	hgsc.bcm.edu	37	5	78533050	78533050	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:78533050A>G	ENST00000396137.4	+	1	1039	c.577A>G	c.(577-579)Ata>Gta	p.I193V	DMGDH_ENST00000520388.1_5'Flank	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	193					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		CTCCGAGGAGATAGAGGTGCT	0.701																																					p.I193V		Atlas-SNP	.											.	JMY	82	.	0			c.A577G						.						14.0	20.0	18.0					5																	78533050		692	1590	2282	SO:0001583	missense	133746	exon1			GAGGAGATAGAGG	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.577A>G	chr5.hg19:g.78533050A>G	ENSP00000379441:p.Ile193Val	206.0	0.0		121.0	5.0	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	A	16.82	3.229082	0.58777	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.08008	3.14	3.84	2.65	0.31530	.	2.723900	0.02643	U	0.105502	T	0.12860	0.0312	L	0.54323	1.7	0.25529	N	0.987294	B	0.20780	0.048	B	0.24541	0.054	T	0.35001	-0.9806	10	0.54805	T	0.06	.	8.3538	0.32318	0.7999:0.2001:0.0:0.0	.	193	Q8N9B5	JMY_HUMAN	V	193	ENSP00000379441:I193V	ENSP00000282259:I193V	I	+	1	0	JMY	78568806	1.000000	0.71417	0.049000	0.19019	0.904000	0.53231	1.637000	0.37155	0.524000	0.28502	0.379000	0.24179	ATA	.	.		0.701	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
CMYA5	202333	hgsc.bcm.edu	37	5	79034137	79034137	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79034137G>T	ENST00000446378.2	+	2	9580	c.9549G>T	c.(9547-9549)ctG>ctT	p.L3183L		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3183					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CAGAATTTCTGGAGGAGCCAC	0.428																																					p.L3183L		Atlas-SNP	.											.	CMYA5	643	.	0			c.G9549T						.						46.0	46.0	46.0					5																	79034137		1850	4093	5943	SO:0001819	synonymous_variant	202333	exon2			ATTTCTGGAGGAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9549G>T	chr5.hg19:g.79034137G>T		111.0	0.0		86.0	4.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.428	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
THBS4	7060	hgsc.bcm.edu	37	5	79351663	79351663	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79351663C>T	ENST00000350881.2	+	3	538	c.348C>T	c.(346-348)aaC>aaT	p.N116N	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Silent_p.N25N	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	116	Laminin G-like.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TTTTCAACAACCTGCAGCTGG	0.567																																					p.N116N		Atlas-SNP	.											.	THBS4	82	.	0			c.C348T						.						166.0	171.0	169.0					5																	79351663		2203	4300	6503	SO:0001819	synonymous_variant	7060	exon3			CAACAACCTGCAG		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.348C>T	chr5.hg19:g.79351663C>T		151.0	0.0		82.0	4.0	NM_003248	B2R909|Q86TG2	Silent	SNP	ENST00000350881.2	hg19	CCDS4049.1																																																																																			.	.		0.567	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
THBS4	7060	hgsc.bcm.edu	37	5	79355537	79355537	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79355537T>C	ENST00000350881.2	+	7	986	c.796T>C	c.(796-798)Ttt>Ctt	p.F266L	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.F175L	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	266					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TCCTCTCAAGTTTCAGTCTCC	0.527																																					p.F266L		Atlas-SNP	.											.	THBS4	82	.	0			c.T796C						.						118.0	118.0	118.0					5																	79355537		2203	4300	6503	SO:0001583	missense	7060	exon7			CTCAAGTTTCAGT		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.796T>C	chr5.hg19:g.79355537T>C	ENSP00000339730:p.Phe266Leu	94.0	0.0		54.0	4.0	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	hg19	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	T	2.198	-0.383767	0.04966	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	T;T	0.27890	1.64;1.64	5.23	-3.23	0.05109	.	1.179790	0.05785	N	0.609271	T	0.12390	0.0301	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	10	0.11794	T	0.64	-1.5851	5.1683	0.15098	0.1103:0.0745:0.4831:0.3322	.	266	P35443	TSP4_HUMAN	L	266;175	ENSP00000339730:F266L;ENSP00000422298:F175L	ENSP00000339730:F266L	F	+	1	0	THBS4	79391293	0.172000	0.23043	0.346000	0.25655	0.151000	0.21798	0.047000	0.14056	-0.130000	0.11599	-0.316000	0.08728	TTT	.	.		0.527	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
ARRDC3	57561	hgsc.bcm.edu	37	5	90670966	90670966	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:90670966C>T	ENST00000265138.3	-	5	909	c.643G>A	c.(643-645)Gag>Aag	p.E215K	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	215					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		GAGCAGTTCTCAATCTCAGCA	0.388																																					p.E215K		Atlas-SNP	.											ARRDC3,bladder,carcinoma,0,1	ARRDC3	56	.	0			c.G643A						.						59.0	54.0	56.0					5																	90670966		2203	4300	6503	SO:0001583	missense	57561	exon5			AGTTCTCAATCTC	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"""alpha-arrestin 3"""	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.643G>A	chr5.hg19:g.90670966C>T	ENSP00000265138:p.Glu215Lys	51.0	0.0		64.0	3.0	NM_020801	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	hg19	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	C	37	6.148985	0.97324	.	.	ENSG00000113369	ENST00000265138	T	0.06933	3.24	6.08	6.08	0.98989	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.36663	0.0975	M	0.87827	2.91	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.02950	-1.1090	10	0.34782	T	0.22	-17.7314	20.6721	0.99693	0.0:1.0:0.0:0.0	.	215	Q96B67	ARRD3_HUMAN	K	215	ENSP00000265138:E215K	ENSP00000265138:E215K	E	-	1	0	ARRDC3	90706722	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.786000	0.85741	2.894000	0.99253	0.591000	0.81541	GAG	.	.		0.388	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801	
MCTP1	79772	hgsc.bcm.edu	37	5	94275844	94275844	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:94275844C>A	ENST00000515393.1	-	5	1116	c.1117G>T	c.(1117-1119)Gga>Tga	p.G373*	MCTP1_ENST00000312216.8_Nonsense_Mutation_p.G152*|MCTP1_ENST00000505208.1_Nonsense_Mutation_p.G152*|MCTP1_ENST00000429576.2_Nonsense_Mutation_p.G152*	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	373					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AAAATGATTCCAAGATCATGG	0.408																																					p.G373X		Atlas-SNP	.											.	MCTP1	110	.	0			c.G1117T						.						170.0	172.0	171.0					5																	94275844		2203	4300	6503	SO:0001587	stop_gained	79772	exon5			TGATTCCAAGATC		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1117G>T	chr5.hg19:g.94275844C>A	ENSP00000424126:p.Gly373*	124.0	0.0		82.0	4.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Nonsense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	7.936443|7.936443	0.98571|0.98571	.|.	.|.	ENSG00000175471|ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568;ENST00000415885;ENST00000507214;ENST00000514780|ENST00000503301	.|.	.|.	.|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79992	.|0.4542	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77593	.|-0.2530	.|3	0.66056|.	D|.	0.02|.	-12.3737|-12.3737	20.0396|20.0396	0.97574|0.97574	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	373;152;152;152;34;152;13;114;134;133|181	.|.	ENSP00000308957:G152X|.	G|W	-|-	1|2	0|0	MCTP1|MCTP1	94301600|94301600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	6.394000|6.394000	0.73223|0.73223	2.814000|2.814000	0.96858|0.96858	0.563000|0.563000	0.77884|0.77884	GGA|TGG	.	.		0.408	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
ARSK	153642	hgsc.bcm.edu	37	5	94939217	94939217	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:94939217C>A	ENST00000380009.4	+	8	1803	c.1598C>A	c.(1597-1599)cCa>cAa	p.P533Q		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	533					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		CATATGAATCCAAGAGCAGTT	0.303																																					p.P533Q		Atlas-SNP	.											.	ARSK	29	.	0			c.C1598A						.						38.0	38.0	38.0					5																	94939217		2203	4299	6502	SO:0001583	missense	153642	exon8			TGAATCCAAGAGC		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"""Arylsulfatase family"""	25239	protein-coding gene	gene with protein product		610011	"""arylsulfatase K"""			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1598C>A	chr5.hg19:g.94939217C>A	ENSP00000369346:p.Pro533Gln	74.0	0.0		73.0	4.0	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	hg19	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	C	9.667	1.145640	0.21288	.	.	ENSG00000164291	ENST00000380009	D	0.98362	-4.89	4.86	1.47	0.22746	.	1.526730	0.03754	N	0.257001	D	0.95089	0.8409	L	0.44542	1.39	0.09310	N	1	B	0.28512	0.214	B	0.23574	0.047	D	0.87413	0.2377	10	0.29301	T	0.29	0.1729	0.0796	0.00030	0.2785:0.2289:0.2308:0.2618	.	533	Q6UWY0	ARSK_HUMAN	Q	533	ENSP00000369346:P533Q	ENSP00000369346:P533Q	P	+	2	0	ARSK	94964973	0.084000	0.21492	0.000000	0.03702	0.026000	0.11368	0.067000	0.14510	0.548000	0.28955	-0.137000	0.14449	CCA	.	.		0.303	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150	
TRPC7	57113	hgsc.bcm.edu	37	5	135692571	135692571	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:135692571T>C	ENST00000513104.1	-	2	787	c.505A>G	c.(505-507)Atc>Gtc	p.I169V	TRPC7_ENST00000355180.3_Missense_Mutation_p.I169V|TRPC7_ENST00000426057.2_Missense_Mutation_p.I169V	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	169					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCGCCAGGATGATGGGCGTG	0.637																																					p.I169V		Atlas-SNP	.											.	TRPC7	126	.	0			c.A505G						.						132.0	142.0	138.0					5																	135692571		2203	4300	6503	SO:0001583	missense	57113	exon2			CCAGGATGATGGG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.505A>G	chr5.hg19:g.135692571T>C	ENSP00000426070:p.Ile169Val	116.0	0.0		93.0	4.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.55|16.55	3.154030|3.154030	0.57259|0.57259	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753|ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	.|T;T;T	.|0.70869	.|-0.52;-0.52;-0.52	5.26|5.26	5.26|5.26	0.73747|0.73747	.|Ankyrin repeat-containing domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76248|0.76248	0.3961|0.3961	M|M	0.79475|0.79475	2.455|2.455	0.29723|0.29723	N|N	0.838498|0.838498	.|B;D;B;B	.|0.55385	.|0.001;0.971;0.032;0.032	.|B;P;B;B	.|0.47603	.|0.001;0.551;0.071;0.102	T|T	0.77955|0.77955	-0.2393|-0.2393	5|10	.|0.56958	.|D	.|0.05	-22.9787|-22.9787	15.3565|15.3565	0.74431|0.74431	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|169;169;169;169	.|Q8IWP7;F5H5U9;Q70T25;Q9HCX4	.|.;.;.;TRPC7_HUMAN	R|V	168|169	.|ENSP00000347312:I169V;ENSP00000441628:I169V;ENSP00000426070:I169V	.|ENSP00000265193:I169V	H|I	-|-	2|1	0|0	TRPC7|TRPC7	135720470|135720470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.022000|5.022000	0.64078|0.64078	2.205000|2.205000	0.71048|0.71048	0.528000|0.528000	0.53228|0.53228	CAT|ATC	.	.		0.637	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389	
KIF20A	10112	hgsc.bcm.edu	37	5	137518950	137518950	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:137518950T>C	ENST00000394894.3	+	8	1151	c.925T>C	c.(925-927)Tac>Cac	p.Y309H	KIF20A_ENST00000508792.1_Missense_Mutation_p.Y291H	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	309	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTTTGAGATCTACAACGAACT	0.493																																					p.Y309H		Atlas-SNP	.											.	KIF20A	53	.	0			c.T925C						.						66.0	63.0	64.0					5																	137518950		2203	4300	6503	SO:0001583	missense	10112	exon8			GAGATCTACAACG	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"""Kinesins"""	9787	protein-coding gene	gene with protein product		605664	"""RAB6 interacting, kinesin-like (rabkinesin6)"""	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.925T>C	chr5.hg19:g.137518950T>C	ENSP00000378356:p.Tyr309His	83.0	0.0		84.0	4.0	NM_005733	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	hg19	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694220	0.68386	.	.	ENSG00000112984	ENST00000394894;ENST00000508792	D;D	0.87334	-2.24;-2.24	5.4	5.4	0.78164	Kinesin, motor domain (4);	0.000000	0.40908	D	0.000992	D	0.93471	0.7917	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94349	0.7577	10	0.87932	D	0	-11.4603	15.4415	0.75187	0.0:0.0:0.0:1.0	.	291;309	B4DL79;O95235	.;KI20A_HUMAN	H	309;291	ENSP00000378356:Y309H;ENSP00000420880:Y291H	ENSP00000378356:Y309H	Y	+	1	0	KIF20A	137546849	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	7.698000	0.84413	2.061000	0.61500	0.533000	0.62120	TAC	.	.		0.493	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733	
ETF1	2107	hgsc.bcm.edu	37	5	137844000	137844000	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:137844000G>A	ENST00000360541.5	-	11	1529	c.1308C>T	c.(1306-1308)gaC>gaT	p.D436D	ETF1_ENST00000503014.1_Silent_p.D422D|ETF1_ENST00000499810.2_Silent_p.D403D	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	436					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTACCTAGTAGTCATCAAGGT	0.488																																					p.D436D		Atlas-SNP	.											.	ETF1	38	.	0			c.C1308T						.						56.0	47.0	50.0					5																	137844000		2203	4300	6503	SO:0001819	synonymous_variant	2107	exon11			CTAGTAGTCATCA	AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"""sup45 (yeast omnipotent suppressor 45) homolog-like 1"", ""polypeptide chain release factor 1"""	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.1308C>T	chr5.hg19:g.137844000G>A		96.0	0.0		124.0	19.0	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Silent	SNP	ENST00000360541.5	hg19	CCDS4207.1																																																																																			.	.		0.488	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730	
PSD2	84249	hgsc.bcm.edu	37	5	139189371	139189371	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:139189371C>A	ENST00000274710.3	+	2	551	c.346C>A	c.(346-348)Cca>Aca	p.P116T		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	116					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCCTCTACCCAGATGCTGA	0.592																																					p.P116T		Atlas-SNP	.											.	PSD2	88	.	0			c.C346A						.						65.0	73.0	71.0					5																	139189371		2203	4300	6503	SO:0001583	missense	84249	exon2			CTCTACCCAGATG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"""Pleckstrin homology (PH) domain containing"""	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.346C>A	chr5.hg19:g.139189371C>A	ENSP00000274710:p.Pro116Thr	64.0	0.0		113.0	5.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	2.704	-0.270254	0.05716	.	.	ENSG00000146005	ENST00000274710	T	0.26223	1.75	4.75	-1.13	0.09775	.	1.428600	0.04426	N	0.368474	T	0.17365	0.0417	N	0.19112	0.55	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.30119	-0.9989	10	0.25106	T	0.35	.	9.8505	0.41055	0.0:0.3107:0.5936:0.0957	.	116	Q9BQI7	PSD2_HUMAN	T	116	ENSP00000274710:P116T	ENSP00000274710:P116T	P	+	1	0	PSD2	139169555	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.314000	0.19432	-0.331000	0.08501	-0.367000	0.07326	CCA	.	.		0.592	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347691	140347691	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140347691C>A	ENST00000289269.5	+	1	1872	c.1340C>A	c.(1339-1341)cCg>cAg	p.P447Q	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA13_ENST00000289272.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	447	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGGAATACCGCAGCTCACA	0.537																																					p.P447Q	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C1340A						.						110.0	113.0	112.0					5																	140347691		2203	4300	6503	SO:0001583	missense	56134	exon1			GAATACCGCAGCT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1340C>A	chr5.hg19:g.140347691C>A	ENSP00000289269:p.Pro447Gln	151.0	0.0		87.0	5.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977428	0.74360	.	.	ENSG00000243232	ENST00000289269	T	0.55588	0.51	5.92	5.92	0.95590	Cadherin (4);Cadherin-like (1);	0.000000	0.41712	D	0.000834	D	0.82838	0.5124	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87312	0.2312	10	0.87932	D	0	.	20.3248	0.98698	0.0:1.0:0.0:0.0	.	447;447	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	Q	447	ENSP00000289269:P447Q	ENSP00000289269:P447Q	P	+	2	0	PCDHAC2	140327875	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.818000	0.86416	2.818000	0.97014	0.655000	0.94253	CCG	.	.		0.537	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719523	140719523	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140719523A>G	ENST00000394576.2	+	1	985	c.985A>G	c.(985-987)Acc>Gcc	p.T329A	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	329	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCCTTCTAACCAGAGCGAA	0.428																																					p.T329A		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.A985G						.						154.0	159.0	157.0					5																	140719523		2203	4300	6503	SO:0001583	missense	56113	exon1			CTTCTAACCAGAG	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.985A>G	chr5.hg19:g.140719523A>G	ENSP00000378077:p.Thr329Ala	149.0	0.0		98.0	4.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	0.392	-0.922845	0.02377	.	.	ENSG00000081853	ENST00000394576	T	0.02709	4.19	5.26	4.09	0.47781	Cadherin (4);Cadherin-like (1);	0.590193	0.13742	U	0.365898	T	0.01287	0.0042	N	0.04043	-0.29	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.13407	0.005;0.009	T	0.47935	-0.9078	10	0.02654	T	1	.	5.6812	0.17776	0.7463:0.0:0.2537:0.0	.	329;329	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	A	329	ENSP00000378077:T329A	ENSP00000378077:T329A	T	+	1	0	PCDHGA2	140699707	0.000000	0.05858	1.000000	0.80357	0.688000	0.40055	-0.472000	0.06623	2.125000	0.65367	0.533000	0.62120	ACC	.	.		0.428	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
PCDHGA6	56109	hgsc.bcm.edu	37	5	140754660	140754660	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140754660T>C	ENST00000517434.1	+	1	1010	c.1010T>C	c.(1009-1011)aTc>aCc	p.I337T	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	337	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTAATAACTATCTTGGATGTC	0.443																																					p.I337T		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.T1010C						.						149.0	156.0	154.0					5																	140754660		1912	4114	6026	SO:0001583	missense	56109	exon1			TAACTATCTTGGA	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1010T>C	chr5.hg19:g.140754660T>C	ENSP00000429601:p.Ile337Thr	151.0	0.0		98.0	6.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	18.57	3.651515	0.67472	.	.	ENSG00000253731	ENST00000517434	T	0.58940	0.3	5.25	5.25	0.73442	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.677552	0.11059	U	0.604160	T	0.74741	0.3756	M	0.81942	2.565	0.09310	N	1	P;P	0.45634	0.731;0.863	P;P	0.54590	0.462;0.756	T	0.67221	-0.5725	10	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	337;337	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	T	337	ENSP00000429601:I337T	ENSP00000429601:I337T	I	+	2	0	PCDHGA6	140734844	0.237000	0.23815	0.984000	0.44739	0.976000	0.68499	3.360000	0.52299	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.443	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
PCDHGA7	56108	hgsc.bcm.edu	37	5	140762724	140762724	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140762724T>C	ENST00000518325.1	+	1	258	c.258T>C	c.(256-258)acT>acC	p.T86T	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	86	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTGGTCACTGCGGGCAGGA	0.577																																					p.T86T		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.T258C						.						49.0	58.0	55.0					5																	140762724		2191	4296	6487	SO:0001819	synonymous_variant	56108	exon1			GGTCACTGCGGGC	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.258T>C	chr5.hg19:g.140762724T>C		160.0	0.0		97.0	4.0	NM_032087	B2RN87|Q9Y5D0	Silent	SNP	ENST00000518325.1	hg19	CCDS54927.1																																																																																			.	.		0.577	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768682	140768682	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140768682G>T	ENST00000519479.1	+	1	1231	c.1231G>T	c.(1231-1233)Gag>Tag	p.E411*	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTAGACCGCGAGCAGAATCC	0.433																																					p.E411X		Atlas-SNP	.											PCDHGB4,NS,carcinoma,0,1	PCDHGB4	125	.	0			c.G1231T						.						133.0	135.0	134.0					5																	140768682		1941	4139	6080	SO:0001587	stop_gained	8641	exon1			GACCGCGAGCAGA	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1231G>T	chr5.hg19:g.140768682G>T	ENSP00000428288:p.Glu411*	92.0	0.0		83.0	4.0	NM_032098	O15099|Q2M267|Q9UN64	Nonsense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	21.5	4.164694	0.78339	.	.	ENSG00000253953	ENST00000519479	.	.	.	5.14	4.27	0.50696	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.6028	0.62029	0.0758:0.0:0.9242:0.0	.	.	.	.	X	411	.	ENSP00000428288:E411X	E	+	1	0	PCDHGB4	140748866	1.000000	0.71417	0.024000	0.17045	0.048000	0.14542	9.706000	0.98722	1.304000	0.44892	0.650000	0.86243	GAG	.	.		0.433	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769224	140769224	+	Silent	SNP	G	G	T	rs372714152	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140769224G>T	ENST00000519479.1	+	1	1773	c.1773G>T	c.(1771-1773)gcG>gcT	p.A591A	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	591	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTAGTGGCGGTGGACGCAG	0.672																																					p.A591A		Atlas-SNP	.											PCDHGB4,colon,carcinoma,0,1	PCDHGB4	125	.	0			c.G1773T						.						40.0	47.0	45.0					5																	140769224		2189	4291	6480	SO:0001819	synonymous_variant	8641	exon1			AGTGGCGGTGGAC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1773G>T	chr5.hg19:g.140769224G>T		81.0	0.0		63.0	3.0	NM_032098	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	hg19	CCDS54928.1																																																																																			.	.		0.672	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
DIAPH1	1729	hgsc.bcm.edu	37	5	140953135	140953135	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140953135G>T	ENST00000398557.4	-	16	2422	c.2282C>A	c.(2281-2283)cCa>cAa	p.P761Q	DIAPH1_ENST00000389057.5_Missense_Mutation_p.P752Q|DIAPH1_ENST00000389054.3_Missense_Mutation_p.P761Q|DIAPH1_ENST00000518047.1_Missense_Mutation_p.P752Q|DIAPH1_ENST00000253811.6_Missense_Mutation_p.P761Q|DIAPH1_ENST00000398566.3_Missense_Mutation_p.P752Q|DIAPH1_ENST00000398562.2_Missense_Mutation_p.P740Q|DIAPH1_ENST00000520569.1_Missense_Mutation_p.P707Q	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	761	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCAGAACTGGGGCTGCAGG	0.542																																					p.P761Q		Atlas-SNP	.											.	DIAPH1	64	.	0			c.C2282A						.						50.0	54.0	53.0					5																	140953135		1849	4093	5942	SO:0001583	missense	1729	exon16			AGAACTGGGGCTG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2282C>A	chr5.hg19:g.140953135G>T	ENSP00000381565:p.Pro761Gln	133.0	0.0		94.0	5.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365931	0.61513	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047;ENST00000546094	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.65	4.65	0.58169	Actin-binding FH2 (1);Formin Homology 1 (1);	0.000000	0.64402	D	0.000007	T	0.77751	0.4177	M	0.75777	2.31	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75830	-0.3179	10	0.29301	T	0.29	.	16.4522	0.83994	0.0:0.0:1.0:0.0	.	707;752;761	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	Q	761;707;740;752;752;761;761;752;200	ENSP00000373706:P761Q;ENSP00000429282:P707Q;ENSP00000381570:P740Q;ENSP00000373709:P752Q;ENSP00000381572:P752Q;ENSP00000381565:P761Q;ENSP00000253811:P761Q;ENSP00000428268:P752Q	ENSP00000253811:P761Q	P	-	2	0	DIAPH1	140933319	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.136000	0.71703	2.418000	0.82041	0.591000	0.81541	CCA	.	.		0.542	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219	
PDE6A	5145	hgsc.bcm.edu	37	5	149278051	149278051	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:149278051C>A	ENST00000255266.5	-	10	1401	c.1282G>T	c.(1282-1284)Ggc>Tgc	p.G428C		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	428	GAF 2.				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)	ACAGACCAGCCCAGAAATTGA	0.358																																					p.G428C		Atlas-SNP	.											.	PDE6A	98	.	0			c.G1282T						.						65.0	64.0	65.0					5																	149278051		2203	4300	6503	SO:0001583	missense	5145	exon10			ACCAGCCCAGAAA		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.1282G>T	chr5.hg19:g.149278051C>A	ENSP00000255266:p.Gly428Cys	52.0	0.0		57.0	4.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205999	0.79127	.	.	ENSG00000132915	ENST00000255266	T	0.70399	-0.48	5.74	4.87	0.63330	GAF (2);	0.000000	0.85682	D	0.000000	D	0.86867	0.6036	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89634	0.3857	10	0.87932	D	0	.	12.7212	0.57144	0.0:0.9205:0.0:0.0795	.	428	P16499	PDE6A_HUMAN	C	428	ENSP00000255266:G428C	ENSP00000255266:G428C	G	-	1	0	PDE6A	149258244	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.427000	0.80284	1.574000	0.49760	0.561000	0.74099	GGC	.	.		0.358	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
NDST1	3340	hgsc.bcm.edu	37	5	149927823	149927823	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:149927823T>C	ENST00000261797.6	+	12	2691	c.2189T>C	c.(2188-2190)tTc>tCc	p.F730S	NDST1_ENST00000523767.1_Intron	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	730	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTACACCTTCCATGAGGTG	0.617																																					p.F730S		Atlas-SNP	.											.	NDST1	79	.	0			c.T2189C						.						87.0	61.0	70.0					5																	149927823		2203	4300	6503	SO:0001583	missense	3340	exon12			ACACCTTCCATGA	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.2189T>C	chr5.hg19:g.149927823T>C	ENSP00000261797:p.Phe730Ser	133.0	0.0		104.0	5.0	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.711708	0.89112	.	.	ENSG00000070614	ENST00000261797	T	0.58210	0.35	4.76	4.76	0.60689	Sulfotransferase domain (1);	0.043601	0.85682	D	0.000000	T	0.72244	0.3436	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75485	-0.3301	10	0.52906	T	0.07	.	14.6042	0.68466	0.0:0.0:0.0:1.0	.	730	P52848	NDST1_HUMAN	S	730	ENSP00000261797:F730S	ENSP00000261797:F730S	F	+	2	0	NDST1	149908016	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.989000	0.88205	1.909000	0.55274	0.533000	0.62120	TTC	.	.		0.617	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
TIMD4	91937	hgsc.bcm.edu	37	5	156349214	156349214	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:156349214G>T	ENST00000274532.2	-	7	964	c.908C>A	c.(907-909)cCc>cAc	p.P303H	TIMD4_ENST00000406964.1_Missense_Mutation_p.P5H|TIMD4_ENST00000407087.3_Missense_Mutation_p.P275H	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	303						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CATTGACATGGGTATTCCATC	0.502																																					p.P303H		Atlas-SNP	.											.	TIMD4	94	.	0			c.C908A						.						191.0	172.0	178.0					5																	156349214		2203	4300	6503	SO:0001583	missense	91937	exon7			GACATGGGTATTC	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"""Immunoglobulin superfamily / V-set domain containing"""	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.908C>A	chr5.hg19:g.156349214G>T	ENSP00000274532:p.Pro303His	125.0	0.0		82.0	5.0	NM_138379	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	9.327	1.059540	0.19987	.	.	ENSG00000145850	ENST00000274532;ENST00000406964;ENST00000407087	T;T;T	0.70631	-0.5;-0.5;-0.5	1.27	-1.17	0.09648	.	24.147000	0.00807	U	0.001463	T	0.66963	0.2843	N	0.19112	0.55	0.09310	N	1	D;D	0.67145	0.996;0.996	P;P	0.56823	0.807;0.807	T	0.55347	-0.8155	10	0.59425	D	0.04	.	3.8138	0.08808	0.5788:0.0:0.4212:0.0	.	275;303	B5MCL9;Q96H15	.;TIMD4_HUMAN	H	303;5;275	ENSP00000274532:P303H;ENSP00000385882:P5H;ENSP00000385973:P275H	ENSP00000274532:P303H	P	-	2	0	TIMD4	156281792	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.761000	0.04751	-0.270000	0.09285	-0.266000	0.10368	CCC	.	.		0.502	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379	
C5orf52	100190949	hgsc.bcm.edu	37	5	157102111	157102111	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:157102111C>A	ENST00000409999.3	+	2	286	c.224C>A	c.(223-225)tCc>tAc	p.S75Y		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	75										endometrium(2)|lung(1)	3						TTAATGAATTCCAGTGAAGCA	0.493																																					p.S75Y		Atlas-SNP	.											.	C5orf52	17	.	0			c.C224A						.						76.0	71.0	72.0					5																	157102111		692	1591	2283	SO:0001583	missense	100190949	exon2			TGAATTCCAGTGA	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.224C>A	chr5.hg19:g.157102111C>A	ENSP00000387027:p.Ser75Tyr	157.0	0.0		90.0	4.0	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	hg19	CCDS47329.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.549357	0.27652	.	.	ENSG00000187658	ENST00000409999	T	0.36340	1.26	2.22	2.22	0.28083	.	.	.	.	.	T	0.41858	0.1177	L	0.29908	0.895	0.25738	N	0.985193	D	0.69078	0.997	D	0.65010	0.931	T	0.13872	-1.0493	9	0.72032	D	0.01	-18.2894	7.8836	0.29637	0.0:1.0:0.0:0.0	.	75	A6NGY3	CE052_HUMAN	Y	75	ENSP00000387027:S75Y	ENSP00000387027:S75Y	S	+	2	0	C5orf52	157034689	0.988000	0.35896	1.000000	0.80357	0.313000	0.28021	0.181000	0.16880	1.235000	0.43724	0.313000	0.20887	TCC	.	.		0.493	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
GABRA1	2554	hgsc.bcm.edu	37	5	161300201	161300201	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:161300201C>A	ENST00000428797.2	+	6	689	c.334C>A	c.(334-336)Cgg>Agg	p.R112R	GABRA1_ENST00000023897.6_Silent_p.R112R|GABRA1_ENST00000444819.1_Silent_p.R112R|GABRA1_ENST00000437025.2_Silent_p.R112R|GABRA1_ENST00000420560.1_Silent_p.R112R|GABRA1_ENST00000393943.4_Silent_p.R112R	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	112			R -> Q (in EIEE19). {ECO:0000269|PubMed:24623842}.		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACAGTCCTCCGGTTAAATAA	0.388																																					p.R112R		Atlas-SNP	.											.	GABRA1	132	.	0			c.C334A						.						80.0	82.0	81.0					5																	161300201		2203	4300	6503	SO:0001819	synonymous_variant	2554	exon6			GTCCTCCGGTTAA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.334C>A	chr5.hg19:g.161300201C>A		167.0	0.0		133.0	42.0	NM_001127643	D3DQK6|Q8N629	Silent	SNP	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.		0.388	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	
TENM2	57451	hgsc.bcm.edu	37	5	167675305	167675305	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:167675305C>T	ENST00000518659.1	+	27	7400	c.7361C>T	c.(7360-7362)cCc>cTc	p.P2454L	TENM2_ENST00000519204.1_Missense_Mutation_p.P2333L|TENM2_ENST00000545108.1_Missense_Mutation_p.P2453L|TENM2_ENST00000403607.2_Missense_Mutation_p.P2278L|TENM2_ENST00000520394.1_Missense_Mutation_p.P2215L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2454					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GAGCCGGCCCCCTTTAACCTG	0.512																																					p.P2445L		Atlas-SNP	.											.	.	.	.	0			c.C7334T						.						60.0	61.0	60.0					5																	167675305		1934	4131	6065	SO:0001583	missense	57451	exon27			CGGCCCCCTTTAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7361C>T	chr5.hg19:g.167675305C>T	ENSP00000429430:p.Pro2454Leu	144.0	0.0		98.0	4.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.3	3.974209	0.74246	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89875	-2.11;-2.1;-2.21;-2.55;-2.58	4.95	4.95	0.65309	Rhs repeat-associated core (1);	0.000000	0.85682	D	0.000000	D	0.95611	0.8573	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.996	D	0.96330	0.9243	10	0.72032	D	0.01	.	18.6074	0.91271	0.0:1.0:0.0:0.0	.	2453;2454;2215	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	2454;2453;2333;2215;2278	ENSP00000429430:P2454L;ENSP00000438635:P2453L;ENSP00000428964:P2333L;ENSP00000427874:P2215L;ENSP00000384905:P2278L	ENSP00000384905:P2278L	P	+	2	0	ODZ2	167607883	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.773000	0.85462	2.475000	0.83589	0.556000	0.70494	CCC	.	.		0.512	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TENM2	57451	hgsc.bcm.edu	37	5	167689229	167689229	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:167689229G>T	ENST00000518659.1	+	29	7778	c.7739G>T	c.(7738-7740)cGg>cTg	p.R2580L	TENM2_ENST00000519204.1_Missense_Mutation_p.R2459L|TENM2_ENST00000545108.1_Missense_Mutation_p.R2579L|TENM2_ENST00000403607.2_Missense_Mutation_p.R2404L|TENM2_ENST00000520394.1_Missense_Mutation_p.R2341L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2580					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AAAGAAGGGCGGGTGACCACG	0.557																																					p.R2571L		Atlas-SNP	.											.	.	.	.	0			c.G7712T						.						29.0	33.0	32.0					5																	167689229		2034	4204	6238	SO:0001583	missense	57451	exon29			AAGGGCGGGTGAC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7739G>T	chr5.hg19:g.167689229G>T	ENSP00000429430:p.Arg2580Leu	115.0	0.0		89.0	6.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.85	2.062122	0.36373	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90197	-2.15;-2.14;-2.26;-2.61;-2.63	5.42	4.53	0.55603	.	0.108147	0.64402	D	0.000006	D	0.86422	0.5929	L	0.49126	1.545	0.35424	D	0.793446	B;B;P	0.35226	0.125;0.076;0.491	B;B;B	0.33521	0.165;0.079;0.092	D	0.88191	0.2877	10	0.48119	T	0.1	.	10.0276	0.42081	0.1599:0.0:0.8401:0.0	.	2579;2580;2341	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	2580;2579;2459;2341;2404	ENSP00000429430:R2580L;ENSP00000438635:R2579L;ENSP00000428964:R2459L;ENSP00000427874:R2341L;ENSP00000384905:R2404L	ENSP00000384905:R2404L	R	+	2	0	ODZ2	167621807	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.017000	0.64047	1.349000	0.45751	0.655000	0.94253	CGG	.	.		0.557	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
CDHR2	54825	hgsc.bcm.edu	37	5	175995734	175995734	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:175995734T>C	ENST00000510636.1	+	4	454	c.180T>C	c.(178-180)taT>taC	p.Y60Y	CDHR2_ENST00000261944.5_Silent_p.Y60Y|CDHR2_ENST00000506348.1_Silent_p.Y60Y	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	60	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTCTGACCTATGGGATGAGCG	0.602																																					p.Y60Y		Atlas-SNP	.											.	CDHR2	152	.	0			c.T180C						.						109.0	102.0	104.0					5																	175995734		2203	4300	6503	SO:0001819	synonymous_variant	54825	exon4			GACCTATGGGATG	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.180T>C	chr5.hg19:g.175995734T>C		121.0	0.0		98.0	4.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	hg19	CCDS34297.1																																																																																			.	.		0.602	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
UIMC1	51720	hgsc.bcm.edu	37	5	176396709	176396709	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176396709T>C	ENST00000377227.4	-	5	490		c.e5-2		UIMC1_ENST00000511320.1_Splice_Site|UIMC1_ENST00000506128.1_Splice_Site|UIMC1_ENST00000377219.2_Splice_Site|UIMC1_ENST00000503273.1_5'Flank			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1						double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGGCAACTCTGAAACAAGTG	0.483																																					.		Atlas-SNP	.											.	UIMC1	55	.	0			c.358-2A>G						.						86.0	83.0	84.0					5																	176396709		2203	4300	6503	SO:0001630	splice_region_variant	51720	exon6			CAACTCTGAAACA	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.358-2A>G	chr5.hg19:g.176396709T>C		107.0	0.0		89.0	4.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Splice_Site	SNP	ENST00000377227.4	hg19	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.199603	0.58126	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000509236	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7632	0.69619	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	UIMC1	176329315	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.803000	0.62546	2.226000	0.72624	0.459000	0.35465	.	.	.		0.483	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	Intron
ZNF346	23567	hgsc.bcm.edu	37	5	176477805	176477805	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176477805C>T	ENST00000358149.3	+	5	614	c.571C>T	c.(571-573)Cat>Tat	p.H191Y	ZNF346_ENST00000506693.1_Missense_Mutation_p.H93Y|ZNF346_ENST00000503039.1_Missense_Mutation_p.H216Y|ZNF346_ENST00000261948.4_Missense_Mutation_p.H216Y|ZNF346_ENST00000503425.1_Missense_Mutation_p.H159Y|ZNF346_ENST00000512315.1_Intron|ZNF346-IT1_ENST00000515264.1_RNA|ZNF346_ENST00000511834.1_Missense_Mutation_p.H207Y	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346	191					positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGCCTCTGCCATGCAACTTT	0.483																																					p.H191Y		Atlas-SNP	.											.	ZNF346	24	.	0			c.C571T						.						119.0	110.0	113.0					5																	176477805		2203	4300	6503	SO:0001583	missense	23567	exon5			CTCTGCCATGCAA	AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.571C>T	chr5.hg19:g.176477805C>T	ENSP00000350869:p.His191Tyr	129.0	0.0		71.0	4.0	NM_012279	B7Z367|Q68CV9|Q6ZMW1	Missense_Mutation	SNP	ENST00000358149.3	hg19	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.461267	0.84317	.	.	ENSG00000113761	ENST00000358149;ENST00000506693;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97	5.47	4.59	0.56863	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.261330	0.45606	D	0.000360	T	0.38401	0.1039	L	0.54323	1.7	0.38262	D	0.941917	P;P;D;P	0.62365	0.945;0.954;0.991;0.953	P;P;P;P	0.59221	0.74;0.816;0.854;0.768	T	0.42699	-0.9436	10	0.72032	D	0.01	.	16.2029	0.82102	0.0:0.8666:0.1334:0.0	.	93;159;216;191	B7Z4J8;B7Z367;Q9UL40-2;Q9UL40	.;.;.;ZN346_HUMAN	Y	191;93;159;216;207;216	ENSP00000350869:H191Y;ENSP00000423515:H93Y;ENSP00000421212:H159Y;ENSP00000261948:H216Y;ENSP00000425725:H207Y;ENSP00000424495:H216Y	ENSP00000261948:H216Y	H	+	1	0	ZNF346	176410411	1.000000	0.71417	0.913000	0.36048	0.952000	0.60782	5.175000	0.65021	1.266000	0.44231	0.655000	0.94253	CAT	.	.		0.483	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279	
FGFR4	2264	hgsc.bcm.edu	37	5	176523334	176523334	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176523334G>T	ENST00000292408.4	+	15	2236	c.1991G>T	c.(1990-1992)cGg>cTg	p.R664L	FGFR4_ENST00000292410.3_Missense_Mutation_p.R624L|FGFR4_ENST00000393648.2_Missense_Mutation_p.R596L|FGFR4_ENST00000393637.1_Missense_Mutation_p.R624L|FGFR4_ENST00000502906.1_Missense_Mutation_p.R664L	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	TTGTTTGACCGGGTGTACACA	0.642										TSP Lung(9;0.080)																											p.R664L		Atlas-SNP	.											FGFR4_ENST00000292408,colon,carcinoma,0,2	FGFR4	174	.	0			c.G1991T						.						81.0	79.0	80.0					5																	176523334		2203	4300	6503	SO:0001583	missense	2264	exon15			TTGACCGGGTGTA	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1991G>T	chr5.hg19:g.176523334G>T	ENSP00000292408:p.Arg664Leu	127.0	0.0		75.0	3.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	g	29.8	5.033067	0.93575	.	.	ENSG00000160867	ENST00000292408;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	4.65	4.65	0.58169	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87370	0.6160	L	0.37800	1.135	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.89220	0.3570	10	0.87932	D	0	.	17.1688	0.86824	0.0:0.0:1.0:0.0	.	596;624;664	B4DVP5;P22455-2;P22455	.;.;FGFR4_HUMAN	L	664;596;664;624;624;892	ENSP00000292408:R664L;ENSP00000377259:R596L;ENSP00000424960:R664L;ENSP00000292410:R624L;ENSP00000377254:R624L	ENSP00000292408:R664L	R	+	2	0	FGFR4	176455940	1.000000	0.71417	0.988000	0.46212	0.843000	0.47879	9.866000	0.99616	2.142000	0.66516	0.556000	0.70494	CGG	.	.		0.642	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
NSD1	64324	hgsc.bcm.edu	37	5	176722236	176722236	+	Missense_Mutation	SNP	A	A	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176722236A>C	ENST00000439151.2	+	23	7912	c.7867A>C	c.(7867-7869)Agt>Cgt	p.S2623R	NSD1_ENST00000347982.4_Missense_Mutation_p.S2354R|NSD1_ENST00000361032.4_Missense_Mutation_p.S2520R|NSD1_ENST00000354179.4_Missense_Mutation_p.S2354R	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2623					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CACAGAGCAAAGTCCCTGGGC	0.587			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2623R		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.A7867C						.						67.0	70.0	69.0					5																	176722236		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GAGCAAAGTCCCT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7867A>C	chr5.hg19:g.176722236A>C	ENSP00000395929:p.Ser2623Arg	151.0	0.0		110.0	39.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.756162	0.31137	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93604	-3.15;-3.15;-3.15;-3.25	4.71	3.54	0.40534	.	0.227351	0.31636	N	0.007312	D	0.86936	0.6053	N	0.19112	0.55	0.27574	N	0.949798	B;B	0.21905	0.062;0.037	B;B	0.26969	0.075;0.048	T	0.79820	-0.1642	10	0.42905	T	0.14	.	11.1301	0.48341	0.835:0.165:0.0:0.0	.	2354;2623	Q96L73-2;Q96L73	.;NSD1_HUMAN	R	2354;2623;2354;2520	ENSP00000346111:S2354R;ENSP00000395929:S2623R;ENSP00000343209:S2354R;ENSP00000354310:S2520R	ENSP00000343209:S2354R	S	+	1	0	NSD1	176654842	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.691000	0.47010	1.980000	0.57719	0.379000	0.24179	AGT	.	.		0.587	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
NSD1	64324	hgsc.bcm.edu	37	5	176722361	176722361	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176722361T>C	ENST00000439151.2	+	23	8037	c.7992T>C	c.(7990-7992)tcT>tcC	p.S2664S	NSD1_ENST00000347982.4_Silent_p.S2395S|NSD1_ENST00000361032.4_Silent_p.S2561S|NSD1_ENST00000354179.4_Silent_p.S2395S	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2664					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CTTGCTGGTCTCTTGGAAGAG	0.537			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2664S		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T7992C						.						67.0	71.0	70.0					5																	176722361		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CTGGTCTCTTGGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7992T>C	chr5.hg19:g.176722361T>C		139.0	0.0		96.0	5.0	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.537	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
F12	2161	hgsc.bcm.edu	37	5	176833015	176833015	+	Silent	SNP	G	G	T	rs201132135		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176833015G>T	ENST00000253496.3	-	3	211	c.163C>A	c.(163-165)Cgg>Agg	p.R55R	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	55	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	TACAGCTGCCGGTGGTACTGG	0.607									Hereditary Angioedema																												p.R55R		Atlas-SNP	.											.	F12	35	.	0			c.C163A						.						93.0	96.0	95.0					5																	176833015		2203	4300	6503	SO:0001819	synonymous_variant	2161	exon3	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GCTGCCGGTGGTA	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.163C>A	chr5.hg19:g.176833015G>T		127.0	0.0		87.0	4.0	NM_000505	P78339	Silent	SNP	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.		0.607	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1		
ZNF354C	30832	hgsc.bcm.edu	37	5	178506014	178506014	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:178506014G>T	ENST00000315475.6	+	5	887	c.581G>T	c.(580-582)gGg>gTg	p.G194V		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TATACATTTGGGAAAGATTTT	0.363																																					p.G194V		Atlas-SNP	.											.	ZNF354C	77	.	0			c.G581T						.						54.0	58.0	57.0					5																	178506014		2201	4299	6500	SO:0001583	missense	30832	exon5			CATTTGGGAAAGA		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.581G>T	chr5.hg19:g.178506014G>T	ENSP00000324064:p.Gly194Val	71.0	0.0		70.0	5.0	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	hg19	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.743763	0.49151	.	.	ENSG00000177932	ENST00000315475	T	0.36520	1.25	3.94	1.59	0.23543	.	.	.	.	.	T	0.57417	0.2052	M	0.90870	3.155	0.53688	D	0.999975	D	0.63880	0.993	P	0.59012	0.85	T	0.58306	-0.7659	9	0.66056	D	0.02	-4.7609	6.9571	0.24578	0.2915:0.0:0.7085:0.0	.	194	Q86Y25	Z354C_HUMAN	V	194	ENSP00000324064:G194V	ENSP00000324064:G194V	G	+	2	0	ZNF354C	178438620	1.000000	0.71417	0.004000	0.12327	0.011000	0.07611	3.680000	0.54641	0.202000	0.20498	-0.229000	0.12294	GGG	.	.		0.363	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
MGAT1	4245	hgsc.bcm.edu	37	5	180219412	180219412	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180219412C>A	ENST00000446023.2	-	3	1310	c.560G>T	c.(559-561)cGc>cTc	p.R187L	MGAT1_ENST00000307826.4_Missense_Mutation_p.R187L|MGAT1_ENST00000427865.2_Missense_Mutation_p.R187L|MGAT1_ENST00000393340.3_Missense_Mutation_p.R187L|MGAT1_ENST00000333055.3_Missense_Mutation_p.R187L	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	187					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCGGTAGTGGCGCGCGATCTT	0.682																																					p.R187L		Atlas-SNP	.											.	MGAT1	48	.	0			c.G560T						.						39.0	46.0	44.0					5																	180219412		2201	4296	6497	SO:0001583	missense	4245	exon3			TAGTGGCGCGCGA	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.560G>T	chr5.hg19:g.180219412C>A	ENSP00000404718:p.Arg187Leu	110.0	0.0		91.0	30.0	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	hg19	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640519	0.87859	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000427865;ENST00000504671	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.94182	0.8133	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.94464	0.7679	10	0.87932	D	0	-28.1319	16.3966	0.83607	0.0:1.0:0.0:0.0	.	187	P26572	MGAT1_HUMAN	L	187	ENSP00000332073:R187L;ENSP00000311888:R187L;ENSP00000404718:R187L;ENSP00000377010:R187L;ENSP00000402838:R187L;ENSP00000424891:R187L	ENSP00000311888:R187L	R	-	2	0	MGAT1	180152018	0.815000	0.29118	0.614000	0.29051	0.849000	0.48306	6.801000	0.75170	2.811000	0.96726	0.655000	0.94253	CGC	.	.		0.682	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
TRIM41	90933	hgsc.bcm.edu	37	5	180651055	180651055	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180651055T>C	ENST00000315073.5	+	1	766	c.56T>C	c.(55-57)gTg>gCg	p.V19A	CTC-338M12.7_ENST00000499096.2_RNA|MIR4638_ENST00000581158.1_RNA|TRIM41_ENST00000351937.5_Missense_Mutation_p.V19A	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	19					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGAGGCGGTGTGCGCCATC	0.617																																					p.V19A		Atlas-SNP	.											.	TRIM41	96	.	0			c.T56C						.						55.0	47.0	50.0					5																	180651055		2203	4300	6503	SO:0001583	missense	90933	exon1			AGGCGGTGTGCGC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.56T>C	chr5.hg19:g.180651055T>C	ENSP00000320869:p.Val19Ala	115.0	0.0		100.0	4.0	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.478351	0.63849	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	D;D	0.83673	-1.75;-1.75	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);	0.181068	0.26442	N	0.024350	T	0.72374	0.3452	N	0.11892	0.195	0.28931	N	0.891565	P;P;P	0.49783	0.779;0.859;0.928	B;P;P	0.47573	0.348;0.55;0.55	T	0.69537	-0.5119	10	0.56958	D	0.05	.	8.4849	0.33065	0.0:0.0:0.1968:0.8032	.	19;19;19	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	A	19;19;6	ENSP00000336749:V19A;ENSP00000320869:V19A	ENSP00000320869:V19A	V	+	2	0	TRIM41	180583661	0.970000	0.33590	1.000000	0.80357	0.975000	0.68041	1.108000	0.31123	1.720000	0.51447	0.260000	0.18958	GTG	.	.		0.617	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
GNB2L1	10399	hgsc.bcm.edu	37	5	180668513	180668513	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180668513A>G	ENST00000512805.1	-	3	816	c.408T>C	c.(406-408)ggT>ggC	p.G136G	GNB2L1_ENST00000511566.1_Silent_p.G136G|GNB2L1_ENST00000456394.2_Silent_p.G136G|GNB2L1_ENST00000376817.4_Silent_p.G92G|SNORD96A_ENST00000606577.1_RNA|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000505461.1_5'UTR|GNB2L1_ENST00000511900.1_Intron|SNORD95_ENST00000579879.1_RNA|GNB2L1_ENST00000514455.1_5'Flank	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	136					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		ATTTGCACACACCCAGGGTAT	0.458																																					p.G136G		Atlas-SNP	.											.	GNB2L1	22	.	0			c.T408C						.						148.0	156.0	153.0					5																	180668513		2203	4300	6503	SO:0001819	synonymous_variant	10399	exon3			GCACACACCCAGG	M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628		"""WD repeat domain containing"""	4399	protein-coding gene	gene with protein product	"""Receptor for Activated C Kinase 1"""	176981				8302854, 2499885	Standard	NM_006098		Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000512805.1:c.408T>C	chr5.hg19:g.180668513A>G		76.0	0.0		76.0	5.0	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	hg19	CCDS34324.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.36|11.36	1.616192|1.616192	0.28801|0.28801	.|.	.|.	ENSG00000204628|ENSG00000204628	ENST00000502905;ENST00000504128|ENST00000507756;ENST00000512968	.|T	.|0.53206	.|0.63	5.88|5.88	0.607|0.607	0.17564|0.17564	.|.	.|.	.|.	.|.	.|.	T|T	0.35248|0.35248	0.0925|0.0925	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.16158|0.16158	-1.0412|-1.0412	4|5	.|.	.|.	.|.	-19.8633|-19.8633	0.5266|0.5266	0.00621|0.00621	0.4199:0.1374:0.1534:0.2893|0.4199:0.1374:0.1534:0.2893	.|.	.|.	.|.	.|.	R|A	54;43|67;111	.|ENSP00000425008:V111A	.|.	C|V	-|-	1|2	0|0	GNB2L1|GNB2L1	180601119|180601119	0.086000|0.086000	0.21541|0.21541	0.930000|0.930000	0.37139|0.37139	0.968000|0.968000	0.65278|0.65278	-0.529000|-0.529000	0.06186|0.06186	-0.121000|-0.121000	0.11787|0.11787	-0.290000|-0.290000	0.09829|0.09829	TGT|GTG	.	.		0.458	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098	
SLC22A23	63027	hgsc.bcm.edu	37	6	3416016	3416016	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:3416016C>T	ENST00000406686.3	-	2	727	c.728G>A	c.(727-729)gGc>gAc	p.G243D	SLC22A23_ENST00000380298.2_Missense_Mutation_p.G243D|SLC22A23_ENST00000490273.1_5'UTR|SLC22A23_ENST00000436008.2_Missense_Mutation_p.G243D|SLC22A23_ENST00000380302.4_5'UTR	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	243					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TATTAGGTAGCCAAAGATTAA	0.458																																					p.G243D		Atlas-SNP	.											.	SLC22A23	89	.	0			c.G728A						.						164.0	144.0	150.0					6																	3416016		692	1591	2283	SO:0001583	missense	63027	exon2			AGGTAGCCAAAGA	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.728G>A	chr6.hg19:g.3416016C>T	ENSP00000385028:p.Gly243Asp	174.0	0.0		104.0	5.0	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	hg19	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	C	31	5.102966	0.94245	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000485307;ENST00000467177;ENST00000380298	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.	.	.	.	D	0.94335	0.8179	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94692	0.7875	9	0.87932	D	0	-17.0608	19.1812	0.93623	0.0:1.0:0.0:0.0	.	243;243	C9J4Z0;A1A5C7	.;S22AN_HUMAN	D	243;243;71;69;243	ENSP00000410245:G243D;ENSP00000385028:G243D;ENSP00000418134:G71D;ENSP00000418985:G69D;ENSP00000369653:G243D	ENSP00000369653:G243D	G	-	2	0	SLC22A23	3361015	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.313000	0.78978	2.530000	0.85305	0.563000	0.77884	GGC	.	.		0.458	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
GCNT2	2651	hgsc.bcm.edu	37	6	10621632	10621632	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:10621632C>T	ENST00000379597.3	+	2	1530	c.974C>T	c.(973-975)gCt>gTt	p.A325V	GCNT2_ENST00000316170.3_Missense_Mutation_p.A323V|GCNT2_ENST00000495262.1_Missense_Mutation_p.A325V|GCNT2_ENST00000410107.1_Missense_Mutation_p.A39V|GCNT2_ENST00000265012.4_Missense_Mutation_p.A325V|GCNT2_ENST00000397423.2_3'UTR			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	325					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AACCTCAGAGCTATAAAGTGG	0.512																																					p.A325V		Atlas-SNP	.											.	GCNT2	123	.	0			c.C974T						.						94.0	80.0	85.0					6																	10621632		2203	4300	6503	SO:0001583	missense	2651	exon4			TCAGAGCTATAAA	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.974C>T	chr6.hg19:g.10621632C>T	ENSP00000368917:p.Ala325Val	90.0	0.0		87.0	4.0	NM_145649		Missense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896631	0.91962	.	.	ENSG00000111846	ENST00000410107;ENST00000495262;ENST00000379597;ENST00000316170;ENST00000265012	T;T;T;T;T	0.42900	0.96;2.84;2.84;2.84;2.84	5.51	5.51	0.81932	.	0.000000	0.56097	D	0.000032	T	0.56645	0.1999	M	0.72118	2.19	0.51482	D	0.999925	P;D;P;B	0.89917	0.885;1.0;0.885;0.392	P;D;P;B	0.91635	0.823;0.999;0.771;0.349	T	0.52328	-0.8590	10	0.35671	T	0.21	-24.6358	17.2045	0.86914	0.0:1.0:0.0:0.0	.	325;39;325;323	Q8N0V5;B7ZBL3;Q8NFS9;Q06430	GNT2A_HUMAN;.;GNT2C_HUMAN;GNT2B_HUMAN	V	39;325;325;323;325	ENSP00000386321:A39V;ENSP00000419411:A325V;ENSP00000368917:A325V;ENSP00000314844:A323V;ENSP00000265012:A325V	ENSP00000265012:A325V	A	+	2	0	GCNT2	10729618	0.999000	0.42202	0.955000	0.39395	0.897000	0.52465	5.198000	0.65147	2.600000	0.87896	0.655000	0.94253	GCT	.	.		0.512	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
TBC1D7	51256	hgsc.bcm.edu	37	6	13316857	13316857	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:13316857G>T	ENST00000379300.3	-	5	708	c.465C>A	c.(463-465)acC>acA	p.T155T	TBC1D7_ENST00000607658.1_Silent_p.T128T|TBC1D7_ENST00000343141.4_Intron|TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000379307.2_Silent_p.T128T|TBC1D7_ENST00000356436.4_Silent_p.T155T	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	155	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			CAAAGCGTCGGGTGATCCAGT	0.423																																					p.T155T		Atlas-SNP	.											.	TBC1D7	34	.	0			c.C465A						.						196.0	204.0	201.0					6																	13316857		2203	4300	6503	SO:0001819	synonymous_variant	51256	exon5			GCGTCGGGTGATC	AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.465C>A	chr6.hg19:g.13316857G>T		101.0	0.0		96.0	4.0	NM_001143965	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Silent	SNP	ENST00000379300.3	hg19	CCDS4523.1																																																																																			.	.		0.423	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495	
SOX4	6659	hgsc.bcm.edu	37	6	21595158	21595158	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:21595158G>A	ENST00000244745.1	+	1	1187	c.393G>A	c.(391-393)agG>agA	p.R131R	SOX4_ENST00000543472.1_Silent_p.R131R	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	131					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|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 transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			ACCGGCCCAGGAAGAAGGTGA	0.642																																					p.R131R		Atlas-SNP	.											SOX4,bladder,carcinoma,0,1	SOX4	11	.	0			c.G393A						.						21.0	26.0	25.0					6																	21595158		2202	4299	6501	SO:0001819	synonymous_variant	6659	exon1			GCCCAGGAAGAAG	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"""SRY (sex determining region Y)-boxes"""	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.393G>A	chr6.hg19:g.21595158G>A		96.0	0.0		59.0	4.0	NM_003107		Silent	SNP	ENST00000244745.1	hg19	CCDS4547.1																																																																																			.	.		0.642	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727451	25727451	+	Silent	SNP	G	G	T	rs145569895		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:25727451G>T	ENST00000274764.2	+	1	315	c.315G>T	c.(313-315)ccG>ccT	p.P105P	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	105					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						TGCTACTGCCGGGAGAGCTGG	0.517																																					p.P105P		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.G315T						.						271.0	196.0	221.0					6																	25727451		2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			ACTGCCGGGAGAG	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.315G>T	chr6.hg19:g.25727451G>T		124.0	0.0		125.0	6.0	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	hg19	CCDS4563.1																																																																																			.	G|1.000;C|0.000		0.517	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
HLA-V	352962	hgsc.bcm.edu	37	6	29760408	29760408	+	RNA	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:29760408A>G	ENST00000457107.1	+	0	278									major histocompatibility complex, class I, V (pseudogene)																		GGAGACAGGGACCGCCAAGGC	0.657																																					p.T165A		Atlas-SNP	.											.	.	.	.	0			c.A493G						.																																					0	exon2			ACAGGGACCGCCA	M96332		6p21.3	2012-10-05	2007-12-12	2007-12-12	ENSG00000181126	ENSG00000181126		"""Histocompatibility complex"""	23482	pseudogene	pseudogene			"""HLA-75 pseudogene"""	HLA-75			Standard	NG_002729		Approved	dJ377H14.4			OTTHUMG00000031277		chr6.hg19:g.29760408A>G		37.0	0.0		83.0	5.0	NM_001207043		Missense_Mutation	SNP	ENST00000457107.1	hg19																																																																																				.	.		0.657	HLA-V-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000105231.1	NG_002729	
ATP6V1G2	534	hgsc.bcm.edu	37	6	31513188	31513188	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31513188G>T	ENST00000303892.5	-	3	638	c.354C>A	c.(352-354)gcC>gcA	p.A118A	ATP6V1G2_ENST00000376151.4_Silent_p.A78A|ATP6V1G2_ENST00000483251.1_Silent_p.A77A|DDX39B-AS1_ENST00000420520.1_RNA|DDX39B-AS1_ENST00000416684.1_RNA|ATP6V1G2-DDX39B_ENST00000475917.1_Intron|DDX39B_ENST00000458640.1_5'Flank|NFKBIL1_ENST00000376148.4_5'Flank|ATP6V1G2-DDX39B_ENST00000376185.1_Intron|ATP6V1G2_ENST00000483170.1_5'UTR|DDX39B_ENST00000396172.1_5'Flank|DDX39B_ENST00000417556.2_5'Flank|NFKBIL1_ENST00000376145.4_5'Flank	NM_130463.3|NM_138282.2	NP_569730.1|NP_612139.1	O95670	VATG2_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2	118					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						GGTGGCCCTAGGCAGAAATCC	0.567																																					p.A118A		Atlas-SNP	.											.	ATP6V1G2	15	.	0			c.C354A						.						44.0	39.0	40.0					6																	31513188		2203	4300	6503	SO:0001819	synonymous_variant	534	exon3			GCCCTAGGCAGAA	Y14768	CCDS4698.1, CCDS4699.1, CCDS56413.1	6p21.3	2011-03-29	2006-01-13	2002-05-10	ENSG00000213760	ENSG00000213760		"""ATPases / V-type"""	862	protein-coding gene	gene with protein product		606853	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump)"", ""ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 2"""	ATP6G, ATP6G2		10202016	Standard	NM_138282		Approved	Vma10, NG38, Em:AC004181.3	uc003nua.3	O95670	OTTHUMG00000166618	ENST00000303892.5:c.354C>A	chr6.hg19:g.31513188G>T		56.0	0.0		58.0	4.0	NM_130463	B5MEF0|Q2L6F8|Q5HYU8|Q5RJ63	Silent	SNP	ENST00000303892.5	hg19	CCDS4698.1																																																																																			.	.		0.567	ATP6V1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076399.3	NM_130463	
TNF	7124	hgsc.bcm.edu	37	6	31544346	31544346	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31544346C>A	ENST00000449264.2	+	2	397	c.222C>A	c.(220-222)gcC>gcA	p.A74A		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	74					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	GCCCTCTGGCCCAGGCAGTCA	0.517									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.A74A		Atlas-SNP	.											.	TNF	15	.	0			c.C222A						.						113.0	109.0	111.0					6																	31544346		2203	4300	6503	SO:0001819	synonymous_variant	7124	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TCTGGCCCAGGCA	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"""Tumor necrosis factor (ligand) superfamily"""	11892	protein-coding gene	gene with protein product	"""TNF superfamily, member 2"""	191160	"""tumor necrosis factor (TNF superfamily, member 2)"""	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.222C>A	chr6.hg19:g.31544346C>A		73.0	0.0		74.0	4.0	NM_000594	O43647|Q9P1Q2|Q9UIV3	Silent	SNP	ENST00000449264.2	hg19	CCDS4702.1																																																																																			.	.		0.517	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2		
CLIC1	1192	hgsc.bcm.edu	37	6	31698776	31698776	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31698776A>G	ENST00000375780.2	-	7	1141	c.569T>C	c.(568-570)gTg>gCg	p.V190A	CLIC1_ENST00000375784.3_Missense_Mutation_p.V190A|CLIC1_ENST00000375779.2_Missense_Mutation_p.V190A|DDAH2_ENST00000375787.2_5'Flank|DDAH2_ENST00000375792.3_5'Flank|DDAH2_ENST00000480913.1_5'Flank|DDAH2_ENST00000375789.2_5'Flank|CLIC1_ENST00000395892.1_Missense_Mutation_p.V190A			O00299	CLIC1_HUMAN	chloride intracellular channel 1	190	GST C-terminal.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|platelet aggregation (GO:0070527)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of mitochondrial membrane potential (GO:0051881)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|brush border (GO:0005903)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)|skin(1)	7						CTTCTTACACACCACCTGAGG	0.572																																					p.V190A		Atlas-SNP	.											.	CLIC1	15	.	0			c.T569C						.						43.0	33.0	37.0					6																	31698776		1510	2708	4218	SO:0001583	missense	1192	exon6			TTACACACCACCT	U93205	CCDS4719.1	6p21.3	2012-09-26			ENSG00000213719	ENSG00000213719		"""Ion channels / Chloride channels : Intracellular"""	2062	protein-coding gene	gene with protein product		602872				9139710	Standard	NM_001288		Approved	NCC27, p64CLCP	uc003nwr.3	O00299	OTTHUMG00000031103	ENST00000375780.2:c.569T>C	chr6.hg19:g.31698776A>G	ENSP00000364935:p.Val190Ala	96.0	0.0		123.0	5.0	NM_001288	Q15089|Q502X1	Missense_Mutation	SNP	ENST00000375780.2	hg19	CCDS4719.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.865033	0.51482	.	.	ENSG00000213719	ENST00000375784;ENST00000375779;ENST00000375780;ENST00000395892	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	4.64	4.64	0.57946	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.64402	U	0.000015	T	0.76227	0.3958	N	0.25144	0.715	0.80722	D	1	B	0.32507	0.373	B	0.37888	0.26	T	0.75701	-0.3226	10	0.02654	T	1	-10.7814	12.0341	0.53415	1.0:0.0:0.0:0.0	.	190	O00299	CLIC1_HUMAN	A	190	ENSP00000364940:V190A;ENSP00000364934:V190A;ENSP00000364935:V190A;ENSP00000379229:V190A	ENSP00000364934:V190A	V	-	2	0	CLIC1	31806755	1.000000	0.71417	0.987000	0.45799	0.960000	0.62799	5.679000	0.68160	1.948000	0.56530	0.459000	0.35465	GTG	.	.		0.572	CLIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076167.3	NM_001288	
TNXB	7148	hgsc.bcm.edu	37	6	32029479	32029479	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32029479G>T	ENST00000375244.3	-	21	7388	c.7187C>A	c.(7186-7188)cCc>cAc	p.P2396H	TNXB_ENST00000375247.2_Missense_Mutation_p.P2396H			P22105	TENX_HUMAN	tenascin XB	2456	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGTGGGGCTGGGGGTCTCTTC	0.627																																					p.P2396H		Atlas-SNP	.											.	TNXB	553	.	0			c.C7187A						.						45.0	55.0	52.0					6																	32029479		1204	2520	3724	SO:0001583	missense	7148	exon21			GGGCTGGGGGTCT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7187C>A	chr6.hg19:g.32029479G>T	ENSP00000364393:p.Pro2396His	131.0	0.0		115.0	5.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.77	3.471565	0.63737	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59772	0.42;0.24	3.99	3.99	0.46301	.	0.113838	0.39475	N	0.001348	T	0.61413	0.2345	M	0.86028	2.79	0.23838	N	0.996701	P	0.45176	0.852	P	0.53549	0.729	T	0.56463	-0.7975	10	0.56958	D	0.05	.	11.4331	0.50052	0.0:0.0:1.0:0.0	.	2396	P22105-3	.	H	2396	ENSP00000364393:P2396H;ENSP00000364396:P2396H	ENSP00000364393:P2396H	P	-	2	0	TNXB	32137457	0.990000	0.36364	0.937000	0.37676	0.947000	0.59692	2.392000	0.44433	2.033000	0.60031	0.585000	0.79938	CCC	.	.		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	hgsc.bcm.edu	37	6	32038106	32038106	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32038106G>T	ENST00000375244.3	-	14	5277	c.5076C>A	c.(5074-5076)ctC>ctA	p.L1692L	TNXB_ENST00000375247.2_Silent_p.L1692L			P22105	TENX_HUMAN	tenascin XB	1774	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCGTCCAGGAGAGGCGCAGTG	0.657																																					p.L1692L		Atlas-SNP	.											.	TNXB	553	.	0			c.C5076A						.						20.0	21.0	21.0					6																	32038106		1915	4123	6038	SO:0001819	synonymous_variant	7148	exon14			CCAGGAGAGGCGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5076C>A	chr6.hg19:g.32038106G>T		187.0	0.0		166.0	31.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.657	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
RNF5	6048	hgsc.bcm.edu	37	6	32148076	32148076	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32148076C>T	ENST00000375094.3	+	6	674	c.516C>T	c.(514-516)ttC>ttT	p.F172F	RNF5_ENST00000427134.2_Intron|AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|AGPAT1_ENST00000375104.2_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	172					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						TCGCCATCTTCTTCTTTTTTT	0.537																																					p.F172F		Atlas-SNP	.											.	RNF5	16	.	0			c.C516T						.						170.0	184.0	179.0					6																	32148076		1511	2708	4219	SO:0001819	synonymous_variant	6048	exon6			CATCTTCTTCTTT	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.516C>T	chr6.hg19:g.32148076C>T		44.0	0.0		63.0	4.0	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	hg19	CCDS4745.1																																																																																			.	.		0.537	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
SLC39A7	7922	hgsc.bcm.edu	37	6	33170874	33170874	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:33170874C>A	ENST00000374677.3	+	6	1501	c.1128C>A	c.(1126-1128)agC>agA	p.S376R	RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.S376R|SLC39A7_ENST00000463972.1_3'UTR|HSD17B8_ENST00000374662.3_5'Flank|RXRB_ENST00000413614.2_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	376				S -> T (in Ref. 1; BAA11528 and 2; AAD12305). {ECO:0000305}.	transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CTGGCTGCAGCAAAAAGCAGG	0.527																																					p.S376R		Atlas-SNP	.											.	SLC39A7	32	.	0			c.C1128A						.						113.0	131.0	124.0					6																	33170874		1399	2635	4034	SO:0001583	missense	7922	exon6			CTGCAGCAAAAAG	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"""Solute carriers"""	4927	protein-coding gene	gene with protein product		601416	"""HLA class II region expressed gene KE4"""	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1128C>A	chr6.hg19:g.33170874C>A	ENSP00000363809:p.Ser376Arg	119.0	0.0		84.0	4.0	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	hg19	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.136882	0.77662	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.53206	0.63;0.63	5.02	5.02	0.67125	.	0.051265	0.85682	D	0.000000	T	0.58864	0.2152	M	0.83483	2.645	0.52099	D	0.999942	P;D	0.55172	0.885;0.97	P;P	0.60415	0.833;0.874	T	0.64317	-0.6436	10	0.62326	D	0.03	-9.1565	11.5361	0.50639	0.0:0.8195:0.1805:0.0	.	357;376	B4DVK8;Q92504	.;S39A7_HUMAN	R	376;357;281;376	ENSP00000363807:S376R;ENSP00000363809:S376R	ENSP00000363807:S376R	S	+	3	2	SLC39A7	33278852	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.542000	0.53625	2.603000	0.88011	0.448000	0.29417	AGC	.	.		0.527	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979	
DEF6	50619	hgsc.bcm.edu	37	6	35288753	35288753	+	Splice_Site	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35288753T>A	ENST00000316637.5	+	10	1677		c.e10+2		DEF6_ENST00000542066.1_Splice_Site	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)							cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						AGCCTGGAGGTGAGAAGGAAT	0.572																																					.		Atlas-SNP	.											.	DEF6	36	.	0			c.1672+2T>A						.						54.0	51.0	52.0					6																	35288753		2203	4300	6503	SO:0001630	splice_region_variant	50619	exon10			TGGAGGTGAGAAG	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"""Pleckstrin homology (PH) domain containing"""	2760	protein-coding gene	gene with protein product	"""SWAP-70-like adaptor protein of T cells"""	610094	"""differentially expressed in FDCP (mouse homolog) 6"""			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.1672+2T>A	chr6.hg19:g.35288753T>A		134.0	0.0		93.0	4.0	NM_022047	Q86VF4	Splice_Site	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.081657	0.76528	.	.	ENSG00000023892	ENST00000542066;ENST00000316637	.	.	.	5.42	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6434	0.56721	0.0:0.0:0.1381:0.8619	.	.	.	.	.	-1	.	.	.	+	.	.	DEF6	35396731	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.789000	0.69029	0.877000	0.35895	0.459000	0.35465	.	.	.		0.572	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	Intron
FKBP5	2289	hgsc.bcm.edu	37	6	35604882	35604882	+	Silent	SNP	A	A	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35604882A>C	ENST00000539068.1	-	3	361	c.159T>G	c.(157-159)gtT>gtG	p.V53V	FKBP5_ENST00000536438.1_Silent_p.V53V|FKBP5_ENST00000357266.4_Silent_p.V53V|FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Silent_p.V53V	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	53	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						AATGGACATAAACTTTGTCTC	0.363																																					p.V53V		Atlas-SNP	.											.	FKBP5	64	.	0			c.T159G						.						112.0	102.0	105.0					6																	35604882		2203	4300	6503	SO:0001819	synonymous_variant	2289	exon4			GACATAAACTTTG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.159T>G	chr6.hg19:g.35604882A>C		204.0	0.0		117.0	40.0	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	hg19	CCDS4808.1																																																																																			.	.		0.363	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
SLC26A8	116369	hgsc.bcm.edu	37	6	35918964	35918964	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35918964C>A	ENST00000490799.1	-	19	2801	c.2448G>T	c.(2446-2448)cgG>cgT	p.R816R	SLC26A8_ENST00000355574.2_Silent_p.R816R|SLC26A8_ENST00000394602.2_Silent_p.R711R	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						AGTAGGTTTCCCGTATCACTG	0.542																																					p.R816R		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G2448T						.						140.0	119.0	126.0					6																	35918964		2203	4300	6503	SO:0001819	synonymous_variant	116369	exon19			GGTTTCCCGTATC	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2448G>T	chr6.hg19:g.35918964C>A		146.0	0.0		99.0	4.0	NM_052961		Silent	SNP	ENST00000490799.1	hg19	CCDS4813.1																																																																																			.	.		0.542	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
TREM2	54209	hgsc.bcm.edu	37	6	41130810	41130810	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:41130810A>G	ENST00000373113.3	-	1	104	c.11T>C	c.(10-12)cTc>cCc	p.L4P	TREM2_ENST00000338469.3_Missense_Mutation_p.L4P|TREM2_ENST00000373122.4_Missense_Mutation_p.L4P	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	4					axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					GAGCAGCCGGAGAGGCTCCAT	0.567																																					p.L4P		Atlas-SNP	.											.	TREM2	35	.	0			c.T11C						.						118.0	89.0	99.0					6																	41130810		2203	4300	6503	SO:0001583	missense	54209	exon1			AGCCGGAGAGGCT	AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"""Immunoglobulin superfamily / V-set domain containing"""	17761	protein-coding gene	gene with protein product		605086	"""triggering receptor expressed on myeloid cells 2a"""			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.11T>C	chr6.hg19:g.41130810A>G	ENSP00000362205:p.Leu4Pro	139.0	0.0		88.0	4.0	NM_018965	Q8N5H8|Q8WYN6	Missense_Mutation	SNP	ENST00000373113.3	hg19	CCDS4852.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.703761	0.48412	.	.	ENSG00000095970	ENST00000373113;ENST00000338469;ENST00000373122	T;T;T	0.59224	0.28;0.56;0.39	4.8	2.36	0.29203	.	.	.	.	.	T	0.53738	0.1815	L	0.53249	1.67	0.21652	N	0.999608	D;D;B	0.76494	0.999;0.997;0.011	D;D;B	0.67548	0.952;0.931;0.008	T	0.38845	-0.9642	9	0.87932	D	0	19.6202	7.4957	0.27487	0.8232:0.0:0.1768:0.0	.	4;4;4	Q9NZC2-2;Q9NZC2-3;Q9NZC2	.;.;TREM2_HUMAN	P	4	ENSP00000362205:L4P;ENSP00000342651:L4P;ENSP00000362214:L4P	ENSP00000342651:L4P	L	-	2	0	TREM2	41238788	0.152000	0.22762	0.025000	0.17156	0.155000	0.21991	2.089000	0.41672	0.863000	0.35553	0.459000	0.35465	CTC	.	.		0.567	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965	
KLHL31	401265	hgsc.bcm.edu	37	6	53516499	53516499	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:53516499G>T	ENST00000407079.1	-	2	1801	c.1802C>A	c.(1801-1803)cCc>cAc	p.P601H	KLHL31_ENST00000370905.3_Missense_Mutation_p.P601H			Q9H511	KLH31_HUMAN	kelch-like family member 31	601					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					AGTGGCCTCGGGTAGCTCGTC	0.607											OREG0017507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P601H		Atlas-SNP	.											.	KLHL31	48	.	0			c.C1802A						.						121.0	105.0	110.0					6																	53516499		2203	4300	6503	SO:0001583	missense	401265	exon3			GCCTCGGGTAGCT		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"""Kelch-like"", ""BTB/POZ domain containing"""	21353	protein-coding gene	gene with protein product		610749	"""kelch repeat and BTB (POZ) domain containing 1"", ""kelch-like 31 (Drosophila)"""	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1802C>A	chr6.hg19:g.53516499G>T	ENSP00000384644:p.Pro601His	133.0	0.0	993	88.0	5.0	NM_001003760	A6N9J2|B2RP49	Missense_Mutation	SNP	ENST00000407079.1	hg19	CCDS34478.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519413	0.85495	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.71341	-0.56;-0.56	5.77	5.77	0.91146	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.78836	0.4346	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.72017	-0.4417	10	0.23891	T	0.37	.	20.3473	0.98799	0.0:0.0:1.0:0.0	.	601	Q9H511	KLH31_HUMAN	H	601	ENSP00000359942:P601H;ENSP00000384644:P601H	ENSP00000359942:P601H	P	-	2	0	KLHL31	53624458	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.884000	0.98904	0.655000	0.94253	CCC	.	.		0.607	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760	
DST	667	hgsc.bcm.edu	37	6	56350122	56350122	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56350122G>T	ENST00000361203.3	-	83	20242	c.20235C>A	c.(20233-20235)atC>atA	p.I6745I	DST_ENST00000244364.6_Silent_p.I4442I|DST_ENST00000312431.6_3'UTR|DST_ENST00000370769.4_Silent_p.I6856I|DST_ENST00000370754.5_Silent_p.I7034I|DST_ENST00000421834.2_Silent_p.I4768I|DST_ENST00000370788.2_Silent_p.I4659I|DST_ENST00000446842.2_Silent_p.I6530I			Q03001	DYST_HUMAN	dystonin	6744					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.I6856I(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGTGATTATCGATCAGATTCA	0.363																																					p.I4442I		Atlas-SNP	.											DST_ENST00000370769,pharynx,carcinoma,0,1	DST	1427	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C13326A						.						128.0	122.0	124.0					6																	56350122		1841	4084	5925	SO:0001819	synonymous_variant	667	exon69			ATTATCGATCAGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20235C>A	chr6.hg19:g.56350122G>T		150.0	0.0		106.0	5.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
DST	667	hgsc.bcm.edu	37	6	56365936	56365936	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56365936T>C	ENST00000361203.3	-	75	18885	c.18878A>G	c.(18877-18879)gAg>gGg	p.E6293G	DST_ENST00000244364.6_Missense_Mutation_p.E3990G|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'UTR|DST_ENST00000370769.4_Missense_Mutation_p.E6404G|DST_ENST00000370754.5_Missense_Mutation_p.E6582G|DST_ENST00000421834.2_Missense_Mutation_p.E4316G|DST_ENST00000370788.2_Missense_Mutation_p.E4207G|DST_ENST00000446842.2_Missense_Mutation_p.E6078G			Q03001	DYST_HUMAN	dystonin	6292					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGGTTTCTGCTCACTTAGCAA	0.478																																					p.E3990G		Atlas-SNP	.											.	DST	1427	.	0			c.A11969G						.						99.0	96.0	97.0					6																	56365936		1947	4142	6089	SO:0001583	missense	667	exon61			TTCTGCTCACTTA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.18878A>G	chr6.hg19:g.56365936T>C	ENSP00000354508:p.Glu6293Gly	103.0	0.0		77.0	5.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.02	3.283157	0.59867	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.88	5.88	0.94601	.	0.000000	0.53938	D	0.000042	T	0.57755	0.2075	M	0.62154	1.92	0.33747	D	0.620107	D;D;D;P;B	0.69078	0.96;0.997;0.993;0.896;0.093	P;D;D;P;B	0.73380	0.859;0.98;0.926;0.562;0.059	T	0.57837	-0.7742	9	0.39692	T	0.17	.	16.2744	0.82636	0.0:0.0:0.0:1.0	.	4316;6404;6582;6402;3990	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	G	3990;6582;6404;4316;6078;4207;6293	ENSP00000244364:E3990G;ENSP00000359790:E6582G;ENSP00000359805:E6404G;ENSP00000400883:E4316G;ENSP00000393645:E6078G;ENSP00000359824:E4207G;ENSP00000354508:E6293G	ENSP00000244364:E3990G	E	-	2	0	DST	56473895	1.000000	0.71417	0.957000	0.39632	0.686000	0.39977	5.093000	0.64517	2.237000	0.73441	0.482000	0.46254	GAG	.	.		0.478	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
DST	667	hgsc.bcm.edu	37	6	56376052	56376052	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56376052T>C	ENST00000361203.3	-	68	17770	c.17763A>G	c.(17761-17763)aaA>aaG	p.K5921K	DST_ENST00000244364.6_Silent_p.K3618K|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'UTR|DST_ENST00000370769.4_Silent_p.K6032K|DST_ENST00000370754.5_Silent_p.K6210K|DST_ENST00000421834.2_Silent_p.K3944K|DST_ENST00000370788.2_Silent_p.K3835K|DST_ENST00000446842.2_Silent_p.K5706K			Q03001	DYST_HUMAN	dystonin	5922					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGACATCTTCTTTAATTTGAC	0.428																																					p.K3618K		Atlas-SNP	.											.	DST	1427	.	0			c.A10854G						.						61.0	56.0	58.0					6																	56376052		1882	4109	5991	SO:0001819	synonymous_variant	667	exon54			ATCTTCTTTAATT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17763A>G	chr6.hg19:g.56376052T>C		164.0	0.0		132.0	6.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
EYS	346007	hgsc.bcm.edu	37	6	66094343	66094343	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:66094343C>T	ENST00000370621.3	-	8	1761	c.1235G>A	c.(1234-1236)tGt>tAt	p.C412Y	EYS_ENST00000393380.2_Missense_Mutation_p.C412Y|EYS_ENST00000370618.3_Missense_Mutation_p.C412Y|EYS_ENST00000503581.1_Missense_Mutation_p.C412Y|EYS_ENST00000342421.5_Missense_Mutation_p.C412Y|EYS_ENST00000370616.2_Missense_Mutation_p.C412Y			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	412					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GAGCAGTTTACAGTGGTCAAT	0.299																																					p.C412Y		Atlas-SNP	.											.	EYS	527	.	0			c.G1235A						.						101.0	98.0	99.0					6																	66094343		2202	4295	6497	SO:0001583	missense	346007	exon8			AGTTTACAGTGGT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1235G>A	chr6.hg19:g.66094343C>T	ENSP00000359655:p.Cys412Tyr	131.0	0.0		83.0	4.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.44	2.834902	0.50951	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;D;D;D	0.96685	1.35;1.35;1.35;-4.09;-4.09;-4.09	6.07	5.21	0.72293	.	.	.	.	.	D	0.98365	0.9457	H	0.95645	3.7	0.30964	N	0.723299	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.962;0.982;0.96	D	0.97376	0.9979	9	0.87932	D	0	.	14.343	0.66641	0.0:0.9296:0.0:0.0704	.	412;412;412	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	Y	412	ENSP00000424243:C412Y;ENSP00000359655:C412Y;ENSP00000359650:C412Y;ENSP00000377042:C412Y;ENSP00000341818:C412Y;ENSP00000359652:C412Y	ENSP00000341818:C412Y	C	-	2	0	EYS	66151064	1.000000	0.71417	0.008000	0.14137	0.409000	0.31022	5.635000	0.67841	1.578000	0.49821	0.655000	0.94253	TGT	.	.		0.299	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
BAI3	577	hgsc.bcm.edu	37	6	69666002	69666002	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:69666002A>G	ENST00000370598.1	+	7	2103	c.1282A>G	c.(1282-1284)Act>Gct	p.T428A		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	428	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CCGGCAGTGCACTGCAGCTGC	0.542																																					p.T428A		Atlas-SNP	.											.	BAI3	451	.	0			c.A1282G						.						76.0	68.0	71.0					6																	69666002		2203	4300	6503	SO:0001583	missense	577	exon7			CAGTGCACTGCAG	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1282A>G	chr6.hg19:g.69666002A>G	ENSP00000359630:p.Thr428Ala	93.0	0.0		70.0	4.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.646796	0.47258	.	.	ENSG00000135298	ENST00000370598	T	0.50548	0.74	5.71	4.53	0.55603	.	0.127331	0.53938	D	0.000049	T	0.22975	0.0555	L	0.37697	1.125	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.07462	-1.0771	10	0.54805	T	0.06	.	12.2372	0.54522	0.8725:0.0:0.0:0.1275	.	428	O60242	BAI3_HUMAN	A	428	ENSP00000359630:T428A	ENSP00000359630:T428A	T	+	1	0	BAI3	69722723	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	5.837000	0.69381	0.976000	0.38417	0.482000	0.46254	ACT	.	.		0.542	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
COL19A1	1310	hgsc.bcm.edu	37	6	70897949	70897949	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:70897949G>T	ENST00000322773.4	+	47	3129	c.3027G>T	c.(3025-3027)ccG>ccT	p.P1009P	COL19A1_ENST00000393344.1_Splice_Site_p.P631P	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	1009	Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CTGGCATTCCGGTAAGTAGTG	0.522																																					p.P1009P		Atlas-SNP	.											COL19A1,right_upper_lobe,carcinoma,+1,1	COL19A1	232	.	0			c.G3027T						.						43.0	43.0	43.0					6																	70897949		2203	4300	6503	SO:0001630	splice_region_variant	1310	exon47			CATTCCGGTAAGT		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.3027+1G>T	chr6.hg19:g.70897949G>T		120.0	1.0		97.0	4.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.		0.522	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		Silent
TMEM30A	55754	hgsc.bcm.edu	37	6	75970580	75970580	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:75970580T>C	ENST00000230461.6	-	4	830	c.501A>G	c.(499-501)ccA>ccG	p.P167P	TMEM30A_ENST00000475111.2_Silent_p.P131P|TMEM30A_ENST00000370050.5_Silent_p.P48P	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	167					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAGGAGCAATTGGTTTGTCTT	0.338																																					p.P167P		Atlas-SNP	.											.	TMEM30A	40	.	0			c.A501G						.						165.0	151.0	156.0					6																	75970580		2203	4300	6503	SO:0001819	synonymous_variant	55754	exon4			AGCAATTGGTTTG	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.501A>G	chr6.hg19:g.75970580T>C		263.0	0.0		189.0	69.0	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Silent	SNP	ENST00000230461.6	hg19	CCDS4983.1																																																																																			.	.		0.338	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
MYO6	4646	hgsc.bcm.edu	37	6	76542624	76542624	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:76542624T>A	ENST00000369977.3	+	6	596	c.457T>A	c.(457-459)Tca>Aca	p.S153T	MYO6_ENST00000369985.4_Missense_Mutation_p.S153T|MYO6_ENST00000369981.3_Missense_Mutation_p.S153T|MYO6_ENST00000369975.1_Missense_Mutation_p.S153T	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	153	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		ATCTGGAGAATCAGGAGCCGG	0.373																																					p.S153T		Atlas-SNP	.											.	MYO6	124	.	0			c.T457A						.						83.0	89.0	87.0					6																	76542624		2203	4300	6503	SO:0001583	missense	4646	exon6			GGAGAATCAGGAG	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.457T>A	chr6.hg19:g.76542624T>A	ENSP00000358994:p.Ser153Thr	109.0	0.0		84.0	4.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852950	0.91355	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.98614	0.9536	H	0.97896	4.1	0.80722	D	1	D;D	0.71674	0.998;0.96	D;D	0.79108	0.992;0.923	D	0.99802	1.1036	10	0.87932	D	0	.	15.8146	0.78589	0.0:0.0:0.0:1.0	.	153;153	Q9UM54-2;Q9UM54-1	.;.	T	153	ENSP00000358998:S153T;ENSP00000359002:S153T;ENSP00000358994:S153T;ENSP00000358992:S153T	ENSP00000358992:S153T	S	+	1	0	MYO6	76599344	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.630000	0.83225	2.193000	0.70182	0.528000	0.53228	TCA	.	.		0.373	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
SNAP91	9892	hgsc.bcm.edu	37	6	84300973	84300973	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:84300973A>G	ENST00000439399.2	-	22	2287	c.1971T>C	c.(1969-1971)tcT>tcC	p.S657S	SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000521743.1_Silent_p.S657S|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000521485.1_Silent_p.S657S|SNAP91_ENST00000195649.6_Silent_p.S657S|SNAP91_ENST00000369694.2_Silent_p.S657S|SNAP91_ENST00000520302.1_Silent_p.S627S|SNAP91_ENST00000428679.2_Silent_p.S657S	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	657					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AAGCAGCCTGAGATGCAGGTT	0.363																																					p.S657S		Atlas-SNP	.											.	SNAP91	199	.	0			c.T1971C						.						124.0	118.0	120.0					6																	84300973		1865	4103	5968	SO:0001819	synonymous_variant	9892	exon21			AGCCTGAGATGCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1971T>C	chr6.hg19:g.84300973A>G		87.0	0.0		44.0	4.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	hg19	CCDS47455.1																																																																																			.	.		0.363	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577355	90577355	+	RNA	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:90577355C>T	ENST00000551025.1	+	0	5783									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTACCATCGCCTCTGAAGTCA	0.398																																					p.P1449L	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C4346T						.						91.0	89.0	90.0					6																	90577355		1890	4110	6000			9994	exon8			CATCGCCTCTGAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90577355C>T		105.0	0.0		79.0	4.0	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.398	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
BACH2	60468	hgsc.bcm.edu	37	6	90661010	90661010	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:90661010C>A	ENST00000257749.4	-	7	1522	c.815G>T	c.(814-816)aGg>aTg	p.R272M	BACH2_ENST00000343122.3_Missense_Mutation_p.R272M|RP3-512E2.2_ENST00000445838.1_RNA|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.R272M	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	272						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		AATCTGCCCCCTGGCAAGCCC	0.532																																					p.R272M		Atlas-SNP	.											.	BACH2	224	.	0			c.G815T						.						76.0	78.0	77.0					6																	90661010		2203	4300	6503	SO:0001583	missense	60468	exon5			TGCCCCCTGGCAA	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.815G>T	chr6.hg19:g.90661010C>A	ENSP00000257749:p.Arg272Met	135.0	0.0		95.0	4.0	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	hg19	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	C	1.851	-0.464926	0.04476	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.35605	1.3;1.3;1.3	5.03	1.12	0.20585	.	0.868689	0.10677	N	0.646818	T	0.06781	0.0173	N	0.03608	-0.345	0.23607	N	0.997304	B	0.02656	0.0	B	0.01281	0.0	T	0.39251	-0.9623	10	0.45353	T	0.12	-22.7857	12.7214	0.57144	0.5957:0.4043:0.0:0.0	.	272	Q9BYV9	BACH2_HUMAN	M	272	ENSP00000257749:R272M;ENSP00000437473:R272M;ENSP00000345642:R272M	ENSP00000257749:R272M	R	-	2	0	BACH2	90717731	0.997000	0.39634	0.726000	0.30738	0.426000	0.31534	2.704000	0.47118	0.051000	0.15978	-1.321000	0.01291	AGG	.	.		0.532	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
MANEA	79694	hgsc.bcm.edu	37	6	96034523	96034523	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:96034523G>A	ENST00000358812.4	+	2	342	c.208G>A	c.(208-210)Gaa>Aaa	p.E70K	MANEA_ENST00000369293.1_Missense_Mutation_p.E70K	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	70	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		AATCAACAGTGAAACAAATAC	0.358																																					p.E70K		Atlas-SNP	.											.	MANEA	58	.	0			c.G208A						.						83.0	86.0	85.0					6																	96034523		2203	4300	6503	SO:0001583	missense	79694	exon2			AACAGTGAAACAA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.208G>A	chr6.hg19:g.96034523G>A	ENSP00000351669:p.Glu70Lys	111.0	0.0		96.0	4.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	hg19	CCDS5032.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374741	0.42105	.	.	ENSG00000172469	ENST00000358812;ENST00000369293;ENST00000542500	.	.	.	5.82	4.77	0.60923	.	0.314947	0.38548	N	0.001645	T	0.33614	0.0869	L	0.57536	1.79	0.43317	D	0.995333	B;P	0.38597	0.041;0.639	B;B	0.34652	0.048;0.187	T	0.30534	-0.9975	9	0.07482	T	0.82	-23.6425	14.8901	0.70604	0.0804:0.0:0.9196:0.0	.	70;70	Q5SRI9;Q8WWX4	MANEA_HUMAN;.	K	70	.	ENSP00000351669:E70K	E	+	1	0	MANEA	96141244	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	1.586000	0.36611	2.754000	0.94517	0.650000	0.86243	GAA	.	.		0.358	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
BEND3	57673	hgsc.bcm.edu	37	6	107390471	107390471	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:107390471G>T	ENST00000369042.1	-	4	2114	c.1924C>A	c.(1924-1926)Cgc>Agc	p.R642S	BEND3_ENST00000429433.2_Missense_Mutation_p.R642S			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	642	BEN 3. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						CGCCGGCAGCGCTCATCCAGT	0.637																																					p.R642S		Atlas-SNP	.											.	BEND3	70	.	0			c.C1924A						.						23.0	26.0	25.0					6																	107390471		2202	4299	6501	SO:0001583	missense	57673	exon5			GGCAGCGCTCATC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1924C>A	chr6.hg19:g.107390471G>T	ENSP00000358038:p.Arg642Ser	94.0	0.0		77.0	4.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928665	0.34002	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	T;T	0.44083	0.93;0.93	4.62	2.61	0.31194	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.20700	0.0498	L	0.29908	0.895	0.49915	D	0.999832	P	0.43909	0.821	P	0.46237	0.508	T	0.04565	-1.0942	10	0.72032	D	0.01	-8.309	6.9748	0.24669	0.0:0.1256:0.4778:0.3965	.	642	Q5T5X7	BEND3_HUMAN	S	642	ENSP00000358038:R642S;ENSP00000411268:R642S	ENSP00000358038:R642S	R	-	1	0	BEND3	107497164	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	2.710000	0.47169	1.126000	0.42016	0.555000	0.69702	CGC	.	.		0.637	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
WASF1	8936	hgsc.bcm.edu	37	6	110426738	110426738	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:110426738T>C	ENST00000392589.1	-	8	1421	c.585A>G	c.(583-585)agA>agG	p.R195R	WASF1_ENST00000359451.2_Silent_p.R195R|WASF1_ENST00000392586.1_Silent_p.R195R|WASF1_ENST00000392587.2_Silent_p.R195R|WASF1_ENST00000392588.1_Silent_p.R195R	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	195					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		CATGAGGTGCTCTTGGCACTT	0.418																																					p.R195R		Atlas-SNP	.											.	WASF1	35	.	0			c.A585G						.						101.0	96.0	98.0					6																	110426738		2203	4300	6503	SO:0001819	synonymous_variant	8936	exon7			AGGTGCTCTTGGC	D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"""A-kinase anchor proteins"""	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.585A>G	chr6.hg19:g.110426738T>C		103.0	0.0		95.0	4.0	NM_001024935	E1P5F2|Q5SZK7	Silent	SNP	ENST00000392589.1	hg19	CCDS5080.1																																																																																			.	.		0.418	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931	
HS3ST5	222537	hgsc.bcm.edu	37	6	114383915	114383915	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:114383915C>A	ENST00000312719.5	-	4	1283	c.95G>T	c.(94-96)gGg>gTg	p.G32V	HS3ST5_ENST00000411826.1_Missense_Mutation_p.G32V|RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	32					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		ATCCAAGCTCCCAACTCTGGC	0.478																																					p.G32V		Atlas-SNP	.											.	HS3ST5	80	.	0			c.G95T						.						153.0	152.0	152.0					6																	114383915		2203	4300	6503	SO:0001583	missense	222537	exon1			AAGCTCCCAACTC	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"""Sulfotransferases, membrane-bound"""	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.95G>T	chr6.hg19:g.114383915C>A	ENSP00000427888:p.Gly32Val	125.0	0.0		100.0	4.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	hg19	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371444	0.82573	.	.	ENSG00000249853	ENST00000312719;ENST00000411826	T;T	0.48836	0.8;0.8	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53725	-0.8398	10	0.56958	D	0.05	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	32	Q8IZT8	HS3S5_HUMAN	V	32	ENSP00000427888:G32V;ENSP00000440332:G32V	ENSP00000427888:G32V	G	-	2	0	HS3ST5	114490608	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.022000	0.76431	2.885000	0.99019	0.655000	0.94253	GGG	.	.		0.478	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
ZUFSP	221302	hgsc.bcm.edu	37	6	116988328	116988328	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:116988328T>C	ENST00000368576.3	-	2	271	c.28A>G	c.(28-30)Aca>Gca	p.T10A	ZUFSP_ENST00000471919.1_Intron|ZUFSP_ENST00000368573.1_Missense_Mutation_p.T10A	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	10							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GAGGTTACTGTTTCACCACAA	0.328																																					p.T10A		Atlas-SNP	.											.	ZUFSP	46	.	0			c.A28G						.						72.0	74.0	74.0					6																	116988328		2187	4291	6478	SO:0001583	missense	221302	exon2			TTACTGTTTCACC	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"""Zinc fingers, C2H2-type"""	21224	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 113"""	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.28A>G	chr6.hg19:g.116988328T>C	ENSP00000357565:p.Thr10Ala	120.0	0.0		99.0	4.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.846093	0.32606	.	.	ENSG00000153975	ENST00000368576;ENST00000368573	T;T	0.41400	1.0;1.67	5.94	3.47	0.39725	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.317816	0.34484	N	0.003921	T	0.09158	0.0226	L	0.29908	0.895	0.25697	N	0.985626	B	0.26400	0.148	B	0.22386	0.039	T	0.18085	-1.0348	10	0.10902	T	0.67	-10.347	4.3961	0.11363	0.0:0.1566:0.1762:0.6671	.	10	Q96AP4	ZUFSP_HUMAN	A	10	ENSP00000357565:T10A;ENSP00000357562:T10A	ENSP00000357562:T10A	T	-	1	0	ZUFSP	117095021	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.412000	0.34714	2.272000	0.75746	0.459000	0.35465	ACA	.	.		0.328	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062	
GOPC	57120	hgsc.bcm.edu	37	6	117884507	117884507	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:117884507T>C	ENST00000368498.2	-	9	1374	c.1299A>G	c.(1297-1299)ggA>ggG	p.G433G	GOPC_ENST00000535237.1_Silent_p.G433G|GOPC_ENST00000467125.1_Intron|DCBLD1_ENST00000296955.8_Intron|GOPC_ENST00000052569.6_Silent_p.G425G	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	433					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		TGCCCAGGTCTCCATTTTCAT	0.363			O	ROS1	glioblastoma																																p.G433G		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.A1299G						.						132.0	123.0	126.0					6																	117884507		2203	4300	6503	SO:0001819	synonymous_variant	57120	exon9			CAGGTCTCCATTT	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.1299A>G	chr6.hg19:g.117884507T>C		129.0	0.0		96.0	4.0	NM_020399	A6NM30|Q59FS4|Q969U8	Silent	SNP	ENST00000368498.2	hg19	CCDS5117.1																																																																																			.	.		0.363	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399	
RNF146	81847	hgsc.bcm.edu	37	6	127607967	127607967	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:127607967G>T	ENST00000368314.1	+	3	633	c.209G>T	c.(208-210)cGg>cTg	p.R70L	RNF146_ENST00000477776.1_3'UTR|RNF146_ENST00000309649.3_Missense_Mutation_p.R69L|RNF146_ENST00000608991.1_Missense_Mutation_p.R69L|RNF146_ENST00000480444.1_3'UTR|RNF146_ENST00000610153.1_Missense_Mutation_p.R70L|RNF146_ENST00000356799.2_3'UTR|RNF146_ENST00000489534.1_3'UTR|RNF146_ENST00000476956.1_3'UTR	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	70					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		CTTGGAAAGCGGTGTGCTCTT	0.458																																					p.R70L		Atlas-SNP	.											.	RNF146	31	.	0			c.G209T						.						136.0	116.0	123.0					6																	127607967		2203	4300	6503	SO:0001583	missense	81847	exon3			GAAAGCGGTGTGC	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"""RING-type (C3HC4) zinc fingers"""	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.209G>T	chr6.hg19:g.127607967G>T	ENSP00000357297:p.Arg70Leu	243.0	0.0		200.0	9.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Missense_Mutation	SNP	ENST00000368314.1	hg19	CCDS56449.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.545107	0.86022	.	.	ENSG00000118518	ENST00000368314;ENST00000356799;ENST00000309649	D;D;D	0.86097	-2.07;-2.07;-2.07	5.8	5.8	0.92144	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.87775	0.6262	L	0.38733	1.17	0.80722	D	1	D	0.71674	0.998	D	0.69142	0.962	D	0.88401	0.3015	10	0.72032	D	0.01	1.2613	20.0734	0.97734	0.0:0.0:1.0:0.0	.	70	Q9NTX7	RN146_HUMAN	L	70;69;69	ENSP00000357297:R70L;ENSP00000349253:R69L;ENSP00000309365:R69L	ENSP00000309365:R69L	R	+	2	0	RNF146	127649660	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	9.809000	0.99208	2.748000	0.94277	0.655000	0.94253	CGG	.	.		0.458	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963	
THEMIS	387357	hgsc.bcm.edu	37	6	128134090	128134090	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:128134090T>C	ENST00000368248.2	-	4	1844	c.1696A>G	c.(1696-1698)Aca>Gca	p.T566A	THEMIS_ENST00000368250.1_Missense_Mutation_p.T487A|THEMIS_ENST00000537166.1_Missense_Mutation_p.T531A|THEMIS_ENST00000543064.1_Missense_Mutation_p.T566A	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	566					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GTTAACTTTGTTTCCTCTACT	0.483																																					p.T566A		Atlas-SNP	.											.	THEMIS	168	.	0			c.A1696G						.						140.0	143.0	142.0					6																	128134090		2203	4300	6503	SO:0001583	missense	387357	exon4			ACTTTGTTTCCTC	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"""thymocyte expressed molecule involved in selection"""	613607	"""chromosome 6 open reading frame 207"", ""chromosome 6 open reading frame 190"", ""thymocyte selection pathway associated"""	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1696A>G	chr6.hg19:g.128134090T>C	ENSP00000357231:p.Thr566Ala	88.0	0.0		95.0	4.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.041446	0.00402	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.17054	2.3;2.31;2.3;2.3	5.96	2.33	0.28932	.	0.600804	0.16591	N	0.207743	T	0.03095	0.0091	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.46816	-0.9164	10	0.11182	T	0.66	-0.125	5.2204	0.15366	0.0:0.3037:0.1454:0.5509	.	566;566	F5H1J9;Q8N1K5	.;THMS1_HUMAN	A	487;566;566;531	ENSP00000357233:T487A;ENSP00000439594:T566A;ENSP00000357231:T566A;ENSP00000439863:T531A	ENSP00000357231:T566A	T	-	1	0	THEMIS	128175783	0.006000	0.16342	0.001000	0.08648	0.023000	0.10783	1.016000	0.29976	0.171000	0.19730	0.533000	0.62120	ACA	.	.		0.483	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923	
ENPP3	5169	hgsc.bcm.edu	37	6	131996238	131996238	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:131996238T>C	ENST00000414305.1	+	10	1109	c.781T>C	c.(781-783)Tat>Cat	p.Y261H	ENPP3_ENST00000543135.1_Missense_Mutation_p.Y227H|ENPP3_ENST00000427148.2_3'UTR|ENPP3_ENST00000358229.5_Missense_Mutation_p.Y261H|ENPP3_ENST00000357639.3_Missense_Mutation_p.Y261H			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	261	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GACAGCAATGTATCAAGGTTT	0.398																																					p.Y261H		Atlas-SNP	.											.	ENPP3	117	.	0			c.T781C						.						92.0	88.0	89.0					6																	131996238		2203	4300	6503	SO:0001583	missense	5169	exon9			GCAATGTATCAAG	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.781T>C	chr6.hg19:g.131996238T>C	ENSP00000406261:p.Tyr261His	92.0	0.0		84.0	4.0	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.921957	0.33908	.	.	ENSG00000154269	ENST00000414305;ENST00000357639;ENST00000543135;ENST00000358229	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.52	1.65	0.23941	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.203901	0.34178	N	0.004181	T	0.33118	0.0852	N	0.25286	0.73	0.80722	D	1	B	0.15719	0.014	B	0.23852	0.049	T	0.09271	-1.0682	10	0.29301	T	0.29	-11.3445	6.093	0.20005	0.2494:0.0713:0.0:0.6794	.	261	O14638	ENPP3_HUMAN	H	261;261;227;261	ENSP00000406261:Y261H;ENSP00000350265:Y261H;ENSP00000440810:Y227H;ENSP00000350964:Y261H	ENSP00000350265:Y261H	Y	+	1	0	ENPP3	132037931	1.000000	0.71417	0.998000	0.56505	0.887000	0.51463	1.583000	0.36579	0.356000	0.24157	0.363000	0.22086	TAT	.	.		0.398	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
ENPP3	5169	hgsc.bcm.edu	37	6	132068028	132068028	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:132068028A>G	ENST00000414305.1	+	26	2888	c.2560A>G	c.(2560-2562)Aaa>Gaa	p.K854E	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.K854E			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	854	Nuclease.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		CTATCAGGATAAAGTGCAGCC	0.363																																					p.K854E		Atlas-SNP	.											.	ENPP3	117	.	0			c.A2560G						.						67.0	70.0	69.0					6																	132068028		2203	4300	6503	SO:0001583	missense	5169	exon25			CAGGATAAAGTGC	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2560A>G	chr6.hg19:g.132068028A>G	ENSP00000406261:p.Lys854Glu	217.0	0.0		151.0	37.0	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	A	8.833	0.940494	0.18281	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.73258	-0.73;-0.73	5.45	5.45	0.79879	DNA/RNA non-specific endonuclease (1);Extracellular Endonuclease, subunit A (1);	0.249386	0.35378	N	0.003250	T	0.59702	0.2213	M	0.68317	2.08	0.30983	N	0.722258	B	0.32467	0.372	B	0.39771	0.309	T	0.61382	-0.7074	10	0.37606	T	0.19	-20.724	11.7667	0.51935	0.8531:0.1469:0.0:0.0	.	854	O14638	ENPP3_HUMAN	E	854	ENSP00000406261:K854E;ENSP00000350265:K854E	ENSP00000350265:K854E	K	+	1	0	ENPP3	132109721	0.430000	0.25538	0.028000	0.17463	0.009000	0.06853	3.820000	0.55693	2.190000	0.69967	0.482000	0.46254	AAA	.	.		0.363	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
VNN2	8875	hgsc.bcm.edu	37	6	133071001	133071001	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:133071001A>G	ENST00000326499.6	-	6	1328	c.1204T>C	c.(1204-1206)Tgc>Cgc	p.C402R	VNN2_ENST00000525289.1_Missense_Mutation_p.C181R|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525270.1_Missense_Mutation_p.C349R	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	402					cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		AGCAGTGTGCAGACCTATGTG	0.403																																					p.C402R		Atlas-SNP	.											.	VNN2	83	.	0			c.T1204C						.						84.0	75.0	78.0					6																	133071001		2203	4300	6503	SO:0001583	missense	8875	exon6			GTGTGCAGACCTA	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.1204T>C	chr6.hg19:g.133071001A>G	ENSP00000322276:p.Cys402Arg	115.0	0.0		93.0	4.0	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Missense_Mutation	SNP	ENST00000326499.6	hg19	CCDS5161.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268007	0.59540	.	.	ENSG00000112303	ENST00000326499;ENST00000525270;ENST00000525289	D;D;D	0.96041	-3.89;-3.89;-3.89	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000002	D	0.98134	0.9384	H	0.94264	3.515	0.44643	D	0.997629	D;D	0.89917	1.0;1.0	D;D	0.91635	0.967;0.999	D	0.99466	1.0944	10	0.87932	D	0	-10.9792	14.0292	0.64604	1.0:0.0:0.0:0.0	.	181;402	O95498-2;O95498	.;VNN2_HUMAN	R	402;349;181	ENSP00000322276:C402R;ENSP00000436822:C349R;ENSP00000436935:C181R	ENSP00000322276:C402R	C	-	1	0	VNN2	133112694	1.000000	0.71417	0.119000	0.21687	0.003000	0.03518	5.911000	0.69939	1.967000	0.57214	0.533000	0.62120	TGC	.	.		0.403	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
PEX7	5191	hgsc.bcm.edu	37	6	137193356	137193356	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:137193356T>C	ENST00000318471.4	+	8	849	c.768T>C	c.(766-768)tcT>tcC	p.S256S	PEX7_ENST00000541292.1_3'UTR	NM_000288.3	NP_000279.1	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7	256					endochondral ossification (GO:0001958)|ether lipid biosynthetic process (GO:0008611)|fatty acid beta-oxidation (GO:0006635)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-2 binding (GO:0005053)|protein homodimerization activity (GO:0042803)			lung(7)|prostate(1)	8	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)		TTCATGCTTCTGTGCTGGCCT	0.323																																					p.S256S		Atlas-SNP	.											.	PEX7	24	.	0			c.T768C						.						144.0	148.0	147.0					6																	137193356		2202	4297	6499	SO:0001819	synonymous_variant	5191	exon8			TGCTTCTGTGCTG	AF180814	CCDS5180.1	6q21-q22.2	2013-01-10			ENSG00000112357	ENSG00000112357		"""WD repeat domain containing"""	8860	protein-coding gene	gene with protein product	"""Refsum disease"""	601757				9090381, 10673331	Standard	NM_000288		Approved	PTS2R, RD	uc003qhd.3	O00628	OTTHUMG00000015650	ENST00000318471.4:c.768T>C	chr6.hg19:g.137193356T>C		100.0	0.0		92.0	5.0	NM_000288	C0H5X6	Silent	SNP	ENST00000318471.4	hg19	CCDS5180.1																																																																																			.	.		0.323	PEX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042387.2	NM_000288	
NHSL1	57224	hgsc.bcm.edu	37	6	138745873	138745873	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:138745873G>A	ENST00000427025.2	-	7	4806	c.4178C>T	c.(4177-4179)cCc>cTc	p.P1393L	NHSL1_ENST00000343505.5_Missense_Mutation_p.P1389L	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1393										breast(2)|endometrium(4)|kidney(1)	7						AGCGCCGGTGGGTGTCACGGG	0.532																																					p.P1393L		Atlas-SNP	.											.	NHSL1	99	.	0			c.C4178T						.						34.0	35.0	35.0					6																	138745873		692	1591	2283	SO:0001583	missense	57224	exon7			CCGGTGGGTGTCA	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4178C>T	chr6.hg19:g.138745873G>A	ENSP00000394546:p.Pro1393Leu	136.0	0.0		105.0	5.0	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Missense_Mutation	SNP	ENST00000427025.2	hg19	CCDS55063.1	.	.	.	.	.	.	.	.	.	.	G	35	5.443609	0.96187	.	.	ENSG00000135540	ENST00000427025;ENST00000343505	T;T	0.47177	0.85;1.34	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.74881	2.28	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.73380	0.98;0.98	T	0.67684	-0.5607	10	0.87932	D	0	-23.1883	20.4561	0.99145	0.0:0.0:1.0:0.0	.	1389;1393	E2QRJ1;Q5SYE7	.;NHSL1_HUMAN	L	1393;1389	ENSP00000394546:P1393L;ENSP00000344672:P1389L	ENSP00000344672:P1389L	P	-	2	0	NHSL1	138787566	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.864000	0.99589	2.847000	0.97988	0.591000	0.81541	CCC	.	.		0.532	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152098	151152098	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:151152098A>G	ENST00000358517.2	+	15	2062	c.1851A>G	c.(1849-1851)acA>acG	p.T617T	PLEKHG1_ENST00000367328.1_Silent_p.T617T			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	617							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)		AGAGCAACACATGCCCTCCTG	0.557																																					p.T617T		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A1851G						.						60.0	55.0	57.0					6																	151152098		2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			CAACACATGCCCT	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.1851A>G	chr6.hg19:g.151152098A>G		114.0	0.0		62.0	4.0	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.557	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
ARID1B	57492	hgsc.bcm.edu	37	6	157502170	157502170	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:157502170A>G	ENST00000350026.5	+	11	3165	c.3164A>G	c.(3163-3165)gAg>gGg	p.E1055G	ARID1B_ENST00000275248.4_Missense_Mutation_p.E1050G|ARID1B_ENST00000478761.2_3'UTR|ARID1B_ENST00000367148.1_Missense_Mutation_p.E1108G|ARID1B_ENST00000346085.5_Missense_Mutation_p.E1068G	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1055	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AATGAGCCAGAGAGAAAGCTC	0.577																																					p.E1068G		Atlas-SNP	.											.	ARID1B	320	.	0			c.A3203G						.						92.0	76.0	82.0					6																	157502170		2203	4296	6499	SO:0001583	missense	57492	exon12			AGCCAGAGAGAAA	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3164A>G	chr6.hg19:g.157502170A>G	ENSP00000055163:p.Glu1055Gly	73.0	0.0		38.0	4.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	28.7	4.946609	0.92593	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584;ENST00000400790	T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.76	5.76	0.90799	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	T	0.61223	0.2330	M	0.68317	2.08	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.91635	0.998;0.999;0.998;0.998	T	0.66432	-0.5925	10	0.87932	D	0	.	16.0796	0.80995	1.0:0.0:0.0:0.0	.	305;1055;1068;1050	Q8NFD5-4;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	G	1068;1055;1108;1050;525;577;530;122	ENSP00000344546:E1068G;ENSP00000055163:E1055G;ENSP00000356116:E1108G;ENSP00000275248:E1050G;ENSP00000412835:E577G;ENSP00000313006:E530G;ENSP00000383596:E122G	ENSP00000275248:E1050G	E	+	2	0	ARID1B	157543862	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	9.339000	0.96797	2.195000	0.70347	0.528000	0.53228	GAG	.	.		0.577	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
ARID1B	57492	hgsc.bcm.edu	37	6	157502190	157502190	+	Silent	SNP	C	C	A	rs387907144		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:157502190C>A	ENST00000350026.5	+	11	3185	c.3184C>A	c.(3184-3186)Cga>Aga	p.R1062R	ARID1B_ENST00000275248.4_Silent_p.R1057R|ARID1B_ENST00000478761.2_3'UTR|ARID1B_ENST00000367148.1_Silent_p.R1115R|ARID1B_ENST00000346085.5_Silent_p.R1075R	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1062	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTGGGTCGACCGATACCTCAC	0.562																																					p.R1075R		Atlas-SNP	.											ARID1B_ENST00000346085,NS,adenocarcinoma,0,2	ARID1B	320	.	0			c.C3223A						.						96.0	81.0	86.0					6																	157502190		2203	4296	6499	SO:0001819	synonymous_variant	57492	exon12			GTCGACCGATACC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3184C>A	chr6.hg19:g.157502190C>A		78.0	0.0		43.0	3.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.		0.562	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
FNDC1	84624	hgsc.bcm.edu	37	6	159618551	159618551	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:159618551C>A	ENST00000297267.9	+	2	398	c.198C>A	c.(196-198)acC>acA	p.T66T	FNDC1_ENST00000340366.6_Silent_p.T66T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	66	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AAGATGCTACCAGTAGACCTG	0.463																																					p.T66T		Atlas-SNP	.											.	FNDC1	250	.	0			c.C198A						.						170.0	162.0	165.0					6																	159618551		1965	4150	6115	SO:0001819	synonymous_variant	84624	exon2			TGCTACCAGTAGA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.198C>A	chr6.hg19:g.159618551C>A		134.0	0.0		96.0	4.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.361524	0.24684	.	.	ENSG00000164694	ENST00000329629	.	.	.	6.11	6.11	0.99139	.	.	.	.	.	T	0.66366	0.2782	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63056	-0.6722	4	.	.	.	-7.2994	16.3193	0.82939	0.0:1.0:0.0:0.0	.	.	.	.	K	25	.	.	Q	+	1	0	FNDC1	159538539	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.939000	0.63526	2.928000	0.99379	0.638000	0.83543	CAG	.	.		0.463	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
IGF2R	3482	hgsc.bcm.edu	37	6	160450671	160450671	+	Missense_Mutation	SNP	C	C	A	rs373279911		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160450671C>A	ENST00000356956.1	+	7	1014	c.866C>A	c.(865-867)cCg>cAg	p.P289Q		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	289					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTGTTTGCCCGTCGGAGCGG	0.562																																					p.P289Q		Atlas-SNP	.											.	IGF2R	251	.	0			c.C866A						.						115.0	94.0	101.0					6																	160450671		2203	4300	6503	SO:0001583	missense	3482	exon7			TTTGCCCGTCGGA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.866C>A	chr6.hg19:g.160450671C>A	ENSP00000349437:p.Pro289Gln	168.0	0.0		125.0	5.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411954	0.62511	.	.	ENSG00000197081	ENST00000356956	T	0.13657	2.57	4.91	4.91	0.64330	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.36744	0.0978	M	0.87827	2.91	0.48830	D	0.999717	D	0.89917	1.0	D	0.97110	1.0	T	0.40997	-0.9533	10	0.66056	D	0.02	-32.3188	17.4451	0.87575	0.0:1.0:0.0:0.0	.	289	P11717	MPRI_HUMAN	Q	289	ENSP00000349437:P289Q	ENSP00000349437:P289Q	P	+	2	0	IGF2R	160370661	1.000000	0.71417	0.042000	0.18584	0.322000	0.28314	5.926000	0.70070	2.433000	0.82419	0.655000	0.94253	CCG	.	.		0.562	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
SLC22A2	6582	hgsc.bcm.edu	37	6	160663434	160663434	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160663434T>C	ENST00000366953.3	-	8	1538	c.1280A>G	c.(1279-1281)gAt>gGt	p.D427G	SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	427					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CCATTGTAGATCTAAGAGGGA	0.448																																					p.D427G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A1280G						.						128.0	117.0	120.0					6																	160663434		2203	4300	6503	SO:0001630	splice_region_variant	6582	exon8			TGTAGATCTAAGA	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1280-1A>G	chr6.hg19:g.160663434T>C		124.0	0.0		61.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	2.403	-0.337027	0.05278	.	.	ENSG00000112499	ENST00000366953	T	0.57107	0.42	5.13	2.71	0.32032	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.432615	0.27442	N	0.019345	T	0.21631	0.0521	L	0.48218	1.51	0.80722	D	1	B	0.17038	0.02	B	0.17979	0.02	T	0.06734	-1.0810	10	0.31617	T	0.26	.	4.3124	0.10977	0.1234:0.0688:0.1288:0.679	.	427	O15244	S22A2_HUMAN	G	427	ENSP00000355920:D427G	ENSP00000355920:D427G	D	-	2	0	SLC22A2	160583424	0.803000	0.28956	0.490000	0.27465	0.006000	0.05464	0.922000	0.28734	0.490000	0.27771	-0.336000	0.08194	GAT	.	.		0.448	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	Missense_Mutation
SLC22A2	6582	hgsc.bcm.edu	37	6	160666525	160666525	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160666525T>C	ENST00000366953.3	-	6	1268	c.1010A>G	c.(1009-1011)gAc>gGc	p.D337G	SLC22A2_ENST00000491092.1_5'UTR|SLC22A2_ENST00000366952.1_Missense_Mutation_p.D316G	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	337					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	TCTGACCAAGTCAAGAAATGA	0.358																																					p.D337G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A1010G						.						98.0	92.0	94.0					6																	160666525		2203	4300	6503	SO:0001583	missense	6582	exon6			ACCAAGTCAAGAA	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1010A>G	chr6.hg19:g.160666525T>C	ENSP00000355920:p.Asp337Gly	85.0	0.0		79.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439366	0.83885	.	.	ENSG00000112499	ENST00000366953;ENST00000366952	T;T	0.73897	-0.79;-0.79	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.88336	0.6409	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.91638	0.5324	10	0.87932	D	0	.	15.1705	0.72869	0.0:0.0:0.0:1.0	.	337;337	O15244;O15244-2	S22A2_HUMAN;.	G	337;316	ENSP00000355920:D337G;ENSP00000355919:D316G	ENSP00000355919:D316G	D	-	2	0	SLC22A2	160586515	1.000000	0.71417	0.978000	0.43139	0.755000	0.42902	7.593000	0.82686	2.159000	0.67721	0.533000	0.62120	GAC	.	.		0.358	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	
MAP3K4	4216	hgsc.bcm.edu	37	6	161508771	161508771	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:161508771G>A	ENST00000392142.4	+	10	2756	c.2608G>A	c.(2608-2610)Gct>Act	p.A870T	MAP3K4_ENST00000366919.2_Missense_Mutation_p.A870T|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A870T|MAP3K4_ENST00000348824.7_Missense_Mutation_p.A870T	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	870					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGACACTCTTGCTGAGGAGAA	0.393																																					p.A870T		Atlas-SNP	.											.	MAP3K4	364	.	0			c.G2608A						.						103.0	102.0	102.0					6																	161508771		2203	4300	6503	SO:0001583	missense	4216	exon10			ACTCTTGCTGAGG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2608G>A	chr6.hg19:g.161508771G>A	ENSP00000375986:p.Ala870Thr	129.0	0.0		92.0	4.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306302	0.40795	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.73	4.84	0.62591	.	0.382460	0.27544	N	0.018900	T	0.34337	0.0894	N	0.16478	0.41	0.09310	N	0.999998	B;B;B	0.15473	0.013;0.013;0.008	B;B;B	0.14023	0.007;0.01;0.005	T	0.11348	-1.0591	10	0.21014	T	0.42	-22.1873	13.8761	0.63653	0.0:0.0:0.7222:0.2778	.	870;870;870	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	T	870	ENSP00000355886:A870T;ENSP00000375986:A870T;ENSP00000355887:A870T;ENSP00000297332:A870T	ENSP00000297332:A870T	A	+	1	0	MAP3K4	161428761	0.990000	0.36364	0.265000	0.24526	0.964000	0.63967	3.493000	0.53266	1.514000	0.48869	0.655000	0.94253	GCT	.	.		0.393	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
RNASET2	8635	hgsc.bcm.edu	37	6	167356557	167356557	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:167356557C>T	ENST00000508775.1	-	5	801	c.282G>A	c.(280-282)agG>agA	p.R94R	RP11-514O12.4_ENST00000507747.1_Missense_Mutation_p.G75E|RNASET2_ENST00000496851.2_5'UTR|RNASET2_ENST00000476238.2_Silent_p.R94R|RNASET2_ENST00000366855.6_Silent_p.R56R	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	94					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		GCCAGTATGCCCTCATTTCTG	0.413																																					p.R94R		Atlas-SNP	.											.	RNASET2	18	.	0			c.G282A						.						71.0	64.0	66.0					6																	167356557		2203	4300	6503	SO:0001819	synonymous_variant	8635	exon5			GTATGCCCTCATT	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.282G>A	chr6.hg19:g.167356557C>T		72.0	0.0		70.0	4.0	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Silent	SNP	ENST00000508775.1	hg19	CCDS5295.1	.	.	.	.	.	.	.	.	.	.	C	0.403	-0.917518	0.02396	.	.	ENSG00000249141	ENST00000507747	.	.	.	4.62	2.73	0.32206	.	.	.	.	.	T	0.31544	0.0800	.	.	.	0.53005	D	0.999961	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	-5.6199	3.7476	0.08554	0.1703:0.5676:0.1657:0.0964	.	.	.	.	E	75	.	.	G	-	2	0	RP11-514O12.4	167276547	0.053000	0.20554	0.532000	0.27989	0.056000	0.15407	0.540000	0.23191	1.009000	0.39289	0.655000	0.94253	GGG	.	.		0.413	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
ADAP1	11033	hgsc.bcm.edu	37	7	975141	975141	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:975141T>C	ENST00000265846.5	-	2	302	c.83A>G	c.(82-84)gAt>gGt	p.D28G	ADAP1_ENST00000539900.1_Splice_Site_p.D39G|ADAP1_ENST00000463358.1_5'UTR	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	28	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						CCAGTCGGGATCTGCAAGGGA	0.662																																					p.D28G		Atlas-SNP	.											.	ADAP1	23	.	0			c.A83G						.						39.0	38.0	39.0					7																	975141		2189	4272	6461	SO:0001630	splice_region_variant	11033	exon2			TCGGGATCTGCAA	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16486	protein-coding gene	gene with protein product		608114	"""centaurin, alpha 1"""	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.83-1A>G	chr7.hg19:g.975141T>C		143.0	0.0		93.0	4.0	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	hg19	CCDS5318.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.563398	0.27915	.	.	ENSG00000105963	ENST00000265846;ENST00000539900;ENST00000435943	T;T;T	0.42131	0.98;0.98;0.98	4.62	3.37	0.38596	.	0.119179	0.53938	U	0.000044	T	0.33933	0.0880	L	0.49513	1.565	0.80722	D	1	B	0.02656	0.0	B	0.12837	0.008	T	0.12192	-1.0557	10	0.19147	T	0.46	.	10.8326	0.46669	0.0:0.0:0.1584:0.8416	.	28	O75689	ADAP1_HUMAN	G	28;39;15	ENSP00000265846:D28G;ENSP00000442682:D39G;ENSP00000394973:D15G	ENSP00000265846:D28G	D	-	2	0	ADAP1	941667	1.000000	0.71417	0.971000	0.41717	0.351000	0.29236	2.828000	0.48120	1.716000	0.51395	0.454000	0.30748	GAT	.	.		0.662	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	Missense_Mutation
IQCE	23288	hgsc.bcm.edu	37	7	2644523	2644523	+	Silent	SNP	G	G	A	rs201471152		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:2644523G>A	ENST00000402050.2	+	19	1825	c.1641G>A	c.(1639-1641)gtG>gtA	p.V547V	IQCE_ENST00000325979.7_Silent_p.V482V|IQCE_ENST00000438376.2_Silent_p.V531V|IQCE_ENST00000404984.1_Silent_p.V496V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	547	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		AGGCGGCTGTGGTGCTTCAGG	0.642																																					p.V547V		Atlas-SNP	.											.	IQCE	66	.	0			c.G1641A						.						41.0	48.0	46.0					7																	2644523		2081	4219	6300	SO:0001819	synonymous_variant	23288	exon19			GGCTGTGGTGCTT	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1641G>A	chr7.hg19:g.2644523G>A		111.0	0.0		91.0	4.0	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	hg19	CCDS43542.1																																																																																			.	G|1.000;T|0.000		0.642	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
RADIL	55698	hgsc.bcm.edu	37	7	4917718	4917718	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:4917718T>C	ENST00000399583.3	-	2	240	c.53A>G	c.(52-54)aAg>aGg	p.K18R	RADIL_ENST00000536091.1_Missense_Mutation_p.K18R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	18					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GCTCTGCCGCTTCAGTTTGCT	0.587																																					p.K18R		Atlas-SNP	.											.	RADIL	110	.	0			c.A53G						.						22.0	26.0	24.0					7																	4917718		2085	4204	6289	SO:0001583	missense	55698	exon2			TGCCGCTTCAGTT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.53A>G	chr7.hg19:g.4917718T>C	ENSP00000382492:p.Lys18Arg	98.0	0.0		83.0	4.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487848	0.64074	.	.	ENSG00000157927	ENST00000399583;ENST00000536091;ENST00000457174	T;T	0.26660	3.11;1.72	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.28764	0.0713	L	0.43152	1.355	0.35318	D	0.784559	P	0.48503	0.911	P	0.49387	0.609	T	0.18429	-1.0337	10	0.10377	T	0.69	-53.8006	13.9572	0.64157	0.0:0.0:0.0:1.0	.	18	Q96JH8	RADIL_HUMAN	R	18	ENSP00000382492:K18R;ENSP00000442533:K18R	ENSP00000382492:K18R	K	-	2	0	RADIL	4884244	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.365000	0.59486	2.235000	0.73313	0.459000	0.35465	AAG	.	.		0.587	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
FAM220A	84792	hgsc.bcm.edu	37	7	6370275	6370275	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:6370275G>T	ENST00000313324.4	-	2	978	c.511C>A	c.(511-513)Cca>Aca	p.P171T	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	171						nucleus (GO:0005634)											GCACTTGGTGGGTCATCCTGA	0.577																																					p.P171T		Atlas-SNP	.											.	.	.	.	0			c.C511A						.						56.0	67.0	63.0					7																	6370275		2203	4300	6503	SO:0001583	missense	84792	exon2			TTGGTGGGTCATC	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.511C>A	chr7.hg19:g.6370275G>T	ENSP00000317289:p.Pro171Thr	139.0	0.0		118.0	5.0	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	hg19	CCDS34599.1	.	.	.	.	.	.	.	.	.	.	G	4.819	0.152269	0.09185	.	.	ENSG00000178397	ENST00000313324	T	0.08896	3.04	5.28	4.4	0.53042	.	0.732533	0.11678	U	0.540083	T	0.14356	0.0347	L	0.55481	1.735	0.09310	N	1	D	0.58268	0.982	P	0.52189	0.692	T	0.17961	-1.0352	10	0.42905	T	0.14	-1.7872	6.0625	0.19846	0.1679:0.1552:0.6769:0.0	.	171	Q7Z4H9	SIPAR_HUMAN	T	171	ENSP00000317289:P171T	ENSP00000317289:P171T	P	-	1	0	C7orf70	6336800	0.003000	0.15002	0.001000	0.08648	0.067000	0.16453	0.920000	0.28705	1.211000	0.43351	0.655000	0.94253	CCA	.	.		0.577	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
DAGLB	221955	hgsc.bcm.edu	37	7	6474496	6474496	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:6474496A>G	ENST00000297056.6	-	4	744	c.575T>C	c.(574-576)gTg>gCg	p.V192A	DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000428902.2_Missense_Mutation_p.V65A|DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000436575.1_Missense_Mutation_p.V151A	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	192					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GGTTTCCCACACGCTTGTAGC	0.502																																					p.V192A		Atlas-SNP	.											.	DAGLB	74	.	0			c.T575C						.						165.0	159.0	161.0					7																	6474496		2203	4300	6503	SO:0001583	missense	221955	exon4			TCCCACACGCTTG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.575T>C	chr7.hg19:g.6474496A>G	ENSP00000297056:p.Val192Ala	190.0	0.0		114.0	6.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	hg19	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361846	0.82353	.	.	ENSG00000164535	ENST00000297056;ENST00000436575;ENST00000471132;ENST00000428902	T;T	0.44083	0.94;0.93	5.37	5.37	0.77165	.	0.068629	0.64402	D	0.000019	T	0.49372	0.1553	M	0.78637	2.42	0.80722	D	1	D	0.53745	0.962	P	0.46389	0.515	T	0.51371	-0.8714	10	0.16420	T	0.52	.	15.3683	0.74541	1.0:0.0:0.0:0.0	.	192	Q8NCG7	DGLB_HUMAN	A	192;151;192;65	ENSP00000297056:V192A;ENSP00000404785:V151A	ENSP00000297056:V192A	V	-	2	0	DAGLB	6441021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.834000	0.92094	2.024000	0.59613	0.482000	0.46254	GTG	.	.		0.502	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
GRID2IP	392862	hgsc.bcm.edu	37	7	6561059	6561059	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:6561059C>T	ENST00000457091.2	-	6	1084		c.e6+1		GRID2IP_ENST00000452113.1_Splice_Site|GRID2IP_ENST00000435185.1_Splice_Site	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein						long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GGGGGTCTCACCACTGGCAAA	0.617																																					.		Atlas-SNP	.											.	GRID2IP	82	.	0			c.1084+1G>A						.						48.0	52.0	51.0					7																	6561059		692	1591	2283	SO:0001630	splice_region_variant	392862	exon7			GTCTCACCACTGG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.1084+1G>A	chr7.hg19:g.6561059C>T		144.0	0.0		97.0	5.0	NM_001145118		Splice_Site	SNP	ENST00000457091.2	hg19	CCDS47537.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343749	0.61073	.	.	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	.	.	.	4.96	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6134	0.39676	0.0:0.9019:0.0:0.0981	.	.	.	.	.	-1	.	.	.	-	.	.	GRID2IP	6527584	1.000000	0.71417	0.989000	0.46669	0.797000	0.45037	3.008000	0.49544	1.227000	0.43598	0.561000	0.74099	.	.	.		0.617	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	Intron
ITGB8	3696	hgsc.bcm.edu	37	7	20444277	20444277	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:20444277T>C	ENST00000222573.4	+	11	2398	c.1714T>C	c.(1714-1716)Tgc>Cgc	p.C572R	ITGB8_ENST00000537992.1_Missense_Mutation_p.C437R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	572	Cysteine-rich tandem repeats.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AGCAGGCAGATGCCAATGCTT	0.522																																					p.C572R		Atlas-SNP	.											.	ITGB8	159	.	0			c.T1714C						.						117.0	97.0	104.0					7																	20444277		2203	4300	6503	SO:0001583	missense	3696	exon11			GGCAGATGCCAAT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1714T>C	chr7.hg19:g.20444277T>C	ENSP00000222573:p.Cys572Arg	136.0	0.0		100.0	6.0	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543454	0.86022	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.99724	-3.57;-6.54	5.77	5.77	0.91146	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.95260	3.645	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96891	0.9653	10	0.87932	D	0	.	16.3818	0.83467	0.0:0.0:0.0:1.0	.	572	P26012	ITB8_HUMAN	R	437;572	ENSP00000441561:C437R;ENSP00000222573:C572R	ENSP00000222573:C572R	C	+	1	0	ITGB8	20410802	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	7.348000	0.79366	2.330000	0.79161	0.528000	0.53228	TGC	.	.		0.522	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
CBX3	11335	hgsc.bcm.edu	37	7	26248156	26248156	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:26248156C>A	ENST00000337620.4	+	4	739	c.311C>A	c.(310-312)tCa>tAa	p.S104*	CBX3_ENST00000396386.2_Nonsense_Mutation_p.S104*|CBX3_ENST00000409747.1_Missense_Mutation_p.Q80K|CBX3_ENST00000497498.1_3'UTR	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	104					chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GACAGCAAATCAAAGAAGAAA	0.328																																					p.S104X		Atlas-SNP	.											.	CBX3	25	.	0			c.C311A						.						36.0	39.0	38.0					7																	26248156		2200	4298	6498	SO:0001587	stop_gained	11335	exon4			GCAAATCAAAGAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.311C>A	chr7.hg19:g.26248156C>A	ENSP00000336687:p.Ser104*	139.0	0.0		116.0	5.0	NM_016587	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Nonsense_Mutation	SNP	ENST00000337620.4	hg19	CCDS5398.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.650357|7.650357	0.98412|0.98412	.|.	.|.	ENSG00000122565|ENSG00000122565	ENST00000409747|ENST00000337620;ENST00000396386	.|.	.|.	.|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.228637	.|0.43260	.|D	.|0.000594	T|.	0.27489|.	0.0675|.	.|.	.|.	.|.	0.26827|0.26827	N|N	0.968673|0.968673	B|.	0.12630|.	0.006|.	B|.	0.11329|.	0.006|.	T|.	0.13872|.	-1.0493|.	7|.	0.30078|0.02654	T|T	0.28|1	.|.	19.424|19.424	0.94734|0.94734	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	80|.	B8ZZ43|.	.|.	K|X	80|104	.|.	ENSP00000387348:Q80K|ENSP00000336687:S104X	Q|S	+|+	1|2	0|0	CBX3|CBX3	26214681|26214681	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.507000|2.507000	0.45442|0.45442	2.661000|2.661000	0.90470|0.90470	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.		0.328	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	
SKAP2	8935	hgsc.bcm.edu	37	7	26779530	26779530	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:26779530C>T	ENST00000345317.2	-	5	674	c.361G>A	c.(361-363)Ggc>Agc	p.G121S	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	121	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TCAAGGTAGCCAGCCTTTAGA	0.373																																					p.G121S		Atlas-SNP	.											.	SKAP2	40	.	0			c.G361A						.						75.0	71.0	72.0					7																	26779530		2203	4300	6503	SO:0001583	missense	8935	exon5			GGTAGCCAGCCTT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"""Pleckstrin homology (PH) domain containing"""	15687	protein-coding gene	gene with protein product		605215	"""src family associated phosphoprotein 2"""	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.361G>A	chr7.hg19:g.26779530C>T	ENSP00000005587:p.Gly121Ser	162.0	0.0		99.0	4.0	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	hg19	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844708	0.91197	.	.	ENSG00000005020	ENST00000345317;ENST00000535331;ENST00000432747	T;T	0.73897	-0.79;-0.79	5.81	4.93	0.64822	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.045894	0.85682	D	0.000000	D	0.87265	0.6134	H	0.96996	3.92	0.80722	D	1	P;D	0.54397	0.887;0.966	P;P	0.54270	0.457;0.747	D	0.90186	0.4246	10	0.72032	D	0.01	-4.3258	11.4594	0.50202	0.0:0.9166:0.0:0.0834	.	106;121	B7Z5N4;O75563	.;SKAP2_HUMAN	S	121;106;106	ENSP00000005587:G121S;ENSP00000408163:G106S	ENSP00000005587:G121S	G	-	1	0	SKAP2	26746055	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.209000	0.58493	2.746000	0.94184	0.591000	0.81541	GGC	.	.		0.373	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1		
CREB5	9586	hgsc.bcm.edu	37	7	28547292	28547292	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:28547292C>A	ENST00000357727.2	+	4	618	c.228C>A	c.(226-228)agC>agA	p.S76R	CREB5_ENST00000409603.1_Missense_Mutation_p.S43R|CREB5_ENST00000396299.2_Missense_Mutation_p.S43R|CREB5_ENST00000396300.2_Missense_Mutation_p.S69R	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	76					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S76S(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						GCCTCTTCAGCGAGCTGGACT	0.547																																					p.S76R		Atlas-SNP	.											CREB5,colon,carcinoma,0,2	CREB5	115	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C228A						.						106.0	112.0	110.0					7																	28547292		2203	4300	6503	SO:0001583	missense	9586	exon4			CTTCAGCGAGCTG	L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"""basic leucine zipper proteins"""	16844	protein-coding gene	gene with protein product	"""cAMP response element binding protein CRE-Bpa"""					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.228C>A	chr7.hg19:g.28547292C>A	ENSP00000350359:p.Ser76Arg	162.0	0.0		119.0	5.0	NM_182898	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	hg19	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.691046	0.30052	.	.	ENSG00000146592	ENST00000396299;ENST00000424599;ENST00000357727;ENST00000396300;ENST00000409603	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.6	-6.46	0.01908	.	0.415223	0.29676	N	0.011491	T	0.19886	0.0478	L	0.29908	0.895	0.80722	D	1	B	0.21520	0.057	B	0.17433	0.018	T	0.01130	-1.1442	10	0.72032	D	0.01	0.5969	16.2367	0.82380	0.0:0.6286:0.0:0.3714	.	76	Q02930	CREB5_HUMAN	R	43;69;76;69;43	ENSP00000379593:S43R;ENSP00000394088:S69R;ENSP00000350359:S76R;ENSP00000379594:S69R;ENSP00000387197:S43R	ENSP00000350359:S76R	S	+	3	2	CREB5	28513817	0.011000	0.17503	0.003000	0.11579	0.417000	0.31264	-0.458000	0.06737	-1.555000	0.01697	-0.793000	0.03317	AGC	.	.		0.547	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904	
VPS41	27072	hgsc.bcm.edu	37	7	38798051	38798051	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:38798051C>A	ENST00000310301.4	-	18	1507	c.1453G>T	c.(1453-1455)Gga>Tga	p.G485*	VPS41_ENST00000395969.2_Nonsense_Mutation_p.G460*	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	485					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TACAGATCTCCAGGCCATTCT	0.358																																					p.G485X		Atlas-SNP	.											.	VPS41	102	.	0			c.G1453T						.						133.0	129.0	130.0					7																	38798051		2203	4300	6503	SO:0001587	stop_gained	27072	exon18			GATCTCCAGGCCA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1453G>T	chr7.hg19:g.38798051C>A	ENSP00000309457:p.Gly485*	150.0	0.0		95.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Nonsense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	C	38	7.054453	0.98032	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-28.0693	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	485;460	.	ENSP00000309457:G485X	G	-	1	0	VPS41	38764576	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	GGA	.	.		0.358	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
INHBA	3624	hgsc.bcm.edu	37	7	41729530	41729530	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:41729530G>T	ENST00000242208.4	-	3	1245	c.999C>A	c.(997-999)atC>atA	p.I333I	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Silent_p.I333I	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	333					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.I333I(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CATTCCAGCCGATGTCCTTGA	0.557										TSP Lung(11;0.080)																											p.I333I		Atlas-SNP	.											INHBA,NS,carcinoma,0,1	INHBA	118	.	1	Substitution - coding silent(1)	lung(1)	c.C999A						.						123.0	123.0	123.0					7																	41729530		2203	4300	6503	SO:0001819	synonymous_variant	3624	exon3			CCAGCCGATGTCC		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.999C>A	chr7.hg19:g.41729530G>T		50.0	1.0		32.0	2.0	NM_002192	Q14599	Silent	SNP	ENST00000242208.4	hg19	CCDS5464.1																																																																																			.	.		0.557	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
NACAD	23148	hgsc.bcm.edu	37	7	45125286	45125286	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:45125286A>G	ENST00000490531.2	-	2	512	c.493T>C	c.(493-495)Tcc>Ccc	p.S165P		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	165					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						GGGGGAGGGGAAGGCACAGAA	0.667																																					p.S165P		Atlas-SNP	.											.	NACAD	44	.	0			c.T493C						.						3.0	4.0	4.0					7																	45125286		635	1514	2149	SO:0001583	missense	23148	exon2			GAGGGGAAGGCAC	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.493T>C	chr7.hg19:g.45125286A>G	ENSP00000420477:p.Ser165Pro	78.0	0.0		80.0	4.0	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	hg19	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	A	4.395	0.072954	0.08436	.	.	ENSG00000136274	ENST00000490531	T	0.13538	2.58	4.4	3.21	0.36854	.	3.352960	0.00913	N	0.002481	T	0.11623	0.0283	N	0.19112	0.55	0.24255	N	0.995303	B	0.15141	0.012	B	0.16722	0.016	T	0.27536	-1.0071	10	0.30854	T	0.27	-2.1458	7.8093	0.29221	0.7876:0.2124:0.0:0.0	.	165	O15069	NACAD_HUMAN	P	165	ENSP00000420477:S165P	ENSP00000420477:S165P	S	-	1	0	NACAD	45091811	.	.	0.690000	0.30148	0.099000	0.18886	.	.	0.693000	0.31634	0.379000	0.24179	TCC	.	.		0.667	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
PKD1L1	168507	hgsc.bcm.edu	37	7	47870945	47870945	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47870945T>C	ENST00000289672.2	-	42	6393	c.6343A>G	c.(6343-6345)Agc>Ggc	p.S2115G		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2115					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AAACCACTGCTGGGTGCTGCG	0.577																																					p.S2115G		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A6343G						.						76.0	72.0	73.0					7																	47870945		2203	4300	6503	SO:0001583	missense	168507	exon42			CACTGCTGGGTGC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6343A>G	chr7.hg19:g.47870945T>C	ENSP00000289672:p.Ser2115Gly	129.0	0.0		92.0	4.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	7.042	0.562675	0.13498	.	.	ENSG00000158683	ENST00000289672	T	0.19532	2.14	4.96	-9.93	0.00452	.	3.234350	0.00899	N	0.002326	T	0.06645	0.0170	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.21314	-1.0249	10	0.20046	T	0.44	0.9118	2.2761	0.04103	0.1146:0.358:0.2339:0.2935	.	2115	Q8TDX9	PK1L1_HUMAN	G	2115	ENSP00000289672:S2115G	ENSP00000289672:S2115G	S	-	1	0	PKD1L1	47837470	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.638000	0.02013	-1.574000	0.01657	0.379000	0.24179	AGC	.	.		0.577	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
PKD1L1	168507	hgsc.bcm.edu	37	7	47874578	47874578	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47874578G>T	ENST00000289672.2	-	39	6164	c.6114C>A	c.(6112-6114)acC>acA	p.T2038T		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2038					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGGGTGCCTCGGTCTGTGCTC	0.527																																					p.T2038T		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C6114A						.						80.0	86.0	84.0					7																	47874578		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon39			TGCCTCGGTCTGT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6114C>A	chr7.hg19:g.47874578G>T		109.0	0.0		84.0	4.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.527	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
PKD1L1	168507	hgsc.bcm.edu	37	7	47898327	47898327	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47898327T>C	ENST00000289672.2	-	27	4356	c.4306A>G	c.(4306-4308)Aag>Gag	p.K1436E		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1436	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACTTCCTCCTTCGAGTTTTCT	0.428																																					p.K1436E		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A4306G						.						176.0	174.0	175.0					7																	47898327		2203	4300	6503	SO:0001583	missense	168507	exon27			CCTCCTTCGAGTT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.4306A>G	chr7.hg19:g.47898327T>C	ENSP00000289672:p.Lys1436Glu	80.0	0.0		77.0	4.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489285	0.26686	.	.	ENSG00000158683	ENST00000289672	T	0.19250	2.16	5.03	-0.218	0.13142	Egg jelly receptor, REJ-like (1);	1.115740	0.06704	N	0.771982	T	0.11495	0.0280	L	0.34521	1.04	0.09310	N	1	B	0.28082	0.2	B	0.23716	0.048	T	0.26883	-1.0090	10	0.05436	T	0.98	-8.1515	4.2509	0.10695	0.0:0.1874:0.3461:0.4665	.	1436	Q8TDX9	PK1L1_HUMAN	E	1436	ENSP00000289672:K1436E	ENSP00000289672:K1436E	K	-	1	0	PKD1L1	47864852	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.309000	0.19332	0.020000	0.15106	-0.321000	0.08615	AAG	.	.		0.428	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
PKD1L1	168507	hgsc.bcm.edu	37	7	47947753	47947753	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47947753G>T	ENST00000289672.2	-	9	1373	c.1323C>A	c.(1321-1323)gcC>gcA	p.A441A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	441					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACGCAGACACGGCCTCATGGC	0.458																																					p.A441A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C1323A						.						118.0	102.0	107.0					7																	47947753		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon9			AGACACGGCCTCA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1323C>A	chr7.hg19:g.47947753G>T		75.0	0.0		75.0	4.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.458	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
ZNF107	51427	hgsc.bcm.edu	37	7	64166707	64166707	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:64166707T>C	ENST00000395391.1	+	4	1400	c.25T>C	c.(25-27)Tct>Cct	p.S9P	ZNF107_ENST00000423627.1_Missense_Mutation_p.S9P|ZNF107_ENST00000344930.3_Missense_Mutation_p.S9P			Q9UII5	ZN107_HUMAN	zinc finger protein 107	9					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(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TTCAGTAATGTCTTTTCATTT	0.299																																					p.S9P		Atlas-SNP	.											.	ZNF107	107	.	0			c.T25C						.						39.0	40.0	40.0					7																	64166707		2194	4295	6489	SO:0001583	missense	51427	exon7			GTAATGTCTTTTC	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.25T>C	chr7.hg19:g.64166707T>C	ENSP00000378789:p.Ser9Pro	78.0	0.0		63.0	4.0	NM_016220		Missense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	9.217	1.032386	0.19590	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T;T	0.08370	4.81;3.1;3.1;3.1	0.596	0.596	0.17496	.	.	.	.	.	T	0.07007	0.0178	L	0.38175	1.15	0.23628	N	0.997252	B	0.02656	0.0	B	0.01281	0.0	T	0.32877	-0.9890	8	0.59425	D	0.04	.	.	.	.	.	9	Q9UII5	ZN107_HUMAN	P	9	ENSP00000353234:S9P;ENSP00000343443:S9P;ENSP00000400037:S9P;ENSP00000378789:S9P	ENSP00000343443:S9P	S	+	1	0	ZNF107	63804142	0.000000	0.05858	0.057000	0.19452	0.129000	0.20672	-0.013000	0.12678	0.478000	0.27488	0.254000	0.18369	TCT	.	.		0.299	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
GUSB	2990	hgsc.bcm.edu	37	7	65435344	65435344	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:65435344G>T	ENST00000304895.4	-	9	1531	c.1401C>A	c.(1399-1401)atC>atA	p.I467I	GUSB_ENST00000421103.1_Silent_p.I321I|GUSB_ENST00000345660.6_Silent_p.I416I	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	467					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TGGTGTGAGCGATCACCATCC	0.577																																					p.I467I		Atlas-SNP	.											.	GUSB	52	.	0			c.C1401A						.						85.0	82.0	83.0					7																	65435344		2203	4300	6503	SO:0001819	synonymous_variant	2990	exon9			GTGAGCGATCACC	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1401C>A	chr7.hg19:g.65435344G>T		82.0	0.0		89.0	5.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.577	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
WBSCR17	64409	hgsc.bcm.edu	37	7	70880904	70880904	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:70880904G>A	ENST00000333538.5	+	4	1253	c.619G>A	c.(619-621)Gtc>Atc	p.V207I	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	207	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AGAGGAGTATGTCCACAAACG	0.507																																					p.V207I		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G619A						.						72.0	67.0	69.0					7																	70880904		2203	4300	6503	SO:0001583	missense	64409	exon4			GAGTATGTCCACA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.619G>A	chr7.hg19:g.70880904G>A	ENSP00000329654:p.Val207Ile	154.0	0.0		86.0	21.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908797	0.72868	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.61040	0.31;0.14	5.17	4.23	0.50019	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.65260	0.2674	L	0.43646	1.37	0.58432	D	0.999996	D	0.76494	0.999	D	0.73708	0.981	T	0.58951	-0.7545	10	0.20519	T	0.43	.	13.5761	0.61875	0.0:0.0:0.8442:0.1558	.	207	Q6IS24	GLTL3_HUMAN	I	207;185	ENSP00000329654:V207I;ENSP00000392019:V185I	ENSP00000329654:V207I	V	+	1	0	WBSCR17	70518840	1.000000	0.71417	0.994000	0.49952	0.944000	0.59088	7.462000	0.80851	2.421000	0.82119	0.563000	0.77884	GTC	.	.		0.507	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
FGL2	10875	hgsc.bcm.edu	37	7	76828978	76828978	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:76828978T>C	ENST00000248598.5	-	1	165	c.133A>G	c.(133-135)Agc>Ggc	p.S45G	CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	45						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TTCCCTCTGCTTTCTAGTCTC	0.498																																					p.S45G		Atlas-SNP	.											.	FGL2	40	.	0			c.A133G						.						120.0	116.0	118.0					7																	76828978		2203	4300	6503	SO:0001583	missense	10875	exon1			CTCTGCTTTCTAG	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"""Fibrinogen C domain containing"""	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.133A>G	chr7.hg19:g.76828978T>C	ENSP00000248598:p.Ser45Gly	112.0	0.0		89.0	4.0	NM_006682		Missense_Mutation	SNP	ENST00000248598.5	hg19	CCDS5591.1	.	.	.	.	.	.	.	.	.	.	T	2.182	-0.387245	0.04932	.	.	ENSG00000127951	ENST00000248598	T	0.58210	0.35	5.38	0.0476	0.14281	.	0.335611	0.39274	N	0.001418	T	0.25121	0.0610	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	10	0.21014	T	0.42	.	5.6955	0.17853	0.0:0.2206:0.1313:0.6481	.	45	Q14314	FGL2_HUMAN	G	45	ENSP00000248598:S45G	ENSP00000248598:S45G	S	-	1	0	FGL2	76666914	0.206000	0.23470	0.051000	0.19133	0.454000	0.32378	-0.074000	0.11450	0.114000	0.18032	-1.054000	0.02325	AGC	.	.		0.498	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682	
AKAP9	10142	hgsc.bcm.edu	37	7	91652178	91652178	+	Missense_Mutation	SNP	A	A	C	rs111673064|rs10644111|rs397825978	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:91652178A>C	ENST00000359028.2	+	15	4264	c.4039A>C	c.(4039-4041)Aaa>Caa	p.K1347Q	AKAP9_ENST00000356239.3_Missense_Mutation_p.K1335Q|AKAP9_ENST00000358100.2_Missense_Mutation_p.K1347Q			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1347			K -> KQ. {ECO:0000269|PubMed:10202149}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K1335_L1336insQ(1)|p.K1347_L1348insQ(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAAAAAACTAAACTTGAAGA	0.313			T	BRAF	papillary thyroid																																p.K1335Q		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.,2	AKAP9	788	.	2	Insertion - In frame(2)	ovary(2)	c.A4003C						.						45.0	46.0	46.0					7																	91652178		2203	4300	6503	SO:0001583	missense	10142	exon14			AAAACTAAACTTG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4039A>C	chr7.hg19:g.91652178A>C	ENSP00000351922:p.Lys1347Gln	50.0	2.0		116.0	7.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.162	-1.080695	0.01888	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.02974	4.09;4.09;4.1	4.68	2.19	0.27852	.	0.840174	0.09958	N	0.733777	T	0.01254	0.0041	N	0.00210	-1.845	0.09310	N	1	P;B;B;B	0.51791	0.948;0.004;0.02;0.115	P;B;B;B	0.49528	0.614;0.007;0.037;0.083	T	0.50625	-0.8806	10	0.23302	T	0.38	.	8.1855	0.31337	0.7884:0.134:0.0775:0.0	.	1347;1335;1335;1347	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	Q	1335;1347;1347;1347;1347	ENSP00000348573:K1335Q;ENSP00000351922:K1347Q;ENSP00000350813:K1347Q	ENSP00000348573:K1335Q	K	+	1	0	AKAP9	91490114	0.545000	0.26449	0.005000	0.12908	0.028000	0.11728	2.404000	0.44539	0.033000	0.15463	-1.431000	0.01090	AAA	.	.		0.313	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CDK6	1021	hgsc.bcm.edu	37	7	92300836	92300836	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:92300836C>T	ENST00000265734.4	-	5	962	c.551G>A	c.(550-552)tGg>tAg	p.W184*	CDK6_ENST00000424848.2_Nonsense_Mutation_p.W184*	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TGCTCTGTACCACAGCGTGAC	0.502			T	MLLT10	ALL																																p.W184X		Atlas-SNP	.		Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	.	CDK6	30	.	0			c.G551A						.						103.0	89.0	94.0					7																	92300836		2203	4300	6503	SO:0001587	stop_gained	1021	exon5			CTGTACCACAGCG		CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"""Cyclin-dependent kinases"""	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.551G>A	chr7.hg19:g.92300836C>T	ENSP00000265734:p.Trp184*	92.0	0.0		137.0	6.0	NM_001259	A4D1G0	Nonsense_Mutation	SNP	ENST00000265734.4	hg19	CCDS5628.1	.	.	.	.	.	.	.	.	.	.	C	39	7.555246	0.98355	.	.	ENSG00000105810	ENST00000265734;ENST00000424848	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1808	19.1725	0.93585	0.0:1.0:0.0:0.0	.	.	.	.	X	184	.	ENSP00000265734:W184X	W	-	2	0	CDK6	92138772	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.746000	0.85057	2.620000	0.88729	0.305000	0.20034	TGG	.	.		0.502	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2		
ARPC1B	10095	hgsc.bcm.edu	37	7	98988562	98988562	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:98988562A>G	ENST00000451682.1	+	8	856	c.547A>G	c.(547-549)Acc>Gcc	p.T183A	ARPC1B_ENST00000252725.5_Missense_Mutation_p.T183A|PDAP1_ENST00000496335.1_5'Flank			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	183					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GCCGGCACCCACCCCGTGGGG	0.592																																					p.T183A		Atlas-SNP	.											.	ARPC1B	41	.	0			c.A547G						.						48.0	48.0	48.0					7																	98988562		2203	4300	6503	SO:0001583	missense	10095	exon6			GCACCCACCCCGT	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	704	protein-coding gene	gene with protein product	"""ARP2/3 protein complex subunit p41"", ""actin related protein 2/3 complex, subunit 1A (41 kD)"""	604223	"""actin related protein 2/3 complex, subunit 1B (41 kD)"""			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.547A>G	chr7.hg19:g.98988562A>G	ENSP00000389631:p.Thr183Ala	36.0	0.0		70.0	4.0	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	hg19	CCDS5661.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902590	0.92035	.	.	ENSG00000130429	ENST00000252725;ENST00000451682	T;T	0.65364	-0.15;-0.15	5.69	5.69	0.88448	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.69824	0.3154	M	0.81497	2.545	0.80722	D	1	P;P	0.45715	0.865;0.865	P;P	0.45829	0.494;0.494	T	0.73104	-0.4088	10	0.44086	T	0.13	-49.599	15.6192	0.76793	1.0:0.0:0.0:0.0	.	183;183	A4D275;O15143	.;ARC1B_HUMAN	A	183	ENSP00000252725:T183A;ENSP00000389631:T183A	ENSP00000252725:T183A	T	+	1	0	ARPC1B	98826498	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.373000	0.79623	2.176000	0.68965	0.459000	0.35465	ACC	.	.		0.592	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
ZNF655	79027	hgsc.bcm.edu	37	7	99169920	99169920	+	Silent	SNP	G	G	T	rs531904406		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99169920G>T	ENST00000394163.2	+	3	372	c.189G>T	c.(187-189)tcG>tcT	p.S63S	ZNF655_ENST00000425063.1_3'UTR|ZNF655_ENST00000252713.4_Silent_p.S63S|ZNF655_ENST00000419215.2_3'UTR|GS1-259H13.10_ENST00000455905.1_Intron|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Silent_p.S98S|ZNF655_ENST00000493277.1_Silent_p.S98S	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	63					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					AGAAAATTTCGGAAGAAGTGC	0.378																																					p.S98S		Atlas-SNP	.											.	ZNF655	75	.	0			c.G294T						.						82.0	85.0	84.0					7																	99169920		2203	4300	6503	SO:0001819	synonymous_variant	79027	exon4			AATTTCGGAAGAA	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.189G>T	chr7.hg19:g.99169920G>T		64.0	0.0		123.0	5.0	NM_001085368	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	hg19	CCDS5669.1																																																																																			.	.		0.378	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494	
TAF6	6878	hgsc.bcm.edu	37	7	99709449	99709449	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99709449G>T	ENST00000344095.4	-	9	1327	c.802C>A	c.(802-804)Cgt>Agt	p.R268S	TAF6_ENST00000472509.1_Missense_Mutation_p.R325S|TAF6_ENST00000453269.2_Missense_Mutation_p.R268S|TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_Missense_Mutation_p.R268S|TAF6_ENST00000437822.2_Missense_Mutation_p.R305S|TAF6_ENST00000418432.2_Missense_Mutation_p.R192S	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	268					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R268C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACGTTCACACGGACCTGTGGG	0.567																																					p.R305S		Atlas-SNP	.											TAF6,NS,carcinoma,0,1	TAF6	55	.	1	Substitution - Missense(1)	breast(1)	c.C913A						.						116.0	107.0	110.0					7																	99709449		2203	4300	6503	SO:0001583	missense	6878	exon9			TCACACGGACCTG		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"""TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD"", ""transcription initiation factor TFIID 70 kD subunit"""	602955	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"""	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.802C>A	chr7.hg19:g.99709449G>T	ENSP00000344537:p.Arg268Ser	154.0	0.0		125.0	5.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588749	0.86851	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.71384	0.3333	L	0.47190	1.495	0.80722	D	1	D;D;D;P;D	0.67145	0.994;0.996;0.994;0.897;0.994	P;D;P;P;P	0.65874	0.871;0.939;0.871;0.462;0.871	T	0.64198	-0.6464	10	0.18276	T	0.48	-11.6477	17.4922	0.87707	0.0:0.0:1.0:0.0	.	305;268;258;268;192	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	S	268;325;268;268;192;305	ENSP00000389575:R268S;ENSP00000419760:R325S;ENSP00000416396:R268S;ENSP00000344537:R268S;ENSP00000407980:R192S;ENSP00000399982:R305S	ENSP00000344537:R268S	R	-	1	0	TAF6	99547385	1.000000	0.71417	1.000000	0.80357	0.493000	0.33554	7.345000	0.79337	2.724000	0.93272	0.561000	0.74099	CGT	.	.		0.567	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641	
C7orf43	55262	hgsc.bcm.edu	37	7	99754538	99754538	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99754538T>C	ENST00000316937.3	-	6	1108	c.923A>G	c.(922-924)aAt>aGt	p.N308S	C7orf43_ENST00000419841.1_Missense_Mutation_p.N76S|C7orf43_ENST00000394035.2_5'Flank|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000457641.1_Missense_Mutation_p.N39S|C7orf43_ENST00000498638.1_5'UTR	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	308										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCCAGGGCATTCAGCGGGCA	0.602																																					p.N308S		Atlas-SNP	.											.	C7orf43	28	.	0			c.A923G						.						58.0	69.0	65.0					7																	99754538		2203	4300	6503	SO:0001583	missense	55262	exon6			AGGGCATTCAGCG		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.923A>G	chr7.hg19:g.99754538T>C	ENSP00000324741:p.Asn308Ser	53.0	0.0		58.0	4.0	NM_018275	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Missense_Mutation	SNP	ENST00000316937.3	hg19	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	T	2.682	-0.275060	0.05679	.	.	ENSG00000146826	ENST00000457641;ENST00000316937;ENST00000419841	T;T;T	0.27104	1.69;1.69;1.69	5.58	2.78	0.32641	.	0.106937	0.64402	N	0.000011	T	0.07593	0.0191	N	0.02539	-0.55	0.25997	N	0.982169	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36939	-0.9727	10	0.07030	T	0.85	-0.7826	6.4336	0.21811	0.0:0.6983:0.0:0.3017	.	76;308	E9PFF9;Q8WVR3	.;CG043_HUMAN	S	39;308;76	ENSP00000396432:N39S;ENSP00000324741:N308S;ENSP00000406326:N76S	ENSP00000324741:N308S	N	-	2	0	C7orf43	99592474	0.987000	0.35691	0.993000	0.49108	0.850000	0.48378	1.049000	0.30392	0.714000	0.32081	-0.464000	0.05259	AAT	.	.		0.602	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275	
AGFG2	3268	hgsc.bcm.edu	37	7	100161852	100161852	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100161852G>T	ENST00000300176.4	+	11	1434	c.1312G>T	c.(1312-1314)Ggg>Tgg	p.G438W	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_Intron	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	438					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCTTCCTTCGGGGACTTAGG	0.627											OREG0018204	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G438W		Atlas-SNP	.											.	AGFG2	44	.	0			c.G1312T						.						41.0	35.0	37.0					7																	100161852		2203	4300	6503	SO:0001583	missense	3268	exon11			TCCTTCGGGGACT	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1312G>T	chr7.hg19:g.100161852G>T	ENSP00000300176:p.Gly438Trp	117.0	0.0	1349	93.0	4.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.416311	0.62511	.	.	ENSG00000106351	ENST00000300176	T	0.23552	1.9	4.59	3.62	0.41486	.	0.455087	0.21940	N	0.066882	T	0.34106	0.0886	L	0.36672	1.1	0.80722	D	1	D	0.71674	0.998	D	0.64410	0.925	T	0.08229	-1.0732	10	0.87932	D	0	-0.6479	7.1738	0.25732	0.1344:0.0:0.8656:0.0	.	438	O95081	AGFG2_HUMAN	W	438	ENSP00000300176:G438W	ENSP00000300176:G438W	G	+	1	0	AGFG2	99999788	0.079000	0.21365	0.974000	0.42286	0.912000	0.54170	1.019000	0.30014	0.995000	0.38917	0.555000	0.69702	GGG	.	.		0.627	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
LRCH4	4034	hgsc.bcm.edu	37	7	100175328	100175328	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100175328T>C	ENST00000310300.6	-	9	1127	c.1075A>G	c.(1075-1077)Agc>Ggc	p.S359G	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	359					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGACATGGCTGTCGATGAAG	0.667																																					p.S359G		Atlas-SNP	.											.	LRCH4	53	.	0			c.A1075G						.						117.0	102.0	107.0					7																	100175328		2203	4300	6503	SO:0001583	missense	4034	exon9			CATGGCTGTCGAT	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1075A>G	chr7.hg19:g.100175328T>C	ENSP00000309689:p.Ser359Gly	67.0	0.0		72.0	4.0	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	hg19	CCDS34706.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429146	0.62844	.	.	ENSG00000077454	ENST00000310300	T	0.36340	1.26	5.52	3.0	0.34707	.	0.141094	0.64402	N	0.000006	T	0.48187	0.1486	M	0.76170	2.325	0.80722	D	1	D	0.60160	0.987	P	0.57101	0.813	T	0.46261	-0.9204	10	0.54805	T	0.06	-4.1156	6.4083	0.21676	0.0:0.0849:0.1586:0.7565	.	359	O75427	LRCH4_HUMAN	G	359	ENSP00000309689:S359G	ENSP00000309689:S359G	S	-	1	0	LRCH4	100013264	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	3.290000	0.51755	0.931000	0.37242	0.439000	0.28862	AGC	.	.		0.667	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
SLC12A9	56996	hgsc.bcm.edu	37	7	100454532	100454532	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100454532A>G	ENST00000354161.3	+	5	616	c.491A>G	c.(490-492)tAc>tGc	p.Y164C	SLC12A9_ENST00000275729.3_Missense_Mutation_p.Y75C|SLC12A9_ENST00000428758.1_Missense_Mutation_p.Y164C|SLC12A9_ENST00000415287.1_Missense_Mutation_p.Y75C|SLC12A9_ENST00000540482.1_Missense_Mutation_p.Y164C	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	164					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCCAGGGCTACGGCTGGAAC	0.662																																					p.Y164C		Atlas-SNP	.											.	SLC12A9	81	.	0			c.A491G						.						52.0	54.0	54.0					7																	100454532		2203	4300	6503	SO:0001583	missense	56996	exon5			AGGGCTACGGCTG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.491A>G	chr7.hg19:g.100454532A>G	ENSP00000275730:p.Tyr164Cys	83.0	0.0		84.0	4.0	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.671349	0.67814	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161	D;D;D;D;D	0.98835	-2.65;-2.65;-5.17;-5.17;-2.94	4.62	4.62	0.57501	Amino acid permease domain (1);	0.000000	0.64402	D	0.000001	D	0.99007	0.9661	M	0.85197	2.74	0.58432	D	0.999994	D;P	0.89917	1.0;0.83	D;P	0.87578	0.998;0.676	D	0.99346	1.0913	10	0.46703	T	0.11	.	11.9565	0.52984	1.0:0.0:0.0:0.0	.	75;164	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	C	164;164;75;75;164	ENSP00000443702:Y164C;ENSP00000408301:Y164C;ENSP00000275729:Y75C;ENSP00000413796:Y75C;ENSP00000275730:Y164C	ENSP00000275729:Y75C	Y	+	2	0	SLC12A9	100292468	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	8.795000	0.91872	1.711000	0.51337	0.379000	0.24179	TAC	.	.		0.662	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
MUC17	140453	hgsc.bcm.edu	37	7	100675798	100675798	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100675798T>C	ENST00000306151.4	+	3	1165	c.1101T>C	c.(1099-1101)acT>acC	p.T367T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	367	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TTGTGACCACTTCTACTGAAC	0.468																																					p.T367T		Atlas-SNP	.											.	MUC17	804	.	0			c.T1101C						.						189.0	196.0	194.0					7																	100675798		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GACCACTTCTACT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.1101T>C	chr7.hg19:g.100675798T>C		70.0	0.0		83.0	4.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CUX1	1523	hgsc.bcm.edu	37	7	101840082	101840082	+	Missense_Mutation	SNP	C	C	A	rs569218052		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:101840082C>A	ENST00000292535.7	+	15	1429	c.1391C>A	c.(1390-1392)tCc>tAc	p.S464Y	SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.S464Y|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.S475Y|CUX1_ENST00000550008.2_Missense_Mutation_p.S464Y|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	464					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TTCAGCTCATCCCTGGCAAGC	0.532													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16575	0.0		0.0	False		,,,				2504	0.0				p.S475Y		Atlas-SNP	.											.	CUX1	253	.	0			c.C1424A						.						70.0	73.0	72.0					7																	101840082		2203	4300	6503	SO:0001583	missense	1523	exon15			GCTCATCCCTGGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1391C>A	chr7.hg19:g.101840082C>A	ENSP00000292535:p.Ser464Tyr	162.0	0.0		146.0	6.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476486	0.44044	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.60797	0.18;0.17;0.16;0.17	5.71	4.8	0.61643	.	0.294006	0.28635	N	0.014644	T	0.52500	0.1738	N	0.22421	0.69	0.80722	D	1	P;P	0.42649	0.681;0.786	B;P	0.47251	0.254;0.542	T	0.53012	-0.8498	10	0.40728	T	0.16	-6.8901	15.6421	0.77012	0.1423:0.8577:0.0:0.0	.	464;475	P39880;P39880-3	CUX1_HUMAN;.	Y	475;464;464;464	ENSP00000353401:S475Y;ENSP00000292535:S464Y;ENSP00000446630:S464Y;ENSP00000447373:S464Y	ENSP00000292535:S464Y	S	+	2	0	CUX1	101626802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.111000	0.50360	1.350000	0.45770	0.561000	0.74099	TCC	.	.		0.532	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
LAMB4	22798	hgsc.bcm.edu	37	7	107706357	107706357	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:107706357C>A	ENST00000388781.3	-	21	2769	c.2686G>T	c.(2686-2688)Gat>Tat	p.D896Y	LAMB4_ENST00000388780.3_Missense_Mutation_p.D896Y|LAMB4_ENST00000205386.4_Missense_Mutation_p.D896Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	896	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TAGTAACCATCAATACACCTG	0.428																																					p.D896Y		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2686T						.						114.0	113.0	113.0					7																	107706357		2203	4300	6503	SO:0001583	missense	22798	exon21			AACCATCAATACA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2686G>T	chr7.hg19:g.107706357C>A	ENSP00000373433:p.Asp896Tyr	65.0	0.0		81.0	5.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.904909	0.52333	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	T;T;T	0.64991	-0.13;-0.13;-0.13	4.69	1.83	0.25207	EGF-like, laminin (4);	0.116598	0.38005	N	0.001844	T	0.75064	0.3799	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.72557	-0.4257	10	0.66056	D	0.02	.	6.1473	0.20293	0.0:0.6432:0.1348:0.222	.	896	A4D0S4	LAMB4_HUMAN	Y	896	ENSP00000205386:D896Y;ENSP00000373433:D896Y;ENSP00000373432:D896Y	ENSP00000205386:D896Y	D	-	1	0	LAMB4	107493593	0.864000	0.29904	0.925000	0.36789	0.932000	0.56968	1.861000	0.39438	0.277000	0.22141	0.563000	0.77884	GAT	.	.		0.428	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
LAMB4	22798	hgsc.bcm.edu	37	7	107720067	107720067	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:107720067A>G	ENST00000388781.3	-	15	1949	c.1866T>C	c.(1864-1866)atT>atC	p.I622I	LAMB4_ENST00000414450.2_Silent_p.I622I|LAMB4_ENST00000388780.3_Silent_p.I622I|LAMB4_ENST00000418464.1_Silent_p.I622I|LAMB4_ENST00000205386.4_Silent_p.I622I	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	622	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AGTGAATGGCAATGGTGAAGT	0.463																																					p.I622I		Atlas-SNP	.											.	LAMB4	253	.	0			c.T1866C						.						93.0	86.0	89.0					7																	107720067		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon15			AATGGCAATGGTG	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1866T>C	chr7.hg19:g.107720067A>G		74.0	0.0		49.0	4.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.		0.463	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
IMPDH1	3614	hgsc.bcm.edu	37	7	128034563	128034563	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:128034563T>C	ENST00000480861.1	-	12	1448	c.1371A>G	c.(1369-1371)gcA>gcG	p.A457A	IMPDH1_ENST00000419067.2_Silent_p.A514A|IMPDH1_ENST00000496200.1_Silent_p.A437A|IMPDH1_ENST00000338791.6_Silent_p.A547A|IMPDH1_ENST00000348127.6_Silent_p.A511A|IMPDH1_ENST00000470772.1_Silent_p.A461A|IMPDH1_ENST00000354269.5_Silent_p.A537A|IMPDH1_ENST00000343214.4_Silent_p.A437A|IMPDH1_ENST00000378717.4_Silent_p.A478A	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						GTTGGATGCCTGCTATGAGGT	0.597																																					p.A547A		Atlas-SNP	.											.	IMPDH1	38	.	0			c.A1641G						.						84.0	81.0	82.0					7																	128034563		2203	4300	6503	SO:0001819	synonymous_variant	3614	exon15			GATGCCTGCTATG		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1371A>G	chr7.hg19:g.128034563T>C		96.0	0.0		91.0	4.0	NM_000883		Silent	SNP	ENST00000480861.1	hg19	CCDS55161.1																																																																																			.	.		0.597	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883	
FLNC	2318	hgsc.bcm.edu	37	7	128494726	128494726	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:128494726C>A	ENST00000325888.8	+	41	7248	c.6987C>A	c.(6985-6987)gcC>gcA	p.A2329A	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.A2296A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2329					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GAGGTGTGGCCGGCGTGCCAG	0.672																																					p.A2329A		Atlas-SNP	.											.	FLNC	339	.	0			c.C6987A						.						16.0	20.0	19.0					7																	128494726		2172	4257	6429	SO:0001819	synonymous_variant	2318	exon41			TGTGGCCGGCGTG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6987C>A	chr7.hg19:g.128494726C>A		113.0	0.0		95.0	4.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.672	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
KIAA1549	57670	hgsc.bcm.edu	37	7	138554406	138554406	+	Silent	SNP	G	G	A	rs575482000		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:138554406G>A	ENST00000422774.1	-	14	4701	c.4653C>T	c.(4651-4653)gaC>gaT	p.D1551D	KIAA1549_ENST00000242365.4_Silent_p.D1501D|KIAA1549_ENST00000440172.1_Silent_p.D1551D			Q9HCM3	K1549_HUMAN	KIAA1549	1551						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						AGGACAGGTCGTCTACCACCG	0.652			O	BRAF	pilocytic astrocytoma								g|||	1	0.000199681	0.0	0.0	5008	,	,		15717	0.0		0.0	False		,,,				2504	0.001				p.D1551D	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,NS,carcinoma,0,2	KIAA1549	314	.	0			c.C4653T						.						39.0	48.0	45.0					7																	138554406		2066	4198	6264	SO:0001819	synonymous_variant	57670	exon14			CAGGTCGTCTACC		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4653C>T	chr7.hg19:g.138554406G>A		161.0	0.0		194.0	31.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.652	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
TRPV6	55503	hgsc.bcm.edu	37	7	142574527	142574527	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:142574527T>C	ENST00000359396.3	-	5	796	c.551A>G	c.(550-552)gAg>gGg	p.E184G	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	184					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					AGCTCCATGCTCAATGAGCAG	0.597																																					p.E184G		Atlas-SNP	.											.	TRPV6	108	.	0			c.A551G						.						101.0	89.0	93.0					7																	142574527		2203	4300	6503	SO:0001583	missense	55503	exon5			CCATGCTCAATGA	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.551A>G	chr7.hg19:g.142574527T>C	ENSP00000352358:p.Glu184Gly	148.0	0.0		119.0	5.0	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	hg19	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669128	0.47677	.	.	ENSG00000165125	ENST00000359396	T	0.68765	-0.35	4.67	3.52	0.40303	Ankyrin repeat-containing domain (4);	0.340540	0.33834	N	0.004503	T	0.64907	0.2641	M	0.69823	2.125	0.41978	D	0.990788	B	0.21381	0.055	B	0.28709	0.093	T	0.62895	-0.6757	10	0.59425	D	0.04	-12.3191	9.3236	0.37980	0.0:0.0857:0.0:0.9143	.	184	Q9H1D0	TRPV6_HUMAN	G	184	ENSP00000352358:E184G	ENSP00000352358:E184G	E	-	2	0	TRPV6	142284649	0.999000	0.42202	0.984000	0.44739	0.861000	0.49209	6.011000	0.70760	0.657000	0.30906	-0.250000	0.11733	GAG	.	.		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
AGAP3	116988	hgsc.bcm.edu	37	7	150814236	150814236	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:150814236A>G	ENST00000397238.2	+	3	445	c.445A>G	c.(445-447)Acg>Gcg	p.T149A	AGAP3_ENST00000335367.3_Missense_Mutation_p.T329A|AGAP3_ENST00000463381.1_5'UTR|AGAP3_ENST00000479901.1_Missense_Mutation_p.T149A|AGAP3_ENST00000473312.1_Missense_Mutation_p.T149A|AGAP3_ENST00000476375.1_3'UTR	NM_031946.4	NP_114152.3	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	113	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						CCGCTATCTGACGGGGACCTA	0.662																																					p.T149A		Atlas-SNP	.											.	AGAP3	121	.	0			c.A445G						.						57.0	61.0	60.0					7																	150814236		2099	4266	6365	SO:0001583	missense	116988	exon3			TATCTGACGGGGA	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16923	protein-coding gene	gene with protein product			"""centaurin, gamma 3"""	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000397238.2:c.445A>G	chr7.hg19:g.150814236A>G	ENSP00000380413:p.Thr149Ala	121.0	0.0		100.0	4.0	NM_001042535	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000397238.2	hg19	CCDS43681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.4|28.4	4.917500|4.917500	0.92249|0.92249	.|.	.|.	ENSG00000133612|ENSG00000133612	ENST00000473312;ENST00000479901;ENST00000397238;ENST00000335355;ENST00000335367|ENST00000469901	T;T;T;T|.	0.22743|.	1.94;1.94;1.94;1.94|.	4.42|4.42	4.42|4.42	0.53409|0.53409	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.80834|.	0.4699|.	M|M	0.91717|0.91717	3.235|3.235	0.80722|0.80722	D|D	1|1	P;P;P;D|.	0.58268|.	0.843;0.648;0.774;0.982|.	P;P;B;P|.	0.58130|.	0.68;0.538;0.307;0.833|.	D|.	0.85152|.	0.0987|.	10|.	0.87932|.	D|.	0|.	.|.	13.0143|13.0143	0.58749|0.58749	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	149;329;149;149|.	C9J975;E7ESL9;Q96P47-4;E9PAL8|.	.;.;.;.|.	A|W	149;149;149;113;329|84	ENSP00000418921:T149A;ENSP00000418125:T149A;ENSP00000380413:T149A;ENSP00000335589:T329A|.	ENSP00000334157:T113A|.	T|X	+|+	1|3	0|0	AGAP3|AGAP3	150445169|150445169	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.986000|0.986000	0.74619|0.74619	9.039000|9.039000	0.93777|0.93777	1.868000|1.868000	0.54150|0.54150	0.334000|0.334000	0.21626|0.21626	ACG|TGA	.	.		0.662	AGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351908.3	NM_031946	
ASB10	136371	hgsc.bcm.edu	37	7	150878505	150878505	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:150878505C>A	ENST00000420175.2	-	3	649	c.625G>T	c.(625-627)Ggt>Tgt	p.G209C	ASB10_ENST00000422024.1_Missense_Mutation_p.G254C|ASB10_ENST00000275838.1_Missense_Mutation_p.G209C|ASB10_ENST00000434669.1_Missense_Mutation_p.G254C|ASB10_ENST00000377867.3_Missense_Mutation_p.G194C			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	209					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCGGACCGACCATCCACTCTC	0.632																																					p.G209C		Atlas-SNP	.											.	ASB10	99	.	0			c.G625T						.						27.0	25.0	26.0					7																	150878505		2200	4291	6491	SO:0001583	missense	136371	exon3			ACCGACCATCCAC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.625G>T	chr7.hg19:g.150878505C>A	ENSP00000391137:p.Gly209Cys	120.0	0.0		94.0	4.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236302	0.58886	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.14	5.14	0.70334	Ankyrin repeat-containing domain (4);	0.054132	0.85682	D	0.000000	T	0.53753	0.1816	N	0.02697	-0.525	0.50039	D	0.999842	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.995;0.999	T	0.61869	-0.6974	10	0.62326	D	0.03	-9.5834	7.2454	0.26119	0.0:0.7308:0.1744:0.0948	.	194;209;254	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	C	209;194;254;254;209	ENSP00000275838:G209C;ENSP00000367098:G194C;ENSP00000401369:G254C;ENSP00000398247:G254C;ENSP00000391137:G209C	ENSP00000275838:G209C	G	-	1	0	ASB10	150509438	0.161000	0.22892	0.996000	0.52242	0.637000	0.38172	1.447000	0.35101	2.549000	0.85964	0.655000	0.94253	GGT	.	.		0.632	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
PAXIP1	22976	hgsc.bcm.edu	37	7	154738503	154738503	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:154738503T>C	ENST00000404141.1	-	18	3097	c.2943A>G	c.(2941-2943)acA>acG	p.T981T	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Silent_p.T981T			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	981	BRCT 6. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		AGATTCCAGGTGTGATGTAAA	0.363																																					p.T981T		Atlas-SNP	.											.	PAXIP1	150	.	0			c.A2943G						.						50.0	45.0	46.0					7																	154738503		1845	4112	5957	SO:0001819	synonymous_variant	22976	exon18			TCCAGGTGTGATG	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2943A>G	chr7.hg19:g.154738503T>C		44.0	0.0		49.0	4.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.363	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
UBE3C	9690	hgsc.bcm.edu	37	7	156961778	156961778	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:156961778C>A	ENST00000348165.5	+	3	517	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	UBE3C_ENST00000389103.4_Intron	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	53	Cis-determinant of acceptor ubiquitin- binding.|IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		AATAATTATCCAGTCATTTAT	0.358																																					p.Q53K		Atlas-SNP	.											.	UBE3C	124	.	0			c.C157A						.						97.0	93.0	95.0					7																	156961778		2203	4300	6503	SO:0001583	missense	9690	exon3			ATTATCCAGTCAT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.157C>A	chr7.hg19:g.156961778C>A	ENSP00000309198:p.Gln53Lys	90.0	0.0		73.0	4.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860561	0.71834	.	.	ENSG00000009335	ENST00000348165	T	0.75154	-0.91	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	D	0.82430	0.5035	M	0.80422	2.495	0.80722	D	1	P;D	0.53312	0.748;0.959	B;P	0.51079	0.318;0.658	D	0.86368	0.1721	10	0.87932	D	0	.	17.8605	0.88779	0.0:1.0:0.0:0.0	.	53;53	Q15386;Q15386-2	UBE3C_HUMAN;.	K	53	ENSP00000309198:Q53K	ENSP00000309198:Q53K	Q	+	1	0	UBE3C	156654539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.994000	0.70623	2.273000	0.75805	0.655000	0.94253	CAG	.	.		0.358	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959974	157959974	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:157959974G>T	ENST00000389418.4	-	6	568	c.559C>A	c.(559-561)Cgc>Agc	p.R187S	PTPRN2_ENST00000409483.1_Missense_Mutation_p.R149S|PTPRN2_ENST00000389413.3_Missense_Mutation_p.R187S|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R210S|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R170S	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	187					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCGGAGAAGCGGTCATCACCC	0.597																																					p.R187S		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C559A						.						64.0	64.0	64.0					7																	157959974		2203	4300	6503	SO:0001583	missense	5799	exon6			AGAAGCGGTCATC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.559C>A	chr7.hg19:g.157959974G>T	ENSP00000374069:p.Arg187Ser	71.0	0.0		95.0	5.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.531298	0.00145	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02656	4.22;4.23;4.22;4.22;4.21	4.3	-5.53	0.02552	.	1.669860	0.04103	N	0.313279	T	0.00936	0.0031	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.44329	-0.9335	10	0.07482	T	0.82	.	0.1714	0.00113	0.2905:0.266:0.1773:0.2662	.	210;149;187;170;187	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	S	149;187;170;187;210	ENSP00000387114:R149S;ENSP00000374064:R187S;ENSP00000374067:R170S;ENSP00000374069:R187S;ENSP00000385464:R210S	ENSP00000374064:R187S	R	-	1	0	PTPRN2	157652735	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.298000	0.08265	-0.884000	0.03976	-0.266000	0.10368	CGC	.	.		0.597	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
CSMD1	64478	hgsc.bcm.edu	37	8	2967694	2967694	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:2967694A>G	ENST00000520002.1	-	44	7152	c.6597T>C	c.(6595-6597)gaT>gaC	p.D2199D	CSMD1_ENST00000602723.1_Silent_p.D2199D|CSMD1_ENST00000400186.3_Silent_p.D2199D|CSMD1_ENST00000542608.1_Silent_p.D2198D|CSMD1_ENST00000602557.1_Silent_p.D2199D|CSMD1_ENST00000537824.1_Silent_p.D2198D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2199	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGCAATGTAATCGTTGACAG	0.433																																					p.D2198D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T6594C						.						89.0	87.0	88.0					8																	2967694		1947	4132	6079	SO:0001819	synonymous_variant	64478	exon43			AATGTAATCGTTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6597T>C	chr8.hg19:g.2967694A>G		72.0	0.0		52.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19																																																																																				.	.		0.433	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SGK223	157285	hgsc.bcm.edu	37	8	8185764	8185764	+	Missense_Mutation	SNP	G	G	T	rs150737128	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:8185764G>T	ENST00000520004.1	-	5	2792	c.2528C>A	c.(2527-2529)cCc>cAc	p.P843H	SGK223_ENST00000330777.4_Missense_Mutation_p.P843H			Q86YV5	SG223_HUMAN		845							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTTCAGCTTGGGGCTTGCTGT	0.587																																					p.P843H	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C2528A						.						135.0	147.0	143.0					8																	8185764		1988	4147	6135	SO:0001583	missense	0	exon4			AGCTTGGGGCTTG																												ENST00000520004.1:c.2528C>A	chr8.hg19:g.8185764G>T	ENSP00000428054:p.Pro843His	149.0	0.0		72.0	4.0	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.063106	0.55432	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.65364	-0.15;-0.15	4.97	4.97	0.65823	.	0.081584	0.48286	D	0.000185	T	0.76723	0.4027	M	0.63843	1.955	0.51767	D	0.999935	D	0.89917	1.0	D	0.91635	0.999	T	0.78540	-0.2165	10	0.87932	D	0	.	15.906	0.79430	0.0:0.0:1.0:0.0	.	843	Q86YV5	SG223_HUMAN	H	843	ENSP00000330930:P843H;ENSP00000428054:P843H	ENSP00000330930:P843H	P	-	2	0	AC068353.1	8223174	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	5.320000	0.65841	2.751000	0.94390	0.563000	0.77884	CCC	.	G|1.000;A|0.000		0.587	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10468763	10468763	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:10468763G>A	ENST00000382483.3	-	4	3068	c.2845C>T	c.(2845-2847)Ccc>Tcc	p.P949S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	949					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GACGAGCGGGGCAGAGAGCTG	0.642																																					p.P949S		Atlas-SNP	.											RP1L1,right_upper_lobe,carcinoma,0,1	RP1L1	453	.	0			c.C2845T						.						41.0	49.0	46.0					8																	10468763		2021	4171	6192	SO:0001583	missense	94137	exon4			AGCGGGGCAGAGA	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2845C>T	chr8.hg19:g.10468763G>A	ENSP00000371923:p.Pro949Ser	103.0	0.0		44.0	2.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035997	0.54896	.	.	ENSG00000183638	ENST00000382483	T	0.76186	-1.0	4.73	4.73	0.59995	.	0.000000	0.34628	N	0.003817	T	0.79851	0.4517	L	0.32530	0.975	0.45899	D	0.99874	D	0.89917	1.0	D	0.91635	0.999	T	0.82163	-0.0593	10	0.87932	D	0	-24.7821	14.9928	0.71401	0.0:0.0:1.0:0.0	.	949	A6NKC6	.	S	949	ENSP00000371923:P949S	ENSP00000371923:P949S	P	-	1	0	RP1L1	10506173	1.000000	0.71417	0.994000	0.49952	0.020000	0.10135	6.864000	0.75494	2.441000	0.82636	0.462000	0.41574	CCC	.	.		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MSR1	4481	hgsc.bcm.edu	37	8	15967718	15967718	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:15967718G>A	ENST00000262101.5	-	10	1353	c.1232C>T	c.(1231-1233)cCa>cTa	p.P411L	MSR1_ENST00000445506.2_Missense_Mutation_p.P429L|MSR1_ENST00000350896.3_Missense_Mutation_p.P348L|MSR1_ENST00000355282.2_Missense_Mutation_p.P348L			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	411	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.P411Q(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CAGCCATATTGGACCAGTACC	0.373																																					p.P411L		Atlas-SNP	.											MSR1,NS,carcinoma,0,1	MSR1	140	.	1	Substitution - Missense(1)	lung(1)	c.C1232T						.						91.0	94.0	93.0					8																	15967718		2203	4300	6503	SO:0001583	missense	4481	exon10			CATATTGGACCAG	D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"""CD molecules"""	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.1232C>T	chr8.hg19:g.15967718G>A	ENSP00000262101:p.Pro411Leu	132.0	0.0		73.0	3.0	NM_138715	D3DSP3|O60505|P21759|Q45F10	Missense_Mutation	SNP	ENST00000262101.5	hg19	CCDS5995.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748979	0.49257	.	.	ENSG00000038945	ENST00000350896;ENST00000262101;ENST00000445506;ENST00000355282	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.08	4.19	0.49359	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.48286	D	0.000194	T	0.54759	0.1878	M	0.74546	2.27	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.75484	0.95;0.973;0.986	T	0.50651	-0.8803	10	0.30854	T	0.27	.	10.1036	0.42519	0.0983:0.0:0.9017:0.0	.	429;348;411	B4DDJ5;P21757-3;P21757	.;.;MSRE_HUMAN	L	348;411;429;348	ENSP00000262100:P348L;ENSP00000262101:P411L;ENSP00000405453:P429L;ENSP00000347430:P348L	ENSP00000262101:P411L	P	-	2	0	MSR1	16012089	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.821000	0.39041	2.515000	0.84797	0.650000	0.86243	CCA	.	.		0.373	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2		
MICU3	286097	hgsc.bcm.edu	37	8	16921741	16921741	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:16921741C>A	ENST00000318063.5	+	2	572	c.530C>A	c.(529-531)cCc>cAc	p.P177H		NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	177						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										ACAGATGAGCCCAAAGGTAAG	0.338																																					p.P177H		Atlas-SNP	.											.	EFHA2	60	.	0			c.C530A						.						92.0	84.0	87.0					8																	16921741		2203	4300	6503	SO:0001583	missense	286097	exon2			ATGAGCCCAAAGG	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"""EF-hand domain containing"""	27820	protein-coding gene	gene with protein product		610633	"""EF hand domain family A2"", ""EF-hand domain family, member A2"""	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.530C>A	chr8.hg19:g.16921741C>A	ENSP00000321455:p.Pro177His	130.0	0.0		87.0	4.0	NM_181723	Q8IYZ3	Missense_Mutation	SNP	ENST00000318063.5	hg19	CCDS5999.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.29|17.29	3.352511|3.352511	0.61293|0.61293	.|.	.|.	ENSG00000155970|ENSG00000155970	ENST00000318063|ENST00000519044	D|D	0.90620|0.90444	-2.7|-2.67	4.83|4.83	3.92|3.92	0.45320|0.45320	.|.	0.114638|0.114638	0.64402|0.64402	D|D	0.000011|0.000011	D|D	0.93785|0.93785	0.8013|0.8013	M|M	0.81942|0.81942	2.565|2.565	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|D	0.93055|0.93055	0.6469|0.6469	10|8	0.72032|0.35671	D|T	0.01|0.21	-21.2422|-21.2422	15.3036|15.3036	0.73976|0.73976	0.0:0.8587:0.1413:0.0|0.0:0.8587:0.1413:0.0	.|.	177|.	Q86XE3|.	EFHA2_HUMAN|.	H|T	177|35	ENSP00000321455:P177H|ENSP00000427765:P35T	ENSP00000321455:P177H|ENSP00000427765:P35T	P|P	+|+	2|1	0|0	EFHA2|EFHA2	16966112|16966112	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.896000|0.896000	0.52359|0.52359	6.206000|6.206000	0.72154|0.72154	1.297000|1.297000	0.44761|0.44761	0.591000|0.591000	0.81541|0.81541	CCC|CCA	.	.		0.338	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723	
VPS37A	137492	hgsc.bcm.edu	37	8	17126365	17126365	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:17126365T>C	ENST00000324849.4	+	4	990	c.316T>C	c.(316-318)Ttt>Ctt	p.F106L	VPS37A_ENST00000521829.1_Splice_Site_p.F81L|VPS37A_ENST00000324815.3_Splice_Site_p.F106L	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	106					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		TTACTTTCAGTTTACAATGCA	0.333																																					p.F106L		Atlas-SNP	.											.	VPS37A	22	.	0			c.T316C						.						86.0	84.0	85.0					8																	17126365		2203	4297	6500	SO:0001630	splice_region_variant	137492	exon4			TTTCAGTTTACAA		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"""hepatocellular carcinoma related protein 1"""	609927	"""vacuolar protein sorting 37A (yeast)"", ""polyglutamine binding protein 2"""	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.316-1T>C	chr8.hg19:g.17126365T>C		117.0	0.0		79.0	4.0	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	hg19	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897638	0.91962	.	.	ENSG00000155975	ENST00000324849;ENST00000324815;ENST00000521829	T;T	0.65549	-0.16;-0.08	5.0	5.0	0.66597	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.66107	0.2756	M	0.71581	2.175	0.80722	D	1	P;B	0.48230	0.907;0.412	P;B	0.45712	0.491;0.134	T	0.69101	-0.5234	9	.	.	.	-17.9103	15.0191	0.71613	0.0:0.0:0.0:1.0	.	81;106	Q8NEZ2-2;Q8NEZ2	.;VP37A_HUMAN	L	106;106;81	ENSP00000318629:F106L;ENSP00000429680:F81L	.	F	+	1	0	VPS37A	17170736	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	7.262000	0.78410	2.011000	0.59026	0.533000	0.62120	TTT	.	.		0.333	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415	Missense_Mutation
EGR3	1960	hgsc.bcm.edu	37	8	22548215	22548215	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:22548215C>T	ENST00000317216.2	-	2	1292	c.935G>A	c.(934-936)cGg>cAg	p.R312Q	EGR3_ENST00000519492.1_3'UTR|RP11-459E5.1_ENST00000523627.1_RNA|EGR3_ENST00000524088.1_5'UTR|EGR3_ENST00000522910.1_Missense_Mutation_p.R274Q	NM_001199881.1|NM_004430.2	NP_001186810.1|NP_004421.2	Q06889	EGR3_HUMAN	early growth response 3	312					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|circadian rhythm (GO:0007623)|endothelial cell chemotaxis (GO:0035767)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)		GCTGAAGCTCCGCATGCAGAT	0.667																																					p.R312Q		Atlas-SNP	.											.	EGR3	33	.	0			c.G935A						.						62.0	63.0	63.0					8																	22548215		2203	4300	6503	SO:0001583	missense	1960	exon2			AAGCTCCGCATGC	X63741	CCDS6033.1, CCDS56528.1	8p23-p21	2013-01-08			ENSG00000179388	ENSG00000179388		"""Zinc fingers, C2H2-type"""	3240	protein-coding gene	gene with protein product	"""zinc finger protein pilot"""	602419				1906159, 11909874	Standard	NM_004430		Approved	PILOT	uc003xcm.1	Q06889	OTTHUMG00000097825	ENST00000317216.2:c.935G>A	chr8.hg19:g.22548215C>T	ENSP00000318057:p.Arg312Gln	207.0	0.0		100.0	4.0	NM_004430	A8K8U9|B4DHJ5|E7EW38|Q2M3W2	Missense_Mutation	SNP	ENST00000317216.2	hg19	CCDS6033.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770789	0.90108	.	.	ENSG00000179388	ENST00000317216;ENST00000522910;ENST00000435199	T;T	0.18960	2.18;2.18	5.62	5.62	0.85841	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	L	0.48877	1.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.15983	-1.0418	10	0.87932	D	0	-12.7178	17.155	0.86788	0.0:1.0:0.0:0.0	.	274;312	E7EW38;Q06889	.;EGR3_HUMAN	Q	312;274;153	ENSP00000318057:R312Q;ENSP00000430310:R274Q	ENSP00000318057:R312Q	R	-	2	0	EGR3	22604160	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.976000	0.63785	2.643000	0.89663	0.655000	0.94253	CGG	.	.		0.667	EGR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215098.1	NM_004430	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23003279	23003279	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:23003279A>G	ENST00000312584.3	-	5	732	c.638T>C	c.(637-639)cTt>cCt	p.L213P		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	213					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TATGATGATAAGGTAGTGATA	0.468																																					p.L213P		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.T638C						.						144.0	128.0	134.0					8																	23003279		2203	4300	6503	SO:0001583	missense	8793	exon5			ATGATAAGGTAGT	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.638T>C	chr8.hg19:g.23003279A>G	ENSP00000310263:p.Leu213Pro	101.0	0.0		56.0	4.0	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	a	3.465	-0.109254	0.06924	.	.	ENSG00000173530	ENST00000312584	D	0.83755	-1.76	1.38	-1.89	0.07689	.	.	.	.	.	T	0.67144	0.2862	N	0.22421	0.69	0.09310	N	0.999997	B	0.24651	0.108	B	0.23018	0.043	T	0.50857	-0.8778	9	0.36615	T	0.2	.	5.2822	0.15682	0.5563:0.0:0.4437:0.0	.	213	Q9UBN6	TR10D_HUMAN	P	213	ENSP00000310263:L213P	ENSP00000310263:L213P	L	-	2	0	TNFRSF10D	23059224	0.042000	0.20092	0.000000	0.03702	0.000000	0.00434	0.003000	0.13083	-0.687000	0.05162	-1.587000	0.00848	CTT	.	.		0.468	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
DPYSL2	1808	hgsc.bcm.edu	37	8	26439530	26439530	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:26439530C>A	ENST00000311151.5	+	2	497	c.85C>A	c.(85-87)Cag>Aag	p.Q29K	DPYSL2_ENST00000521913.1_5'UTR|DPYSL2_ENST00000523027.1_5'UTR	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	29					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TAATGATGACCAGTCGTTCTA	0.398																																					p.Q134K		Atlas-SNP	.											.	DPYSL2	49	.	0			c.C400A						.						152.0	128.0	136.0					8																	26439530		2203	4300	6503	SO:0001583	missense	1808	exon2			GATGACCAGTCGT	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.85C>A	chr8.hg19:g.26439530C>A	ENSP00000309539:p.Gln29Lys	126.0	0.0		85.0	4.0	NM_001197293	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	hg19	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816092	0.70912	.	.	ENSG00000092964	ENST00000493789;ENST00000311151;ENST00000522745	D;D;D	0.86627	-2.15;-1.92;-1.92	5.13	5.13	0.70059	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.87148	0.6105	L	0.35593	1.075	0.80722	D	1	B;P;P	0.49961	0.032;0.732;0.93	B;P;P	0.57679	0.009;0.625;0.825	T	0.81927	-0.0709	10	0.07325	T	0.83	-19.4567	18.7656	0.91871	0.0:1.0:0.0:0.0	.	29;29;85	Q53ET2;Q16555;Q59GB4	.;DPYL2_HUMAN;.	K	101;29;29	ENSP00000427954:Q101K;ENSP00000309539:Q29K;ENSP00000428909:Q29K	ENSP00000309539:Q29K	Q	+	1	0	DPYSL2	26495447	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.647000	0.83462	2.666000	0.90696	0.561000	0.74099	CAG	.	.		0.398	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386	
CHRNA2	1135	hgsc.bcm.edu	37	8	27320754	27320754	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:27320754G>A	ENST00000520933.2	-	5	1359	c.1206C>T	c.(1204-1206)caC>caT	p.H402H	CHRNA2_ENST00000407991.1_Silent_p.H402H|CHRNA2_ENST00000240132.2_Silent_p.H387H			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	402					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	TCTCCAGCCAGTGATAAGAGG	0.657																																					p.H402H		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C1206T						.						71.0	64.0	66.0					8																	27320754		2203	4300	6503	SO:0001819	synonymous_variant	1135	exon6			CAGCCAGTGATAA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.1206C>T	chr8.hg19:g.27320754G>A		79.0	0.0		37.0	4.0	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	hg19	CCDS6059.1																																																																																			.	.		0.657	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
ESCO2	157570	hgsc.bcm.edu	37	8	27633887	27633887	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:27633887A>G	ENST00000305188.8	+	3	300	c.62A>G	c.(61-63)cAc>cGc	p.H21R	RNU6-1276P_ENST00000365372.1_RNA|ESCO2_ENST00000397418.2_5'UTR	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	21					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		AGCCTTTTACACTTCACTGAA	0.308									SC Phocomelia syndrome																												p.H21R		Atlas-SNP	.											.	ESCO2	50	.	0			c.A62G						.						27.0	29.0	28.0					8																	27633887		2199	4299	6498	SO:0001583	missense	157570	exon3	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	TTTTACACTTCAC	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"""Roberts syndrome"", ""establishment of cohesion 1 homolog 2 (S. cerevisiae)"""	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.62A>G	chr8.hg19:g.27633887A>G	ENSP00000306999:p.His21Arg	143.0	0.0		79.0	4.0	NM_001017420	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	A	0.055	-1.237731	0.01493	.	.	ENSG00000171320	ENST00000523566;ENST00000305188;ENST00000519637	T;T;T	0.61742	1.09;0.08;1.09	5.02	2.6	0.31112	.	2.157160	0.02081	N	0.052398	T	0.31358	0.0794	N	0.02539	-0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37197	-0.9716	10	0.16896	T	0.51	6.3879	4.5927	0.12315	0.7389:0.0:0.0925:0.1686	.	21;21	E5RFE4;Q56NI9	.;ESCO2_HUMAN	R	21	ENSP00000428435:H21R;ENSP00000306999:H21R;ENSP00000428027:H21R	ENSP00000306999:H21R	H	+	2	0	ESCO2	27689806	0.765000	0.28485	0.046000	0.18839	0.224000	0.24922	0.774000	0.26675	0.329000	0.23460	-1.114000	0.02060	CAC	.	.		0.308	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420	
HTRA4	203100	hgsc.bcm.edu	37	8	38845473	38845473	+	Silent	SNP	C	C	T	rs576647651		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:38845473C>T	ENST00000302495.4	+	9	1387	c.1287C>T	c.(1285-1287)caC>caT	p.H429H		NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	429	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			TGAGAGATCACGATGTAATTG	0.358																																					p.H429H		Atlas-SNP	.											.	HTRA4	25	.	0			c.C1287T						.						103.0	89.0	94.0					8																	38845473		2203	4300	6503	SO:0001819	synonymous_variant	203100	exon9			AGATCACGATGTA	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.1287C>T	chr8.hg19:g.38845473C>T		87.0	0.0		46.0	4.0	NM_153692	Q542Z4|Q6PF13	Silent	SNP	ENST00000302495.4	hg19	CCDS6110.1																																																																																			.	.		0.358	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692	
ADAM9	8754	hgsc.bcm.edu	37	8	38934925	38934925	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:38934925G>A	ENST00000487273.2	+	16	1954	c.1876G>A	c.(1876-1878)Gga>Aga	p.G626R	ADAM9_ENST00000484143.1_3'UTR	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	626	Cys-rich.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ATGTGGTGCTGGAAAGGTAAT	0.348																																					p.G626R		Atlas-SNP	.											.	ADAM9	66	.	0			c.G1876A						.						52.0	49.0	50.0					8																	38934925		2203	4300	6503	SO:0001583	missense	8754	exon16			GGTGCTGGAAAGG	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.1876G>A	chr8.hg19:g.38934925G>A	ENSP00000419446:p.Gly626Arg	173.0	0.0		85.0	4.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	hg19	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816101	0.50527	.	.	ENSG00000168615	ENST00000487273	T	0.16597	2.33	5.55	5.55	0.83447	ADAM, cysteine-rich (1);	0.251101	0.40728	N	0.001028	T	0.37598	0.1009	L	0.58428	1.81	0.40269	D	0.978263	D	0.54772	0.968	P	0.59703	0.862	T	0.02901	-1.1096	10	0.54805	T	0.06	.	19.8769	0.96880	0.0:0.0:1.0:0.0	.	626	Q13443	ADAM9_HUMAN	R	626	ENSP00000419446:G626R	ENSP00000369249:G626R	G	+	1	0	ADAM9	39054082	1.000000	0.71417	0.886000	0.34754	0.278000	0.26855	6.128000	0.71650	2.767000	0.95098	0.557000	0.71058	GGA	.	.		0.348	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2		
ADAM2	2515	hgsc.bcm.edu	37	8	39678655	39678655	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:39678655T>C	ENST00000265708.4	-	6	482	c.379A>G	c.(379-381)Ata>Gta	p.I127V	ADAM2_ENST00000347580.4_Missense_Mutation_p.I127V|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.I127V|ADAM2_ENST00000379853.2_Missense_Mutation_p.I127V	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	127					adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		AGGGGTTCTATTCCATAACTA	0.318																																					p.I127V		Atlas-SNP	.											.	ADAM2	124	.	0			c.A379G						.						49.0	49.0	49.0					8																	39678655		2203	4297	6500	SO:0001583	missense	2515	exon6			GTTCTATTCCATA	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"""ADAM metallopeptidase domain containing"""	198	protein-coding gene	gene with protein product	"""cancer/testis antigen 15"""	601533	"""fertilin beta"""	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.379A>G	chr8.hg19:g.39678655T>C	ENSP00000265708:p.Ile127Val	163.0	0.0		99.0	5.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867809	0.72065	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.13901	2.55;2.55;2.55;2.55	5.47	5.47	0.80525	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.41419	0.1158	M	0.84585	2.705	0.36139	D	0.846633	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.85130	0.99;0.995;0.993;0.997	T	0.56565	-0.7958	8	.	.	.	.	13.5152	0.61537	0.0:0.0:0.0:1.0	.	127;127;127;127	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	V	127	ENSP00000343854:I127V;ENSP00000369182:I127V;ENSP00000265708:I127V;ENSP00000429352:I127V	.	I	-	1	0	ADAM2	39797812	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.868000	0.56055	2.076000	0.62316	0.533000	0.62120	ATA	.	.		0.318	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464	
KAT6A	7994	hgsc.bcm.edu	37	8	41790607	41790607	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:41790607A>G	ENST00000396930.3	-	18	5674	c.5131T>C	c.(5131-5133)Ttc>Ctc	p.F1711L	KAT6A_ENST00000265713.2_Missense_Mutation_p.F1711L|KAT6A_ENST00000406337.1_Missense_Mutation_p.F1711L	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1711	Interaction with PML.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GCTGGGGTGAAACTGTTATTC	0.572																																					p.F1711L		Atlas-SNP	.											.	.	.	.	0			c.T5131C						.						75.0	78.0	77.0					8																	41790607		2203	4300	6503	SO:0001583	missense	7994	exon18			GGGTGAAACTGTT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.5131T>C	chr8.hg19:g.41790607A>G	ENSP00000380136:p.Phe1711Leu	185.0	0.0		72.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	6.821	0.520527	0.13005	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.67523	-0.27;-0.27;-0.27	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.70798	0.3265	L	0.34521	1.04	0.58432	D	0.999996	D	0.69078	0.997	D	0.70716	0.97	T	0.65179	-0.6231	10	0.10636	T	0.68	-17.5726	15.8462	0.78895	1.0:0.0:0.0:0.0	.	1711	Q92794	KAT6A_HUMAN	L	1711	ENSP00000265713:F1711L;ENSP00000385888:F1711L;ENSP00000380136:F1711L	ENSP00000265713:F1711L	F	-	1	0	KAT6A	41909764	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	8.890000	0.92477	2.136000	0.66102	0.528000	0.53228	TTC	.	.		0.572	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
POLB	5423	hgsc.bcm.edu	37	8	42214709	42214709	+	Missense_Mutation	SNP	A	A	G	rs200554507		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:42214709A>G	ENST00000265421.4	+	8	615	c.445A>G	c.(445-447)Aga>Gga	p.R149G	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	149					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	CTTTGAAAAAAGAATTCCTCG	0.289								DNA polymerases (catalytic subunits)																													p.R149G		Atlas-SNP	.											.	POLB	60	.	0			c.A445G						.																																			SO:0001583	missense	5423	exon8			GAAAAAAGAATTC		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"""DNA polymerases"""	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.445A>G	chr8.hg19:g.42214709A>G	ENSP00000265421:p.Arg149Gly	181.0	0.0		99.0	4.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Missense_Mutation	SNP	ENST00000265421.4	hg19	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.87|16.87	3.242315|3.242315	0.58995|0.58995	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000521290|ENST00000532157;ENST00000265421;ENST00000518925	T|T;T	0.14391|0.51071	2.51|0.72;0.72	5.93|5.93	5.93|5.93	0.95920|0.95920	.|DNA-directed DNA polymerase X (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.53753|0.53753	0.1816|0.1816	M|M	0.85945|0.85945	2.785|2.785	0.80722|0.80722	D|D	1|1	.|B;B	.|0.28055	.|0.199;0.166	.|B;B	.|0.30782	.|0.12;0.06	T|T	0.59434|0.59434	-0.7455|-0.7455	7|10	0.54805|0.87932	T|D	0.06|0	-0.5562|-0.5562	10.3894|10.3894	0.44160|0.44160	0.8359:0.1641:0.0:0.0|0.8359:0.1641:0.0:0.0	.|.	.|149;149	.|Q53EV2;P06746	.|.;DPOLB_HUMAN	R|G	79|35;149;184	ENSP00000429597:K79R|ENSP00000265421:R149G;ENSP00000430784:R184G	ENSP00000429597:K79R|ENSP00000265421:R149G	K|R	+|+	2|1	0|2	POLB|POLB	42333866|42333866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	6.432000|6.432000	0.73400|0.73400	2.263000|2.263000	0.75096|0.75096	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	A|0.999;G|0.001		0.289	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690	
PRKDC	5591	hgsc.bcm.edu	37	8	48707064	48707064	+	Splice_Site	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:48707064T>A	ENST00000523565.1	-	74	10514		c.e74-2		PRKDC_ENST00000338368.3_Splice_Site|PRKDC_ENST00000314191.2_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GGAAGAGATCTAAAACAGAGA	0.408								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.10458-2A>T						.						54.0	50.0	52.0					8																	48707064		1894	4133	6027	SO:0001630	splice_region_variant	5591	exon75			GAGATCTAAAACA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.2995-2A>T	chr8.hg19:g.48707064T>A		81.0	0.0		73.0	4.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.85	2.361541	0.41801	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7929	0.78380	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	48869617	1.000000	0.71417	0.911000	0.35937	0.077000	0.17291	7.358000	0.79466	2.123000	0.65237	0.533000	0.62120	.	.	.		0.408	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron
CHD7	55636	hgsc.bcm.edu	37	8	61765595	61765595	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:61765595C>T	ENST00000423902.2	+	31	6790	c.6311C>T	c.(6310-6312)gCt>gTt	p.A2104V	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2104					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTGGTTGGTGCTGCTAAACAC	0.537																																					p.A2104V		Atlas-SNP	.											.	CHD7	534	.	0			c.C6311T						.						103.0	114.0	111.0					8																	61765595		2074	4209	6283	SO:0001583	missense	55636	exon31			TTGGTGCTGCTAA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6311C>T	chr8.hg19:g.61765595C>T	ENSP00000392028:p.Ala2104Val	241.0	1.0		220.0	95.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.153143	0.57259	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.87966	-2.32	5.41	4.52	0.55395	.	0.063732	0.64402	D	0.000007	D	0.83303	0.5225	L	0.28115	0.83	0.58432	D	0.999999	B	0.25169	0.119	B	0.36885	0.235	T	0.78909	-0.2018	10	0.34782	T	0.22	-14.0265	16.0296	0.80570	0.0:0.8653:0.1347:0.0	.	2104	Q9P2D1	CHD7_HUMAN	V	2104	ENSP00000392028:A2104V	ENSP00000307304:A2104V	A	+	2	0	CHD7	61928149	1.000000	0.71417	0.583000	0.28640	0.991000	0.79684	6.090000	0.71397	1.252000	0.44001	0.655000	0.94253	GCT	.	.		0.537	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
RRS1	23212	hgsc.bcm.edu	37	8	67342183	67342183	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:67342183C>T	ENST00000320270.2	+	1	921	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	ADHFE1_ENST00000379385.4_5'Flank|RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000396623.3_5'Flank|ADHFE1_ENST00000415254.1_5'Flank	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	273					hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GGAGCTGCTTCGTGTCATGAA	0.557																																					p.R273C		Atlas-SNP	.											.	RRS1	13	.	0			c.C817T						.						26.0	31.0	29.0					8																	67342183		2203	4300	6503	SO:0001583	missense	23212	exon1			CTGCTTCGTGTCA	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.817C>T	chr8.hg19:g.67342183C>T	ENSP00000322396:p.Arg273Cys	58.0	0.0		73.0	5.0	NM_015169	Q9BUX8	Missense_Mutation	SNP	ENST00000320270.2	hg19	CCDS6189.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.486862	0.44249	.	.	ENSG00000179041	ENST00000320270	D	0.86497	-2.13	5.26	3.33	0.38152	.	0.132508	0.48286	D	0.000193	D	0.88676	0.6501	L	0.47716	1.5	0.49915	D	0.999839	D	0.76494	0.999	P	0.58391	0.838	D	0.89186	0.3547	10	0.62326	D	0.03	-4.8295	12.8419	0.57809	0.3984:0.6016:0.0:0.0	.	273	Q15050	RRS1_HUMAN	C	273	ENSP00000322396:R273C	ENSP00000322396:R273C	R	+	1	0	RRS1	67504737	1.000000	0.71417	0.998000	0.56505	0.454000	0.32378	1.181000	0.32017	1.343000	0.45638	0.650000	0.86243	CGT	.	.		0.557	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169	
PREX2	80243	hgsc.bcm.edu	37	8	69104651	69104651	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:69104651G>A	ENST00000288368.4	+	37	4772	c.4495G>A	c.(4495-4497)Gca>Aca	p.A1499T		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1499					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGCTGCCTGTGCAAACACAGC	0.537																																					p.A1499T		Atlas-SNP	.											PREX2,colon,carcinoma,0,1	PREX2	614	.	0			c.G4495A						.						78.0	64.0	69.0					8																	69104651		2203	4300	6503	SO:0001583	missense	80243	exon37			GCCTGTGCAAACA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4495G>A	chr8.hg19:g.69104651G>A	ENSP00000288368:p.Ala1499Thr	73.0	0.0		68.0	17.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.636432	0.67130	.	.	ENSG00000046889	ENST00000288368	T	0.59906	0.23	4.89	4.89	0.63831	.	0.494062	0.21652	N	0.071168	T	0.42539	0.1207	N	0.11560	0.145	0.35876	D	0.828574	B	0.10296	0.003	B	0.17098	0.017	T	0.45056	-0.9287	10	0.39692	T	0.17	.	18.4181	0.90577	0.0:0.0:1.0:0.0	.	1499	Q70Z35	PREX2_HUMAN	T	1499	ENSP00000288368:A1499T	ENSP00000288368:A1499T	A	+	1	0	PREX2	69267205	0.992000	0.36948	0.982000	0.44146	0.991000	0.79684	5.460000	0.66691	2.427000	0.82271	0.467000	0.42956	GCA	.	.		0.537	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
LY96	23643	hgsc.bcm.edu	37	8	74941217	74941217	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:74941217T>C	ENST00000284818.2	+	5	502	c.411T>C	c.(409-411)gcT>gcC	p.A137A	LY96_ENST00000518893.1_Silent_p.A107A	NM_015364.4	NP_056179	Q9Y6Y9	LY96_HUMAN	lymphocyte antigen 96	137					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endosome membrane (GO:0010008)|extracellular region (GO:0005576)|lipopolysaccharide receptor complex (GO:0046696)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|lipopolysaccharide receptor activity (GO:0001875)			endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			TTGTTGAAGCTATTTCTGGGA	0.299																																					p.A137A	GBM(131;1357 1748 34893 50149 52212)	Atlas-SNP	.											.	LY96	17	.	0			c.T411C						.						76.0	77.0	77.0					8																	74941217		2203	4298	6501	SO:0001819	synonymous_variant	23643	exon5			TGAAGCTATTTCT	AB018549	CCDS6216.1, CCDS56540.1	8q13.3	2004-01-22			ENSG00000154589	ENSG00000154589			17156	protein-coding gene	gene with protein product		605243				10359581, 11466383	Standard	NM_015364		Approved	MD-2	uc003yad.3	Q9Y6Y9	OTTHUMG00000164504	ENST00000284818.2:c.411T>C	chr8.hg19:g.74941217T>C		84.0	0.0		94.0	4.0	NM_015364	B3Y6A5|E5RJJ7	Silent	SNP	ENST00000284818.2	hg19	CCDS6216.1																																																																																			.	.		0.299	LY96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379032.2	NM_015364	
MRPS28	28957	hgsc.bcm.edu	37	8	80942312	80942312	+	Silent	SNP	G	G	T	rs147337080	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:80942312G>T	ENST00000276585.4	-	1	194	c.172C>A	c.(172-174)Cgg>Agg	p.R58R	MRPS28_ENST00000521605.1_Silent_p.R58R|MRPS28_ENST00000522987.1_5'UTR|MRPS28_ENST00000521434.1_5'Flank|RP11-92K15.3_ENST00000607017.1_lincRNA|TPD52_ENST00000537855.1_Intron	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	58						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			TCCGAGTGCCGCTCCAACGCG	0.642																																					p.R58R		Atlas-SNP	.											.	MRPS28	11	.	0			c.C172A						.						30.0	30.0	30.0					8																	80942312		2203	4300	6503	SO:0001819	synonymous_variant	28957	exon1			AGTGCCGCTCCAA	AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586		"""Mitochondrial ribosomal proteins / small subunits"""	14513	protein-coding gene	gene with protein product		611990				11279123, 11042152	Standard	NM_014018		Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.172C>A	chr8.hg19:g.80942312G>T		58.0	0.0		89.0	4.0	NM_014018	B2RDZ7|Q96Q21	Silent	SNP	ENST00000276585.4	hg19	CCDS6226.1	.	.	.	.	.	.	.	.	.	.	G	5.653	0.305105	0.10678	.	.	ENSG00000147586	ENST00000518271	.	.	.	5.28	4.4	0.53042	.	.	.	.	.	T	0.62466	0.2430	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60964	-0.7158	4	.	.	.	.	11.0826	0.48068	0.0:0.0:0.8152:0.1847	.	.	.	.	R	52	.	.	S	-	3	2	MRPS28	81104867	0.743000	0.28239	0.992000	0.48379	0.229000	0.25112	0.950000	0.29122	1.442000	0.47568	0.655000	0.94253	AGC	.	G|0.997;A|0.003		0.642	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379526.1	NM_014018	
WWP1	11059	hgsc.bcm.edu	37	8	87439874	87439874	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:87439874G>T	ENST00000517970.1	+	11	1467	c.1160G>T	c.(1159-1161)tGg>tTg	p.W387L	WWP1_ENST00000349423.2_Missense_Mutation_p.W169L|WWP1_ENST00000265428.4_Missense_Mutation_p.W387L|WWP1_ENST00000341922.2_Missense_Mutation_p.W257L	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	387	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TGTGGTAGTTGGGAAAGAAGA	0.338																																					p.W387L		Atlas-SNP	.											.	WWP1	97	.	0			c.G1160T						.						116.0	120.0	119.0					8																	87439874		2203	4300	6503	SO:0001583	missense	11059	exon11			GTAGTTGGGAAAG	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1160G>T	chr8.hg19:g.87439874G>T	ENSP00000427793:p.Trp387Leu	129.0	0.0		130.0	6.0	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	31	5.083754	0.94050	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	D;D;D;D	0.99766	-6.69;-6.69;-6.69;-6.69	5.54	5.54	0.83059	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	H	0.98951	4.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96263	0.9192	10	0.72032	D	0.01	.	19.4875	0.95035	0.0:0.0:1.0:0.0	.	169;387	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	L	387;387;257;169	ENSP00000427793:W387L;ENSP00000265428:W387L;ENSP00000340564:W257L;ENSP00000342665:W169L	ENSP00000265428:W387L	W	+	2	0	WWP1	87508990	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.585000	0.87301	0.650000	0.86243	TGG	.	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
KIAA1429	25962	hgsc.bcm.edu	37	8	95531221	95531221	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:95531221T>C	ENST00000297591.5	-	9	2580	c.2505A>G	c.(2503-2505)gaA>gaG	p.E835E	KIAA1429_ENST00000437199.1_Silent_p.E835E|KIAA1429_ENST00000421249.2_Silent_p.E835E	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	835					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACCCCAAGGCTTCTTTGGAAT	0.333																																					p.E835E		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A2505G						.						50.0	56.0	54.0					8																	95531221		2191	4299	6490	SO:0001819	synonymous_variant	25962	exon9			CAAGGCTTCTTTG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2505A>G	chr8.hg19:g.95531221T>C		64.0	0.0		68.0	4.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	hg19	CCDS34923.1																																																																																			.	.		0.333	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
MTDH	92140	hgsc.bcm.edu	37	8	98656988	98656988	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:98656988C>T	ENST00000336273.3	+	1	582	c.254C>T	c.(253-255)cCg>cTg	p.P85L	MTDH_ENST00000519934.1_Missense_Mutation_p.P62L	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	85	Interaction with BCCIP.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			CGGAGGAGCCCGCCCCGCAAG	0.711																																					p.P85L		Atlas-SNP	.											.	MTDH	54	.	0			c.C254T						.						5.0	7.0	6.0					8																	98656988		1866	3849	5715	SO:0001583	missense	92140	exon1			GGAGCCCGCCCCG	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"""astrocyte elevated gene 1"""	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.254C>T	chr8.hg19:g.98656988C>T	ENSP00000338235:p.Pro85Leu	28.0	0.0		32.0	4.0	NM_178812	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	hg19	CCDS6274.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434272	0.83776	.	.	ENSG00000147649	ENST00000336273;ENST00000519934	T;T	0.09723	2.95;2.95	5.32	4.44	0.53790	.	0.263023	0.37715	N	0.001978	T	0.08935	0.0221	L	0.29908	0.895	0.50313	D	0.999863	B	0.15141	0.012	B	0.08055	0.003	T	0.11817	-1.0572	10	0.44086	T	0.13	-4.4925	11.3329	0.49487	0.0:0.9141:0.0:0.0859	.	85	Q86UE4	LYRIC_HUMAN	L	85;62	ENSP00000338235:P85L;ENSP00000428168:P62L	ENSP00000338235:P85L	P	+	2	0	MTDH	98726164	0.079000	0.21365	1.000000	0.80357	0.994000	0.84299	0.365000	0.20348	1.371000	0.46172	0.591000	0.81541	CCG	.	.		0.711	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2		
FBXO43	286151	hgsc.bcm.edu	37	8	101153750	101153750	+	Silent	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:101153750T>A	ENST00000428847.2	-	2	1048	c.732A>T	c.(730-732)ctA>ctT	p.L244L		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	244					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			CAACTTCAAATAGGCTACAAT	0.323																																					p.L244L		Atlas-SNP	.											FBXO43_ENST00000428847,colon,carcinoma,0,3	FBXO43	155	.	0			c.A732T						.						37.0	38.0	38.0					8																	101153750		1808	3958	5766	SO:0001819	synonymous_variant	286151	exon2			TTCAAATAGGCTA	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"""F-boxes /  ""other"""""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.732A>T	chr8.hg19:g.101153750T>A		50.0	1.0		50.0	2.0	NM_001029860		Silent	SNP	ENST00000428847.2	hg19	CCDS47904.1																																																																																			.	.		0.323	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110457403	110457403	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:110457403G>T	ENST00000378402.5	+	38	5409	c.5305G>T	c.(5305-5307)Gga>Tga	p.G1769*		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1769	IPT/TIG 10.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCTTATTGAAGGAGAAGGTTT	0.398										HNSCC(38;0.096)																											p.G1769X		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G5305T						.						82.0	77.0	78.0					8																	110457403		1874	4111	5985	SO:0001587	stop_gained	93035	exon38			ATTGAAGGAGAAG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5305G>T	chr8.hg19:g.110457403G>T	ENSP00000367655:p.Gly1769*	62.0	0.0		59.0	4.0	NM_177531	Q567P2|Q9UF27	Nonsense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	46	12.168009	0.99643	.	.	ENSG00000205038	ENST00000378402	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	.	.	.	X	1769	.	ENSP00000367655:G1769X	G	+	1	0	PKHD1L1	110526579	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.545000	0.82128	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.398	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CSMD3	114788	hgsc.bcm.edu	37	8	113650925	113650925	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:113650925C>T	ENST00000297405.5	-	21	3770	c.3526G>A	c.(3526-3528)Gaa>Aaa	p.E1176K	CSMD3_ENST00000455883.2_Splice_Site_p.E1072K|CSMD3_ENST00000343508.3_Splice_Site_p.E1136K|CSMD3_ENST00000352409.3_Splice_Site_p.E1176K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1176	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTTTCTCACCAGAGAATGTT	0.308										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E1176K		Atlas-SNP	.											CSMD3_ENST00000343508,left_upper_lobe,carcinoma,0,2	CSMD3	2325	.	0			c.G3526A						.						33.0	36.0	35.0					8																	113650925		2201	4300	6501	SO:0001630	splice_region_variant	114788	exon21			TCTCACCAGAGAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3526+1G>A	chr8.hg19:g.113650925C>T		26.0	0.0		25.0	2.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960401	0.92791	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.91	4.91	0.64330	CUB (3);	0.000000	0.64402	D	0.000001	T	0.58466	0.2124	M	0.79258	2.445	0.49213	D	0.999763	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.85130	0.997;0.993;0.977	T	0.60875	-0.7176	9	.	.	.	.	18.4581	0.90728	0.0:1.0:0.0:0.0	.	1072;1176;1136	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	K	1136;1176;516;1072;1176	ENSP00000345799:E1136K;ENSP00000297405:E1176K;ENSP00000341558:E516K;ENSP00000412263:E1072K;ENSP00000343124:E1176K	.	E	-	1	0	CSMD3	113720101	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.750000	0.85110	2.448000	0.82819	0.491000	0.48974	GAA	.	.		0.308	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Missense_Mutation
KIAA0196	9897	hgsc.bcm.edu	37	8	126093910	126093910	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:126093910G>T	ENST00000318410.7	-	5	860	c.511C>A	c.(511-513)Cga>Aga	p.R171R	KIAA0196_ENST00000521109.1_5'Flank|KIAA0196_ENST00000517845.1_Silent_p.R23R	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	171					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TACCTGTATCGGTAGTAAGAA	0.428																																					p.R171R		Atlas-SNP	.											.	KIAA0196	90	.	0			c.C511A						.						207.0	164.0	179.0					8																	126093910		2203	4300	6503	SO:0001819	synonymous_variant	9897	exon5			TGTATCGGTAGTA		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.511C>A	chr8.hg19:g.126093910G>T		114.0	0.0		121.0	5.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	hg19	CCDS6355.1																																																																																			.	.		0.428	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
ADCY8	114	hgsc.bcm.edu	37	8	131833641	131833641	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:131833641A>G	ENST00000286355.5	-	13	4793	c.2701T>C	c.(2701-2703)Tca>Cca	p.S901P	ADCY8_ENST00000377928.3_Missense_Mutation_p.S770P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	901					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AGTAGCAGTGATACCTCCTTG	0.463										HNSCC(32;0.087)																											p.S901P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T2701C						.						100.0	78.0	86.0					8																	131833641		2203	4300	6503	SO:0001583	missense	114	exon13			GCAGTGATACCTC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2701T>C	chr8.hg19:g.131833641A>G	ENSP00000286355:p.Ser901Pro	88.0	0.0		97.0	4.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.367570	0.82463	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.79653	-1.29;-1.28	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.84615	0.5511	L	0.50333	1.59	0.42160	D	0.991596	P;D	0.69078	0.937;0.997	P;P	0.59221	0.671;0.854	D	0.83803	0.0237	10	0.35671	T	0.21	.	15.5593	0.76229	1.0:0.0:0.0:0.0	.	770;901	E7EVL1;P40145	.;ADCY8_HUMAN	P	901;770	ENSP00000286355:S901P;ENSP00000367161:S770P	ENSP00000286355:S901P	S	-	1	0	ADCY8	131902823	1.000000	0.71417	0.111000	0.21465	0.636000	0.38137	8.811000	0.91954	2.277000	0.76020	0.528000	0.53228	TCA	.	.		0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
KCNQ3	3786	hgsc.bcm.edu	37	8	133153569	133153569	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:133153569C>T	ENST00000388996.4	-	10	1692	c.1272G>A	c.(1270-1272)ctG>ctA	p.L424L	KCNQ3_ENST00000519445.1_Silent_p.L424L|KCNQ3_ENST00000521134.1_Silent_p.L304L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	424					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CCAAGAGACCCAGCTTTTGGC	0.423																																					p.L424L		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1272A						.						66.0	69.0	68.0					8																	133153569		2203	4300	6503	SO:0001819	synonymous_variant	3786	exon10			GAGACCCAGCTTT	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1272G>A	chr8.hg19:g.133153569C>T		85.0	0.0		105.0	50.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	hg19	CCDS34943.1																																																																																			.	.		0.423	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
PTK2	5747	hgsc.bcm.edu	37	8	141753415	141753415	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:141753415C>A	ENST00000522684.1	-	20	1878	c.1649G>T	c.(1648-1650)cGg>cTg	p.R550L	PTK2_ENST00000340930.3_Missense_Mutation_p.R550L|PTK2_ENST00000517887.1_Missense_Mutation_p.R594L|PTK2_ENST00000521059.1_Missense_Mutation_p.R550L|PTK2_ENST00000519465.1_Missense_Mutation_p.R178L|PTK2_ENST00000519419.1_Missense_Mutation_p.R594L|PTK2_ENST00000538769.1_Missense_Mutation_p.R218L|PTK2_ENST00000520151.1_3'UTR|PTK2_ENST00000535192.1_Missense_Mutation_p.R550L|PTK2_ENST00000395218.2_Missense_Mutation_p.R550L	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	550	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CAGAACATTCCGAGCAGCAAT	0.338																																					p.R572L		Atlas-SNP	.											.	PTK2	311	.	0			c.G1715T						.						105.0	102.0	103.0					8																	141753415		2203	4300	6503	SO:0001583	missense	5747	exon20			ACATTCCGAGCAG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1649G>T	chr8.hg19:g.141753415C>A	ENSP00000429911:p.Arg550Leu	76.0	0.0		91.0	4.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346651	0.95807	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207	D;D;D;D;D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.997;0.999;0.996;1.0;0.996;0.996;0.999;0.999;0.996	D	0.95265	0.8372	10	0.87932	D	0	.	18.7608	0.91849	0.0:1.0:0.0:0.0	.	550;245;470;550;572;550;502;398;218;178	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	L	550;550;178;594;550;502;550;471;245;222;550;218;594;248;396	ENSP00000429911:R550L;ENSP00000438009:R550L;ENSP00000429170:R178L;ENSP00000429082:R594L;ENSP00000429474:R550L;ENSP00000378644:R550L;ENSP00000428492:R222L;ENSP00000341189:R550L;ENSP00000445742:R218L;ENSP00000429129:R594L;ENSP00000430603:R248L	ENSP00000341189:R550L	R	-	2	0	PTK2	141822597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.642000	0.83385	2.442000	0.82660	0.591000	0.81541	CGG	.	.		0.338	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
GPR20	2843	hgsc.bcm.edu	37	8	142366956	142366956	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:142366956G>T	ENST00000377741.3	-	2	1158	c.1068C>A	c.(1066-1068)ccC>ccA	p.P356P	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	356					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			ACTAAGCCTCGGGCCCATTAG	0.652																																					p.P356P		Atlas-SNP	.											.	GPR20	43	.	0			c.C1068A						.						25.0	25.0	25.0					8																	142366956		2203	4299	6502	SO:0001819	synonymous_variant	2843	exon2			AGCCTCGGGCCCA	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.1068C>A	chr8.hg19:g.142366956G>T		57.0	0.0		73.0	5.0	NM_005293	Q17R96	Silent	SNP	ENST00000377741.3	hg19	CCDS34949.1																																																																																			.	.		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
TSNARE1	203062	hgsc.bcm.edu	37	8	143436037	143436037	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143436037G>A	ENST00000307180.3	-	2	166	c.49C>T	c.(49-51)Cct>Tct	p.P17S	TSNARE1_ENST00000524325.1_Missense_Mutation_p.P17S|TSNARE1_ENST00000519651.1_Missense_Mutation_p.P17S|TSNARE1_ENST00000520166.1_Missense_Mutation_p.P17S	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	17					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCCGAAAGGGCCACGGCTC	0.607																																					p.P17S		Atlas-SNP	.											.	TSNARE1	59	.	0			c.C49T						.						51.0	46.0	47.0					8																	143436037		2203	4300	6503	SO:0001583	missense	203062	exon2			CGAAAGGGCCACG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.49C>T	chr8.hg19:g.143436037G>A	ENSP00000303437:p.Pro17Ser	58.0	0.0		64.0	5.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.392290	0.25118	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651;ENST00000520462;ENST00000518720	T;T;T;T;T;T	0.28666	2.21;2.19;2.21;1.6;1.88;1.85	3.47	2.57	0.30868	.	0.000000	0.32970	U	0.005437	T	0.20251	0.0487	L	0.32530	0.975	0.09310	N	1	B;B;B;B	0.29862	0.141;0.259;0.141;0.141	B;B;B;B	0.26614	0.043;0.071;0.043;0.043	T	0.17961	-1.0352	10	0.87932	D	0	-3.3269	7.0289	0.24956	0.1369:0.0:0.8631:0.0	.	17;17;17;17	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	S	17;17;17;17;17;33	ENSP00000428763:P17S;ENSP00000303437:P17S;ENSP00000427770:P17S;ENSP00000429679:P17S;ENSP00000429626:P17S;ENSP00000430789:P33S	ENSP00000303437:P17S	P	-	1	0	TSNARE1	143433944	0.145000	0.22656	0.002000	0.10522	0.641000	0.38312	0.823000	0.27366	0.728000	0.32382	0.563000	0.77884	CCT	.	.		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
BAI1	575	hgsc.bcm.edu	37	8	143603470	143603470	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143603470G>A	ENST00000517894.1	+	21	4063	c.3169G>A	c.(3169-3171)Ggc>Agc	p.G1057S	BAI1_ENST00000323289.5_Missense_Mutation_p.G1057S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1057					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCTCTGCCTGGGCTGGGGTGA	0.672																																					p.G1057S		Atlas-SNP	.											.	BAI1	146	.	0			c.G3169A						.						32.0	40.0	38.0					8																	143603470		2196	4296	6492	SO:0001583	missense	575	exon20			TGCCTGGGCTGGG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3169G>A	chr8.hg19:g.143603470G>A	ENSP00000430945:p.Gly1057Ser	64.0	0.0		57.0	4.0	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.06	3.016528	0.54468	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	D;D	0.84516	-1.86;-1.86	3.78	3.78	0.43462	.	0.151741	0.43260	U	0.000583	D	0.86969	0.6061	M	0.84219	2.685	0.58432	D	0.999999	B	0.24533	0.105	B	0.30401	0.115	D	0.87356	0.2341	10	0.72032	D	0.01	.	14.6053	0.68475	0.0:0.0:1.0:0.0	.	1057	E9PBK0	.	S	1057	ENSP00000430945:G1057S;ENSP00000313046:G1057S	ENSP00000313046:G1057S	G	+	1	0	BAI1	143600472	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.490000	0.97952	1.641000	0.50575	0.305000	0.20034	GGC	.	.		0.672	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
LYNX1	66004	hgsc.bcm.edu	37	8	143846491	143846491	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143846491G>A	ENST00000335822.5	-	4	849	c.222C>T	c.(220-222)tgC>tgT	p.C74C	RP11-706C16.7_ENST00000523657.1_RNA|LYNX1_ENST00000523332.1_Missense_Mutation_p.A82V|LYNX1_ENST00000317543.7_Silent_p.C40C	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	74	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.C74W(1)|p.C40W(1)		endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AGTCCCTCAGGCATCTGGATC	0.617																																					p.C74C		Atlas-SNP	.											LYNX1_ENST00000317543,NS,carcinoma,0,2	LYNX1	40	.	2	Substitution - Missense(2)	lung(2)	c.C222T						.						76.0	56.0	63.0					8																	143846491		2203	4300	6503	SO:0001819	synonymous_variant	66004	exon4			CCTCAGGCATCTG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.222C>T	chr8.hg19:g.143846491G>A		71.0	0.0		39.0	3.0	NM_023946	D3DWI7|G3XAC2|Q86SR0	Silent	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	G	7.555	0.663421	0.14710	.	.	ENSG00000180155	ENST00000523332	T	0.52754	0.65	3.73	0.841	0.18918	.	.	.	.	.	T	0.45558	0.1348	.	.	.	0.20489	N	0.999892	.	.	.	.	.	.	T	0.42865	-0.9426	6	0.87932	D	0	.	6.5234	0.22287	0.3369:0.0:0.6631:0.0	.	.	.	.	V	82	ENSP00000428713:A82V	ENSP00000428713:A82V	A	-	2	0	LYNX1	143843493	0.881000	0.30235	0.017000	0.16124	0.007000	0.05969	1.215000	0.32431	0.025000	0.15241	-0.492000	0.04666	GCC	.	.		0.617	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476	
PUF60	22827	hgsc.bcm.edu	37	8	144904074	144904074	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144904074A>G	ENST00000526683.1	-	3	676	c.121T>C	c.(121-123)Tcc>Ccc	p.S41P	PUF60_ENST00000313352.7_5'UTR|PUF60_ENST00000349157.6_Missense_Mutation_p.S41P|PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000456095.2_Missense_Mutation_p.S12P|PUF60_ENST00000527197.1_Missense_Mutation_p.S12P|PUF60_ENST00000453551.2_5'UTR	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	41	Inhibits homodimerization.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ATCTTGATGGAGTCTGTGCCC	0.632																																					p.S41P		Atlas-SNP	.											.	PUF60	26	.	0			c.T121C						.						30.0	35.0	33.0					8																	144904074		2050	4183	6233	SO:0001583	missense	22827	exon3			TGATGGAGTCTGT	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"""RNA binding motif (RRM) containing"""	17042	protein-coding gene	gene with protein product	"""siah binding protein 1"", ""FBP interacting repressor"", ""pyrimidine tract binding splicing factor"", ""Ro ribonucleoprotein binding protein 1"""	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.121T>C	chr8.hg19:g.144904074A>G	ENSP00000434359:p.Ser41Pro	61.0	0.0		61.0	4.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Missense_Mutation	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.888214	0.52014	.	.	ENSG00000179950	ENST00000526683;ENST00000456095;ENST00000349157;ENST00000527197;ENST00000526459;ENST00000529999;ENST00000531897;ENST00000533162	T;T;T;T;T;T;T;T	0.21543	2.53;2.59;2.42;2.51;2.59;3.43;3.35;2.0	5.13	-2.14	0.07123	.	.	.	.	.	T	0.08492	0.0211	N	0.08118	0	0.35256	D	0.779152	P;B;P	0.52316	0.952;0.0;0.92	B;B;B	0.44315	0.446;0.0;0.178	T	0.42292	-0.9460	9	0.39692	T	0.17	.	0.7891	0.01054	0.4676:0.1478:0.1474:0.2372	.	12;41;41	Q9UHX1-5;Q9UHX1-2;Q9UHX1	.;.;PUF60_HUMAN	P	41;12;41;12;40;78;78;78	ENSP00000434359:S41P;ENSP00000395417:S12P;ENSP00000322036:S41P;ENSP00000431960:S12P;ENSP00000432610:S40P;ENSP00000434863:S78P;ENSP00000437309:S78P;ENSP00000433403:S78P	ENSP00000322036:S41P	S	-	1	0	PUF60	144976062	0.849000	0.29639	0.513000	0.27749	0.942000	0.58702	0.603000	0.24149	-0.654000	0.05394	0.460000	0.39030	TCC	.	.		0.632	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281	
EPPK1	83481	hgsc.bcm.edu	37	8	144942463	144942463	+	Silent	SNP	G	G	T	rs377506188		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144942463G>T	ENST00000525985.1	-	2	5030	c.4959C>A	c.(4957-4959)acC>acA	p.T1653T				P58107	EPIPL_HUMAN	epiplakin 1	1653						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TATAGGGGTCGGTGTAGCCGG	0.632																																					p.T1653T		Atlas-SNP	.											.	EPPK1	199	.	0			c.C4959A						.						64.0	75.0	71.0					8																	144942463		1996	4154	6150	SO:0001819	synonymous_variant	83481	exon1			GGGGTCGGTGTAG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4959C>A	chr8.hg19:g.144942463G>T		146.0	0.0		152.0	7.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.632	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
PLEC	5339	hgsc.bcm.edu	37	8	144996328	144996328	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144996328T>C	ENST00000322810.4	-	32	8241	c.8072A>G	c.(8071-8073)gAg>gGg	p.E2691G	PLEC_ENST00000357649.2_Missense_Mutation_p.E2558G|PLEC_ENST00000398774.2_Missense_Mutation_p.E2522G|PLEC_ENST00000436759.2_Missense_Mutation_p.E2581G|PLEC_ENST00000356346.3_Missense_Mutation_p.E2540G|PLEC_ENST00000345136.3_Missense_Mutation_p.E2554G|PLEC_ENST00000354589.3_Missense_Mutation_p.E2554G|PLEC_ENST00000527096.1_Missense_Mutation_p.E2577G|PLEC_ENST00000354958.2_Missense_Mutation_p.E2532G	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2691	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCGCCGCGCCTCCTCCATGCT	0.711																																					p.E2691G		Atlas-SNP	.											.	PLEC	1144	.	0			c.A8072G						.						8.0	8.0	8.0					8																	144996328		2098	4151	6249	SO:0001583	missense	5339	exon32			CGCGCCTCCTCCA	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8072A>G	chr8.hg19:g.144996328T>C	ENSP00000323856:p.Glu2691Gly	50.0	0.0		48.0	4.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	7.992|7.992	0.753435|0.753435	0.15778|0.15778	.|.	.|.	ENSG00000178209|ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096|ENST00000527303	T;T;T;T;T;T;T;T;T|.	0.77229|.	-1.04;-1.04;-1.08;-1.08;-1.06;-1.04;-1.04;-1.04;-1.04|.	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.367509|.	0.19788|.	U|.	0.106041|.	T|T	0.58424|0.58424	0.2121|0.2121	L|L	0.43152|0.43152	1.355|1.355	0.36059|0.36059	D|D	0.841329|0.841329	P;P;P;P;P;P;P;P|.	0.42296|.	0.775;0.775;0.775;0.666;0.775;0.775;0.775;0.775|.	B;B;B;B;B;B;B;B|.	0.41412|.	0.356;0.356;0.356;0.194;0.356;0.356;0.356;0.356|.	T|T	0.64601|0.64601	-0.6369|-0.6369	10|5	0.72032|.	D|.	0.01|.	.|.	13.0896|13.0896	0.59160|0.59160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2581;2540;2532;2691;2522;2554;2558;2554|.	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4|.	.;.;.;PLEC_HUMAN;.;.;.;.|.	G|G	2554;2558;2554;2522;2691;2532;2540;2581;2577|124	ENSP00000344848:E2554G;ENSP00000350277:E2558G;ENSP00000346602:E2554G;ENSP00000381756:E2522G;ENSP00000323856:E2691G;ENSP00000347044:E2532G;ENSP00000348702:E2540G;ENSP00000388180:E2581G;ENSP00000434583:E2577G|.	ENSP00000323856:E2691G|.	E|R	-|-	2|1	0|2	PLEC|PLEC	145068316|145068316	0.954000|0.954000	0.32549|0.32549	1.000000|1.000000	0.80357|0.80357	0.415000|0.415000	0.31203|0.31203	2.021000|2.021000	0.41020|0.41020	1.773000|1.773000	0.52216|0.52216	0.364000|0.364000	0.22116|0.22116	GAG|AGG	.	.		0.711	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
EXOSC4	54512	hgsc.bcm.edu	37	8	145135446	145135446	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145135446T>C	ENST00000316052.5	+	3	783	c.680T>C	c.(679-681)cTc>cCc	p.L227P	GPAA1_ENST00000361036.6_5'Flank|GPAA1_ENST00000355091.4_5'Flank|CTD-3065J16.9_ENST00000524499.1_RNA	NM_019037.2	NP_061910.1	Q9NPD3	EXOS4_HUMAN	exosome component 4	227					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)			lung(4)|prostate(1)|upper_aerodigestive_tract(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GTGCACACCCTCTTAGATCGA	0.622																																					p.L227P		Atlas-SNP	.											.	EXOSC4	19	.	0			c.T680C						.						56.0	64.0	62.0					8																	145135446		2203	4300	6503	SO:0001583	missense	54512	exon3			ACACCCTCTTAGA	AF281133	CCDS6414.1	8q24.3	2004-03-26			ENSG00000178896	ENSG00000178896			18189	protein-coding gene	gene with protein product	"""exosome component Rrp41"""	606491				11110791	Standard	NM_019037		Approved	hRrp41p, FLJ20591, Rrp41p, RRP41, RRP41A, Ski6p, SKI6, p12A	uc003zau.3	Q9NPD3	OTTHUMG00000165437	ENST00000316052.5:c.680T>C	chr8.hg19:g.145135446T>C	ENSP00000315476:p.Leu227Pro	71.0	0.0		54.0	6.0	NM_019037		Missense_Mutation	SNP	ENST00000316052.5	hg19	CCDS6414.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.249010	0.59103	.	.	ENSG00000178896	ENST00000316052;ENST00000527954	T	0.74421	-0.84	5.38	5.38	0.77491	Exoribonuclease, phosphorolytic domain 2 (1);	0.384150	0.21994	N	0.066109	T	0.78780	0.4337	L	0.39898	1.24	0.80722	D	1	P	0.36944	0.574	P	0.54026	0.74	T	0.78229	-0.2285	10	0.46703	T	0.11	-32.6333	13.3251	0.60454	0.0:0.0:0.0:1.0	.	227	Q9NPD3	EXOS4_HUMAN	P	227;250	ENSP00000315476:L227P	ENSP00000315476:L227P	L	+	2	0	EXOSC4	145207434	1.000000	0.71417	0.299000	0.25016	0.529000	0.34654	5.537000	0.67186	2.046000	0.60703	0.459000	0.35465	CTC	.	.		0.622	EXOSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384065.1	NM_019037	
CPSF1	29894	hgsc.bcm.edu	37	8	145622853	145622853	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145622853T>C	ENST00000349769.3	-	22	2328	c.2234A>G	c.(2233-2235)gAg>gGg	p.E745G	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	745					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			ATACAGCATCTCCTCCTCGTC	0.692																																					p.E745G	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.A2234G						.						50.0	58.0	55.0					8																	145622853		2201	4296	6497	SO:0001583	missense	29894	exon22			AGCATCTCCTCCT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.2234A>G	chr8.hg19:g.145622853T>C	ENSP00000339353:p.Glu745Gly	70.0	0.0		78.0	4.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.021539	0.93462	.	.	ENSG00000071894	ENST00000349769	T	0.32515	1.45	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.40067	0.1102	L	0.58101	1.795	0.80722	D	1	P	0.51933	0.949	P	0.52343	0.696	T	0.14117	-1.0484	10	0.18276	T	0.48	-6.8196	13.3392	0.60535	0.0:0.0:0.0:1.0	.	745	Q10570	CPSF1_HUMAN	G	745	ENSP00000339353:E745G	ENSP00000339353:E745G	E	-	2	0	CPSF1	145593661	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.114000	0.77103	2.051000	0.60960	0.402000	0.26972	GAG	.	.		0.692	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
SLC39A4	55630	hgsc.bcm.edu	37	8	145640174	145640174	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145640174T>C	ENST00000301305.3	-	5	1016	c.911A>G	c.(910-912)cAg>cGg	p.Q304R	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.Q279R	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	304					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			TCCACTCAGCTGCTGTTGGAG	0.657																																					p.Q304R		Atlas-SNP	.											SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	.	0			c.A911G						.						52.0	54.0	53.0					8																	145640174		2203	4300	6503	SO:0001583	missense	55630	exon5			CTCAGCTGCTGTT	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.911A>G	chr8.hg19:g.145640174T>C	ENSP00000301305:p.Gln304Arg	94.0	1.0		75.0	3.0	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	hg19	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760629	0.69763	.	.	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.60920	0.15;0.34	4.98	4.98	0.66077	.	0.373720	0.26828	N	0.022284	T	0.64549	0.2608	M	0.62723	1.935	0.31638	N	0.648231	B;D	0.67145	0.275;0.996	B;P	0.53649	0.047;0.731	T	0.73116	-0.4084	10	0.72032	D	0.01	-19.829	11.0906	0.48113	0.0:0.0:0.0:1.0	.	304;279	Q6P5W5;A6NDY5	S39A4_HUMAN;.	R	279;304	ENSP00000276833:Q279R;ENSP00000301305:Q304R	ENSP00000276833:Q279R	Q	-	2	0	SLC39A4	145610982	0.996000	0.38824	1.000000	0.80357	0.915000	0.54546	1.317000	0.33631	1.903000	0.55091	0.444000	0.29173	CAG	.	.		0.657	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
TONSL	4796	hgsc.bcm.edu	37	8	145659654	145659654	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145659654G>T	ENST00000409379.3	-	21	3123	c.3094C>A	c.(3094-3096)Caa>Aaa	p.Q1032K	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1032					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						AGCACCTGTTGGTGCTCCCCT	0.662																																					p.Q1032K		Atlas-SNP	.											.	TONSL	128	.	0			c.C3094A						.						14.0	14.0	14.0					8																	145659654		2181	4275	6456	SO:0001583	missense	4796	exon21			CCTGTTGGTGCTC		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3094C>A	chr8.hg19:g.145659654G>T	ENSP00000386239:p.Gln1032Lys	125.0	0.0		90.0	4.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	G	0.058	-1.230958	0.01518	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.38722	1.12	5.08	4.19	0.49359	.	0.894593	0.09740	N	0.761961	T	0.38799	0.1054	L	0.50333	1.59	0.31259	N	0.693062	B	0.15473	0.013	B	0.11329	0.006	T	0.39078	-0.9631	10	0.16896	T	0.51	-1.0722	13.1015	0.59222	0.0:0.1628:0.8372:0.0	.	1032	Q96HA7	TONSL_HUMAN	K	1032;1031	ENSP00000386239:Q1032K	ENSP00000386239:Q1032K	Q	-	1	0	TONSL	145630462	0.997000	0.39634	0.229000	0.23960	0.055000	0.15305	2.490000	0.45294	1.102000	0.41551	0.462000	0.41574	CAA	.	.		0.662	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
SMARCA2	6595	hgsc.bcm.edu	37	9	2056807	2056807	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:2056807A>G	ENST00000382203.1	+	7	1518	c.1309A>G	c.(1309-1311)Aag>Gag	p.K437E	SMARCA2_ENST00000357248.2_Missense_Mutation_p.K437E|SMARCA2_ENST00000382194.1_Missense_Mutation_p.K437E|SMARCA2_ENST00000349721.2_Missense_Mutation_p.K437E			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	437	HSA. {ECO:0000255|PROSITE- ProRule:PRU00549}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GAAGCAGCAGAAGATTGAGCA	0.532																																					p.K437E		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A1309G						.						82.0	77.0	79.0					9																	2056807		2203	4300	6503	SO:0001583	missense	6595	exon7			CAGCAGAAGATTG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1309A>G	chr9.hg19:g.2056807A>G	ENSP00000371638:p.Lys437Glu	107.0	0.0		65.0	4.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.860069	0.91433	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	5.17	5.17	0.71159	Helicase/SANT-associated, DNA binding (1);HAS subgroup (1);HSA (1);	0.000000	0.85682	D	0.000000	D	0.85287	0.5662	M	0.86343	2.81	0.80722	D	1	D;D;D	0.69078	0.992;0.996;0.997	D;D;D	0.79108	0.933;0.987;0.992	D	0.86819	0.2003	10	0.46703	T	0.11	-33.2005	14.69	0.69080	1.0:0.0:0.0:0.0	.	38;437;437	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	E	437	ENSP00000265773:K437E;ENSP00000349788:K437E;ENSP00000392081:K437E;ENSP00000371638:K437E;ENSP00000371629:K437E	ENSP00000265773:K437E	K	+	1	0	SMARCA2	2046807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.305000	0.96197	1.946000	0.56461	0.533000	0.62120	AAG	.	.		0.532	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
ERMP1	79956	hgsc.bcm.edu	37	9	5830996	5830996	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:5830996G>T	ENST00000339450.5	-	2	460	c.371C>A	c.(370-372)cCc>cAc	p.P124H	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_5'Flank	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	124						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TGTAGTCCTGGGGCCAATGGA	0.393																																					p.P124H		Atlas-SNP	.											.	ERMP1	63	.	0			c.C371A						.						98.0	97.0	97.0					9																	5830996		2203	4300	6503	SO:0001583	missense	79956	exon2			GTCCTGGGGCCAA	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.371C>A	chr9.hg19:g.5830996G>T	ENSP00000340427:p.Pro124His	134.0	0.0		89.0	4.0	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	hg19	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.929829	0.73327	.	.	ENSG00000099219	ENST00000339450	T	0.55930	0.49	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.62816	0.2459	M	0.73319	2.225	0.80722	D	1	D;P	0.53462	0.96;0.941	P;P	0.48425	0.46;0.577	T	0.61515	-0.7047	10	0.36615	T	0.2	-15.9811	20.0124	0.97464	0.0:0.0:1.0:0.0	.	124;124	E7ER77;Q7Z2K6	.;ERMP1_HUMAN	H	124	ENSP00000340427:P124H	ENSP00000340427:P124H	P	-	2	0	ERMP1	5820996	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.749000	0.94314	0.655000	0.94253	CCC	.	.		0.393	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
BNC2	54796	hgsc.bcm.edu	37	9	16552604	16552604	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:16552604T>C	ENST00000380672.4	-	5	650	c.593A>G	c.(592-594)aAg>aGg	p.K198R	BNC2_ENST00000380666.2_Missense_Mutation_p.K198R|BNC2_ENST00000380667.2_Missense_Mutation_p.K131R|BNC2_ENST00000545497.1_Missense_Mutation_p.K103R	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CTCCTCTTGCTTCAGGACGCT	0.562																																					p.K198R		Atlas-SNP	.											.	BNC2	166	.	0			c.A593G						.						111.0	81.0	91.0					9																	16552604		2203	4300	6503	SO:0001583	missense	54796	exon5			TCTTGCTTCAGGA	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.593A>G	chr9.hg19:g.16552604T>C	ENSP00000370047:p.Lys198Arg	163.0	0.0		77.0	5.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	T	35	5.446621	0.96205	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	T;T;T;T;T	0.03772	3.81;3.81;3.81;3.81;3.81	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.53249	1.67	0.80722	D	1	D;B;D;D;D;D;B	0.89917	0.999;0.127;0.992;0.996;1.0;0.993;0.272	D;B;D;D;D;D;B	0.91635	0.994;0.109;0.984;0.99;0.999;0.956;0.153	T	0.00054	-1.2182	10	0.66056	D	0.02	-25.3735	16.6512	0.85203	0.0:0.0:0.0:1.0	.	103;131;235;198;24;156;198	F5H586;B1APH0;Q06HC4;Q6ZN30-2;B4E3J2;Q5H9S4;Q6ZN30	.;.;.;.;.;.;BNC2_HUMAN	R	198;155;235;226;131;103;24;198;198	ENSP00000370047:K198R;ENSP00000408370:K155R;ENSP00000370042:K131R;ENSP00000444640:K103R;ENSP00000370041:K198R	ENSP00000370041:K198R	K	-	2	0	BNC2	16542604	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.333000	0.79357	0.482000	0.46254	AAG	.	.		0.562	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
CNTLN	54875	hgsc.bcm.edu	37	9	17332673	17332673	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:17332673A>G	ENST00000380647.3	+	10	1673	c.1589A>G	c.(1588-1590)aAg>aGg	p.K530R	CNTLN_ENST00000425824.1_Missense_Mutation_p.K530R|CNTLN_ENST00000262360.5_Missense_Mutation_p.K530R			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	530					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GAGCTACAGAAGCTGAGAAAA	0.383																																					p.K530R		Atlas-SNP	.											.	CNTLN	128	.	0			c.A1589G						.						73.0	69.0	70.0					9																	17332673		1836	4082	5918	SO:0001583	missense	54875	exon10			TACAGAAGCTGAG	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1589A>G	chr9.hg19:g.17332673A>G	ENSP00000370021:p.Lys530Arg	244.0	0.0		137.0	6.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.626434	0.28978	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.13307	2.6;2.6;2.6	5.54	5.54	0.83059	.	.	.	.	.	T	0.16557	0.0398	L	0.34521	1.04	0.31547	N	0.659277	P;P;P	0.42692	0.787;0.787;0.787	P;P;P	0.46758	0.526;0.526;0.526	T	0.04635	-1.0937	9	0.20519	T	0.43	.	15.3261	0.74164	1.0:0.0:0.0:0.0	.	530;530;530	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	R	530	ENSP00000370021:K530R;ENSP00000392798:K530R;ENSP00000262360:K530R	ENSP00000262360:K530R	K	+	2	0	CNTLN	17322673	1.000000	0.71417	0.986000	0.45419	0.780000	0.44128	3.434000	0.52841	2.098000	0.63641	0.482000	0.46254	AAG	.	.		0.383	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
SH3GL2	6456	hgsc.bcm.edu	37	9	17791315	17791315	+	Silent	SNP	G	G	T	rs150625805	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:17791315G>T	ENST00000380607.4	+	7	831	c.711G>T	c.(709-711)acG>acT	p.T237T	SH3GL2_ENST00000537391.1_Silent_p.T190T	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	237	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		AGCAAGTCACGGTCAGACTGG	0.423																																					p.T237T		Atlas-SNP	.											.	SH3GL2	60	.	0			c.G711T						.						143.0	132.0	136.0					9																	17791315		2203	4300	6503	SO:0001819	synonymous_variant	6456	exon7			AGTCACGGTCAGA	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.711G>T	chr9.hg19:g.17791315G>T		234.0	0.0		91.0	4.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	G|0.998;A|0.002		0.423	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026	
FOCAD	54914	hgsc.bcm.edu	37	9	20907148	20907148	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:20907148G>T	ENST00000380249.1	+	24	2989		c.e24-1		FOCAD_ENST00000605086.1_Splice_Site|FOCAD_ENST00000338382.6_Splice_Site	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin							focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ttttcccataggttcatatcc	0.363																																					.		Atlas-SNP	.											.	.	.	.	0			c.2626-1G>T						.						116.0	107.0	110.0					9																	20907148		2203	4300	6503	SO:0001630	splice_region_variant	54914	exon24			CCCATAGGTTCAT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2626-1G>T	chr9.hg19:g.20907148G>T		80.0	0.0		64.0	4.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Splice_Site	SNP	ENST00000380249.1	hg19	CCDS34993.1																																																																																			.	.		0.363	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	Intron
TEK	7010	hgsc.bcm.edu	37	9	27212778	27212778	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:27212778G>T	ENST00000380036.4	+	17	3202	c.2760G>T	c.(2758-2760)ctG>ctT	p.L920L	TEK_ENST00000519097.1_Silent_p.L772L|TEK_ENST00000406359.4_Silent_p.L877L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	920	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	GCCGTGTGCTGGAGACGGACC	0.597																																					p.L920L		Atlas-SNP	.											.	TEK	250	.	0			c.G2760T						.						97.0	76.0	83.0					9																	27212778		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon17			TGTGCTGGAGACG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2760G>T	chr9.hg19:g.27212778G>T		141.0	0.0		84.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.597	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
NFX1	4799	hgsc.bcm.edu	37	9	33364038	33364038	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:33364038G>T	ENST00000379540.3	+	20	2966	c.2904G>T	c.(2902-2904)gaG>gaT	p.E968D	NFX1_ENST00000379521.4_Missense_Mutation_p.E968D	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	968					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATATCAGTGAGGATTCTGATC	0.403																																					p.E968D		Atlas-SNP	.											.	NFX1	85	.	0			c.G2904T						.						142.0	130.0	134.0					9																	33364038		2203	4300	6503	SO:0001583	missense	4799	exon20			CAGTGAGGATTCT	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.2904G>T	chr9.hg19:g.33364038G>T	ENSP00000368856:p.Glu968Asp	173.0	0.0		136.0	6.0	NM_147133	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	G	8.494	0.862744	0.17178	.	.	ENSG00000086102	ENST00000379540;ENST00000379521	T;T	0.22743	2.27;1.94	6.08	-12.2	0.00006	.	0.561473	0.20789	N	0.085649	T	0.04407	0.0121	N	0.05467	-0.045	0.38185	D	0.939728	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42865	-0.9426	10	0.12430	T	0.62	-1.2131	1.8683	0.03203	0.3128:0.3206:0.2358:0.1309	.	968;968	Q12986;Q12986-2	NFX1_HUMAN;.	D	968	ENSP00000368856:E968D;ENSP00000368836:E968D	ENSP00000368836:E968D	E	+	3	2	NFX1	33354038	0.000000	0.05858	0.495000	0.27527	0.918000	0.54935	-2.966000	0.00670	-2.052000	0.00902	-0.282000	0.10007	GAG	.	.		0.403	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1		
FRMPD1	22844	hgsc.bcm.edu	37	9	37737222	37737222	+	Silent	SNP	C	C	A	rs550100323		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:37737222C>A	ENST00000539465.1	+	14	2124	c.1531C>A	c.(1531-1533)Cgg>Agg	p.R511R	FRMPD1_ENST00000541302.1_Silent_p.R380R|FRMPD1_ENST00000377765.3_Silent_p.R511R|FRMPD1_ENST00000536622.1_Silent_p.R333R|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	511						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		ACAAGCGCACCGGGTATCTGC	0.537																																					p.R511R		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C1531A						.						80.0	73.0	75.0					9																	37737222		2203	4300	6503	SO:0001819	synonymous_variant	22844	exon14			GCGCACCGGGTAT	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1531C>A	chr9.hg19:g.37737222C>A		122.0	0.0		106.0	5.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	hg19	CCDS6612.1																																																																																			.	.		0.537	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
TJP2	9414	hgsc.bcm.edu	37	9	71842715	71842715	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:71842715T>C	ENST00000377245.4	+	8	1453	c.1245T>C	c.(1243-1245)tcT>tcC	p.S415S	TJP2_ENST00000453658.2_Silent_p.S392S|TJP2_ENST00000348208.4_Silent_p.S415S|TJP2_ENST00000265384.7_Silent_p.S415S|TJP2_ENST00000535702.1_Silent_p.S419S|TJP2_ENST00000539225.1_Silent_p.S446S	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	415					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GATCATTTTCTCCAGAGGAGA	0.318																																					p.S446S		Atlas-SNP	.											.	TJP2	120	.	0			c.T1338C						.						76.0	71.0	73.0					9																	71842715		2203	4300	6503	SO:0001819	synonymous_variant	9414	exon8			ATTTTCTCCAGAG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1245T>C	chr9.hg19:g.71842715T>C		142.0	0.0		91.0	5.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	hg19	CCDS6627.1																																																																																			.	.		0.318	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
FAM189A2	9413	hgsc.bcm.edu	37	9	72003281	72003281	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:72003281A>G	ENST00000257515.8	+	10	1484	c.1064A>G	c.(1063-1065)gAa>gGa	p.E355G	FAM189A2_ENST00000455972.1_Missense_Mutation_p.E355G|FAM189A2_ENST00000303068.7_Missense_Mutation_p.E190G|FAM189A2_ENST00000377216.3_Missense_Mutation_p.E142G|FAM189A2_ENST00000469179.1_3'UTR	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2	355						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GACATCCATGAACTTGTAGAA	0.438																																					p.E355G		Atlas-SNP	.											.	FAM189A2	55	.	0			c.A1064G						.						61.0	58.0	59.0					9																	72003281		2203	4300	6503	SO:0001583	missense	9413	exon10			TCCATGAACTTGT	L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"""chromosome 9 open reading frame 61"""	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.1064A>G	chr9.hg19:g.72003281A>G	ENSP00000257515:p.Glu355Gly	140.0	0.0		94.0	4.0	NM_004816	Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Missense_Mutation	SNP	ENST00000257515.8	hg19	CCDS6629.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.924268	0.92319	.	.	ENSG00000135063	ENST00000455972;ENST00000257515;ENST00000303068;ENST00000377225;ENST00000377216	T;T;T	0.35605	2.35;2.35;1.3	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.58524	0.2128	M	0.62723	1.935	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.61068	-0.7137	10	0.72032	D	0.01	-19.6869	16.1549	0.81657	1.0:0.0:0.0:0.0	.	355	Q15884	F1892_HUMAN	G	355;355;190;354;142	ENSP00000395675:E355G;ENSP00000257515:E355G;ENSP00000304435:E190G	ENSP00000257515:E355G	E	+	2	0	FAM189A2	71193101	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.210000	0.95106	2.209000	0.71365	0.533000	0.62120	GAA	.	.		0.438	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816	
MAMDC2	256691	hgsc.bcm.edu	37	9	72728033	72728033	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:72728033T>C	ENST00000377182.4	+	5	1245	c.628T>C	c.(628-630)Ttc>Ctc	p.F210L	MAMDC2-AS1_ENST00000414515.3_RNA|MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	210	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GGATCACACCTTCAAGAGTGA	0.493																																					p.F210L		Atlas-SNP	.											.	MAMDC2	55	.	0			c.T628C						.						92.0	82.0	86.0					9																	72728033		2203	4300	6503	SO:0001583	missense	256691	exon5			CACACCTTCAAGA	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.628T>C	chr9.hg19:g.72728033T>C	ENSP00000366387:p.Phe210Leu	120.0	0.0		96.0	4.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	hg19	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	T	2.869	-0.234515	0.05983	.	.	ENSG00000165072	ENST00000377182	T	0.01804	4.63	5.72	3.39	0.38822	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.662303	0.16615	N	0.206726	T	0.00580	0.0019	N	0.00690	-1.25	0.24804	N	0.992684	B	0.02656	0.0	B	0.08055	0.003	T	0.45264	-0.9273	10	0.07325	T	0.83	-11.9473	4.5903	0.12304	0.0:0.4564:0.0:0.5436	.	210	Q7Z304	MAMC2_HUMAN	L	210	ENSP00000366387:F210L	ENSP00000366387:F210L	F	+	1	0	MAMDC2	71917853	0.475000	0.25894	0.714000	0.30535	0.704000	0.40688	0.784000	0.26816	1.001000	0.39076	0.379000	0.24179	TTC	.	.		0.493	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
PCSK5	5125	hgsc.bcm.edu	37	9	78749051	78749051	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:78749051A>G	ENST00000545128.1	+	10	1773	c.1235A>G	c.(1234-1236)cAg>cGg	p.Q412R	PCSK5_ENST00000376767.3_Missense_Mutation_p.Q412R|PCSK5_ENST00000376752.4_Missense_Mutation_p.Q412R	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	412	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						AGAGACGTACAGCATGTTATT	0.433																																					p.Q412R		Atlas-SNP	.											.	PCSK5	329	.	0			c.A1235G						.						133.0	123.0	126.0					9																	78749051		2203	4300	6503	SO:0001583	missense	5125	exon10			ACGTACAGCATGT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1235A>G	chr9.hg19:g.78749051A>G	ENSP00000446280:p.Gln412Arg	73.0	0.0		72.0	4.0	NM_006200	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	hg19	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.661280	0.88154	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	D	0.93148	0.7818	M	0.76328	2.33	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93660	0.6981	10	0.66056	D	0.02	-22.4224	16.3426	0.83092	1.0:0.0:0.0:0.0	.	412;412	Q92824-2;B1AMG5	.;.	R	412;115;412;412;412;85	ENSP00000446280:Q412R;ENSP00000365958:Q412R;ENSP00000365943:Q412R;ENSP00000411654:Q85R	ENSP00000365943:Q412R	Q	+	2	0	PCSK5	77938871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.317000	0.78254	0.460000	0.39030	CAG	.	.		0.433	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPATA31D1	389763	hgsc.bcm.edu	37	9	84608274	84608274	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:84608274C>A	ENST00000344803.2	+	4	2936	c.2889C>A	c.(2887-2889)tcC>tcA	p.S963S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	963					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCTCTAAGTCCCGTAGTCGAA	0.507																																					p.S963S		Atlas-SNP	.											.	.	.	.	0			c.C2889A						.						102.0	99.0	100.0					9																	84608274		1885	4128	6013	SO:0001819	synonymous_variant	389763	exon4			TAAGTCCCGTAGT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2889C>A	chr9.hg19:g.84608274C>A		107.0	0.0		89.0	4.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.		0.507	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
NTRK2	4915	hgsc.bcm.edu	37	9	87339221	87339221	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:87339221C>T	ENST00000323115.4	+	7	1156	c.803C>T	c.(802-804)gCg>gTg	p.A268V	NTRK2_ENST00000359847.3_Missense_Mutation_p.A268V|NTRK2_ENST00000376208.1_Missense_Mutation_p.A268V|NTRK2_ENST00000376213.1_Missense_Mutation_p.A268V|NTRK2_ENST00000395866.2_Missense_Mutation_p.A112V|NTRK2_ENST00000376214.1_Missense_Mutation_p.A268V|NTRK2_ENST00000395882.1_Missense_Mutation_p.A268V|NTRK2_ENST00000304053.6_Missense_Mutation_p.A268V|NTRK2_ENST00000277120.3_Missense_Mutation_p.A268V			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	268	Ig-like C2-type 1.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TCTTGTGTGGCGGAAAATCTT	0.408										TSP Lung(25;0.17)																											p.A268V		Atlas-SNP	.											.	NTRK2	331	.	0			c.C803T						.						215.0	204.0	208.0					9																	87339221		2203	4300	6503	SO:0001583	missense	4915	exon8			GTGTGGCGGAAAA	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.803C>T	chr9.hg19:g.87339221C>T	ENSP00000314586:p.Ala268Val	188.0	0.0		140.0	35.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067874	0.93950	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.27	5.27	0.74061	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054584	0.64402	D	0.000001	D	0.84566	0.5500	M	0.83692	2.655	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.995;0.995;0.997;0.987;0.977;0.999;0.995	T	0.80966	-0.1146	10	0.15952	T	0.53	.	19.2585	0.93957	0.0:1.0:0.0:0.0	.	112;268;268;268;268;268;314;268	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	V	268;268;268;268;268;268;268;268;112	ENSP00000365387:A268V;ENSP00000365386:A268V;ENSP00000379221:A268V;ENSP00000365381:A268V;ENSP00000306167:A268V;ENSP00000277120:A268V;ENSP00000314586:A268V;ENSP00000352906:A268V;ENSP00000379207:A112V	ENSP00000277120:A268V	A	+	2	0	NTRK2	86529041	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.453000	0.73488	2.627000	0.88993	0.460000	0.39030	GCG	.	.		0.408	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1		
WNK2	65268	hgsc.bcm.edu	37	9	96079837	96079837	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:96079837T>C	ENST00000297954.4	+	29	6663	c.6663T>C	c.(6661-6663)cgT>cgC	p.R2221R	WNK2_ENST00000395477.2_Silent_p.R2184R|WNK2_ENST00000356055.3_3'UTR|WNK2_ENST00000471076.1_3'UTR|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.R1833R|WNK2_ENST00000427277.2_Silent_p.R1796R	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2221					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GGATGCCACGTCTGCCCCCAG	0.637																																					p.R2184R		Atlas-SNP	.											.	WNK2	277	.	0			c.T6552C						.						79.0	70.0	73.0					9																	96079837		2203	4300	6503	SO:0001819	synonymous_variant	65268	exon28			GCCACGTCTGCCC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6663T>C	chr9.hg19:g.96079837T>C		131.0	0.0		96.0	4.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.231|9.231	1.035854|1.035854	0.19590|0.19590	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	.|.	.|.	.|.	5.53|5.53	0.617|0.617	0.17619|0.17619	.|.	.|.	.|.	.|.	.|.	T|T	0.34687|0.34687	0.0906|0.0906	.|.	.|.	.|.	0.23036|0.23036	N|N	0.998394|0.998394	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28202|0.28202	-1.0051|-1.0051	4|4	.|.	.|.	.|.	.|.	9.2033|9.2033	0.37272|0.37272	0.0:0.4499:0.0:0.5501|0.0:0.4499:0.0:0.5501	.|.	.|.	.|.	.|.	P|A	1676|2180;981	.|.	.|.	S|V	+|+	1|2	0|0	WNK2|WNK2	95119658|95119658	0.878000|0.878000	0.30173|0.30173	0.136000|0.136000	0.22124|0.22124	0.825000|0.825000	0.46686|0.46686	0.410000|0.410000	0.21098|0.21098	-0.118000|-0.118000	0.11851|0.11851	0.528000|0.528000	0.53228|0.53228	TCT|GTC	.	.		0.637	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
PTPDC1	138639	hgsc.bcm.edu	37	9	96827014	96827014	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:96827014A>G	ENST00000375360.3	+	2	334		c.e2-1			NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1						cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						TTTTTCCAACAGACTACCATG	0.388																																					.		Atlas-SNP	.											.	PTPDC1	134	.	0			.						.						88.0	87.0	88.0					9																	96827014		2203	4300	6503	SO:0001630	splice_region_variant	138639	.			TCCAACAGACTAC	BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	30184	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase PTP9Q22"""					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.-6-1A>G	chr9.hg19:g.96827014A>G		78.0	0.0		46.0	4.0	.	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Splice_Site	SNP	ENST00000375360.3	hg19	CCDS6707.1																																																																																			.	.		0.388	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422	Intron
HIATL1	84641	hgsc.bcm.edu	37	9	97218607	97218607	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:97218607T>C	ENST00000375344.3	+	10	1383	c.1114T>C	c.(1114-1116)Tca>Cca	p.S372P	HIATL1_ENST00000428393.2_Intron	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	372					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				GAATGCAGAGTCAGATCAGCA	0.567																																					p.S372P	Pancreas(77;1260 1915 1973 10423)	Atlas-SNP	.											.	HIATL1	31	.	0			c.T1114C						.						115.0	90.0	99.0					9																	97218607		2203	4300	6503	SO:0001583	missense	84641	exon10			GCAGAGTCAGATC	AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.1114T>C	chr9.hg19:g.97218607T>C	ENSP00000364493:p.Ser372Pro	112.0	0.0		84.0	4.0	NM_032558	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Missense_Mutation	SNP	ENST00000375344.3	hg19	CCDS6710.2	.	.	.	.	.	.	.	.	.	.	T	3.671	-0.067489	0.07273	.	.	ENSG00000148110	ENST00000375344;ENST00000277183	T	0.54071	0.59	4.96	1.4	0.22301	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.122256	0.36338	N	0.002646	T	0.17238	0.0414	N	0.01431	-0.87	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.05194	-1.0900	10	0.09338	T	0.73	-1.2852	3.9325	0.09292	0.0:0.3154:0.1895:0.4951	.	372	Q5SR56	HIAL1_HUMAN	P	372;77	ENSP00000364493:S372P	ENSP00000277183:S77P	S	+	1	0	HIATL1	96258428	0.620000	0.27068	1.000000	0.80357	0.993000	0.82548	0.504000	0.22626	0.468000	0.27243	0.533000	0.62120	TCA	.	.		0.567	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98643510	98643510	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:98643510G>A	ENST00000288985.7	+	2	744	c.439G>A	c.(439-441)Gga>Aga	p.G147R	ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	147	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										GTTTCTTTATGGACACTACAT	0.373																																					p.G147R		Atlas-SNP	.											.	.	.	.	0			c.G439A						.						78.0	79.0	79.0					9																	98643510		2203	4300	6503	SO:0001583	missense	375748	exon2			CTTTATGGACACT	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.439G>A	chr9.hg19:g.98643510G>A	ENSP00000288985:p.Gly147Arg	96.0	0.0		79.0	4.0	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	hg19	CCDS35072.1	.	.	.	.	.	.	.	.	.	.	G	1.646	-0.515159	0.04200	.	.	ENSG00000182150	ENST00000288985	D	0.92397	-3.03	5.32	2.49	0.30216	DEAD-like helicase (2);SNF2-related (1);	0.740189	0.12278	N	0.483201	T	0.73837	0.3638	N	0.01297	-0.9	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.60989	-0.7153	10	0.16420	T	0.52	-1.7485	4.7574	0.13092	0.3734:0.0:0.4875:0.1391	.	147	Q5T890	RAD26_HUMAN	R	147	ENSP00000288985:G147R	ENSP00000288985:G147R	G	+	1	0	C9orf102	97683331	0.999000	0.42202	0.990000	0.47175	0.841000	0.47740	0.630000	0.24553	0.376000	0.24707	0.591000	0.81541	GGA	.	.		0.373	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	
CCDC180	100499483	hgsc.bcm.edu	37	9	100080840	100080840	+	Missense_Mutation	SNP	G	G	T	rs368120179		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:100080840G>T	ENST00000357054.1	+	24	2539	c.1604G>T	c.(1603-1605)cGg>cTg	p.R535L	RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_Intron|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.R396L|CCDC180_ENST00000411667.2_Missense_Mutation_p.R393L|CCDC180_ENST00000529487.1_Missense_Mutation_p.R396L			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	535						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R535Q(1)									CAGCAAAGGCGGCTGAAGCAT	0.602																																					p.R396L		Atlas-SNP	.											KIAA1529,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1187T						.						78.0	63.0	68.0					9																	100080840		2203	4300	6503	SO:0001583	missense	0	exon10			AAAGGCGGCTGAA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.1604G>T	chr9.hg19:g.100080840G>T	ENSP00000349562:p.Arg535Leu	36.0	0.0		26.0	2.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.93	2.977491	0.53720	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	4.61	4.61	0.57282	.	0.229630	0.36409	N	0.002610	T	0.48822	0.1521	M	0.74258	2.255	0.20307	N	0.999916	D;D;D;D	0.89917	0.962;1.0;1.0;1.0	B;D;D;D	0.91635	0.358;0.999;0.999;0.999	T	0.34925	-0.9809	10	0.37606	T	0.19	-25.4457	13.1516	0.59492	0.0:0.0:1.0:0.0	.	393;535;396;535	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	L	535;396;393;419;396	ENSP00000349562:R535L;ENSP00000364348:R396L;ENSP00000414000:R393L;ENSP00000434727:R396L	ENSP00000349562:R535L	R	+	2	0	C9orf174	99120661	0.860000	0.29831	0.335000	0.25508	0.014000	0.08584	3.458000	0.53014	2.548000	0.85928	0.563000	0.77884	CGG	.	.		0.602	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
C9orf156	51531	hgsc.bcm.edu	37	9	100667081	100667081	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:100667081G>T	ENST00000375119.3	-	5	1336	c.1260C>A	c.(1258-1260)atC>atA	p.I420I		NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	420					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				AAGCCGGCTTGATCCTCAGCA	0.522																																					p.I420I		Atlas-SNP	.											.	C9orf156	35	.	0			c.C1260A						.						111.0	104.0	106.0					9																	100667081		2203	4300	6503	SO:0001819	synonymous_variant	51531	exon5			CGGCTTGATCCTC	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.1260C>A	chr9.hg19:g.100667081G>T		122.0	0.0		106.0	6.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	hg19	CCDS6730.1																																																																																			.	.		0.522	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
TEX10	54881	hgsc.bcm.edu	37	9	103090232	103090232	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:103090232T>C	ENST00000374902.4	-	8	1814	c.1638A>G	c.(1636-1638)aaA>aaG	p.K546K	TEX10_ENST00000535814.1_Silent_p.K549K	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	546						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GGGATAACACTTTACTACGAT	0.348																																					p.K549K		Atlas-SNP	.											.	TEX10	99	.	0			c.A1647G						.						79.0	67.0	71.0					9																	103090232		2203	4300	6503	SO:0001819	synonymous_variant	54881	exon8			TAACACTTTACTA	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"""testis expressed gene 10"", ""testis expressed sequence 10"""			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1638A>G	chr9.hg19:g.103090232T>C		113.0	0.0		113.0	5.0	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	hg19	CCDS6748.1																																																																																			.	.		0.348	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	
CYLC2	1539	hgsc.bcm.edu	37	9	105767096	105767096	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:105767096A>G	ENST00000374798.3	+	4	370	c.300A>G	c.(298-300)aaA>aaG	p.K100K	CYLC2_ENST00000487798.1_Silent_p.K100K	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	100	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				AGCCTCTCAAACCAACTCGTA	0.378																																					p.K100K		Atlas-SNP	.											CYLC2,NS,carcinoma,0,1	CYLC2	109	.	0			c.A300G						.						60.0	60.0	60.0					9																	105767096		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon4			TCTCAAACCAACT	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.300A>G	chr9.hg19:g.105767096A>G		65.0	0.0		46.0	2.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.378	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340	
SMC2	10592	hgsc.bcm.edu	37	9	106877083	106877083	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:106877083A>G	ENST00000286398.7	+	13	1932	c.1644A>G	c.(1642-1644)cgA>cgG	p.R548R	SMC2_ENST00000374793.3_Silent_p.R548R|SMC2_ENST00000303219.8_Silent_p.R548R|SMC2_ENST00000374787.3_Silent_p.R548R	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	548	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						CTGGAGAACGACTCTACAATG	0.338																																					p.R548R		Atlas-SNP	.											SMC2L1,NS,carcinoma,0,2	SMC2	127	.	0			c.A1644G						.						91.0	87.0	89.0					9																	106877083		2203	4300	6503	SO:0001819	synonymous_variant	10592	exon13			AGAACGACTCTAC	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.1644A>G	chr9.hg19:g.106877083A>G		99.0	2.0		81.0	4.0	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	hg19	CCDS35086.1																																																																																			.	.		0.338	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
OR13D1	286365	hgsc.bcm.edu	37	9	107457666	107457666	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:107457666T>C	ENST00000318763.5	+	1	1007	c.964T>C	c.(964-966)Tat>Cat	p.Y322H		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	322						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCCCATCATCTATAGCCTCAG	0.388																																					p.Y322H		Atlas-SNP	.											.	OR13D1	42	.	0			c.T964C						.						87.0	90.0	89.0					9																	107457666		2203	4300	6503	SO:0001583	missense	286365	exon1			ATCATCTATAGCC		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.964T>C	chr9.hg19:g.107457666T>C	ENSP00000317357:p.Tyr322His	137.0	0.0		90.0	4.0	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	hg19	CCDS35094.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.899063	0.33535	.	.	ENSG00000179055	ENST00000318763	T	0.61859	0.07	3.65	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41294	D	0.000901	T	0.76659	0.4018	M	0.92026	3.265	0.41997	D	0.990879	D	0.76494	0.999	D	0.67103	0.949	T	0.80317	-0.1433	10	0.87932	D	0	.	8.5813	0.33630	0.0:0.0:0.0:1.0	.	322	Q8NGV5	O13D1_HUMAN	H	322	ENSP00000317357:Y322H	ENSP00000317357:Y322H	Y	+	1	0	OR13D1	106497487	1.000000	0.71417	0.264000	0.24511	0.100000	0.18952	5.656000	0.67988	1.515000	0.48885	0.418000	0.28097	TAT	.	.		0.388	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
RAD23B	5887	hgsc.bcm.edu	37	9	110045933	110045933	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:110045933T>C	ENST00000358015.3	+	1	374	c.23T>C	c.(22-24)cTc>cCc	p.L8P	RAD23B_ENST00000416373.2_5'Flank	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	8	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CTGAAGACCCTCCAGCAGCAG	0.756								Direct reversal of damage;Nucleotide excision repair (NER)																													p.L8P		Atlas-SNP	.											.	RAD23B	31	.	0			c.T23C						.						9.0	7.0	8.0					9																	110045933		2060	4010	6070	SO:0001583	missense	5887	exon1			AGACCCTCCAGCA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.23T>C	chr9.hg19:g.110045933T>C	ENSP00000350708:p.Leu8Pro	76.0	0.0		39.0	4.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	t	11.88	1.769288	0.31320	.	.	ENSG00000119318	ENST00000419616;ENST00000358015	T;T	0.75821	-0.97;-0.97	4.3	4.3	0.51218	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.64402	D	0.000004	D	0.88998	0.6590	H	0.95402	3.665	0.80722	D	1	D;D	0.69078	0.997;0.993	D;D	0.81914	0.995;0.995	D	0.91075	0.4895	10	0.87932	D	0	-6.4507	11.0015	0.47609	0.0:0.0:0.0:1.0	.	8;8	B4DEA3;P54727	.;RD23B_HUMAN	P	8	ENSP00000416868:L8P;ENSP00000350708:L8P	ENSP00000350708:L8P	L	+	2	0	RAD23B	109085754	1.000000	0.71417	0.996000	0.52242	0.045000	0.14185	3.417000	0.52714	1.575000	0.49775	0.451000	0.29950	CTC	.	.		0.756	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
IKBKAP	8518	hgsc.bcm.edu	37	9	111665171	111665171	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:111665171A>G	ENST00000374647.5	-	16	2109	c.1802T>C	c.(1801-1803)gTt>gCt	p.V601A	IKBKAP_ENST00000537196.1_Missense_Mutation_p.V252A	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	601					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AGGAAACCGAACAGGAAATCC	0.453																																					p.V601A		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T1802C						.						115.0	114.0	114.0					9																	111665171		2203	4300	6503	SO:0001583	missense	8518	exon16			AACCGAACAGGAA	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1802T>C	chr9.hg19:g.111665171A>G	ENSP00000363779:p.Val601Ala	175.0	0.0		120.0	6.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807873	0.70797	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26957	1.7;1.7	5.52	5.52	0.82312	.	0.267708	0.35970	N	0.002871	T	0.31199	0.0789	L	0.60904	1.88	0.23528	N	0.99749	P	0.45283	0.855	P	0.44447	0.45	T	0.22941	-1.0202	10	0.41790	T	0.15	-7.0671	13.5958	0.61988	1.0:0.0:0.0:0.0	.	601	O95163	ELP1_HUMAN	A	601;252	ENSP00000363779:V601A;ENSP00000439367:V252A	ENSP00000363779:V601A	V	-	2	0	IKBKAP	110704992	0.994000	0.37717	0.074000	0.20217	0.751000	0.42716	7.128000	0.77217	2.096000	0.63516	0.454000	0.30748	GTT	.	.		0.453	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
IKBKAP	8518	hgsc.bcm.edu	37	9	111685163	111685163	+	Missense_Mutation	SNP	G	G	A	rs202179488		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:111685163G>A	ENST00000374647.5	-	6	818	c.511C>T	c.(511-513)Cat>Tat	p.H171Y	IKBKAP_ENST00000537196.1_Intron	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	171					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TCTGATCCATGGAACTGTGTC	0.408																																					p.H171Y		Atlas-SNP	.											.	IKBKAP	122	.	0			c.C511T						.						214.0	188.0	196.0					9																	111685163		2203	4300	6503	SO:0001583	missense	8518	exon6			ATCCATGGAACTG	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.511C>T	chr9.hg19:g.111685163G>A	ENSP00000363779:p.His171Tyr	110.0	0.0		100.0	4.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773896	0.90108	.	.	ENSG00000070061	ENST00000374647	T	0.30182	1.54	5.62	5.62	0.85841	.	0.044217	0.85682	D	0.000000	T	0.64405	0.2595	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71431	-0.4595	10	0.72032	D	0.01	-9.2614	17.1551	0.86790	0.0:0.0:1.0:0.0	.	171	O95163	ELP1_HUMAN	Y	171	ENSP00000363779:H171Y	ENSP00000363779:H171Y	H	-	1	0	IKBKAP	110724984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.088000	0.94132	2.639000	0.89480	0.650000	0.86243	CAT	.	G|0.999;C|0.001		0.408	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
EPB41L4B	54566	hgsc.bcm.edu	37	9	112013790	112013790	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:112013790T>C	ENST00000374566.3	-	13	1798	c.1281A>G	c.(1279-1281)gcA>gcG	p.A427A	EPB41L4B_ENST00000374557.4_Splice_Site_p.A427A	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	427					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTGGGTTGCTTGCTATAAAGG	0.428																																					p.A427A		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.A1281G						.						145.0	152.0	150.0					9																	112013790		1958	4155	6113	SO:0001630	splice_region_variant	54566	exon13			GTTGCTTGCTATA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1280-1A>G	chr9.hg19:g.112013790T>C		135.0	0.0		121.0	5.0	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	hg19	CCDS43859.1																																																																																			.	.		0.428	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	Silent
AKAP2	11217	hgsc.bcm.edu	37	9	112899145	112899145	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:112899145A>G	ENST00000259318.7	+	2	835	c.628A>G	c.(628-630)Agg>Ggg	p.R210G	AKAP2_ENST00000374525.1_Missense_Mutation_p.R299G|AKAP2_ENST00000434623.2_Missense_Mutation_p.R299G|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.R441G|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.R441G|AKAP2_ENST00000555236.1_Missense_Mutation_p.R441G|AKAP2_ENST00000510514.5_Missense_Mutation_p.R441G	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	210										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						TAGAAAAGTGAGGCCTTCAGA	0.512																																					p.R441G		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.A1321G						.						66.0	68.0	67.0					9																	112899145		2203	4300	6503	SO:0001583	missense	445815	exon8			AAAGTGAGGCCTT	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.628A>G	chr9.hg19:g.112899145A>G	ENSP00000259318:p.Arg210Gly	130.0	0.0		93.0	4.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533409	0.27387	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	6.16	3.81	0.43845	.	0.044099	0.85682	D	0.000000	T	0.66157	0.2761	M	0.70275	2.135	0.49798	D	0.999821	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.993;1.0;0.999;0.996;0.996;0.993	D;D;P;D;D;P;P;P	0.85130	0.996;0.997;0.782;0.997;0.994;0.892;0.892;0.782	T	0.67484	-0.5659	10	0.72032	D	0.01	-29.5922	12.6715	0.56870	0.7178:0.2822:0.0:0.0	.	210;299;293;299;300;441;441;259	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	G	441;441;441;441;299;299;259;210	ENSP00000363654:R441G;ENSP00000305861:R441G;ENSP00000451476:R441G;ENSP00000421522:R441G;ENSP00000404782:R299G;ENSP00000363649:R299G;ENSP00000419268:R259G;ENSP00000259318:R210G	ENSP00000259318:R210G	R	+	1	2	PALM2-AKAP2;AKAP2	111938966	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	3.660000	0.54496	0.544000	0.28883	-0.319000	0.08680	AGG	.	.		0.512	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
KIAA0368	23392	hgsc.bcm.edu	37	9	114172333	114172333	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:114172333T>C	ENST00000338205.5	-	22	2757	c.2538A>G	c.(2536-2538)aaA>aaG	p.K846K	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Silent_p.K1024K|KIAA0368_ENST00000374378.3_5'Flank			Q5VYK3	ECM29_HUMAN	KIAA0368	852					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TATTTGTTTCTTTACTGGAAG	0.353																																					p.K1024K		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A3072G						.						24.0	23.0	23.0					9																	114172333		1812	4073	5885	SO:0001819	synonymous_variant	23392	exon24			TGTTTCTTTACTG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2538A>G	chr9.hg19:g.114172333T>C		109.0	0.0		122.0	5.0	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	hg19																																																																																				.	.		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
C9orf84	158401	hgsc.bcm.edu	37	9	114480520	114480520	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:114480520T>C	ENST00000318737.4	-	14	2116	c.1988A>G	c.(1987-1989)cAt>cGt	p.H663R	C9orf84_ENST00000394777.4_Intron|C9orf84_ENST00000374287.3_Missense_Mutation_p.H663R|C9orf84_ENST00000394779.3_Missense_Mutation_p.H624R	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	663										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TACCAGAAGATGTAAGAGAGC	0.333																																					p.H663R		Atlas-SNP	.											.	C9orf84	207	.	0			c.A1988G						.						106.0	99.0	101.0					9																	114480520		2203	4300	6503	SO:0001583	missense	158401	exon14			AGAAGATGTAAGA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1988A>G	chr9.hg19:g.114480520T>C	ENSP00000322108:p.His663Arg	133.0	0.0		80.0	4.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	T	14.69	2.611816	0.46631	.	.	ENSG00000165181	ENST00000394779;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T	0.07567	3.18;3.19;3.19	5.25	5.25	0.73442	.	0.000000	0.52532	D	0.000062	T	0.19927	0.0479	L	0.34521	1.04	0.32601	N	0.525949	D;D	0.89917	1.0;0.992	D;P	0.85130	0.997;0.868	T	0.07829	-1.0752	10	0.87932	D	0	-9.0295	15.1394	0.72599	0.0:0.0:0.0:1.0	.	663;624	Q5VXU9;A2A2V3	CI084_HUMAN;.	R	624;277;663;663	ENSP00000378259:H624R;ENSP00000363405:H663R;ENSP00000322108:H663R	ENSP00000322108:H663R	H	-	2	0	C9orf84	113520341	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	5.371000	0.66150	1.987000	0.57996	0.482000	0.46254	CAT	.	.		0.333	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
PRPF4	9128	hgsc.bcm.edu	37	9	116053881	116053881	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:116053881G>A	ENST00000374198.4	+	14	1612	c.1510G>A	c.(1510-1512)Ggg>Agg	p.G504R	PRPF4_ENST00000374199.4_Missense_Mutation_p.G503R	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	504					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						TTCTTCCGATGGGCAGCTCAT	0.512																																					p.G504R		Atlas-SNP	.											.	PRPF4	56	.	0			c.G1510A						.						95.0	87.0	90.0					9																	116053881		2203	4300	6503	SO:0001583	missense	9128	exon14			TCCGATGGGCAGC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1510G>A	chr9.hg19:g.116053881G>A	ENSP00000363313:p.Gly504Arg	135.0	0.0		78.0	4.0	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	hg19	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893442	0.91889	.	.	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.65549	-0.16;-0.16	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.097634	0.64402	D	0.000001	D	0.84151	0.5409	M	0.93978	3.48	0.80722	D	1	D;D	0.63880	0.987;0.993	D;D	0.63703	0.909;0.917	D	0.87581	0.2484	10	0.72032	D	0.01	.	19.0588	0.93078	0.0:0.0:1.0:0.0	.	519;504	Q59EL4;O43172	.;PRP4_HUMAN	R	503;504	ENSP00000363315:G503R;ENSP00000363313:G504R	ENSP00000363313:G504R	G	+	1	0	PRPF4	115093702	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.102000	0.94226	2.744000	0.94065	0.655000	0.94253	GGG	.	.		0.512	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
COL27A1	85301	hgsc.bcm.edu	37	9	117068856	117068856	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:117068856C>A	ENST00000356083.3	+	58	5386	c.4995C>A	c.(4993-4995)acC>acA	p.T1665T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1665	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TCTTTAAAACCTTACACTACC	0.567											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T1665T		Atlas-SNP	.											.	COL27A1	200	.	0			c.C4995A						.						77.0	77.0	77.0					9																	117068856		2203	4300	6503	SO:0001819	synonymous_variant	85301	exon58			TAAAACCTTACAC	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4995C>A	chr9.hg19:g.117068856C>A		77.0	0.0	1478	84.0	4.0	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	hg19	CCDS6802.1																																																																																			.	.		0.567	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
FBXW2	26190	hgsc.bcm.edu	37	9	123526947	123526947	+	Missense_Mutation	SNP	C	C	T	rs374464211		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123526947C>T	ENST00000608872.1	-	8	1442	c.1255G>A	c.(1255-1257)Gaa>Aaa	p.E419K	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Missense_Mutation_p.E354K	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	419					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						CAGGATGCTTCGCCTGCCAGG	0.542																																					p.E419K		Atlas-SNP	.											.	FBXW2	34	.	0			c.G1255A						.	C	LYS/GLU	1,4167		0,1,2083	127.0	137.0	134.0		1255	4.9	1.0	9		134	0,8458		0,0,4229	no	missense	FBXW2	NM_012164.3	56	0,1,6312	TT,TC,CC		0.0,0.024,0.0079	benign	419/455	123526947	1,12625	2084	4229	6313	SO:0001583	missense	26190	exon8			ATGCTTCGCCTGC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13608	protein-coding gene	gene with protein product		609071	"""F-box and WD-40 domain protein 2"""			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1255G>A	chr9.hg19:g.123526947C>T	ENSP00000476369:p.Glu419Lys	115.0	0.0		95.0	5.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000785	0.74818	2.4E-4	0.0	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;T	0.80480	0.29;-1.38	4.95	4.95	0.65309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.106728	0.64402	D	0.000005	T	0.66386	0.2784	N	0.22421	0.69	0.53688	D	0.999978	P;P;B	0.43352	0.774;0.804;0.428	B;B;B	0.29716	0.106;0.039;0.027	T	0.74426	-0.3669	10	0.72032	D	0.01	-8.1105	16.037	0.80638	0.0:1.0:0.0:0.0	.	354;419;419	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	K	419;354;419	ENSP00000363036:E419K;ENSP00000341161:E354K	ENSP00000341161:E354K	E	-	1	0	FBXW2	122566768	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.978000	0.70501	2.447000	0.82792	0.563000	0.77884	GAA	.	.		0.542	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2		
FBXW2	26190	hgsc.bcm.edu	37	9	123526956	123526956	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123526956G>T	ENST00000608872.1	-	8	1433	c.1246C>A	c.(1246-1248)Ctg>Atg	p.L416M	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Missense_Mutation_p.L351M	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	416					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						TCGCCTGCCAGGAAGCTTGAG	0.542																																					p.L416M		Atlas-SNP	.											.	FBXW2	34	.	0			c.C1246A						.						136.0	142.0	140.0					9																	123526956		2032	4212	6244	SO:0001583	missense	26190	exon8			CTGCCAGGAAGCT	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13608	protein-coding gene	gene with protein product		609071	"""F-box and WD-40 domain protein 2"""			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1246C>A	chr9.hg19:g.123526956G>T	ENSP00000476369:p.Leu416Met	105.0	0.0		96.0	4.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038947	0.55003	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;D	0.83992	-0.09;-1.79	4.95	3.8	0.43715	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84492	0.5484	L	0.44542	1.39	0.51482	D	0.999925	D;D;D	0.71674	0.994;0.998;0.994	P;D;D	0.77557	0.827;0.99;0.99	D	0.84080	0.0384	10	0.87932	D	0	-2.4718	5.0892	0.14698	0.2566:0.0:0.7434:0.0	.	351;416;416	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	M	416;351;416	ENSP00000363036:L416M;ENSP00000341161:L351M	ENSP00000341161:L351M	L	-	1	2	FBXW2	122566777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.734000	0.55037	2.447000	0.82792	0.563000	0.77884	CTG	.	.		0.542	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2		
PHF19	26147	hgsc.bcm.edu	37	9	123636996	123636996	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123636996T>C	ENST00000373896.3	-	2	276	c.24A>G	c.(22-24)ccA>ccG	p.P8P	PHF19_ENST00000312189.6_Silent_p.P8P	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	8					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCCGAGTCCCTGGATCCAGAG	0.552																																					p.P8P		Atlas-SNP	.											.	PHF19	47	.	0			c.A24G						.						77.0	78.0	78.0					9																	123636996		2203	4300	6503	SO:0001819	synonymous_variant	26147	exon2			AGTCCCTGGATCC	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24566	protein-coding gene	gene with protein product	"""polycomb-like 3"", ""tudor domain containing 19B"""	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.24A>G	chr9.hg19:g.123636996T>C		58.0	0.0		63.0	4.0	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Silent	SNP	ENST00000373896.3	hg19	CCDS35116.1																																																																																			.	.		0.552	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308	
SCAI	286205	hgsc.bcm.edu	37	9	127781126	127781126	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:127781126T>C	ENST00000336505.6	-	9	871	c.813A>G	c.(811-813)ggA>ggG	p.G271G	SCAI_ENST00000373549.4_Silent_p.G294G	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	271					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						GAGACAACTGTCCCACAATCA	0.383																																					p.G294G		Atlas-SNP	.											.	SCAI	84	.	0			c.A882G						.						114.0	109.0	111.0					9																	127781126		1952	4147	6099	SO:0001819	synonymous_variant	286205	exon10			CAACTGTCCCACA	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.813A>G	chr9.hg19:g.127781126T>C		105.0	0.0		82.0	4.0	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	hg19	CCDS48017.1																																																																																			.	.		0.383	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
FAM129B	64855	hgsc.bcm.edu	37	9	130272586	130272586	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130272586A>G	ENST00000373312.3	-	9	1213	c.1000T>C	c.(1000-1002)Tgc>Cgc	p.C334R	FAM129B_ENST00000373314.3_Missense_Mutation_p.C321R|FAM129B_ENST00000468379.1_Intron	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	334					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						TTCCGCACGCACACCTCTGCC	0.642																																					p.C334R		Atlas-SNP	.											.	FAM129B	84	.	0			c.T1000C						.						106.0	102.0	103.0					9																	130272586		2203	4300	6503	SO:0001583	missense	64855	exon9			GCACGCACACCTC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1000T>C	chr9.hg19:g.130272586A>G	ENSP00000362409:p.Cys334Arg	108.0	0.0		66.0	4.0	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Missense_Mutation	SNP	ENST00000373312.3	hg19	CCDS35145.1	.	.	.	.	.	.	.	.	.	.	A	8.958	0.969866	0.18659	.	.	ENSG00000136830	ENST00000373314;ENST00000373312	T;T	0.26067	1.77;1.76	6.04	6.04	0.98038	.	0.174286	0.51477	D	0.000096	T	0.23210	0.0561	L	0.40543	1.245	0.80722	D	1	P;P	0.39094	0.659;0.659	B;B	0.37943	0.261;0.261	T	0.02625	-1.1132	10	0.26408	T	0.33	-23.0447	14.5284	0.67905	1.0:0.0:0.0:0.0	.	321;334	Q96TA1-2;Q96TA1	.;NIBL1_HUMAN	R	321;334	ENSP00000362411:C321R;ENSP00000362409:C334R	ENSP00000362409:C334R	C	-	1	0	FAM129B	129312407	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	3.207000	0.51106	2.317000	0.78254	0.459000	0.35465	TGC	.	.		0.642	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
C9orf117	286207	hgsc.bcm.edu	37	9	130473684	130473684	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130473684T>C	ENST00000373295.2	+	4	804	c.764T>C	c.(763-765)cTc>cCc	p.L255P	C9orf117_ENST00000373293.5_5'Flank	NM_001012502.2	NP_001012520.2	Q5JU67	CI117_HUMAN	chromosome 9 open reading frame 117	255										breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AATGAGCAGCTCAAGGGAAGA	0.557																																					p.L255P		Atlas-SNP	.											.	C9orf117	21	.	0			c.T764C						.						68.0	70.0	69.0					9																	130473684		2018	4194	6212	SO:0001583	missense	286207	exon4			AGCAGCTCAAGGG	AK094948	CCDS43878.1	9q34.11	2012-04-02			ENSG00000160401	ENSG00000160401			27843	protein-coding gene	gene with protein product							Standard	NM_001012502		Approved		uc004brn.1	Q5JU67	OTTHUMG00000020709	ENST00000373295.2:c.764T>C	chr9.hg19:g.130473684T>C	ENSP00000362392:p.Leu255Pro	121.0	0.0		70.0	4.0	NM_001012502	A5D8T9	Missense_Mutation	SNP	ENST00000373295.2	hg19	CCDS43878.1	.	.	.	.	.	.	.	.	.	.	T	15.23	2.773137	0.49680	.	.	ENSG00000160401	ENST00000373295	T	0.45276	0.9	5.44	5.44	0.79542	.	0.075738	0.56097	D	0.000029	T	0.64136	0.2571	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.68198	-0.5472	10	0.72032	D	0.01	-22.8891	13.4422	0.61119	0.0:0.0:0.0:1.0	.	255	Q5JU67	CI117_HUMAN	P	255	ENSP00000362392:L255P	ENSP00000362392:L255P	L	+	2	0	C9orf117	129513505	1.000000	0.71417	0.963000	0.40424	0.423000	0.31445	4.822000	0.62686	2.064000	0.61679	0.454000	0.30748	CTC	.	.		0.557	C9orf117-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054215.2	NM_001012502	
LCN2	3934	hgsc.bcm.edu	37	9	130911932	130911932	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130911932A>G	ENST00000373017.1	+	2	365	c.128A>G	c.(127-129)cAg>cGg	p.Q43R	LCN2_ENST00000540948.1_Missense_Mutation_p.Q43R|LCN2_ENST00000277480.2_Missense_Mutation_p.Q43R|LCN2_ENST00000372998.1_Missense_Mutation_p.Q43R|LCN2_ENST00000470902.1_3'UTR|LCN2_ENST00000373013.2_Missense_Mutation_p.Q43R			P80188	NGAL_HUMAN	lipocalin 2	43					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|small molecule binding (GO:0036094)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						CAGAACTTCCAGGACAACCAA	0.627																																					p.Q43R		Atlas-SNP	.											.	LCN2	12	.	0			c.A128G						.						63.0	64.0	63.0					9																	130911932		2203	4300	6503	SO:0001583	missense	3934	exon1			ACTTCCAGGACAA		CCDS6892.1	9q34	2011-10-24	2007-12-18		ENSG00000148346	ENSG00000148346		"""Lipocalins"""	6526	protein-coding gene	gene with protein product	"""oncogene 24p3"", ""neutrophil gelatinase-associated lipocalin"", ""siderocalin"""	600181	"""lipocalin 2 (oncogene 24p3)"""			7683678	Standard	NM_005564		Approved	NGAL, 24p3	uc004bto.1	P80188	OTTHUMG00000020734	ENST00000373017.1:c.128A>G	chr9.hg19:g.130911932A>G	ENSP00000362108:p.Gln43Arg	110.0	0.0		99.0	5.0	NM_005564	A6NII8|B4DWV4|B7ZAA2|P30150|Q5SYV9|Q5SYW0|Q6FGL5|Q92683	Missense_Mutation	SNP	ENST00000373017.1	hg19	CCDS6892.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.256384	0.22965	.	.	ENSG00000148346	ENST00000373017;ENST00000277480;ENST00000373013;ENST00000540948;ENST00000372998	T;T;T;T;T	0.24538	1.87;1.87;1.85;1.86;1.86	3.45	2.32	0.28847	Lipocalin conserved site (1);Calycin-like (1);Calycin (1);	0.875580	0.09640	N	0.775100	T	0.17109	0.0411	L	0.38175	1.15	0.09310	N	1	B;B;B	0.29253	0.239;0.041;0.041	B;B;B	0.24269	0.052;0.035;0.035	T	0.24835	-1.0149	10	0.38643	T	0.18	-6.123	3.66	0.08236	0.7502:0.0:0.2498:0.0	.	43;44;43	P80188-2;B2ZDQ1;P80188	.;.;NGAL_HUMAN	R	43	ENSP00000362108:Q43R;ENSP00000277480:Q43R;ENSP00000362104:Q43R;ENSP00000441666:Q43R;ENSP00000362089:Q43R	ENSP00000277480:Q43R	Q	+	2	0	LCN2	129951753	0.088000	0.21588	0.219000	0.23793	0.625000	0.37756	1.313000	0.33585	0.715000	0.32103	0.374000	0.22700	CAG	.	.		0.627	LCN2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054375.1	NM_005564	
SPTAN1	6709	hgsc.bcm.edu	37	9	131337065	131337065	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:131337065G>T	ENST00000372731.4	+	4	585	c.475G>T	c.(475-477)Gag>Tag	p.E159*	SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.E159*|SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.E159*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	159					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ACGAGAATGTGAGGACGTGAT	0.473																																					p.E159X	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G475T						.						164.0	162.0	162.0					9																	131337065		2203	4300	6503	SO:0001587	stop_gained	6709	exon4			GAATGTGAGGACG	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.475G>T	chr9.hg19:g.131337065G>T	ENSP00000361816:p.Glu159*	124.0	0.0		100.0	4.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	37	6.473816	0.97594	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	6.08	6.08	0.98989	.	0.046712	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	.	.	.	X	159	.	ENSP00000350882:E159X	E	+	1	0	SPTAN1	130376886	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	9.430000	0.97488	2.894000	0.99253	0.655000	0.94253	GAG	.	.		0.473	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
NUP188	23511	hgsc.bcm.edu	37	9	131765691	131765691	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:131765691G>T	ENST00000372577.2	+	38	4413	c.4392G>T	c.(4390-4392)aaG>aaT	p.K1464N	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1464					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						ACTTCATGAAGGAGTGGCACT	0.582																																					p.K1464N		Atlas-SNP	.											.	NUP188	140	.	0			c.G4392T						.						118.0	110.0	113.0					9																	131765691		2203	4300	6503	SO:0001583	missense	23511	exon38			CATGAAGGAGTGG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4392G>T	chr9.hg19:g.131765691G>T	ENSP00000361658:p.Lys1464Asn	67.0	0.0		46.0	4.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803502	0.70682	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.33438	1.41	5.8	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.53249	1.67	0.80722	D	1	P;D	0.76494	0.784;0.999	B;D	0.78314	0.312;0.991	T	0.32428	-0.9907	10	0.39692	T	0.17	-8.8756	9.7807	0.40647	0.2141:0.0:0.7859:0.0	.	797;1464	E9PET9;Q5SRE5	.;NU188_HUMAN	N	1353;1464	ENSP00000361658:K1464N	ENSP00000349125:K1353N	K	+	3	2	NUP188	130805512	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.477000	0.45180	1.455000	0.47813	0.561000	0.74099	AAG	.	.		0.582	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
USP20	10868	hgsc.bcm.edu	37	9	132642472	132642472	+	Missense_Mutation	SNP	C	C	A	rs200854092	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:132642472C>A	ENST00000315480.4	+	25	2823	c.2665C>A	c.(2665-2667)Cgc>Agc	p.R889S	USP20_ENST00000372429.3_Missense_Mutation_p.R889S|USP20_ENST00000472108.1_3'UTR|USP20_ENST00000358355.1_Missense_Mutation_p.R889S			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	889	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GATTGCCATCCGCCAGAGTGT	0.632																																					p.R889S		Atlas-SNP	.											.	USP20	186	.	0			c.C2665A						.						32.0	43.0	39.0					9																	132642472		2066	4205	6271	SO:0001583	missense	10868	exon25			GCCATCCGCCAGA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2665C>A	chr9.hg19:g.132642472C>A	ENSP00000313811:p.Arg889Ser	112.0	0.0		50.0	4.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863098	0.51482	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.18657	2.2;2.2;2.2	5.11	5.11	0.69529	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (2);	0.000000	0.85682	D	0.000000	T	0.48714	0.1515	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.51631	-0.8681	10	0.54805	T	0.06	.	13.2032	0.59780	0.1698:0.8302:0.0:0.0	.	889	Q9Y2K6	UBP20_HUMAN	S	889	ENSP00000361506:R889S;ENSP00000313811:R889S;ENSP00000351122:R889S	ENSP00000313811:R889S	R	+	1	0	USP20	131682293	1.000000	0.71417	0.998000	0.56505	0.054000	0.15201	1.766000	0.38491	2.387000	0.81309	0.655000	0.94253	CGC	.	C|1.000;T|0.000		0.632	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
NUP214	8021	hgsc.bcm.edu	37	9	134049687	134049687	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:134049687G>A	ENST00000359428.5	+	22	3283	c.3139G>A	c.(3139-3141)Ggt>Agt	p.G1047S	NUP214_ENST00000451030.1_Missense_Mutation_p.G1048S|NUP214_ENST00000411637.2_Missense_Mutation_p.G1037S			P35658	NU214_HUMAN	nucleoporin 214kDa	1047	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCTTCACCTGGTGTGATGGG	0.483			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.G1047S	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G3139A						.						78.0	68.0	71.0					9																	134049687		2203	4300	6503	SO:0001583	missense	8021	exon22			TCACCTGGTGTGA	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.3139G>A	chr9.hg19:g.134049687G>A	ENSP00000352400:p.Gly1047Ser	153.0	0.0		93.0	4.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.611743	0.46631	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.31510	1.49;1.49;1.49	5.81	1.13	0.20643	.	0.672958	0.12990	N	0.422559	T	0.10637	0.0260	N	0.08118	0	0.22710	N	0.998825	B;B;B;B	0.16603	0.001;0.0;0.018;0.0	B;B;B;B	0.17722	0.004;0.003;0.015;0.019	T	0.34378	-0.9831	10	0.05525	T	0.97	-5.2842	2.9419	0.05833	0.3673:0.0:0.4403:0.1924	.	1036;641;1037;1047	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	S	1047;1037;1048;1036;641;476	ENSP00000352400:G1047S;ENSP00000396576:G1037S;ENSP00000405014:G1048S	ENSP00000352400:G1047S	G	+	1	0	NUP214	133039508	0.780000	0.28664	0.018000	0.16275	0.853000	0.48598	1.415000	0.34748	0.301000	0.22738	-0.982000	0.02568	GGT	.	.		0.483	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
SETX	23064	hgsc.bcm.edu	37	9	135218087	135218087	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:135218087G>T	ENST00000224140.5	-	5	670	c.488C>A	c.(487-489)cCc>cAc	p.P163H	SETX_ENST00000372169.2_Missense_Mutation_p.P163H|SETX_ENST00000393220.1_Missense_Mutation_p.P163H	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	163					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CATTTCATTGGGATGGACTAA	0.398																																					p.P163H		Atlas-SNP	.											.	SETX	234	.	0			c.C488A						.						202.0	209.0	207.0					9																	135218087		2203	4300	6503	SO:0001583	missense	23064	exon5			TCATTGGGATGGA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.488C>A	chr9.hg19:g.135218087G>T	ENSP00000224140:p.Pro163His	104.0	0.0		74.0	5.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258512	0.80246	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.89196	-2.48;-2.48;-2.48	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.91845	0.7419	L	0.34521	1.04	0.42482	D	0.992865	D	0.89917	1.0	D	0.91635	0.999	D	0.92843	0.6290	10	0.87932	D	0	.	18.6094	0.91279	0.0:0.0:1.0:0.0	.	163	Q7Z333	SETX_HUMAN	H	163	ENSP00000224140:P163H;ENSP00000361242:P163H;ENSP00000376913:P163H	ENSP00000224140:P163H	P	-	2	0	SETX	134207908	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.041000	0.64196	2.636000	0.89361	0.557000	0.71058	CCC	.	.		0.398	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
TSC1	7248	hgsc.bcm.edu	37	9	135779080	135779080	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:135779080C>A	ENST00000298552.3	-	17	2387	c.2166G>T	c.(2164-2166)aaG>aaT	p.K722N	TSC1_ENST00000545250.1_Missense_Mutation_p.K671N|TSC1_ENST00000440111.2_Missense_Mutation_p.K722N	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	722					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.R721fs*9(1)|p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTTTGATCACCTTGCGGAGGA	0.537			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.K722N		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	2	Unknown(1)|Deletion - Frameshift(1)	ovary(1)|bone(1)	c.G2166T						.						69.0	70.0	70.0					9																	135779080		2203	4300	6503	SO:0001583	missense	7248	exon17	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GATCACCTTGCGG	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2166G>T	chr9.hg19:g.135779080C>A	ENSP00000298552:p.Lys722Asn	94.0	0.0		82.0	33.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085869	0.55861	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;D	0.85339	-1.97;-1.97;-1.84	5.32	3.47	0.39725	.	0.209808	0.49916	D	0.000125	T	0.73976	0.3656	L	0.27053	0.805	0.80722	D	1	P;P	0.36753	0.568;0.568	B;B	0.37550	0.253;0.253	T	0.72887	-0.4156	10	0.66056	D	0.02	-7.8598	5.4933	0.16789	0.0:0.6389:0.0:0.3611	.	671;722	B7Z897;Q92574	.;TSC1_HUMAN	N	722;722;671	ENSP00000298552:K722N;ENSP00000394524:K722N;ENSP00000444017:K671N	ENSP00000298552:K722N	K	-	3	2	TSC1	134768901	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.810000	0.27183	1.242000	0.43836	0.650000	0.86243	AAG	.	.		0.537	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
GBGT1	26301	hgsc.bcm.edu	37	9	136029419	136029419	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136029419G>T	ENST00000372040.3	-	7	900	c.589C>A	c.(589-591)Cgg>Agg	p.R197R	GBGT1_ENST00000372043.3_Silent_p.T190T|GBGT1_ENST00000540636.1_Silent_p.R180R|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	197					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TCCACCTCCCGGTGAGCCCTC	0.602																																					p.R197R		Atlas-SNP	.											.,1	GBGT1	25	.	0			c.C589A						.						91.0	72.0	78.0					9																	136029419		2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CCTCCCGGTGAGC	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.589C>A	chr9.hg19:g.136029419G>T		114.0	0.0		99.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	hg19	CCDS6960.1																																																																																			.	.		0.602	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
GBGT1	26301	hgsc.bcm.edu	37	9	136031411	136031411	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136031411G>T	ENST00000372040.3	-	4	490	c.179C>A	c.(178-180)cCc>cAc	p.P60H	GBGT1_ENST00000372043.3_Missense_Mutation_p.P60H|GBGT1_ENST00000540636.1_Intron|GBGT1_ENST00000372038.3_Silent_p.A72A|RALGDS_ENST00000542690.1_Silent_p.A72A|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	60					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CCATACCACGGGCTGGAGTGG	0.552																																					p.P60H		Atlas-SNP	.											.	GBGT1	25	.	0			c.C179A						.						145.0	121.0	129.0					9																	136031411		2203	4300	6503	SO:0001583	missense	26301	exon4			ACCACGGGCTGGA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.179C>A	chr9.hg19:g.136031411G>T	ENSP00000361110:p.Pro60His	149.0	0.0		83.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	8.952	0.968524	0.18659	.	.	ENSG00000148288	ENST00000372043;ENST00000372040	T;T	0.01228	5.14;5.14	4.65	3.75	0.43078	.	0.357573	0.26279	N	0.025296	T	0.05090	0.0136	M	0.66939	2.045	0.24795	N	0.992734	D;D	0.76494	0.999;0.98	D;P	0.66351	0.943;0.845	T	0.23226	-1.0194	10	0.36615	T	0.2	-13.5243	7.5864	0.27995	0.1982:0.0:0.8018:0.0	.	60;60	Q8N5D6-2;Q8N5D6	.;GBGT1_HUMAN	H	60	ENSP00000361113:P60H;ENSP00000361110:P60H	ENSP00000361110:P60H	P	-	2	0	GBGT1	135021232	0.992000	0.36948	0.060000	0.19600	0.002000	0.02628	2.534000	0.45676	1.068000	0.40764	-0.136000	0.14681	CCC	.	.		0.552	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
CACFD1	11094	hgsc.bcm.edu	37	9	136328625	136328625	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136328625T>C	ENST00000316948.4	+	2	222	c.142T>C	c.(142-144)Ttc>Ctc	p.F48L	CACFD1_ENST00000489519.1_3'UTR|CACFD1_ENST00000291722.7_Missense_Mutation_p.F48L|CACFD1_ENST00000542192.1_Missense_Mutation_p.F48L|CACFD1_ENST00000540581.1_Missense_Mutation_p.F48L	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	48					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										CTCTGGCCTCTTCAACTGCAT	0.622																																					p.F48L		Atlas-SNP	.											.	CACFD1	1	.	0			c.T142C						.						157.0	146.0	150.0					9																	136328625		2203	4300	6503	SO:0001583	missense	11094	exon2			GGCCTCTTCAACT		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"""chromosome 9 open reading frame 7"""	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.142T>C	chr9.hg19:g.136328625T>C	ENSP00000317121:p.Phe48Leu	119.0	0.0		93.0	4.0	NM_001242370	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Missense_Mutation	SNP	ENST00000316948.4	hg19	CCDS6974.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978155	0.53720	.	.	ENSG00000160325	ENST00000291722;ENST00000535514;ENST00000316948;ENST00000540581;ENST00000542192;ENST00000444798	D;T;T;T;T	0.87887	-2.31;1.07;1.07;0.98;1.07	4.81	4.81	0.61882	Membrane protein, Golgi apparatus TVP18/Calcium channel flower (1);	0.177896	0.52532	D	0.000065	T	0.78842	0.4347	N	0.19112	0.55	0.45390	D	0.998373	B;B;B;B	0.31817	0.15;0.119;0.003;0.341	B;B;B;B	0.31101	0.027;0.019;0.016;0.124	T	0.79259	-0.1877	10	0.52906	T	0.07	-31.3281	13.8451	0.63463	0.0:0.0:0.0:1.0	.	48;48;48;48	B7Z5E1;F5GXX4;Q9UGQ2;Q9UGQ2-2	.;.;FLOWR_HUMAN;.	L	48;38;48;48;48;20	ENSP00000291722:F48L;ENSP00000317121:F48L;ENSP00000440832:F48L;ENSP00000444328:F48L;ENSP00000414495:F20L	ENSP00000291722:F48L	F	+	1	0	C9orf7	135318446	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.550000	0.82173	1.940000	0.56252	0.402000	0.26972	TTC	.	.		0.622	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586	
GPSM1	26086	hgsc.bcm.edu	37	9	139250846	139250846	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:139250846C>T	ENST00000440944.1	+	13	1885	c.1665C>T	c.(1663-1665)atC>atT	p.I555I	GPSM1_ENST00000392944.1_Silent_p.I46I|GPSM1_ENST00000429455.1_Silent_p.I46I	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	555	GoLoco 2. {ECO:0000255|PROSITE- ProRule:PRU00097}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		TCGACCTCATCGCCAGCTCCC	0.711																																					p.I555I		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1665T						.						16.0	20.0	19.0					9																	139250846		2195	4291	6486	SO:0001819	synonymous_variant	26086	exon13			CCTCATCGCCAGC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1665C>T	chr9.hg19:g.139250846C>T		76.0	0.0		65.0	19.0	NM_001145638	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
SEC16A	9919	hgsc.bcm.edu	37	9	139370230	139370230	+	Missense_Mutation	SNP	G	G	T	rs371898934		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:139370230G>T	ENST00000371706.3	-	1	1337	c.1304C>A	c.(1303-1305)cCg>cAg	p.P435Q	SEC16A_ENST00000290037.6_Missense_Mutation_p.P435Q|SEC16A_ENST00000313050.7_Missense_Mutation_p.P613Q|SEC16A_ENST00000431893.2_Missense_Mutation_p.P435Q			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	435					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		AGATTTTACCGGTTCGAAAGA	0.522																																					p.P613Q		Atlas-SNP	.											.	SEC16A	249	.	0			c.C1838A						.						36.0	38.0	37.0					9																	139370230		2061	4198	6259	SO:0001583	missense	9919	exon3			TTTACCGGTTCGA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.1304C>A	chr9.hg19:g.139370230G>T	ENSP00000360771:p.Pro435Gln	84.0	0.0		51.0	4.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	G	26.6	4.749388	0.89753	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925	T;T;T;T	0.42900	0.96;1.0;0.98;1.0	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.66167	0.2762	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67639	-0.5619	10	0.87932	D	0	-15.3679	18.9459	0.92622	0.0:0.0:1.0:0.0	.	613;435;435;240	F1T0I1;O15027-5;O15027-4;A4QN19	.;.;.;.	Q	613;435;435;435;240	ENSP00000325827:P613Q;ENSP00000360771:P435Q;ENSP00000290037:P435Q;ENSP00000387583:P435Q	ENSP00000290037:P435Q	P	-	2	0	SEC16A	138490051	1.000000	0.71417	0.997000	0.53966	0.856000	0.48823	7.833000	0.86765	2.796000	0.96246	0.650000	0.86243	CCG	.	.		0.522	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
GRIN1	2902	hgsc.bcm.edu	37	9	140036523	140036523	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140036523C>T	ENST00000371561.3	+	2	1414	c.317C>T	c.(316-318)cCt>cTt	p.P106L	GRIN1_ENST00000371553.3_Missense_Mutation_p.P106L|GRIN1_ENST00000315048.3_Missense_Mutation_p.P106L|GRIN1_ENST00000350902.5_Missense_Mutation_p.P106L|GRIN1_ENST00000371560.3_Missense_Mutation_p.P106L|GRIN1_ENST00000371559.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371555.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371546.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371550.4_Missense_Mutation_p.P106L|GRIN1_ENST00000471122.1_3'UTR	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	106					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACTCCCACCCCTGTCTCCTAC	0.592																																					p.P106L	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.C317T						.						380.0	298.0	326.0					9																	140036523		2203	4300	6503	SO:0001583	missense	2902	exon2			CCACCCCTGTCTC		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4584	protein-coding gene	gene with protein product		138249	"""N-methyl-D-aspartate receptor subunit NR1"""	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.317C>T	chr9.hg19:g.140036523C>T	ENSP00000360616:p.Pro106Leu	287.0	0.0		191.0	32.0	NM_000832	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457243	0.84317	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	D;D;D;D;D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76	3.37	3.37	0.38596	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.84826	0.5558	L	0.29908	0.895	0.80722	D	1	D;B;D;D;D;D	0.89917	0.999;0.144;1.0;1.0;1.0;0.995	D;B;D;D;D;D	0.85130	0.984;0.27;0.995;0.995;0.997;0.956	D	0.84739	0.0750	10	0.41790	T	0.15	.	13.8091	0.63252	0.0:1.0:0.0:0.0	.	106;106;106;106;106;106	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	L	106	ENSP00000360616:P106L;ENSP00000316696:P106L;ENSP00000316915:P106L;ENSP00000360605:P106L;ENSP00000360601:P106L;ENSP00000360610:P106L;ENSP00000360608:P106L;ENSP00000360614:P106L;ENSP00000360615:P106L	ENSP00000316696:P106L	P	+	2	0	GRIN1	139156344	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.016000	0.76393	1.887000	0.54652	0.462000	0.41574	CCT	.	.		0.592	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327	
ANAPC2	29882	hgsc.bcm.edu	37	9	140077667	140077667	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140077667A>G	ENST00000323927.2	-	6	1200	c.1196T>C	c.(1195-1197)cTc>cCc	p.L399P		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	399					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		AGAGATATAGAGGGTGATGAT	0.622																																					p.L399P		Atlas-SNP	.											.	ANAPC2	57	.	0			c.T1196C						.						144.0	141.0	142.0					9																	140077667		2203	4299	6502	SO:0001583	missense	29882	exon6			ATATAGAGGGTGA	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"""Anaphase promoting complex subunits"""	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1196T>C	chr9.hg19:g.140077667A>G	ENSP00000314004:p.Leu399Pro	136.0	0.0		93.0	5.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456193	0.63401	.	.	ENSG00000176248	ENST00000323927	T	0.03124	4.04	4.83	4.83	0.62350	.	0.066268	0.64402	D	0.000019	T	0.11239	0.0274	L	0.55990	1.75	0.80722	D	1	D;D	0.64830	0.994;0.993	P;P	0.62491	0.903;0.843	T	0.07233	-1.0783	10	0.33940	T	0.23	-28.7388	12.3771	0.55285	1.0:0.0:0.0:0.0	.	399;396	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	P	399	ENSP00000314004:L399P	ENSP00000314004:L399P	L	-	2	0	ANAPC2	139197488	1.000000	0.71417	0.981000	0.43875	0.988000	0.76386	8.545000	0.90657	2.034000	0.60081	0.459000	0.35465	CTC	.	.		0.622	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366	
ANAPC2	29882	hgsc.bcm.edu	37	9	140082090	140082090	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140082090T>C	ENST00000323927.2	-	2	587	c.583A>G	c.(583-585)Aca>Gca	p.T195A	SSNA1_ENST00000322310.5_5'Flank	NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	195					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		TCCGGGTCTGTGCCCCCTTCC	0.587																																					p.T195A		Atlas-SNP	.											.	ANAPC2	57	.	0			c.A583G						.						78.0	78.0	78.0					9																	140082090		2203	4300	6503	SO:0001583	missense	29882	exon2			GGTCTGTGCCCCC	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"""Anaphase promoting complex subunits"""	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.583A>G	chr9.hg19:g.140082090T>C	ENSP00000314004:p.Thr195Ala	148.0	0.0		95.0	4.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.308976	0.23821	.	.	ENSG00000176248	ENST00000323927	T	0.76186	-1.0	4.56	4.56	0.56223	.	0.373064	0.32608	N	0.005880	T	0.52917	0.1764	N	0.22421	0.69	0.27736	N	0.944655	B;B	0.24920	0.001;0.114	B;B	0.24394	0.001;0.053	T	0.41342	-0.9514	10	0.06757	T	0.87	-10.2173	6.7051	0.23246	0.0:0.1043:0.0:0.8957	.	195;195	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	A	195	ENSP00000314004:T195A	ENSP00000314004:T195A	T	-	1	0	ANAPC2	139201911	0.973000	0.33851	0.994000	0.49952	0.946000	0.59487	1.708000	0.37899	1.915000	0.55452	0.459000	0.35465	ACA	.	.		0.587	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366	
TOR4A	54863	hgsc.bcm.edu	37	9	140173587	140173587	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140173587A>G	ENST00000357503.2	+	2	642	c.446A>G	c.(445-447)gAc>gGc	p.D149G		NM_017723.2	NP_060193.2	Q9NXH8	TOR4A_HUMAN	torsin family 4, member A	149					chaperone mediated protein folding requiring cofactor (GO:0051085)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)										CAGCGCTATGACCTCGACGGG	0.652																																					p.D149G		Atlas-SNP	.											.	.	.	.	0			c.A446G						.						17.0	15.0	15.0					9																	140173587		2196	4296	6492	SO:0001583	missense	54863	exon2			GCTATGACCTCGA	AK023361	CCDS7041.1	9q34.3	2012-04-03	2012-04-03	2012-04-03	ENSG00000198113	ENSG00000198113			25981	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 167"""	C9orf167			Standard	NM_017723		Approved	FLJ20245	uc004cmn.3	Q9NXH8	OTTHUMG00000131779	ENST00000357503.2:c.446A>G	chr9.hg19:g.140173587A>G	ENSP00000350102:p.Asp149Gly	97.0	0.0		67.0	4.0	NM_017723	A2BFA4	Missense_Mutation	SNP	ENST00000357503.2	hg19	CCDS7041.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.708706	0.68615	.	.	ENSG00000198113	ENST00000357503	T	0.46063	0.88	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.62551	0.2437	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.66492	-0.5910	10	0.66056	D	0.02	-8.8223	13.0926	0.59174	1.0:0.0:0.0:0.0	.	149	Q9NXH8	CI167_HUMAN	G	149	ENSP00000350102:D149G	ENSP00000350102:D149G	D	+	2	0	C9orf167	139293408	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	4.678000	0.61641	1.770000	0.52166	0.459000	0.35465	GAC	.	.		0.652	TOR4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254711.1	NM_017723	
AKR1E2	83592	hgsc.bcm.edu	37	10	4879675	4879675	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:4879675G>T	ENST00000298375.7	+	5	555	c.484G>T	c.(484-486)Ggg>Tgg	p.G162W	AKR1E2_ENST00000334019.4_Missense_Mutation_p.G162W|AKR1E2_ENST00000345253.5_Intron|AKR1E2_ENST00000532248.1_Missense_Mutation_p.G162W|AKR1E2_ENST00000525281.1_3'UTR	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	162						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						GGTGATCACCGGGCTGGTGAA	0.507																																					p.G162W	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.G484T						.						101.0	95.0	97.0					10																	4879675		2203	4300	6503	SO:0001583	missense	83592	exon5			ATCACCGGGCTGG	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"""Aldo-keto reductases"""	23437	protein-coding gene	gene with protein product			"""aldo-keto reductase family 1, member C-like 2"""	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.484G>T	chr10.hg19:g.4879675G>T	ENSP00000298375:p.Gly162Trp	98.0	0.0		81.0	4.0	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	hg19	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166273	0.38217	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019	D;T;T;T	0.87887	-2.31;-0.72;-0.72;-0.72	4.2	3.27	0.37495	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	D	0.95671	0.8592	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96091	0.9061	10	0.87932	D	0	.	11.5482	0.50706	0.0:0.0:0.8199:0.1801	.	123;162;162;162	B7Z7K2;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;AKCL2_HUMAN;.	W	58;166;162;162;162	ENSP00000435436:G166W;ENSP00000298375:G162W;ENSP00000432947:G162W;ENSP00000335034:G162W	ENSP00000298375:G162W	G	+	1	0	AKR1E2	4869675	1.000000	0.71417	0.557000	0.28306	0.012000	0.07955	6.848000	0.75409	1.314000	0.45095	0.455000	0.32223	GGG	.	.		0.507	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436	
ITIH2	3698	hgsc.bcm.edu	37	10	7751027	7751027	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:7751027T>C	ENST00000358415.4	+	4	401	c.235T>C	c.(235-237)Tct>Cct	p.S79P	ITIH2_ENST00000480387.1_Intron|ITIH2_ENST00000379587.4_Missense_Mutation_p.S68P	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	79	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TAAAGTCCAGTCTACTATTAC	0.418																																					p.S79P		Atlas-SNP	.											.	ITIH2	144	.	0			c.T235C						.						150.0	148.0	149.0					10																	7751027		2203	4300	6503	SO:0001583	missense	3698	exon4			GTCCAGTCTACTA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.235T>C	chr10.hg19:g.7751027T>C	ENSP00000351190:p.Ser79Pro	107.0	0.0		91.0	4.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.171990	0.38315	.	.	ENSG00000151655	ENST00000358415;ENST00000429820;ENST00000379587	T;T;T	0.28895	1.59;1.59;1.59	5.5	5.5	0.81552	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.099413	0.64402	D	0.000001	T	0.60715	0.2290	M	0.90369	3.11	0.54753	D	0.999981	D	0.76494	0.999	D	0.76575	0.988	T	0.67546	-0.5643	10	0.56958	D	0.05	-23.9638	11.6215	0.51121	0.1331:0.0:0.0:0.8669	.	79	P19823	ITIH2_HUMAN	P	79;54;68	ENSP00000351190:S79P;ENSP00000388826:S54P;ENSP00000368906:S68P	ENSP00000351190:S79P	S	+	1	0	ITIH2	7791033	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	4.079000	0.57613	2.214000	0.71695	0.482000	0.46254	TCT	.	.		0.418	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
NUDT5	11164	hgsc.bcm.edu	37	10	12219831	12219831	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:12219831G>T	ENST00000491614.1	-	5	645	c.250C>A	c.(250-252)Cga>Aga	p.R84R	NUDT5_ENST00000378940.3_Silent_p.R84R|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000537776.1_Silent_p.R84R|NUDT5_ENST00000378927.3_Silent_p.R84R|NUDT5_ENST00000378937.3_Silent_p.R97R			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	84	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				ATTGGTGGTCGGAACTGTTTC	0.522																																					p.R84R		Atlas-SNP	.											NUDT5,caecum,carcinoma,0,1	NUDT5	10	.	0			c.C250A						.						115.0	89.0	98.0					10																	12219831		2203	4300	6503	SO:0001819	synonymous_variant	11164	exon5			GTGGTCGGAACTG	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.250C>A	chr10.hg19:g.12219831G>T		91.0	0.0		54.0	4.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	hg19	CCDS7089.1																																																																																			.	.		0.522	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
NUDT5	11164	hgsc.bcm.edu	37	10	12219892	12219892	+	Silent	SNP	C	C	A	rs371734243		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:12219892C>A	ENST00000491614.1	-	5	584	c.189G>T	c.(187-189)gcG>gcT	p.A63A	NUDT5_ENST00000378940.3_Silent_p.A63A|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000537776.1_Silent_p.A63A|NUDT5_ENST00000378927.3_Silent_p.A63A|NUDT5_ENST00000378937.3_Silent_p.A76A			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	63	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CGGGGATGACCGCGACACCTG	0.502																																					p.A63A		Atlas-SNP	.											.	NUDT5	10	.	0			c.G189T						.						84.0	65.0	72.0					10																	12219892		2203	4300	6503	SO:0001819	synonymous_variant	11164	exon5			GATGACCGCGACA	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.189G>T	chr10.hg19:g.12219892C>A		57.0	0.0		48.0	4.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	hg19	CCDS7089.1																																																																																			.	.		0.502	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
FAM188A	80013	hgsc.bcm.edu	37	10	15821138	15821138	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:15821138G>T	ENST00000277632.3	-	15	1411	c.1191C>A	c.(1189-1191)gtC>gtA	p.V397V	FAM188A_ENST00000477891.1_5'UTR|FAM188A_ENST00000378036.1_Silent_p.V102V	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	397					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						CTACGTACATGACCTGTTGAA	0.398																																					p.V397V	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.C1191A						.						109.0	86.0	93.0					10																	15821138		2202	4300	6502	SO:0001819	synonymous_variant	80013	exon15			GTACATGACCTGT	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"""caspase recruitment domain containing pro-apoptotic protein"", ""CARD-containing protein"""	611649	"""chromosome 10 open reading frame 97"""	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.1191C>A	chr10.hg19:g.15821138G>T		112.0	0.0		69.0	4.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Silent	SNP	ENST00000277632.3	hg19	CCDS7110.1																																																																																			.	.		0.398	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948	
CUBN	8029	hgsc.bcm.edu	37	10	17127716	17127716	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:17127716A>G	ENST00000377833.4	-	16	2055	c.1990T>C	c.(1990-1992)Ttc>Ctc	p.F664L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	664	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTGGTGCAGAACTTCCCAAGA	0.448																																					p.F664L		Atlas-SNP	.											.	CUBN	515	.	0			c.T1990C						.						78.0	78.0	78.0					10																	17127716		2203	4300	6503	SO:0001583	missense	8029	exon16			TGCAGAACTTCCC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1990T>C	chr10.hg19:g.17127716A>G	ENSP00000367064:p.Phe664Leu	152.0	0.0		87.0	4.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.283422	0.59867	.	.	ENSG00000107611	ENST00000377833	T	0.19394	2.15	5.83	4.69	0.59074	CUB (5);	0.000000	0.44285	D	0.000471	T	0.16128	0.0388	L	0.31207	0.915	0.80722	D	1	P	0.35894	0.526	B	0.34301	0.179	T	0.02966	-1.1088	10	0.54805	T	0.06	.	11.6014	0.51006	0.9298:0.0:0.0702:0.0	.	664	O60494	CUBN_HUMAN	L	664	ENSP00000367064:F664L	ENSP00000367064:F664L	F	-	1	0	CUBN	17167722	1.000000	0.71417	0.942000	0.38095	0.327000	0.28475	6.043000	0.71004	1.031000	0.39867	0.533000	0.62120	TTC	.	.		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
STAM	8027	hgsc.bcm.edu	37	10	17747603	17747603	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:17747603T>C	ENST00000377524.3	+	12	1287	c.1072T>C	c.(1072-1074)Tca>Cca	p.S358P	STAM_ENST00000540523.1_Missense_Mutation_p.S247P	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	358					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TTCAGAACTCTCAGAACTTAA	0.323																																					p.S358P		Atlas-SNP	.											STAM,colon,carcinoma,0,1	STAM	60	.	0			c.T1072C						.						91.0	90.0	90.0					10																	17747603		2202	4300	6502	SO:0001583	missense	8027	exon12			GAACTCTCAGAAC	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1072T>C	chr10.hg19:g.17747603T>C	ENSP00000366746:p.Ser358Pro	82.0	0.0		59.0	3.0	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	hg19	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.680564	0.88542	.	.	ENSG00000136738	ENST00000377524;ENST00000540523	T;T	0.42513	1.31;0.97	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.68081	-0.5503	10	0.49607	T	0.09	-18.014	15.8513	0.78934	0.0:0.0:0.0:1.0	.	358	Q92783	STAM1_HUMAN	P	358;247	ENSP00000366746:S358P;ENSP00000438073:S247P	ENSP00000366746:S358P	S	+	1	0	STAM	17787609	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.152000	0.67230	0.533000	0.62120	TCA	.	.		0.323	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473	
ARL5B	221079	hgsc.bcm.edu	37	10	18963040	18963040	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:18963040C>A	ENST00000377275.3	+	5	700	c.467C>A	c.(466-468)tCc>tAc	p.S156Y		NM_178815.3	NP_848930.1	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 5B	156					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(1)|ovary(1)	2						CACATTCAATCCTGCTGTGCT	0.413																																					p.S156Y		Atlas-SNP	.											.	ARL5B	12	.	0			c.C467A						.						108.0	94.0	98.0					10																	18963040		2203	4300	6503	SO:0001583	missense	221079	exon5			TTCAATCCTGCTG	AF494061	CCDS7131.1	10p13	2014-05-09	2005-11-03	2005-11-03	ENSG00000165997	ENSG00000165997		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	23052	protein-coding gene	gene with protein product		608909	"""ADP-ribosylation factor-like 8"""	ARL8		12853149	Standard	XM_005252400		Approved		uc001iqd.1	Q96KC2	OTTHUMG00000017765	ENST00000377275.3:c.467C>A	chr10.hg19:g.18963040C>A	ENSP00000366487:p.Ser156Tyr	85.0	0.0		64.0	4.0	NM_178815		Missense_Mutation	SNP	ENST00000377275.3	hg19	CCDS7131.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739167	0.89573	.	.	ENSG00000165997	ENST00000377275	D	0.82255	-1.59	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.89787	0.6816	M	0.67517	2.055	0.80722	D	1	D	0.63046	0.992	P	0.61722	0.893	D	0.90363	0.4375	10	0.87932	D	0	-3.4532	19.6088	0.95594	0.0:1.0:0.0:0.0	.	156	Q96KC2	ARL5B_HUMAN	Y	156	ENSP00000366487:S156Y	ENSP00000366487:S156Y	S	+	2	0	ARL5B	19003046	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.760000	0.85248	2.636000	0.89361	0.467000	0.42956	TCC	.	.		0.413	ARL5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047078.1	NM_178815	
NEBL	10529	hgsc.bcm.edu	37	10	21104614	21104614	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:21104614G>T	ENST00000377122.4	-	22	2577	c.2181C>A	c.(2179-2181)acC>acA	p.T727T	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	727					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CACTTAAAGTGGTAGCTCTTC	0.323																																					p.T727T		Atlas-SNP	.											.	NEBL	199	.	0			c.C2181A						.						118.0	113.0	114.0					10																	21104614		2203	4300	6503	SO:0001819	synonymous_variant	10529	exon22			TAAAGTGGTAGCT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.2181C>A	chr10.hg19:g.21104614G>T		139.0	0.0		92.0	4.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000377122.4	hg19	CCDS7134.1																																																																																			.	.		0.323	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
MLLT10	8028	hgsc.bcm.edu	37	10	21884283	21884283	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:21884283C>T	ENST00000307729.7	+	5	497	c.319C>T	c.(319-321)Ctg>Ttg	p.L107L	MLLT10_ENST00000377059.3_Silent_p.L107L|MLLT10_ENST00000446906.2_Silent_p.L107L|MLLT10_ENST00000377072.3_Silent_p.L107L|MLLT10_ENST00000495130.1_3'UTR			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	107	Self-association.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						GGTTTGTGCCCTGTATATTCC	0.353			T	"""MLL, PICALM, CDK6"""	AL																																p.L107L		Atlas-SNP	.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	MLLT10_ENST00000377072,colon,carcinoma,0,2	MLLT10	183	.	0			c.C319T						.						100.0	93.0	96.0					10																	21884283		2203	4300	6503	SO:0001819	synonymous_variant	8028	exon4			TGTGCCCTGTATA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.319C>T	chr10.hg19:g.21884283C>T		128.0	0.0		98.0	5.0	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Silent	SNP	ENST00000307729.7	hg19	CCDS55708.1																																																																																			.	.		0.353	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
PIP4K2A	5305	hgsc.bcm.edu	37	10	22880591	22880591	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:22880591G>T	ENST00000376573.4	-	4	687	c.459C>A	c.(457-459)gcC>gcA	p.A153A	PIP4K2A_ENST00000323883.7_5'UTR|PIP4K2A_ENST00000422321.1_5'UTR|PIP4K2A_ENST00000545335.1_Silent_p.A94A	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	153	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						TGTGCATTTCGGCCACGTCTT	0.453																																					p.A153A		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.C459A						.						135.0	123.0	127.0					10																	22880591		2203	4300	6503	SO:0001819	synonymous_variant	5305	exon4			CATTTCGGCCACG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.459C>A	chr10.hg19:g.22880591G>T		125.0	0.0		120.0	6.0	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	hg19	CCDS7141.1																																																																																			.	.		0.453	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
APBB1IP	54518	hgsc.bcm.edu	37	10	26825148	26825148	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:26825148T>C	ENST00000376236.4	+	10	1499		c.e10+2			NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						AAGACTAAGGTCAGAAAAAAA	0.333																																					.		Atlas-SNP	.											.	APBB1IP	117	.	0			c.1044+2T>C						.						64.0	79.0	74.0					10																	26825148		2193	4294	6487	SO:0001630	splice_region_variant	54518	exon10			CTAAGGTCAGAAA	AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"""Pleckstrin homology (PH) domain containing"""	17379	protein-coding gene	gene with protein product	"""Rap1-GTP-interacting adaptor molecule"""	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.1044+2T>C	chr10.hg19:g.26825148T>C		73.0	0.0		80.0	4.0	NM_019043	Q8IWS8|Q8IYL7|Q8IZZ7	Splice_Site	SNP	ENST00000376236.4	hg19	CCDS31167.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517084	0.64634	.	.	ENSG00000077420	ENST00000445780;ENST00000376236	.	.	.	5.93	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6743	0.56884	0.1238:0.0:0.0:0.8762	.	.	.	.	.	-1	.	.	.	+	.	.	APBB1IP	26865154	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	8.040000	0.89188	1.073000	0.40885	-0.258000	0.10820	.	.	.		0.333	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043	Intron
ZNF248	57209	hgsc.bcm.edu	37	10	38126943	38126943	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:38126943G>T	ENST00000395867.3	-	4	662	c.112C>A	c.(112-114)Ctg>Atg	p.L38M	ZNF248_ENST00000494133.1_5'UTR|ZNF248_ENST00000374648.3_Missense_Mutation_p.L38M|ZNF248_ENST00000357328.4_Missense_Mutation_p.L38M	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TAATTTTCCAGGATCACATCT	0.418																																					p.L38M		Atlas-SNP	.											.	ZNF248	61	.	0			c.C112A						.						159.0	151.0	153.0					10																	38126943		2203	4300	6503	SO:0001583	missense	57209	exon4			TTTCCAGGATCAC	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.112C>A	chr10.hg19:g.38126943G>T	ENSP00000379208:p.Leu38Met	148.0	0.0		96.0	4.0	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255122	0.39896	.	.	ENSG00000198105	ENST00000395867;ENST00000374648;ENST00000357328;ENST00000395873;ENST00000395874	T;T;T;T;T	0.58506	4.03;0.33;4.03;0.33;0.33	4.43	3.53	0.40419	Krueppel-associated box (4);	0.000000	0.35495	N	0.003172	T	0.79143	0.4396	M	0.93016	3.37	0.33771	D	0.623008	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86561	0.1841	10	0.87932	D	0	.	10.4631	0.44592	0.097:0.0:0.903:0.0	.	38;38	Q8NDW4;Q8NDV8	ZN248_HUMAN;.	M	38	ENSP00000379208:L38M;ENSP00000363778:L38M;ENSP00000349882:L38M;ENSP00000379214:L38M;ENSP00000379215:L38M	ENSP00000349882:L38M	L	-	1	2	ZNF248	38166949	1.000000	0.71417	0.999000	0.59377	0.244000	0.25665	1.997000	0.40786	1.213000	0.43380	0.563000	0.77884	CTG	.	.		0.418	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
ZNF33A	7581	hgsc.bcm.edu	37	10	38343701	38343701	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:38343701C>A	ENST00000458705.2	+	5	804	c.646C>A	c.(646-648)Cac>Aac	p.H216N	ZNF33A_ENST00000374618.3_Missense_Mutation_p.H217N|ZNF33A_ENST00000307441.9_Missense_Mutation_p.H216N|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.H223N			Q06730	ZN33A_HUMAN	zinc finger protein 33A	216					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AACTTTAGAGCACAATTTTGA	0.353																																					p.H217N		Atlas-SNP	.											.	ZNF33A	103	.	0			c.C649A						.						83.0	82.0	82.0					10																	38343701		2203	4300	6503	SO:0001583	missense	7581	exon5			TTAGAGCACAATT	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.646C>A	chr10.hg19:g.38343701C>A	ENSP00000387713:p.His216Asn	142.0	0.0		118.0	5.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	hg19	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.998246	0.35226	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.05139	3.52;3.49;3.49;3.49	2.26	-0.992	0.10232	.	0.469523	0.15964	N	0.236124	T	0.03263	0.0095	N	0.22421	0.69	0.21841	N	0.999518	B;B;B	0.32467	0.372;0.097;0.184	B;B;B	0.26094	0.051;0.023;0.066	T	0.38178	-0.9673	10	0.56958	D	0.05	.	3.3177	0.07039	0.5539:0.2845:0.0:0.1616	.	223;216;217	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	N	217;223;216;216	ENSP00000363747:H217N;ENSP00000402467:H223N;ENSP00000387713:H216N;ENSP00000304268:H216N	ENSP00000304268:H216N	H	+	1	0	ZNF33A	38383707	0.001000	0.12720	0.344000	0.25628	0.542000	0.35054	-0.069000	0.11542	0.085000	0.17107	0.460000	0.39030	CAC	.	.		0.353	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
ZNF33B	7582	hgsc.bcm.edu	37	10	43088543	43088543	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:43088543A>G	ENST00000359467.3	-	5	1969	c.1855T>C	c.(1855-1857)Tgc>Cgc	p.C619R	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	619					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)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						GACTTCTGGCAGAAGGTTTTT	0.373																																					p.C619R	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.T1855C						.						95.0	95.0	95.0					10																	43088543		2203	4300	6503	SO:0001583	missense	7582	exon5			TCTGGCAGAAGGT	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1855T>C	chr10.hg19:g.43088543A>G	ENSP00000352444:p.Cys619Arg	129.0	0.0		121.0	5.0	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	hg19	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	A	2.623	-0.288063	0.05605	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.07327	3.2	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36740	N	0.002422	T	0.03783	0.0107	N	0.02202	-0.64	0.37728	D	0.925189	B	0.28552	0.215	B	0.34590	0.186	T	0.47497	-0.9113	10	0.35671	T	0.21	.	9.025	0.36224	1.0:0.0:0.0:0.0	.	619	Q06732	ZN33B_HUMAN	R	619;585	ENSP00000352444:C619R	ENSP00000352444:C619R	C	-	1	0	ZNF33B	42408549	0.012000	0.17670	0.995000	0.50966	0.982000	0.71751	0.506000	0.22658	1.446000	0.47643	0.336000	0.21669	TGC	.	.		0.373	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
RASGEF1A	221002	hgsc.bcm.edu	37	10	43698747	43698747	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:43698747T>C	ENST00000395809.1	-	3	2826	c.320A>G	c.(319-321)aAg>aGg	p.K107R	RASGEF1A_ENST00000374459.1_Splice_Site_p.K115R|RASGEF1A_ENST00000395810.1_Splice_Site_p.K107R|RASGEF1A_ENST00000472864.1_5'UTR			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	107	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						CCGCCTCACCTTTTCAGGCCC	0.697																																					p.K107R		Atlas-SNP	.											.	RASGEF1A	66	.	0			c.A320G						.						8.0	8.0	8.0					10																	43698747		2136	4212	6348	SO:0001630	splice_region_variant	221002	exon3			CTCACCTTTTCAG	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.321+1A>G	chr10.hg19:g.43698747T>C		91.0	0.0		100.0	4.0	NM_145313	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	hg19	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	T	14.62	2.590975	0.46214	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.51574	0.7;0.7;0.7	5.33	5.33	0.75918	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.071891	0.56097	D	0.000027	T	0.43299	0.1241	L	0.48642	1.525	0.53688	D	0.999972	B;B	0.12630	0.006;0.005	B;B	0.20767	0.031;0.018	T	0.28038	-1.0056	10	0.35671	T	0.21	.	14.4595	0.67440	0.0:0.0:0.0:1.0	.	107;115	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	R	115;107;107	ENSP00000363583:K115R;ENSP00000379155:K107R;ENSP00000379154:K107R	ENSP00000363583:K115R	K	-	2	0	RASGEF1A	43018753	1.000000	0.71417	0.988000	0.46212	0.061000	0.15899	6.668000	0.74457	2.017000	0.59298	0.402000	0.26972	AAG	.	.		0.697	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313	Missense_Mutation
TMEM72	643236	hgsc.bcm.edu	37	10	45429084	45429084	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:45429084G>T	ENST00000544540.1	+	3	339		c.e3-1		TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						CCTCTCCCCAGGTGTCAACCA	0.607																																					.		Atlas-SNP	.											.	TMEM72	25	.	0			c.210-1G>T						.						59.0	60.0	59.0					10																	45429084		1568	3582	5150	SO:0001630	splice_region_variant	643236	exon4			TCCCCAGGTGTCA	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-145-1G>T	chr10.hg19:g.45429084G>T		63.0	0.0		52.0	4.0	NM_001123376	A1L181|Q5T740	Splice_Site	SNP	ENST00000544540.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.78	1.447607	0.26074	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4359	0.75146	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM72	44749090	1.000000	0.71417	0.999000	0.59377	0.127000	0.20565	6.353000	0.73032	2.788000	0.95919	0.650000	0.86243	.	.	.		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	Intron
C10orf71	118461	hgsc.bcm.edu	37	10	50532329	50532329	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50532329C>T	ENST00000374144.3	+	3	2027	c.1739C>T	c.(1738-1740)cCc>cTc	p.P580L	C10orf71_ENST00000323868.4_Missense_Mutation_p.P580L			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	580										endometrium(1)	1						ACAGCTGACCCCAGTGAGCCC	0.547																																					p.P580L		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1739T						.						41.0	42.0	42.0					10																	50532329		1996	4173	6169	SO:0001583	missense	118461	exon3			CTGACCCCAGTGA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1739C>T	chr10.hg19:g.50532329C>T	ENSP00000363259:p.Pro580Leu	133.0	0.0		86.0	4.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457083	0.43634	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.72	5.48	4.47	0.54385	.	0.470679	0.15889	N	0.239636	T	0.08044	0.0201	L	0.36672	1.1	0.09310	N	1	B	0.20988	0.05	B	0.17722	0.019	T	0.45963	-0.9225	10	0.02654	T	1	.	4.8407	0.13489	0.0:0.792:0.0:0.208	.	580	Q711Q0-3	.	L	580	ENSP00000318713:P580L;ENSP00000363259:P580L	ENSP00000318713:P580L	P	+	2	0	C10orf71	50202335	0.006000	0.16342	0.006000	0.13384	0.239000	0.25481	1.931000	0.40134	2.587000	0.87381	0.591000	0.81541	CCC	.	.		0.547	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
CHAT	1103	hgsc.bcm.edu	37	10	50833615	50833615	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50833615C>A	ENST00000337653.2	+	6	1002	c.849C>A	c.(847-849)ccC>ccA	p.P283P	CHAT_ENST00000455728.2_Silent_p.P165P|CHAT_ENST00000395559.2_Silent_p.P165P|CHAT_ENST00000351556.3_Silent_p.P165P|CHAT_ENST00000339797.1_Silent_p.P165P|CHAT_ENST00000395562.2_Silent_p.P201P	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	283					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.P283P(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	ACCGGCTCCCCGGCCATACCC	0.587																																					p.P283P		Atlas-SNP	.											CHAT,NS,carcinoma,0,1	CHAT	162	.	1	Substitution - coding silent(1)	kidney(1)	c.C849A						.						47.0	36.0	40.0					10																	50833615		2203	4300	6503	SO:0001819	synonymous_variant	1103	exon6			GCTCCCCGGCCAT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.849C>A	chr10.hg19:g.50833615C>A		108.0	0.0		71.0	4.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	hg19	CCDS7232.1																																																																																			.	.		0.587	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
OGDHL	55753	hgsc.bcm.edu	37	10	50948862	50948862	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50948862A>G	ENST00000374103.4	-	16	2119	c.2034T>C	c.(2032-2034)caT>caC	p.H678H	OGDHL_ENST00000419399.1_Silent_p.H621H|OGDHL_ENST00000432695.1_Silent_p.H469H|OGDHL_ENST00000490844.1_5'Flank	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	678					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CCTCCTGGTCATGGAGAACAT	0.632																																					p.H678H		Atlas-SNP	.											.	OGDHL	149	.	0			c.T2034C						.						126.0	95.0	105.0					10																	50948862		2203	4300	6503	SO:0001819	synonymous_variant	55753	exon16			CTGGTCATGGAGA	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2034T>C	chr10.hg19:g.50948862A>G		67.0	0.0		47.0	4.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	hg19	CCDS7234.1																																																																																			.	.		0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
SGMS1	259230	hgsc.bcm.edu	37	10	52066912	52066912	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:52066912T>C	ENST00000361781.2	-	11	2191	c.1232A>G	c.(1231-1233)aAt>aGt	p.N411S	SGMS1_ENST00000429490.1_Missense_Mutation_p.N242S	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	417					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						TTATGTGTCATTCACCAGCCG	0.448																																					p.N411S		Atlas-SNP	.											.	SGMS1	40	.	0			c.A1232G						.						100.0	86.0	91.0					10																	52066912		2203	4300	6503	SO:0001583	missense	259230	exon11			GTGTCATTCACCA	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"""Sterile alpha motif (SAM) domain containing"""	29799	protein-coding gene	gene with protein product		611573	"""transmembrane protein 23"""	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.1232A>G	chr10.hg19:g.52066912T>C	ENSP00000354829:p.Asn411Ser	223.0	0.0		149.0	6.0	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	9.604	1.129421	0.21041	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.41400	1.0	5.58	3.22	0.36961	.	0.198210	0.47093	D	0.000258	T	0.17323	0.0416	N	0.03608	-0.345	0.80722	D	1	B;B	0.17038	0.02;0.002	B;B	0.12837	0.008;0.001	T	0.04386	-1.0955	10	0.26408	T	0.33	-11.3741	6.6094	0.22743	0.0:0.2538:0.0:0.7462	.	242;417	B4DJU2;Q86VZ5	.;SMS1_HUMAN	S	211;411;242	ENSP00000354829:N411S	ENSP00000354829:N411S	N	-	2	0	SGMS1	51736918	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.505000	0.22642	1.027000	0.39758	0.533000	0.62120	AAT	.	.		0.448	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156	
A1CF	29974	hgsc.bcm.edu	37	10	52619608	52619608	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:52619608C>A	ENST00000373993.1	-	1	137	c.93G>T	c.(91-93)ttG>ttT	p.L31F	A1CF_ENST00000374001.2_Missense_Mutation_p.L31F|A1CF_ENST00000395495.1_Missense_Mutation_p.L31F|A1CF_ENST00000373997.3_Missense_Mutation_p.L31F|A1CF_ENST00000282641.2_Missense_Mutation_p.L31F|A1CF_ENST00000373995.3_5'UTR|A1CF_ENST00000395489.2_5'UTR			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	31					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CTACCTGGACCAAGCTATATC	0.502																																					p.L31F		Atlas-SNP	.											.	A1CF	190	.	0			c.G93T						.						84.0	74.0	78.0					10																	52619608		2203	4300	6503	SO:0001583	missense	29974	exon3			CTGGACCAAGCTA	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.93G>T	chr10.hg19:g.52619608C>A	ENSP00000363105:p.Leu31Phe	105.0	0.0		80.0	4.0	NM_138932	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242686	0.79912	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000282641;ENST00000395495;ENST00000414883	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;2.54;1.91	5.83	5.83	0.93111	.	0.644585	0.15345	N	0.267300	T	0.58177	0.2104	M	0.82630	2.6	0.80722	D	1	P;P	0.49783	0.846;0.928	B;P	0.47573	0.398;0.55	T	0.64385	-0.6420	10	0.72032	D	0.01	.	17.6277	0.88097	0.0:1.0:0.0:0.0	.	31;31	Q9NQ94;Q9NQ94-2	A1CF_HUMAN;.	F	31	ENSP00000363113:L31F;ENSP00000363105:L31F;ENSP00000363109:L31F;ENSP00000282641:L31F;ENSP00000378873:L31F;ENSP00000397953:L31F	ENSP00000282641:L31F	L	-	3	2	A1CF	52289614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.253000	0.65452	2.770000	0.95276	0.655000	0.94253	TTG	.	.		0.502	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
EGR2	1959	hgsc.bcm.edu	37	10	64575711	64575711	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:64575711G>T	ENST00000242480.3	-	1	404	c.79C>A	c.(79-81)Ccg>Acg	p.P27T	EGR2_ENST00000493899.2_5'UTR|EGR2_ENST00000411732.1_5'UTR|EGR2_ENST00000439032.1_Missense_Mutation_p.P27T	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	27					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					TCCTCCACCGGGTAGATGTTG	0.582																																					p.P27T		Atlas-SNP	.											.	EGR2	77	.	0			c.C79A						.						183.0	166.0	172.0					10																	64575711		2203	4300	6503	SO:0001583	missense	1959	exon1			CCACCGGGTAGAT	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"""Zinc fingers, C2H2-type"""	3239	protein-coding gene	gene with protein product	"""Krox-20 homolog, Drosophila"""	129010	"""early growth response 2 (Krox-20 homolog, Drosophila)"""	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.79C>A	chr10.hg19:g.64575711G>T	ENSP00000242480:p.Pro27Thr	178.0	0.0		122.0	5.0	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	hg19	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.296360	0.60086	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000432380	T;T	0.14766	2.48;2.48	5.1	5.1	0.69264	.	0.131508	0.53938	D	0.000058	T	0.14527	0.0351	L	0.59436	1.845	0.80722	D	1	P	0.43024	0.798	B	0.36289	0.221	T	0.01371	-1.1372	10	0.87932	D	0	-15.2967	11.9405	0.52899	0.0851:0.0:0.9149:0.0	.	27	P11161	EGR2_HUMAN	T	27;27;40	ENSP00000242480:P27T;ENSP00000402040:P27T	ENSP00000242480:P27T	P	-	1	0	EGR2	64245717	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.627000	0.54252	2.548000	0.85928	0.556000	0.70494	CCG	.	.		0.582	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
STOX1	219736	hgsc.bcm.edu	37	10	70645469	70645469	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:70645469T>C	ENST00000298596.6	+	3	2000	c.1917T>C	c.(1915-1917)caT>caC	p.H639H	STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399169.4_Silent_p.H639H|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Silent_p.H529H	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	639						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGACTCCGCATAGTCTGCCAT	0.438																																					p.H639H		Atlas-SNP	.											.	STOX1	75	.	0			c.T1917C						.						128.0	121.0	123.0					10																	70645469		1926	4141	6067	SO:0001819	synonymous_variant	219736	exon3			TCCGCATAGTCTG	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1917T>C	chr10.hg19:g.70645469T>C		60.0	0.0		54.0	4.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.438	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
PRF1	5551	hgsc.bcm.edu	37	10	72357906	72357906	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:72357906C>A	ENST00000441259.1	-	3	1731	c.1571G>T	c.(1570-1572)aGg>aTg	p.R524M	PRF1_ENST00000373209.2_Missense_Mutation_p.R524M	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	524					apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						GGGCAAGCACCTGGCATGATA	0.582			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.R524M		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.G1571T						.						106.0	100.0	102.0					10																	72357906		2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AAGCACCTGGCAT	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1571G>T	chr10.hg19:g.72357906C>A	ENSP00000398568:p.Arg524Met	88.0	0.0		79.0	6.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.667704	0.29604	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91237	-2.81;-2.81	5.97	-11.9	0.00025	.	1.068430	0.07158	N	0.850236	T	0.78553	0.4301	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.11329	0.006	T	0.65849	-0.6068	10	0.49607	T	0.09	-3.7194	12.2817	0.54767	0.0714:0.196:0.6362:0.0964	.	524	P14222	PERF_HUMAN	M	524	ENSP00000362305:R524M;ENSP00000398568:R524M	ENSP00000316746:R524M	R	-	2	0	PRF1	72027912	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.888000	0.01616	-2.925000	0.00303	-2.226000	0.00293	AGG	.	.		0.582	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
PSAP	5660	hgsc.bcm.edu	37	10	73585601	73585601	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:73585601A>G	ENST00000394936.3	-	7	917	c.770T>C	c.(769-771)aTg>aCg	p.M257T	PSAP_ENST00000394934.1_Missense_Mutation_p.M257T			P07602	SAP_HUMAN	prosaposin	257	Saposin B-type 2. {ECO:0000255|PROSITE- ProRule:PRU00415}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TACCATGTGCATCATCATCTG	0.388																																					p.M257T		Atlas-SNP	.											.	PSAP	43	.	0			c.T770C						.						101.0	96.0	98.0					10																	73585601		2203	4300	6503	SO:0001583	missense	5660	exon7			ATGTGCATCATCA	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.770T>C	chr10.hg19:g.73585601A>G	ENSP00000378394:p.Met257Thr	102.0	0.0		88.0	4.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839762	0.71488	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000404083;ENST00000394940	T;T	0.74842	-0.88;-0.88	5.3	5.3	0.74995	Saposin-like (2);Saposin-like type B, 2 (1);Saposin B (2);	0.077004	0.85682	D	0.000000	T	0.79839	0.4515	M	0.76002	2.32	0.58432	D	0.999997	P	0.47191	0.891	P	0.48873	0.593	T	0.81651	-0.0836	10	0.49607	T	0.09	-28.0768	15.2039	0.73162	1.0:0.0:0.0:0.0	.	257	P07602	SAP_HUMAN	T	257;257;257;257;260;182	ENSP00000378394:M257T;ENSP00000378392:M257T	ENSP00000350063:M257T	M	-	2	0	PSAP	73255607	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	4.259000	0.58828	2.143000	0.66587	0.459000	0.35465	ATG	.	.		0.388	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778	
SEC24C	9632	hgsc.bcm.edu	37	10	75526220	75526220	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75526220T>C	ENST00000339365.2	+	13	1882	c.1720T>C	c.(1720-1722)Tct>Cct	p.S574P	SEC24C_ENST00000345254.4_Missense_Mutation_p.S574P|SEC24C_ENST00000411652.2_Missense_Mutation_p.S455P|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000546025.1_3'UTR|SEC24C_ENST00000535742.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	574					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					GATGGTTGTGTCTGATGTGGC	0.502																																					p.S574P		Atlas-SNP	.											.	SEC24C	86	.	0			c.T1720C						.						100.0	83.0	89.0					10																	75526220		2203	4300	6503	SO:0001583	missense	9632	exon12			GTTGTGTCTGATG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1720T>C	chr10.hg19:g.75526220T>C	ENSP00000343405:p.Ser574Pro	69.0	0.0		50.0	4.0	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.229951	0.79688	.	.	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.76186	-1.0;-1.0;-1.0	5.93	5.93	0.95920	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	T	0.79992	0.4542	L	0.39245	1.2	0.80722	D	1	D;D;D	0.64830	0.987;0.992;0.994	P;P;D	0.68943	0.82;0.874;0.961	T	0.75952	-0.3136	10	0.21014	T	0.42	-20.5737	16.3798	0.83452	0.0:0.0:0.0:1.0	.	455;574;574	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	P	574;574;455	ENSP00000321845:S574P;ENSP00000343405:S574P;ENSP00000402913:S455P	ENSP00000343405:S574P	S	+	1	0	SEC24C	75196226	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	8.040000	0.89188	2.271000	0.75665	0.533000	0.62120	TCT	.	.		0.502	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
CAMK2G	818	hgsc.bcm.edu	37	10	75602229	75602229	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75602229C>A	ENST00000351293.3	-	11	947	c.890G>T	c.(889-891)cGg>cTg	p.R297L	CAMK2G_ENST00000423381.1_Missense_Mutation_p.R297L|CAMK2G_ENST00000372765.1_Missense_Mutation_p.R297L|CAMK2G_ENST00000444854.2_Silent_p.P97P|CAMK2G_ENST00000394762.2_Missense_Mutation_p.R297L|CAMK2G_ENST00000322635.3_Missense_Mutation_p.R297L|CAMK2G_ENST00000322680.3_Missense_Mutation_p.R297L|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000305762.7_Missense_Mutation_p.R297L|RP11-574K11.8_ENST00000446730.2_RNA	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	297	Calmodulin-binding.|Calmodulin-binding. {ECO:0000250}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	CAGTTTTCTCCGGGCATTGAA	0.542																																					p.R297L		Atlas-SNP	.											.	CAMK2G	79	.	0			c.G890T						.						128.0	115.0	120.0					10																	75602229		2203	4300	6503	SO:0001583	missense	818	exon11			TTTCTCCGGGCAT	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.890G>T	chr10.hg19:g.75602229C>A	ENSP00000277853:p.Arg297Leu	110.0	0.0		91.0	5.0	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	hg19	CCDS7336.1	.	.	.	.	.	.	.	.	.	.	C	36	5.757903	0.96898	.	.	ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765	T;T;T;T;T;T;T;T	0.70045	-0.38;1.96;-0.39;-0.36;-0.39;-0.45;-0.4;1.96	5.87	5.87	0.94306	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	D	0.83362	0.5238	M	0.86178	2.8	0.80722	D	1	P;P;P;P;B;B;P;D;D	0.60575	0.935;0.807;0.935;0.878;0.186;0.128;0.661;0.975;0.988	P;B;P;P;B;B;B;P;P	0.61477	0.569;0.274;0.569;0.464;0.037;0.04;0.33;0.622;0.889	D	0.85128	0.0973	10	0.87932	D	0	.	20.2079	0.98282	0.0:1.0:0.0:0.0	.	297;289;297;297;297;297;297;297;297	Q13555-2;B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8	.;.;.;.;.;.;KCC2G_HUMAN;.;.	L	297;297;297;297;297;297;232;297;297	ENSP00000277853:R297L;ENSP00000315599:R297L;ENSP00000410298:R297L;ENSP00000319060:R297L;ENSP00000378243:R297L;ENSP00000393784:R232L;ENSP00000307082:R297L;ENSP00000361851:R297L	ENSP00000307082:R297L	R	-	2	0	CAMK2G	75272235	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.810000	0.86072	2.781000	0.95711	0.655000	0.94253	CGG	.	.		0.542	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
C10orf55	414236	hgsc.bcm.edu	37	10	75671984	75671984	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75671984T>C	ENST00000409178.1	-	4	359	c.19A>G	c.(19-21)Agt>Ggt	p.S7G	PLAU_ENST00000372764.3_Missense_Mutation_p.C33R|PLAU_ENST00000446342.1_Missense_Mutation_p.C16R|C10orf55_ENST00000412307.2_Missense_Mutation_p.S7G|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372762.4_Intron	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55	7										endometrium(1)	1	Prostate(51;0.0112)					GAACTGTGACTGTCTAAATGG	0.537																																					p.C33R		Atlas-SNP	.											.	PLAU	47	.	0			c.T97C						.						106.0	95.0	99.0					10																	75671984		2203	4300	6503	SO:0001583	missense	5328	exon4			TGTGACTGTCTAA		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.19A>G	chr10.hg19:g.75671984T>C	ENSP00000386960:p.Ser7Gly	94.0	0.0		93.0	4.0	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	hg19	CCDS53541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.64|15.64	2.891905|2.891905	0.52014|0.52014	.|.	.|.	ENSG00000122861|ENSG00000222047	ENST00000446342;ENST00000372764|ENST00000409178;ENST00000412307	D;D|.	0.89123|.	-2.37;-2.47|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.40067|0.40067	0.1102|0.1102	N|N	0.08118|0.08118	0|0	0.26793|0.26793	N|N	0.969365|0.969365	D;D;D|D	0.89917|0.89917	1.0;1.0;1.0|1.0	D;D;D|D	0.97110|0.72338	0.998;0.998;1.0|0.977	T|T	0.41342|0.41342	-0.9514|-0.9514	9|8	.|0.87932	.|D	.|0	.|.	12.6036|12.6036	0.56511|0.56511	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	16;33;33|7	E7ET40;B2R7F2;P00749|Q5SWW7	.;.;UROK_HUMAN|CJ055_HUMAN	R|G	16;33|7	ENSP00000388474:C16R;ENSP00000361850:C33R|.	.|ENSP00000386960:S7G	C|S	+|-	1|1	0|0	PLAU|C10orf55	75341990|75341990	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.144000|0.144000	0.21451|0.21451	4.825000|4.825000	0.62708|0.62708	2.234000|2.234000	0.73211|0.73211	0.402000|0.402000	0.26972|0.26972	TGT|AGT	.	.		0.537	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
MAT1A	4143	hgsc.bcm.edu	37	10	82039957	82039957	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:82039957G>T	ENST00000372213.3	-	5	781	c.521C>A	c.(520-522)cCc>cAc	p.P174H		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	174					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CCGCAGCCAGGGGAGGAGGCC	0.567																																					p.P174H		Atlas-SNP	.											.	MAT1A	52	.	0			c.C521A						.						67.0	76.0	73.0					10																	82039957		2203	4300	6503	SO:0001583	missense	4143	exon5			AGCCAGGGGAGGA		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.521C>A	chr10.hg19:g.82039957G>T	ENSP00000361287:p.Pro174His	100.0	0.0		70.0	19.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.732975	0.69189	.	.	ENSG00000151224	ENST00000372213;ENST00000372206;ENST00000455001	D;D	0.83250	-1.7;-1.7	4.91	4.91	0.64330	S-adenosylmethionine synthetase, central domain (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.89866	0.6839	M	0.88512	2.96	0.80722	D	1	P	0.52692	0.955	P	0.52909	0.713	D	0.92061	0.5656	10	0.87932	D	0	-27.5525	15.935	0.79694	0.0:0.0:1.0:0.0	.	174	Q00266	METK1_HUMAN	H	174;174;111	ENSP00000361287:P174H;ENSP00000414961:P111H	ENSP00000361280:P174H	P	-	2	0	MAT1A	82029937	1.000000	0.71417	0.997000	0.53966	0.655000	0.38815	7.528000	0.81941	2.442000	0.82660	0.655000	0.94253	CCC	.	.		0.567	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
TSPAN14	81619	hgsc.bcm.edu	37	10	82275975	82275975	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:82275975G>T	ENST00000429989.3	+	8	860	c.637G>T	c.(637-639)Gat>Tat	p.D213Y	TSPAN14_ENST00000372164.3_Missense_Mutation_p.D196Y|TSPAN14_ENST00000372156.1_Missense_Mutation_p.D213Y|TSPAN14_ENST00000481124.1_Missense_Mutation_p.D90Y|TSPAN14_ENST00000341863.6_Missense_Mutation_p.D156Y|TSPAN14_ENST00000265450.5_3'UTR|TSPAN14_ENST00000372158.1_Missense_Mutation_p.D213Y	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	213					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GAGCAAGTGGGATGAGTCCAT	0.562																																					p.D213Y		Atlas-SNP	.											.	TSPAN14	29	.	0			c.G637T						.						135.0	120.0	125.0					10																	82275975		2203	4300	6503	SO:0001583	missense	81619	exon8			AAGTGGGATGAGT	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.637G>T	chr10.hg19:g.82275975G>T	ENSP00000396270:p.Asp213Tyr	154.0	0.0		83.0	4.0	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	hg19	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500877	0.64298	.	.	ENSG00000108219	ENST00000429989;ENST00000481124;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000341863;ENST00000372156	T;T;T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28	5.57	5.57	0.84162	Tetraspanin, EC2 domain (1);	0.523983	0.22284	N	0.062088	T	0.78585	0.4306	N	0.17082	0.46	0.42227	D	0.991878	D;P;P	0.61697	0.99;0.903;0.94	P;P;P	0.60236	0.871;0.722;0.601	T	0.80341	-0.1423	10	0.66056	D	0.02	-21.4631	10.4742	0.44655	0.088:0.0:0.912:0.0	.	90;213;196	B4DHY6;Q8NG11;Q8NG11-2	.;TSN14_HUMAN;.	Y	213;90;183;196;213;156;213	ENSP00000396270:D213Y;ENSP00000418195:D90Y;ENSP00000361230:D183Y;ENSP00000361237:D196Y;ENSP00000361231:D213Y;ENSP00000344076:D156Y;ENSP00000361229:D213Y	ENSP00000344076:D156Y	D	+	1	0	TSPAN14	82265955	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.381000	0.52455	2.643000	0.89663	0.591000	0.81541	GAT	.	.		0.562	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
IFIT2	3433	hgsc.bcm.edu	37	10	91066851	91066851	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:91066851T>C	ENST00000371826.3	+	2	1307	c.1138T>C	c.(1138-1140)Ttt>Ctt	p.F380L	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	380					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				GTATGGCAACTTTCAGCTGTA	0.408																																					p.F380L		Atlas-SNP	.											.	IFIT2	39	.	0			c.T1138C						.						93.0	87.0	89.0					10																	91066851		1914	4128	6042	SO:0001583	missense	3433	exon2			GGCAACTTTCAGC	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.1138T>C	chr10.hg19:g.91066851T>C	ENSP00000360891:p.Phe380Leu	96.0	0.0		91.0	4.0	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741715	0.69304	.	.	ENSG00000119922	ENST00000371826	T	0.20463	2.07	4.58	2.12	0.27331	Tetratricopeptide-like helical (1);	0.078649	0.52532	U	0.000072	T	0.24236	0.0587	L	0.58969	1.84	0.41503	D	0.988297	D	0.54397	0.966	P	0.48598	0.583	T	0.02031	-1.1226	10	0.42905	T	0.14	-8.7326	7.5678	0.27890	0.1403:0.0:0.1468:0.7129	.	380	P09913	IFIT2_HUMAN	L	380	ENSP00000360891:F380L	ENSP00000360891:F380L	F	+	1	0	IFIT2	91056831	0.976000	0.34144	0.994000	0.49952	0.994000	0.84299	2.922000	0.48860	0.449000	0.26747	0.533000	0.62120	TTT	.	.		0.408	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
IDE	3416	hgsc.bcm.edu	37	10	94291601	94291601	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:94291601C>A	ENST00000265986.6	-	4	621	c.565G>T	c.(565-567)Gaa>Taa	p.E189*		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	189					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""""""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"""	TTCTCATGTTCTGAATCAACT	0.398																																					p.E189X		Atlas-SNP	.											.	IDE	77	.	0			c.G565T						.						98.0	90.0	92.0					10																	94291601		2203	4300	6503	SO:0001587	stop_gained	3416	exon4			CATGTTCTGAATC	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"""insulysin"""	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.565G>T	chr10.hg19:g.94291601C>A	ENSP00000265986:p.Glu189*	114.0	0.0		76.0	5.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Nonsense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	C	35	5.577823	0.96565	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.124	19.6584	0.95853	0.0:1.0:0.0:0.0	.	.	.	.	X	189;175	.	ENSP00000265986:E189X	E	-	1	0	IDE	94281581	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.747000	0.85070	2.646000	0.89796	0.655000	0.94253	GAA	.	.		0.398	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	
HPS1	3257	hgsc.bcm.edu	37	10	100182230	100182230	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:100182230C>T	ENST00000325103.6	-	17	1872	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	HPS1_ENST00000361490.4_Missense_Mutation_p.V547M|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	547					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		GTGCGGTCCACATAGATGAAG	0.572									Hermansky-Pudlak syndrome																												p.V547M		Atlas-SNP	.											.	HPS1	65	.	0			c.G1639A						.						114.0	111.0	112.0					10																	100182230		2203	4300	6503	SO:0001583	missense	3257	exon17	Familial Cancer Database	HPS, HPS1-8	GGTCCACATAGAT	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1639G>A	chr10.hg19:g.100182230C>T	ENSP00000326649:p.Val547Met	87.0	0.0		89.0	4.0	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	hg19	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965098	0.74131	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891	T;T	0.32988	1.43;1.43	5.37	1.48	0.22813	.	0.062767	0.64402	D	0.000004	T	0.54727	0.1876	M	0.86178	2.8	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.994	P;D;P	0.91635	0.894;0.999;0.894	T	0.54139	-0.8338	10	0.59425	D	0.04	.	9.8855	0.41260	0.0:0.7252:0.0:0.2748	.	514;547;548	Q92902-2;Q8WXE5;D3DR62	.;.;.	M	547;547;514	ENSP00000326649:V547M;ENSP00000355310:V547M	ENSP00000326649:V547M	V	-	1	0	HPS1	100172220	1.000000	0.71417	0.927000	0.36925	0.822000	0.46500	4.434000	0.59935	0.012000	0.14892	0.561000	0.74099	GTG	.	.		0.572	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
ABCC2	1244	hgsc.bcm.edu	37	10	101567952	101567952	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101567952G>A	ENST00000370449.4	+	13	1894	c.1781G>A	c.(1780-1782)aGc>aAc	p.S594N		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	594	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TTTCCCCTGAGCATGCTTCCC	0.473																																					p.S594N		Atlas-SNP	.											.	ABCC2	160	.	0			c.G1781A						.						241.0	210.0	221.0					10																	101567952		2203	4300	6503	SO:0001583	missense	1244	exon13			CCCTGAGCATGCT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1781G>A	chr10.hg19:g.101567952G>A	ENSP00000359478:p.Ser594Asn	160.0	0.0		115.0	39.0	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	G	2.621	-0.288648	0.05605	.	.	ENSG00000023839	ENST00000370449	T	0.29142	1.58	5.63	1.32	0.21799	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.767826	0.12970	N	0.424253	T	0.22859	0.0552	N	0.25789	0.76	0.58432	D	0.999999	B	0.30326	0.276	B	0.28709	0.093	T	0.14008	-1.0488	10	0.07813	T	0.8	-12.9795	20.8761	0.99795	0.0:0.8123:0.1877:0.0	.	594	Q92887	MRP2_HUMAN	N	594	ENSP00000359478:S594N	ENSP00000359478:S594N	S	+	2	0	ABCC2	101557942	0.003000	0.15002	0.157000	0.22605	0.964000	0.63967	0.116000	0.15561	0.253000	0.21552	0.491000	0.48974	AGC	.	.		0.473	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
CPN1	1369	hgsc.bcm.edu	37	10	101824984	101824984	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101824984G>T	ENST00000370418.3	-	4	971	c.720C>A	c.(718-720)acC>acA	p.T240T		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	240	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		GGGTGCTGGCGGTGCGGCGGA	0.602																																					p.T240T		Atlas-SNP	.											.	CPN1	62	.	0			c.C720A						.						61.0	65.0	64.0					10																	101824984		2203	4300	6503	SO:0001819	synonymous_variant	1369	exon4			GCTGGCGGTGCGG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.720C>A	chr10.hg19:g.101824984G>T		96.0	0.0		87.0	4.0	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	hg19	CCDS7486.1																																																																																			.	.		0.602	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
CHUK	1147	hgsc.bcm.edu	37	10	101964400	101964400	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101964400C>A	ENST00000370397.7	-	13	1456	c.1370G>T	c.(1369-1371)aGa>aTa	p.R457I		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	457	Leucine-zipper.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	AGCATTATATCTAAGAAGACT	0.289																																					p.R457I	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.G1370T						.						89.0	83.0	85.0					10																	101964400		2202	4300	6502	SO:0001583	missense	1147	exon13			TTATATCTAAGAA	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1370G>T	chr10.hg19:g.101964400C>A	ENSP00000359424:p.Arg457Ile	104.0	0.0		115.0	5.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893339	0.91889	.	.	ENSG00000213341	ENST00000370397	T	0.77489	-1.1	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.87152	0.6106	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.87874	0.2673	10	0.87932	D	0	-18.3766	17.3158	0.87224	0.0:1.0:0.0:0.0	.	457	O15111	IKKA_HUMAN	I	457	ENSP00000359424:R457I	ENSP00000359424:R457I	R	-	2	0	CHUK	101954390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.696000	0.92011	0.650000	0.86243	AGA	.	.		0.289	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
CHUK	1147	hgsc.bcm.edu	37	10	101982628	101982628	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101982628G>T	ENST00000370397.7	-	3	396	c.310C>A	c.(310-312)Cga>Aga	p.R104R		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.R104*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	ACTACCTTTCGGAGATCTCCT	0.353																																					p.R104R	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											CHUK,NS,carcinoma,0,1	CHUK	71	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C310A						.						110.0	96.0	101.0					10																	101982628		2203	4300	6503	SO:0001819	synonymous_variant	1147	exon3			CCTTTCGGAGATC	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.310C>A	chr10.hg19:g.101982628G>T		86.0	1.0		98.0	4.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Silent	SNP	ENST00000370397.7	hg19	CCDS7488.1																																																																																			.	.		0.353	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
OBFC1	79991	hgsc.bcm.edu	37	10	105652001	105652001	+	Missense_Mutation	SNP	T	T	C	rs553430081		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:105652001T>C	ENST00000224950.3	-	8	930	c.763A>G	c.(763-765)Aag>Gag	p.K255E	OBFC1_ENST00000369764.1_Missense_Mutation_p.K255E|OBFC1_ENST00000466828.1_5'UTR	NM_024928.4	NP_079204.2	Q9H668	STN1_HUMAN	oligonucleotide/oligosaccharide-binding fold containing 1	255	Winged helix-turn-helix (wHTH) 1.				positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromosome, telomeric region (GO:0000784)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)|single-stranded telomeric DNA binding (GO:0043047)			large_intestine(3)|lung(7)|ovary(1)|pancreas(2)	13		Colorectal(252;0.178)		Epithelial(162;3.39e-10)|all cancers(201;1.32e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0151)		GTGTCCTTCTTAAAATTCACC	0.363													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17281	0.0		0.0	False		,,,				2504	0.0				p.K255E		Atlas-SNP	.											.	OBFC1	33	.	0			c.A763G						.						75.0	76.0	76.0					10																	105652001		2203	4300	6503	SO:0001583	missense	79991	exon8			CCTTCTTAAAATT	BC017400	CCDS7552.1	10q25.1	2011-06-14				ENSG00000107960			26200	protein-coding gene	gene with protein product		613128				12477932	Standard	NM_024928		Approved	FLJ22559, bA541N10.2	uc001kxm.3	Q9H668		ENST00000224950.3:c.763A>G	chr10.hg19:g.105652001T>C	ENSP00000224950:p.Lys255Glu	77.0	0.0		93.0	4.0	NM_024928	D3DR99|Q5TCZ0	Missense_Mutation	SNP	ENST00000224950.3	hg19	CCDS7552.1	.	.	.	.	.	.	.	.	.	.	T	0.046	-1.266407	0.01433	.	.	ENSG00000107960	ENST00000224950;ENST00000369764	T;T	0.43294	0.95;0.95	5.23	2.82	0.32997	Domain of unknown function DUF1879, CTS complex STN1 subunit (1);	0.768337	0.13102	N	0.413671	T	0.29749	0.0743	L	0.37561	1.115	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17258	-1.0375	10	0.27785	T	0.31	-13.7692	7.0044	0.24828	0.0:0.0838:0.1523:0.7639	.	255	Q9H668	STN1_HUMAN	E	255	ENSP00000224950:K255E;ENSP00000358779:K255E	ENSP00000224950:K255E	K	-	1	0	OBFC1	105641991	0.410000	0.25376	0.292000	0.24919	0.203000	0.24098	0.817000	0.27281	0.903000	0.36546	-0.466000	0.05196	AAG	.	.		0.363	OBFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050174.1	NM_024928	
VWA2	340706	hgsc.bcm.edu	37	10	116045927	116045927	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:116045927C>T	ENST00000392982.3	+	11	1477	c.1227C>T	c.(1225-1227)agC>agT	p.S409S	VWA2_ENST00000603594.1_Silent_p.S409S			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	409	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		TGGTCTGGAGCCTCGATGGCA	0.687																																					p.S409S		Atlas-SNP	.											.	VWA2	64	.	0			c.C1227T						.						78.0	71.0	73.0					10																	116045927		2203	4300	6503	SO:0001819	synonymous_variant	340706	exon11			CTGGAGCCTCGAT	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1227C>T	chr10.hg19:g.116045927C>T		159.0	0.0		85.0	4.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	hg19																																																																																				.	.		0.687	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
BTBD16	118663	hgsc.bcm.edu	37	10	124096039	124096039	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:124096039T>C	ENST00000260723.4	+	15	1545	c.1294T>C	c.(1294-1296)Tct>Cct	p.S432P	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Missense_Mutation_p.S433P	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	432										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				GGAATCTCCCTCTGCGGTCTA	0.562																																					p.S432P		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1294C						.						69.0	59.0	62.0					10																	124096039		2203	4300	6503	SO:0001583	missense	118663	exon15			TCTCCCTCTGCGG	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1294T>C	chr10.hg19:g.124096039T>C	ENSP00000260723:p.Ser432Pro	121.0	0.0		93.0	4.0	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	hg19	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.289154	0.23478	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.18502	2.21;2.21	5.49	-3.99	0.04069	.	0.836862	0.10391	N	0.680466	T	0.08268	0.0206	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.33929	-0.9849	10	0.35671	T	0.21	-8.1829	5.1317	0.14913	0.1138:0.0769:0.5034:0.3059	.	433;432	Q32M84-2;Q32M84	.;BTBDG_HUMAN	P	432;433	ENSP00000260723:S432P;ENSP00000357990:S433P	ENSP00000260723:S432P	S	+	1	0	BTBD16	124086029	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.710000	0.05024	-0.257000	0.09459	-0.331000	0.08364	TCT	.	.		0.562	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
DMBT1	1755	hgsc.bcm.edu	37	10	124380739	124380739	+	Silent	SNP	G	G	T	rs374741257		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:124380739G>T	ENST00000338354.3	+	41	5170	c.5064G>T	c.(5062-5064)tcG>tcT	p.S1688S	DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Silent_p.S1678S|DMBT1_ENST00000368956.2_Silent_p.S1060S|DMBT1_ENST00000344338.3_Silent_p.S1678S|DMBT1_ENST00000330163.4_Silent_p.S1060S|DMBT1_ENST00000368909.3_Silent_p.S1688S			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1688	SRCR 13. {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)				GGGCCATGTCGGCCCCAGGAA	0.612																																					p.S1688S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	.	0			c.G5064T						.						156.0	159.0	158.0					10																	124380739		1972	4162	6134	SO:0001819	synonymous_variant	1755	exon41			CATGTCGGCCCCA		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.5064G>T	chr10.hg19:g.124380739G>T		102.0	1.0		49.0	3.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	hg19																																																																																				.	.		0.612	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
CFAP46	54777	hgsc.bcm.edu	37	10	134694527	134694527	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:134694527T>C	ENST00000368586.5	-	28	3737	c.3637A>G	c.(3637-3639)Atg>Gtg	p.M1213V	TTC40_ENST00000368582.2_Missense_Mutation_p.M1213V	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGCCACTCCATCTCAGGCTTC	0.537																																					p.M1213V		Atlas-SNP	.											.	TTC40	100	.	0			c.A3637G						.																																			SO:0001583	missense	54777	exon28			ACTCCATCTCAGG																												ENST00000368586.5:c.3637A>G	chr10.hg19:g.134694527T>C	ENSP00000357575:p.Met1213Val	91.0	0.0		51.0	5.0	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	hg19	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	2.166	-0.391002	0.04932	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.40756	3.0;1.02	3.63	3.63	0.41609	.	.	.	.	.	T	0.40398	0.1115	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.27938	-1.0059	6	0.48119	T	0.1	.	7.829	0.29332	0.1858:0.0:0.0:0.8141	.	.	.	.	V	1213	ENSP00000357575:M1213V;ENSP00000357571:M1213V	ENSP00000357571:M1213V	M	-	1	0	C10orf93	134544517	0.497000	0.26067	0.346000	0.25655	0.011000	0.07611	1.077000	0.30741	1.425000	0.47237	0.402000	0.26972	ATG	.	.		0.537	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GPR123	84435	hgsc.bcm.edu	37	10	134910585	134910585	+	Silent	SNP	C	C	T	rs62624493	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:134910585C>T	ENST00000392607.3	+	3	547	c.111C>T	c.(109-111)gtC>gtT	p.V37V	GPR123_ENST00000607359.1_Silent_p.V757V	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	37					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCTCCTTCGTCACCTACATCG	0.627																																					p.V37V		Atlas-SNP	.											.	GPR123	118	.	0			c.C111T						.						124.0	101.0	109.0					10																	134910585		2203	4300	6503	SO:0001819	synonymous_variant	84435	exon3			CTTCGTCACCTAC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.111C>T	chr10.hg19:g.134910585C>T		35.0	0.0		36.0	8.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	C|0.993;G|0.007		0.627	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
ADAM8	101	hgsc.bcm.edu	37	10	135087474	135087474	+	Missense_Mutation	SNP	G	G	A	rs375135486		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:135087474G>A	ENST00000445355.3	-	4	337	c.287C>T	c.(286-288)aCg>aTg	p.T96M	ADAM8_ENST00000559180.1_5'UTR|ADAM8_ENST00000415217.3_Missense_Mutation_p.T96M|ADAM8_ENST00000485491.2_Silent_p.D61D	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	96					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		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)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		AGGCTGCTCCGTCACCTCGGA	0.701																																					p.T96M		Atlas-SNP	.											.	ADAM8	41	.	0			c.C287T						.		MET/THR,MET/THR,	0,4354		0,0,2177	28.0	29.0	29.0		287,287,183	0.2	0.2	10		29	3,8577		0,3,4287	no	missense,missense,coding-synonymous	ADAM8	NM_001109.4,NM_001164489.1,NM_001164490.1	81,81,	0,3,6464	AA,AG,GG		0.035,0.0,0.0232	probably-damaging,probably-damaging,	96/825,96/743,61/734	135087474	3,12931	2177	4290	6467	SO:0001583	missense	101	exon4			TGCTCCGTCACCT	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.287C>T	chr10.hg19:g.135087474G>A	ENSP00000453302:p.Thr96Met	101.0	0.0		62.0	17.0	NM_001164489	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	hg19	CCDS31319.2																																																																																			.	.		0.701	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	
ECHS1	1892	hgsc.bcm.edu	37	10	135182430	135182430	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:135182430G>T	ENST00000368547.3	-	4	866	c.511C>A	c.(511-513)Cca>Aca	p.P171T	MIR3944_ENST00000581277.1_RNA	NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	171					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		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)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		TCTTTACCTGGGATGGTTCCT	0.512																																					p.P171T	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.C511A						.						126.0	112.0	116.0					10																	135182430		2202	4298	6500	SO:0001583	missense	1892	exon4			TACCTGGGATGGT		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"""enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"""			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.511C>A	chr10.hg19:g.135182430G>T	ENSP00000357535:p.Pro171Thr	135.0	0.0		109.0	6.0	NM_004092	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	hg19	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085421	0.76642	.	.	ENSG00000127884	ENST00000368547	T	0.77229	-1.08	5.81	5.81	0.92471	Crotonase, core (1);	0.000000	0.85682	D	0.000000	D	0.91240	0.7239	M	0.93978	3.48	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.92823	0.6274	10	0.72032	D	0.01	.	17.6318	0.88111	0.0:0.0:1.0:0.0	.	171	P30084	ECHM_HUMAN	T	171	ENSP00000357535:P171T	ENSP00000357535:P171T	P	-	1	0	ECHS1	135032420	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	6.633000	0.74286	2.763000	0.94921	0.650000	0.86243	CCA	.	.		0.512	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1		
PHRF1	57661	hgsc.bcm.edu	37	11	607103	607103	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:607103C>A	ENST00000264555.5	+	14	1775	c.1647C>A	c.(1645-1647)tcC>tcA	p.S549S	PHRF1_ENST00000416188.2_Silent_p.S548S|PHRF1_ENST00000413872.2_Silent_p.S547S|PHRF1_ENST00000533464.1_Silent_p.S545S	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	549					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GCAGTCTGTCCAGAGGGGAAG	0.542																																					p.S548S		Atlas-SNP	.											.	PHRF1	188	.	0			c.C1644A						.						54.0	52.0	53.0					11																	607103		1870	4102	5972	SO:0001819	synonymous_variant	57661	exon14			TCTGTCCAGAGGG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1647C>A	chr11.hg19:g.607103C>A		93.0	0.0		85.0	4.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.542	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
OSBPL5	114879	hgsc.bcm.edu	37	11	3143580	3143580	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:3143580T>C	ENST00000263650.7	-	4	457	c.298A>G	c.(298-300)Aag>Gag	p.K100E	OSBPL5_ENST00000389989.3_Missense_Mutation_p.K100E|OSBPL5_ENST00000542243.1_Missense_Mutation_p.Q15R|OSBPL5_ENST00000525498.1_Missense_Mutation_p.K52E|OSBPL5_ENST00000348039.5_Missense_Mutation_p.K100E	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	100					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGGCTCACCTTGAGAGTCTCC	0.622																																					p.K100E		Atlas-SNP	.											.	OSBPL5	78	.	0			c.A298G						.						54.0	44.0	48.0					11																	3143580		2202	4298	6500	SO:0001583	missense	114879	exon4			TCACCTTGAGAGT	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.298A>G	chr11.hg19:g.3143580T>C	ENSP00000263650:p.Lys100Glu	107.0	0.0		80.0	4.0	NM_145638	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	hg19	CCDS31344.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.630835|4.630835	0.87660|0.87660	.|.	.|.	ENSG00000021762|ENSG00000021762	ENST00000263650;ENST00000389989;ENST00000525498;ENST00000348039;ENST00000533234;ENST00000526122|ENST00000542243	T;T;T;T;T;T|T	0.58210|0.43294	1.02;0.85;0.94;0.85;0.44;0.35|0.95	4.32|4.32	4.32|4.32	0.51571|0.51571	.|.	0.142736|.	0.46145|.	N|.	0.000318|.	T|T	0.53530|0.53530	0.1802|0.1802	M|M	0.66939|0.66939	2.045|2.045	0.30506|0.30506	N|N	0.769943|0.769943	D;D;D;D|.	0.89917|.	1.0;0.997;1.0;1.0|.	D;D;D;D|.	0.85130|.	0.976;0.945;0.997;0.976|.	T|T	0.58629|0.58629	-0.7603|-0.7603	10|7	0.87932|0.59425	D|D	0|0.04	13.4107|13.4107	12.7833|12.7833	0.57489|0.57489	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	52;61;100;100|.	B4DVB0;E7EP03;Q8N596;Q9H0X9|.	.;.;.;OSBL5_HUMAN|.	E|R	100;100;52;100;100;100|15	ENSP00000263650:K100E;ENSP00000374639:K100E;ENSP00000433342:K52E;ENSP00000302872:K100E;ENSP00000436950:K100E;ENSP00000433754:K100E|ENSP00000441551:Q15R	ENSP00000263650:K100E|ENSP00000441551:Q15R	K|Q	-|-	1|2	0|0	OSBPL5|OSBPL5	3100156|3100156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.741000|0.741000	0.42261|0.42261	7.255000|7.255000	0.78338|0.78338	1.817000|1.817000	0.53016|0.53016	0.459000|0.459000	0.35465|0.35465	AAG|CAA	.	.		0.622	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
OR52A1	23538	hgsc.bcm.edu	37	11	5173434	5173434	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:5173434T>C	ENST00000380367.1	-	2	583	c.166A>G	c.(166-168)Agt>Ggt	p.S56G	OR52A1_ENST00000328942.1_Missense_Mutation_p.S56G			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	56					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATGGAGACTGCGCTCAGAT	0.438																																					p.S56G		Atlas-SNP	.											.	OR52A1	58	.	0			c.A166G						.						79.0	74.0	76.0					11																	5173434		2201	4297	6498	SO:0001583	missense	23538	exon1			GGAGACTGCGCTC	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"""GPCR / Class A : Olfactory receptors"""	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.166A>G	chr11.hg19:g.5173434T>C	ENSP00000369725:p.Ser56Gly	132.0	0.0		112.0	5.0	NM_012375	Q6IF31	Missense_Mutation	SNP	ENST00000380367.1	hg19	CCDS31374.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307509	0.40795	.	.	ENSG00000182070	ENST00000380367;ENST00000328942	T;T	0.00464	7.24;7.24	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.209000	0.33732	N	0.004619	T	0.00815	0.0027	M	0.88181	2.935	0.34100	D	0.661778	B	0.15719	0.014	B	0.14578	0.011	T	0.15178	-1.0446	10	0.66056	D	0.02	.	14.3488	0.66685	0.0:0.0:0.0:1.0	.	56	Q9UKL2	O52A1_HUMAN	G	56	ENSP00000369725:S56G;ENSP00000333684:S56G	ENSP00000333684:S56G	S	-	1	0	OR52A1	5130010	0.751000	0.28327	0.984000	0.44739	0.472000	0.32918	3.145000	0.50623	2.257000	0.74773	0.533000	0.62120	AGT	.	.		0.438	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375	
RRP8	23378	hgsc.bcm.edu	37	11	6622399	6622399	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:6622399G>T	ENST00000254605.6	-	3	1014	c.897C>A	c.(895-897)atC>atA	p.I299I	ILK_ENST00000537806.1_5'Flank|ILK_ENST00000528995.1_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|RRP8_ENST00000534343.1_Intron|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000299421.4_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	299					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						GATCCCTGGCGATGCGGTCCA	0.577																																					p.I299I		Atlas-SNP	.											RRP8,NS,adenocarcinoma,0,1	RRP8	40	.	0			c.C897A						.						28.0	28.0	28.0					11																	6622399		2201	4296	6497	SO:0001819	synonymous_variant	23378	exon3			CCTGGCGATGCGG	AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"""KIAA0409"""	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.897C>A	chr11.hg19:g.6622399G>T		54.0	1.0		41.0	2.0	NM_015324	Q7KZ78|Q9BVM6	Silent	SNP	ENST00000254605.6	hg19	CCDS31411.1																																																																																			.	.		0.577	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324	
DCHS1	8642	hgsc.bcm.edu	37	11	6653382	6653382	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:6653382C>T	ENST00000299441.3	-	6	3772	c.3361G>A	c.(3361-3363)Ggg>Agg	p.G1121R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1121	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGCTGGTCCCTGGGGGCTGG	0.597																																					p.G1121R		Atlas-SNP	.											.	DCHS1	277	.	0			c.G3361A						.						62.0	62.0	62.0					11																	6653382		2201	4295	6496	SO:0001583	missense	8642	exon6			TGGTCCCTGGGGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3361G>A	chr11.hg19:g.6653382C>T	ENSP00000299441:p.Gly1121Arg	128.0	0.0		112.0	5.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881772	0.72294	.	.	ENSG00000166341	ENST00000299441	T	0.69806	-0.43	4.66	4.66	0.58398	Cadherin (3);Cadherin-like (1);	0.000000	0.47093	D	0.000245	D	0.86264	0.5891	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89686	0.3894	10	0.66056	D	0.02	.	17.0688	0.86567	0.0:1.0:0.0:0.0	.	1121	Q96JQ0	PCD16_HUMAN	R	1121	ENSP00000299441:G1121R	ENSP00000299441:G1121R	G	-	1	0	DCHS1	6609958	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.297000	0.78799	2.584000	0.87258	0.561000	0.74099	GGG	.	.		0.597	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
NLRP14	338323	hgsc.bcm.edu	37	11	7091661	7091661	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:7091661T>C	ENST00000299481.4	+	11	3466	c.3120T>C	c.(3118-3120)tcT>tcC	p.S1040S		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1040					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TCTTGAAGTCTCCTAAGTGTA	0.393																																					p.S1040S		Atlas-SNP	.											.	NLRP14	187	.	0			c.T3120C						.						88.0	90.0	89.0					11																	7091661		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon11			GAAGTCTCCTAAG	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3120T>C	chr11.hg19:g.7091661T>C		139.0	0.0		96.0	4.0	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.		0.393	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
OR10A3	26496	hgsc.bcm.edu	37	11	7960614	7960614	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:7960614C>A	ENST00000360759.3	-	1	527	c.454G>T	c.(454-456)Ggg>Tgg	p.G152W		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	152					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACCATGATCCCTGAGATCCAT	0.428																																					p.G152W		Atlas-SNP	.											.	OR10A3	54	.	0			c.G454T						.						54.0	52.0	53.0					11																	7960614		2201	4296	6497	SO:0001583	missense	26496	exon1			TGATCCCTGAGAT	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"""GPCR / Class A : Olfactory receptors"""	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.454G>T	chr11.hg19:g.7960614C>A	ENSP00000353988:p.Gly152Trp	117.0	0.0		129.0	6.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	hg19	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	C	4.878	0.163194	0.09287	.	.	ENSG00000170683	ENST00000360759	T	0.40756	1.02	4.95	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	0.376015	0.18862	N	0.129105	T	0.59224	0.2178	H	0.97732	4.065	0.09310	N	1	B	0.25007	0.116	B	0.35278	0.199	T	0.60316	-0.7287	10	0.72032	D	0.01	.	6.3974	0.21620	0.1471:0.6892:0.0:0.1637	.	152	P58181	O10A3_HUMAN	W	152	ENSP00000353988:G152W	ENSP00000353988:G152W	G	-	1	0	OR10A3	7917190	0.000000	0.05858	0.069000	0.20011	0.056000	0.15407	0.321000	0.19558	0.344000	0.23847	0.650000	0.86243	GGG	.	.		0.428	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745	
TRIM66	9866	hgsc.bcm.edu	37	11	8642090	8642090	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:8642090C>T	ENST00000299550.6	-	16	3241	c.3047G>A	c.(3046-3048)aGc>aAc	p.S1016N	TRIM66_ENST00000402157.2_Missense_Mutation_p.S1045N	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	1016						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						CTGGGTCAGGCTGCGGCACAA	0.597																																					p.S1016N		Atlas-SNP	.											.	TRIM66	45	.	0			c.G3047A						.						50.0	43.0	45.0					11																	8642090		692	1591	2283	SO:0001583	missense	9866	exon16			GTCAGGCTGCGGC	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.3047G>A	chr11.hg19:g.8642090C>T	ENSP00000299550:p.Ser1016Asn	167.0	0.0		132.0	34.0	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	hg19		.	.	.	.	.	.	.	.	.	.	C	11.28	1.592835	0.28357	.	.	ENSG00000166436	ENST00000299550;ENST00000402157	D;D	0.84516	-1.86;-1.86	4.68	4.68	0.58851	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Bromodomain (1);Zinc finger, FYVE/PHD-type (1);	0.065897	0.64402	D	0.000014	T	0.68851	0.3046	N	0.12443	0.215	0.27191	N	0.960418	B	0.20261	0.043	B	0.32533	0.147	T	0.56601	-0.7952	10	0.06757	T	0.87	-17.127	5.8163	0.18494	0.0:0.7674:0.0:0.2326	.	1016	O15016	TRI66_HUMAN	N	1016;1045	ENSP00000299550:S1016N;ENSP00000384876:S1045N	ENSP00000299550:S1016N	S	-	2	0	TRIM66	8598666	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.963000	0.49184	2.594000	0.87642	0.555000	0.69702	AGC	.	.		0.597	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
DKK3	27122	hgsc.bcm.edu	37	11	11988502	11988502	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:11988502T>C	ENST00000396505.2	-	6	910	c.672A>G	c.(670-672)agA>agG	p.R224R	DKK3_ENST00000450094.2_Splice_Site_p.R196R|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000525493.1_Splice_Site_p.R224R|DKK3_ENST00000326932.4_Splice_Site_p.R224R	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	224	DKK-type Cys-2.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		GCCACTCACCTCTCTGGAAGG	0.607											OREG0020766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R224R		Atlas-SNP	.											.	DKK3	35	.	0			c.A672G						.						77.0	75.0	76.0					11																	11988502		2201	4294	6495	SO:0001630	splice_region_variant	27122	exon5			CTCACCTCTCTGG	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"""regulated in glioma"""	605416	"""dickkopf (Xenopus laevis) homolog 3"", ""dickkopf 3 homolog (Xenopus laevis)"""			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.673+1A>G	chr11.hg19:g.11988502T>C		232.0	0.0	676	129.0	6.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	hg19	CCDS7808.1																																																																																			.	.		0.607	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	Silent
TEAD1	7003	hgsc.bcm.edu	37	11	12904610	12904610	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:12904610A>G	ENST00000526600.1	+	4	572	c.349A>G	c.(349-351)Aca>Gca	p.T117A	TEAD1_ENST00000527575.1_Missense_Mutation_p.T213A|TEAD1_ENST00000361905.4_Missense_Mutation_p.T198A|TEAD1_ENST00000527636.1_Missense_Mutation_p.T213A|TEAD1_ENST00000334310.6_Missense_Mutation_p.T202A|TEAD1_ENST00000361985.2_Missense_Mutation_p.T213A			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	213					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTCCATTGGCACAACCAAGCT	0.562																																					p.T213A		Atlas-SNP	.											.	TEAD1	40	.	0			c.A637G						.						124.0	107.0	113.0					11																	12904610		2200	4294	6494	SO:0001583	missense	7003	exon9			ATTGGCACAACCA	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"""atrophia areata, peripapillary chorioretinal degeneration"""	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.349A>G	chr11.hg19:g.12904610A>G	ENSP00000435393:p.Thr117Ala	137.0	0.0		97.0	4.0	NM_021961	A4FUP2|E7EV65	Missense_Mutation	SNP	ENST00000526600.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.73	3.686755	0.68157	.	.	ENSG00000187079	ENST00000361905;ENST00000527636;ENST00000527575;ENST00000334310;ENST00000361985;ENST00000526600	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	M	0.76002	2.32	0.80722	D	1	D;B;B	0.54397	0.966;0.237;0.024	P;B;B	0.50934	0.654;0.318;0.108	T	0.38394	-0.9663	10	0.28530	T	0.3	-10.2993	15.4426	0.75200	1.0:0.0:0.0:0.0	.	202;117;213	A4FUP2;E9PKB7;P28347	.;.;TEAD1_HUMAN	A	198;213;213;202;213;117	ENSP00000355332:T198A;ENSP00000435233:T213A;ENSP00000435977:T213A;ENSP00000334754:T202A;ENSP00000354588:T213A;ENSP00000435393:T117A	ENSP00000334754:T202A	T	+	1	0	TEAD1	12861186	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.123000	0.65237	0.533000	0.62120	ACA	.	.		0.562	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961	
ARNTL	406	hgsc.bcm.edu	37	11	13408153	13408153	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:13408153C>A	ENST00000403290.1	+	20	2086	c.1731C>A	c.(1729-1731)ccC>ccA	p.P577P	ARNTL_ENST00000389707.4_Silent_p.P576P|ARNTL_ENST00000403482.3_Silent_p.P575P|ARNTL_ENST00000361003.4_Silent_p.P459P|ARNTL_ENST00000403510.3_Silent_p.P533P|ARNTL_ENST00000396441.3_Silent_p.P576P|ARNTL_ENST00000389708.3_3'UTR|ARNTL_ENST00000401424.1_Silent_p.P534P			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	577	Interaction with CIART. {ECO:0000250|UniProtKB:Q9WTL8}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		GTGAGAACCCCCACATAGGTA	0.413																																					p.P576P		Atlas-SNP	.											.	ARNTL	46	.	0			c.C1728A						.						100.0	99.0	99.0					11																	13408153		2200	4294	6494	SO:0001819	synonymous_variant	406	exon19			GAACCCCCACATA	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"""Basic helix-loop-helix proteins"""	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1731C>A	chr11.hg19:g.13408153C>A		103.0	0.0		72.0	4.0	NM_001030272	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Silent	SNP	ENST00000403290.1	hg19																																																																																				.	.		0.413	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178	
C11orf58	10944	hgsc.bcm.edu	37	11	16774369	16774369	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:16774369T>C	ENST00000228136.4	+	4	624	c.246T>C	c.(244-246)tcT>tcC	p.S82S	C11orf58_ENST00000422258.2_Silent_p.S38S|C11orf58_ENST00000525684.1_Missense_Mutation_p.L62P			O00193	SMAP_HUMAN	chromosome 11 open reading frame 58	82										NS(1)|endometrium(1)|lung(3)|prostate(1)|skin(1)	7						AACTGGAGTCTCAATATCAGC	0.348																																					p.S82S		Atlas-SNP	.											C11orf58,bladder,carcinoma,+1,1	C11orf58	14	.	0			c.T246C						.						124.0	118.0	120.0					11																	16774369		2200	4294	6494	SO:0001819	synonymous_variant	10944	exon4			GGAGTCTCAATAT	BC007103	CCDS7822.1	11p15.1	2012-05-30			ENSG00000110696	ENSG00000110696			16990	protein-coding gene	gene with protein product	"""small acidic protein"""					9263035	Standard	NM_014267		Approved	SMAP	uc001mmk.2	O00193	OTTHUMG00000165910	ENST00000228136.4:c.246T>C	chr11.hg19:g.16774369T>C		145.0	0.0		98.0	5.0	NM_014267	B2RD28	Silent	SNP	ENST00000228136.4	hg19	CCDS7822.1	.	.	.	.	.	.	.	.	.	.	T	9.867	1.197999	0.22037	.	.	ENSG00000110696	ENST00000525684	.	.	.	5.57	1.74	0.24563	.	.	.	.	.	T	0.58466	0.2124	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58411	-0.7641	5	0.59425	D	0.04	.	5.4834	0.16737	0.0:0.1384:0.2831:0.5785	.	.	.	.	P	62	.	ENSP00000432534:L62P	L	+	2	0	C11orf58	16730945	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.984000	0.29565	0.902000	0.36520	0.533000	0.62120	CTC	.	.		0.348	C11orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387023.2	NM_014267	
SAA4	6291	hgsc.bcm.edu	37	11	18253136	18253136	+	Silent	SNP	C	C	A	rs201938371		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:18253136C>A	ENST00000278222.4	-	4	486	c.306G>T	c.(304-306)tcG>tcT	p.S102S	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	102					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)		p.S102S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CGTTGGACTTCGAGTCCTCCA	0.517																																					p.S180S		Atlas-SNP	.											SAA4,colon,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G540T						.						105.0	105.0	105.0					11																	18253136		2199	4293	6492	SO:0001819	synonymous_variant	100528017	exon6			GGACTTCGAGTCC	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.306G>T	chr11.hg19:g.18253136C>A		169.0	0.0		111.0	28.0	NM_001199744	Q6FHJ4	Silent	SNP	ENST00000278222.4	hg19	CCDS7832.1																																																																																			.	C|1.000;T|0.000		0.517	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512	
IGSF22	283284	hgsc.bcm.edu	37	11	18732375	18732375	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:18732375T>C	ENST00000513874.1	-	16	2538	c.2399A>G	c.(2398-2400)gAg>gGg	p.E800G	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	800										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						ACCAGGAGGCTCTGTGGGGGA	0.537																																					p.E800G		Atlas-SNP	.											.	IGSF22	211	.	0			c.A2399G						.						42.0	43.0	43.0					11																	18732375		1943	4139	6082	SO:0001630	splice_region_variant	283284	exon16			GGAGGCTCTGTGG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2399-1A>G	chr11.hg19:g.18732375T>C		137.0	0.0		132.0	6.0	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046319	0.55110	.	.	ENSG00000179057	ENST00000513874	T	0.53640	0.61	4.5	4.5	0.54988	.	0.202751	0.24136	U	0.041218	T	0.23806	0.0576	N	0.03608	-0.345	0.20638	N	0.999878	P	0.38922	0.651	B	0.33521	0.165	T	0.17776	-1.0358	10	0.66056	D	0.02	.	12.1657	0.54129	0.0:0.0:0.0:1.0	.	800	D6RGV7	.	G	800	ENSP00000421191:E800G	ENSP00000322422:E699G	E	-	2	0	IGSF22	18688951	0.815000	0.29118	0.990000	0.47175	0.580000	0.36256	0.999000	0.29757	1.884000	0.54569	0.460000	0.39030	GAG	.	.		0.537	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	Missense_Mutation
LUZP2	338645	hgsc.bcm.edu	37	11	24759781	24759781	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:24759781C>G	ENST00000336930.6	+	4	332	c.266C>G	c.(265-267)tCt>tGt	p.S89C	LUZP2_ENST00000531187.1_3'UTR|LUZP2_ENST00000533227.1_Missense_Mutation_p.S3C			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	89						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GAAATGAAGTCTCTTCAGGAG	0.358																																					p.S89C		Atlas-SNP	.											LUZP2,colon,carcinoma,0,1	LUZP2	90	.	0			c.C266G						.						66.0	69.0	68.0					11																	24759781		2203	4300	6503	SO:0001583	missense	338645	exon4			TGAAGTCTCTTCA	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.266C>G	chr11.hg19:g.24759781C>G	ENSP00000336817:p.Ser89Cys	251.0	1.0		183.0	55.0	NM_001252010	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	hg19	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072033	0.76415	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	T;T;T	0.25749	1.78;1.78;1.78	5.76	5.76	0.90799	.	0.200304	0.43416	D	0.000574	T	0.47710	0.1460	L	0.60455	1.87	0.41438	D	0.987905	D;D	0.89917	1.0;0.999	D;D	0.66351	0.943;0.943	T	0.41034	-0.9531	10	0.72032	D	0.01	-6.6251	17.4398	0.87562	0.0:1.0:0.0:0.0	.	3;89	E9PN53;Q86TE4	.;LUZP2_HUMAN	C	89;89;3	ENSP00000336817:S89C;ENSP00000437032:S89C;ENSP00000432952:S3C	ENSP00000336817:S89C	S	+	2	0	LUZP2	24716357	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.098000	0.71458	2.721000	0.93114	0.650000	0.86243	TCT	.	.		0.358	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909	
WT1	7490	hgsc.bcm.edu	37	11	32452076	32452076	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:32452076C>T	ENST00000379079.2	-	1	283	c.10G>A	c.(10-12)Ggt>Agt	p.G4S	WT1_ENST00000448076.3_Intron|WT1_ENST00000332351.3_Intron|WT1_ENST00000530998.1_Splice_Site_p.G4S	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	148					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CTAGACGAACCCTTCTCCATT	0.577			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.G4S		Atlas-SNP	.	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	0			c.G10A						.						21.0	22.0	21.0					11																	32452076		875	1989	2864	SO:0001630	splice_region_variant	7490	exon1	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	ACGAACCCTTCTC		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.10+1G>A	chr11.hg19:g.32452076C>T		104.0	0.0		63.0	4.0	NM_001198551	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	c	16.84	3.234954	0.58886	.	.	ENSG00000184937	ENST00000379079;ENST00000530998	D;D	0.91351	-2.83;-2.83	3.64	1.76	0.24704	.	.	.	.	.	D	0.90923	0.7147	L	0.43152	1.355	0.48696	D	0.999693	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86984	0.2106	8	.	.	.	.	5.761	0.18201	0.0:0.7552:0.0:0.2448	.	4;4	B3KSA5;P19544-6	.;.	S	4	ENSP00000368370:G4S;ENSP00000435307:G4S	.	G	-	1	0	WT1	32408652	1.000000	0.71417	0.998000	0.56505	0.554000	0.35429	1.640000	0.37186	0.538000	0.28769	0.457000	0.33378	GGT	.	.		0.577	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378	Missense_Mutation
LDLRAD3	143458	hgsc.bcm.edu	37	11	36250861	36250861	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:36250861A>G	ENST00000315571.5	+	6	973	c.952A>G	c.(952-954)Agc>Ggc	p.S318G	LDLRAD3_ENST00000528989.1_Missense_Mutation_p.S269G|LDLRAD3_ENST00000524419.1_Missense_Mutation_p.S308G	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	318					receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				GGAAGACACCAGCCACAGCCC	0.662																																					p.S318G		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A952G						.						56.0	67.0	63.0					11																	36250861		2201	4292	6493	SO:0001583	missense	143458	exon6			GACACCAGCCACA	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.952A>G	chr11.hg19:g.36250861A>G	ENSP00000318607:p.Ser318Gly	127.0	0.0		90.0	4.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.525352	0.00959	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000315571	D;D;D	0.94280	-3.39;-3.25;-3.15	5.12	-10.2	0.00374	.	1.204760	0.05640	N	0.583225	D	0.83385	0.5243	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.71652	-0.4528	10	0.33141	T	0.24	.	10.2419	0.43316	0.6743:0.1099:0.1507:0.0651	.	308;269;318	E9PR86;B7Z1U3;Q86YD5	.;.;LRAD3_HUMAN	G	269;308;318	ENSP00000433954:S269G;ENSP00000434313:S308G;ENSP00000318607:S318G	ENSP00000318607:S318G	S	+	1	0	LDLRAD3	36207437	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-1.570000	0.02140	-2.955000	0.00292	-2.346000	0.00244	AGC	.	.		0.662	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902	
ACCS	84680	hgsc.bcm.edu	37	11	44089232	44089232	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:44089232A>G	ENST00000263776.8	+	2	489	c.55A>G	c.(55-57)Acc>Gcc	p.T19A	ACCS_ENST00000432284.2_Missense_Mutation_p.T19A|ACCS_ENST00000533208.1_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	19					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.T19A(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCTGGGCCCCACCTGCATGCA	0.557																																					p.T19A	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											ACCS,rectum,carcinoma,0,1	ACCS	64	.	1	Substitution - Missense(1)	large_intestine(1)	c.A55G						.						69.0	73.0	72.0					11																	44089232		2203	4300	6503	SO:0001583	missense	84680	exon2			GGCCCCACCTGCA	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.55A>G	chr11.hg19:g.44089232A>G	ENSP00000263776:p.Thr19Ala	127.0	0.0		112.0	5.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	G	0.417	-0.910247	0.02434	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.59364	0.97;0.27;0.97;1.07	5.43	0.0996	0.14503	.	0.861636	0.10406	N	0.678505	T	0.26738	0.0654	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-0.427	7.4529	0.27248	0.2042:0.1334:0.6623:0.0	.	19;19	B4E219;Q96QU6	.;1A1L1_HUMAN	A	19	ENSP00000434156:T19A;ENSP00000263776:T19A;ENSP00000391775:T19A;ENSP00000435919:T19A	ENSP00000263776:T19A	T	+	1	0	ACCS	44045808	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.167000	0.09940	-0.164000	0.10927	-3.370000	0.00041	ACC	.	.		0.557	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
C11orf94	143678	hgsc.bcm.edu	37	11	45928125	45928125	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:45928125G>T	ENST00000449465.1	-	3	328	c.292C>A	c.(292-294)Cta>Ata	p.L98I	RP11-618K13.2_ENST00000533218.1_RNA	NM_001080446.2	NP_001073915.2	C9JXX5	CK094_HUMAN	chromosome 11 open reading frame 94	98						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|ovary(1)|pancreas(1)|prostate(1)	7						TTGGGTCATAGGTGTGCATCA	0.617																																					p.L98I		Atlas-SNP	.											.	C11orf94	13	.	0			c.C292A						.						94.0	96.0	96.0					11																	45928125		1938	4124	6062	SO:0001583	missense	143678	exon3			GTCATAGGTGTGC		CCDS44577.1	11p11.2	2012-08-10			ENSG00000234776	ENSG00000234776			37213	protein-coding gene	gene with protein product							Standard	NM_001080446		Approved		uc001nbs.4	C9JXX5	OTTHUMG00000167004	ENST00000449465.1:c.292C>A	chr11.hg19:g.45928125G>T	ENSP00000401498:p.Leu98Ile	87.0	0.0		82.0	4.0	NM_001080446		Missense_Mutation	SNP	ENST00000449465.1	hg19	CCDS44577.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908906	0.52439	.	.	ENSG00000234776	ENST00000449465	T	0.55052	0.54	4.66	0.388	0.16264	.	.	.	.	.	T	0.34803	0.0910	.	.	.	0.09310	N	1	B	0.21821	0.061	B	0.19148	0.024	T	0.34551	-0.9824	8	0.87932	D	0	-1.7759	1.1397	0.01762	0.2163:0.3268:0.2903:0.1666	.	98	C9JXX5	CK094_HUMAN	I	98	ENSP00000401498:L98I	ENSP00000401498:L98I	L	-	1	2	C11orf94	45884701	0.000000	0.05858	0.032000	0.17829	0.020000	0.10135	0.050000	0.14120	-0.075000	0.12798	-0.181000	0.13052	CTA	.	.		0.617	C11orf94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392395.1	NM_001080446	
LRP4	4038	hgsc.bcm.edu	37	11	46896443	46896443	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:46896443G>T	ENST00000378623.1	-	28	4379	c.4137C>A	c.(4135-4137)gtC>gtA	p.V1379V	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1379					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CAGGAACAGGGACATGCACAT	0.527																																					p.V1379V		Atlas-SNP	.											.	LRP4	160	.	0			c.C4137A						.						163.0	132.0	142.0					11																	46896443		2201	4299	6500	SO:0001819	synonymous_variant	4038	exon28			AACAGGGACATGC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4137C>A	chr11.hg19:g.46896443G>T		134.0	0.0		114.0	31.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	hg19	CCDS31478.1																																																																																			.	.		0.527	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
PACSIN3	29763	hgsc.bcm.edu	37	11	47199984	47199984	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:47199984G>T	ENST00000539589.1	-	10	1434	c.1092C>A	c.(1090-1092)acC>acA	p.T364T	ARFGAP2_ENST00000395449.3_5'Flank|ARFGAP2_ENST00000524782.1_5'Flank|ARFGAP2_ENST00000419701.2_5'Flank|PACSIN3_ENST00000298838.6_Silent_p.T364T|ARFGAP2_ENST00000426335.2_5'Flank|ARFGAP2_ENST00000319543.6_5'Flank	NM_001184975.1	NP_001171904.1	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in neurons 3	364	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endocytosis (GO:0045806)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|cytoskeletal protein binding (GO:0008092)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)	11						CCCGAACCCCGGTGGCAGCCT	0.617																																					p.T364T		Atlas-SNP	.											.	PACSIN3	28	.	0			c.C1092A						.						69.0	69.0	69.0					11																	47199984		2201	4298	6499	SO:0001819	synonymous_variant	29763	exon10			AACCCCGGTGGCA	AF130979	CCDS31481.1	11p12-p11	2008-02-05				ENSG00000165912			8572	protein-coding gene	gene with protein product	"""syndapin III"""	606513				10531379	Standard	NM_016223		Approved	SDPIII	uc001ndx.3	Q9UKS6		ENST00000539589.1:c.1092C>A	chr11.hg19:g.47199984G>T		155.0	0.0		87.0	4.0	NM_016223	A6NH84|Q9H331|Q9NWV9	Silent	SNP	ENST00000539589.1	hg19	CCDS31481.1																																																																																			.	.		0.617	PACSIN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391632.1	NM_016223	
MADD	8567	hgsc.bcm.edu	37	11	47307982	47307982	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:47307982A>G	ENST00000311027.5	+	15	2716		c.e15-1		MADD_ENST00000342922.4_Splice_Site|MADD_ENST00000395336.3_Splice_Site|MADD_ENST00000395344.3_Splice_Site|MADD_ENST00000406482.1_Splice_Site|MADD_ENST00000402192.2_Splice_Site|MADD_ENST00000407859.3_Splice_Site|MADD_ENST00000349238.3_Splice_Site|MADD_ENST00000402799.1_Splice_Site	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TCCCCTTGATAGGCAGCCTCT	0.517																																					.		Atlas-SNP	.											.	MADD	172	.	0			c.2552-2A>G						.						197.0	171.0	180.0					11																	47307982		2201	4298	6499	SO:0001630	splice_region_variant	8567	exon15			CTTGATAGGCAGC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.2552-1A>G	chr11.hg19:g.47307982A>G		102.0	0.0		69.0	4.0	NM_130470		Splice_Site	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579730	0.86645	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.379	0.83439	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MADD	47264558	1.000000	0.71417	0.936000	0.37596	0.992000	0.81027	8.698000	0.91311	2.268000	0.75426	0.455000	0.32223	.	.	.		0.517	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		Intron
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069548	57069548	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:57069548C>A	ENST00000532437.1	-	7	5145	c.4834G>T	c.(4834-4836)Gag>Tag	p.E1612*	TNKS1BP1_ENST00000358252.3_Splice_Site_p.E1612*			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1612	Arg/Glu/Lys-rich (charged).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCAGCCCTACCTGTAGAGTCC	0.592																																					p.E1612X		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4834T						.						131.0	128.0	129.0					11																	57069548		2201	4296	6497	SO:0001630	splice_region_variant	85456	exon8			CCCTACCTGTAGA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4834+1G>T	chr11.hg19:g.57069548C>A		94.0	0.0		82.0	4.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Nonsense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	48	13.939359	0.99771	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	.	.	.	5.22	5.22	0.72569	.	0.128563	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-22.6828	15.687	0.77418	0.0:1.0:0.0:0.0	.	.	.	.	X	1612	.	.	E	-	1	0	TNKS1BP1	56826124	0.988000	0.35896	0.564000	0.28396	0.775000	0.43874	3.002000	0.49496	2.432000	0.82394	0.561000	0.74099	GAG	.	.		0.592	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	Nonsense_Mutation
P2RX3	5024	hgsc.bcm.edu	37	11	57115686	57115686	+	Missense_Mutation	SNP	G	G	T	rs115850675	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:57115686G>T	ENST00000263314.2	+	5	468	c.434G>T	c.(433-435)cGg>cTg	p.R145L		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	145					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						TCTGTGCTCCGGACCTGTGAG	0.627																																					p.R145L		Atlas-SNP	.											.	P2RX3	55	.	0			c.G434T						.						39.0	32.0	34.0					11																	57115686		2200	4296	6496	SO:0001583	missense	5024	exon5			TGCTCCGGACCTG	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.434G>T	chr11.hg19:g.57115686G>T	ENSP00000263314:p.Arg145Leu	57.0	0.0		68.0	5.0	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	hg19	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.620038	0.28801	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04603	3.59	4.79	0.744	0.18353	.	0.837269	0.10699	N	0.644320	T	0.05227	0.0139	L	0.41492	1.28	0.09310	N	1	B	0.31256	0.316	B	0.31946	0.138	T	0.38045	-0.9679	10	0.72032	D	0.01	-3.417	8.0811	0.30746	0.3492:0.0:0.6508:0.0	.	145	P56373	P2RX3_HUMAN	L	145	ENSP00000263314:R145L	ENSP00000263314:R145L	R	+	2	0	P2RX3	56872262	0.002000	0.14202	0.466000	0.27168	0.373000	0.29922	0.350000	0.20079	0.444000	0.26612	-0.258000	0.10820	CGG	.	G|0.996;A|0.004		0.627	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
MS4A13	503497	hgsc.bcm.edu	37	11	60292725	60292725	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:60292725A>T	ENST00000378186.2	+	5	555	c.232A>T	c.(232-234)Att>Ttt	p.I78F	MS4A13_ENST00000527948.1_Intron|MS4A13_ENST00000437058.2_Intron|MS4A13_ENST00000378185.2_Intron	NM_001012417.2	NP_001012417.2	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	122						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						AATTACTACAATTACTGCAGT	0.303																																					p.I78F		Atlas-SNP	.											.	MS4A13	27	.	0			c.A232T						.						41.0	43.0	42.0					11																	60292725		2197	4274	6471	SO:0001583	missense	503497	exon5			ACTACAATTACTG	AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000378186.2:c.232A>T	chr11.hg19:g.60292725A>T	ENSP00000367428:p.Ile78Phe	409.0	0.0		373.0	126.0	NM_001012417	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000378186.2	hg19	CCDS31571.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.588705	0.46110	.	.	ENSG00000204979	ENST00000378186	T	0.02525	4.26	4.55	-5.16	0.02857	.	0.554719	0.14962	N	0.288332	T	0.02083	0.0065	L	0.43757	1.38	0.09310	N	1	B	0.18863	0.031	B	0.20767	0.031	T	0.41858	-0.9485	10	0.27785	T	0.31	-10.0673	3.3356	0.07100	0.2504:0.1477:0.4578:0.1441	.	78	Q5J8X5	M4A13_HUMAN	F	78	ENSP00000367428:I78F	ENSP00000367428:I78F	I	+	1	0	MS4A13	60049301	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.314000	0.01125	-0.906000	0.03866	0.477000	0.44152	ATT	.	.		0.303	MS4A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395408.1	NM_001012417	
PRPF19	27339	hgsc.bcm.edu	37	11	60666657	60666657	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:60666657G>T	ENST00000227524.4	-	11	1153	c.948C>A	c.(946-948)gcC>gcA	p.A316A		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						AGTCGCCAGTGGCATGAAGGC	0.612											OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A316A		Atlas-SNP	.											.	PRPF19	62	.	0			c.C948A						.						53.0	42.0	46.0					11																	60666657		2203	4299	6502	SO:0001819	synonymous_variant	27339	exon11			GCCAGTGGCATGA	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.948C>A	chr11.hg19:g.60666657G>T		110.0	0.0	1047	77.0	4.0	NM_014502		Silent	SNP	ENST00000227524.4	hg19	CCDS7995.1																																																																																			.	.		0.612	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	
TUT1	64852	hgsc.bcm.edu	37	11	62346379	62346379	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:62346379C>A	ENST00000476907.1	-	5	1505	c.814G>T	c.(814-816)Gat>Tat	p.D272Y	TUT1_ENST00000308436.7_Missense_Mutation_p.D310Y|MIR3654_ENST00000496634.2_Missense_Mutation_p.D272Y			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	272	Pro-rich.				mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GCTTCAGAATCCTGGGGAGAA	0.627																																					p.D310Y		Atlas-SNP	.											.	TUT1	122	.	0			c.G928T						.						43.0	50.0	48.0					11																	62346379		2202	4299	6501	SO:0001583	missense	64852	exon5			CAGAATCCTGGGG	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.814G>T	chr11.hg19:g.62346379C>A	ENSP00000419607:p.Asp272Tyr	140.0	0.0		91.0	4.0	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.39	3.818019	0.71028	.	.	ENSG00000149016	ENST00000308436;ENST00000476907;ENST00000278279	T;T	0.39592	1.07;1.09	5.44	5.44	0.79542	.	0.628774	0.14934	N	0.289938	T	0.42899	0.1223	N	0.22421	0.69	0.25198	N	0.99008	P	0.49559	0.925	P	0.51355	0.667	T	0.37753	-0.9692	10	0.72032	D	0.01	-0.4185	14.7726	0.69691	0.0:1.0:0.0:0.0	.	310	F5H0R1	.	Y	310;272;133	ENSP00000308000:D310Y;ENSP00000419607:D272Y	ENSP00000441670:D272Y	D	-	1	0	TUT1	62102955	0.093000	0.21703	0.981000	0.43875	0.978000	0.69477	2.409000	0.44583	2.561000	0.86390	0.563000	0.77884	GAT	.	.		0.627	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
HNRNPUL2	221092	hgsc.bcm.edu	37	11	62488867	62488867	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:62488867T>C	ENST00000301785.5	-	9	1703	c.1511A>G	c.(1510-1512)gAc>gGc	p.D504G	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.D504G	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	504						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GCTTTTGGGGTCCATCTCTGG	0.433																																					p.D504G		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A1511G						.						151.0	156.0	154.0					11																	62488867		1850	4095	5945	SO:0001583	missense	221092	exon9			TTGGGGTCCATCT		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1511A>G	chr11.hg19:g.62488867T>C	ENSP00000301785:p.Asp504Gly	132.0	0.0		90.0	4.0	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.278462	0.40294	.	.	ENSG00000214753	ENST00000301785	T	0.43688	0.94	5.99	5.99	0.97316	Zeta toxin domain (1);	0.158080	0.56097	D	0.000037	T	0.50051	0.1593	L	0.41961	1.31	0.46542	D	0.999093	D	0.59767	0.986	P	0.59595	0.86	T	0.36261	-0.9755	10	0.15952	T	0.53	-26.4567	14.4463	0.67352	0.0:0.0:0.0:1.0	.	504	Q1KMD3	HNRL2_HUMAN	G	504	ENSP00000301785:D504G	ENSP00000301785:D504G	D	-	2	0	HNRNPUL2	62245443	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.648000	0.67930	2.291000	0.77112	0.533000	0.62120	GAC	.	.		0.433	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877	
MACROD1	28992	hgsc.bcm.edu	37	11	63884020	63884020	+	Intron	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:63884020A>G	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.N94S	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						AACCAGATCAACAACGCCGGC	0.562																																					p.N94S		Atlas-SNP	.											.	FLRT1	46	.	0			c.A281G						.						91.0	70.0	77.0					11																	63884020		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGATCAACAACGC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34690T>C	chr11.hg19:g.63884020A>G		65.0	0.0		61.0	5.0	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	hg19	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.365961	0.24684	.	.	ENSG00000126500	ENST00000246841	T	0.02032	4.49	5.57	0.773	0.18516	.	0.315459	0.31660	N	0.007277	T	0.01730	0.0055	L	0.34521	1.04	0.38044	D	0.935546	B	0.21606	0.058	B	0.15052	0.012	T	0.53885	-0.8375	10	0.23891	T	0.37	-34.1717	5.8822	0.18862	0.6576:0.1347:0.2077:0.0	.	66	Q9NZU1	FLRT1_HUMAN	S	94	ENSP00000246841:N94S	ENSP00000246841:N94S	N	+	2	0	FLRT1	63640596	0.999000	0.42202	1.000000	0.80357	0.941000	0.58515	1.347000	0.33975	0.394000	0.25230	0.459000	0.35465	AAC	.	.		0.562	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
STIP1	10963	hgsc.bcm.edu	37	11	63962047	63962047	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:63962047G>T	ENST00000305218.4	+	4	605	c.458G>T	c.(457-459)cGg>cTg	p.R153L	STIP1_ENST00000538945.1_Missense_Mutation_p.R129L|STIP1_ENST00000358794.5_Missense_Mutation_p.R200L|STIP1_ENST00000540501.1_3'UTR|STIP1_ENST00000543847.1_Missense_Mutation_p.R153L	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	153	STI1 1.				response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						CCTACCTACCGGGAGCTGATA	0.483																																					p.R153L		Atlas-SNP	.											.	STIP1	63	.	0			c.G458T						.						102.0	86.0	91.0					11																	63962047		2201	4297	6498	SO:0001583	missense	10963	exon4			CCTACCGGGAGCT	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"""Tetratricopeptide (TTC) repeat domain containing"""	11387	protein-coding gene	gene with protein product	"""Hsp70/Hsp90-organizing protein"""	605063	"""stress-induced-phosphoprotein 1"""			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.458G>T	chr11.hg19:g.63962047G>T	ENSP00000305958:p.Arg153Leu	134.0	0.0		93.0	5.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Missense_Mutation	SNP	ENST00000305218.4	hg19	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.734182	0.30684	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000543847	T;T;T;T	0.22336	2.63;2.87;2.68;1.96	5.57	4.45	0.53987	Heat shock chaperonin-binding (1);	0.062752	0.56097	D	0.000021	T	0.14830	0.0358	L	0.41236	1.265	0.51012	D	0.9999	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.0;0.0;0.004	T	0.07385	-1.0775	10	0.16420	T	0.52	-16.3185	8.2957	0.31984	0.1974:0.0:0.8026:0.0	.	129;153;153	F5H0T1;P31948;F5H783	.;STIP1_HUMAN;.	L	200;153;129;153	ENSP00000351646:R200L;ENSP00000305958:R153L;ENSP00000445957:R129L;ENSP00000442704:R153L	ENSP00000305958:R153L	R	+	2	0	STIP1	63718623	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	3.088000	0.50175	2.788000	0.95919	0.650000	0.86243	CGG	.	.		0.483	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64599915	64599915	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:64599915C>T	ENST00000342711.5	-	27	3071	c.3072G>A	c.(3070-3072)ctG>ctA	p.L1024L	CDC42BPG_ENST00000491280.1_5'UTR	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						AGATGCGTGGCAGGTCCCTGG	0.592																																					p.L1024L		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G3072A						.						63.0	66.0	65.0					11																	64599915		2201	4297	6498	SO:0001819	synonymous_variant	55561	exon27			GCGTGGCAGGTCC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3072G>A	chr11.hg19:g.64599915C>T		119.0	0.0		75.0	4.0	NM_017525		Silent	SNP	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.		0.592	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
MAP3K11	4296	hgsc.bcm.edu	37	11	65373551	65373551	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:65373551C>T	ENST00000530153.1	-	7	1355	c.834G>A	c.(832-834)ttG>ttA	p.L278L	MAP3K11_ENST00000532507.1_5'UTR|MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Splice_Site_p.L535L					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						CTGCAGGCTCCACTGCAGGGG	0.577																																					p.L535L		Atlas-SNP	.											.	MAP3K11	67	.	0			c.G1605A						.						15.0	18.0	17.0					11																	65373551		2199	4296	6495	SO:0001630	splice_region_variant	4296	exon7			AGGCTCCACTGCA		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.833-1G>A	chr11.hg19:g.65373551C>T		48.0	0.0		58.0	4.0	NM_002419		Silent	SNP	ENST00000530153.1	hg19																																																																																				.	.		0.577	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		Silent
KLC2	64837	hgsc.bcm.edu	37	11	66031564	66031564	+	Silent	SNP	G	G	T	rs556408432		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66031564G>T	ENST00000417856.1	+	8	1233	c.990G>T	c.(988-990)ctG>ctT	p.L330L	KLC2_ENST00000394065.2_Silent_p.L191L|KLC2_ENST00000316924.5_Silent_p.L330L|RP11-867G23.1_ENST00000530805.1_RNA|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394066.2_Silent_p.L253L|KLC2_ENST00000394078.1_Intron|KLC2_ENST00000421552.1_Silent_p.L253L|KLC2_ENST00000394067.2_Silent_p.L330L	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	330					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TCAGCAACCTGGCCCTGCTGT	0.637																																					p.L330L		Atlas-SNP	.											.	KLC2	50	.	0			c.G990T						.						27.0	26.0	26.0					11																	66031564		2200	4294	6494	SO:0001819	synonymous_variant	64837	exon8			CAACCTGGCCCTG	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.990G>T	chr11.hg19:g.66031564G>T		118.0	0.0		142.0	18.0	NM_022822	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Silent	SNP	ENST00000417856.1	hg19	CCDS8130.1																																																																																			.	.		0.637	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
BBS1	582	hgsc.bcm.edu	37	11	66283057	66283057	+	Splice_Site	SNP	G	G	T	rs376894444		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66283057G>T	ENST00000318312.7	+	5	530	c.479G>T	c.(478-480)cGg>cTg	p.R160L	BBS1_ENST00000537537.1_Intron|BBS1_ENST00000455748.2_Intron|BBS1_ENST00000393994.2_Splice_Site_p.R160L|CTD-3074O7.11_ENST00000419755.3_Splice_Site_p.R197L|BBS1_ENST00000529766.1_3'UTR	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	160			R -> Q (in BBS1). {ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21344540}.		cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GAGAGCATCCGGTGAGAGGCT	0.587									Bardet-Biedl syndrome																												p.R160L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.G479T						.						112.0	101.0	105.0					11																	66283057		2200	4295	6495	SO:0001630	splice_region_variant	582	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCATCCGGTGAGA	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.479+1G>T	chr11.hg19:g.66283057G>T		132.0	0.0		195.0	8.0	NM_024649	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	hg19	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135798	0.94517	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000525809;ENST00000393994;ENST00000524705	D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;-2.87	5.25	5.25	0.73442	.	.	.	.	.	D	0.94528	0.8238	M	0.67569	2.06	0.80722	D	1	D;D;D;D	0.76494	0.996;0.992;0.999;0.999	D;D;D;D	0.79108	0.992;0.91;0.977;0.977	D	0.94926	0.8078	9	0.72032	D	0.01	.	16.4108	0.83712	0.0:0.0:1.0:0.0	.	160;48;160;197	Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;BBS1_HUMAN;.	L	197;160;69;160;67	ENSP00000398526:R197L;ENSP00000317469:R160L;ENSP00000431187:R69L;ENSP00000377563:R160L;ENSP00000436927:R67L	ENSP00000317469:R160L	R	+	2	0	BBS1;CTD-3074O7.11	66039633	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.932000	0.87634	2.452000	0.82932	0.558000	0.71614	CGG	.	.		0.587	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		Missense_Mutation
RBM14	10432	hgsc.bcm.edu	37	11	66392658	66392658	+	Silent	SNP	C	C	A	rs375934305		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66392658C>A	ENST00000310137.4	+	2	1450	c.1311C>A	c.(1309-1311)gcC>gcA	p.A437A	RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000503028.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	437	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CACAGCCAGCCACAGCTGCTG	0.637																																					p.A437A		Atlas-SNP	.											.	RBM14	59	.	0			c.C1311A						.						68.0	71.0	70.0					11																	66392658		2187	4264	6451	SO:0001819	synonymous_variant	10432	exon2			GCCAGCCACAGCT	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1311C>A	chr11.hg19:g.66392658C>A		40.0	0.0		75.0	4.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	hg19	CCDS8147.1																																																																																			.	.		0.637	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
RBM14	10432	hgsc.bcm.edu	37	11	66392968	66392968	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66392968C>A	ENST00000310137.4	+	2	1760	c.1621C>A	c.(1621-1623)Cgc>Agc	p.R541S	RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000503028.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	541	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						TGCCTCCTACCGCGGCCAGCC	0.652																																					p.R541S		Atlas-SNP	.											.	RBM14	59	.	0			c.C1621A						.						41.0	36.0	38.0					11																	66392968		2200	4295	6495	SO:0001583	missense	10432	exon2			TCCTACCGCGGCC	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1621C>A	chr11.hg19:g.66392968C>A	ENSP00000311747:p.Arg541Ser	88.0	0.0		126.0	6.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851892	0.32699	.	.	ENSG00000239306	ENST00000310137	D	0.83837	-1.77	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.81226	0.4778	N	0.08118	0	0.80722	D	1	D	0.53745	0.962	D	0.65010	0.931	D	0.84711	0.0734	10	0.87932	D	0	-2.0699	14.1553	0.65413	0.0:1.0:0.0:0.0	.	541	Q96PK6	RBM14_HUMAN	S	541	ENSP00000311747:R541S	ENSP00000311747:R541S	R	+	1	0	RBM14	66149544	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.116000	0.31221	2.720000	0.93068	0.655000	0.94253	CGC	.	.		0.652	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
KDM2A	22992	hgsc.bcm.edu	37	11	67017960	67017960	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67017960A>G	ENST00000529006.2	+	17	2905	c.2459A>G	c.(2458-2460)cAg>cGg	p.Q820R	KDM2A_ENST00000530342.1_Missense_Mutation_p.Q381R|KDM2A_ENST00000398645.2_Intron|KDM2A_ENST00000308783.5_Missense_Mutation_p.Q278R|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	820					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						CCCAAGCTGCAGGCCATCACG	0.622																																					p.Q820R		Atlas-SNP	.											.	KDM2A	80	.	0			c.A2459G						.						52.0	59.0	56.0					11																	67017960		2131	4233	6364	SO:0001583	missense	22992	exon17			AGCTGCAGGCCAT	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2459A>G	chr11.hg19:g.67017960A>G	ENSP00000432786:p.Gln820Arg	107.0	0.0		85.0	4.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.041105	0.55003	.	.	ENSG00000173120	ENST00000529006;ENST00000530342;ENST00000308783	T;T;T	0.24723	2.21;1.84;1.89	5.91	5.91	0.95273	.	0.104270	0.64402	D	0.000003	T	0.12817	0.0311	N	0.08118	0	0.58432	D	0.999997	P;P	0.42409	0.779;0.779	B;B	0.34873	0.191;0.145	T	0.17289	-1.0374	9	.	.	.	-6.2752	14.9163	0.70801	1.0:0.0:0.0:0.0	.	278;820	D4QA03;Q9Y2K7	.;KDM2A_HUMAN	R	820;381;278	ENSP00000432786:Q820R;ENSP00000435776:Q381R;ENSP00000309302:Q278R	.	Q	+	2	0	KDM2A	66774536	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.149000	0.64863	2.261000	0.74972	0.533000	0.62120	CAG	.	.		0.622	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308	
ACY3	91703	hgsc.bcm.edu	37	11	67410349	67410349	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67410349T>C	ENST00000255082.3	-	8	976	c.806A>G	c.(805-807)gAc>gGc	p.D269G	ACY3_ENST00000529256.1_Missense_Mutation_p.D148G	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	269	Shielding domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	ATAGAGCAGGTCCTCCCCACT	0.572																																					p.D269G	GBM(56;346 1011 27014 29495 46841)	Atlas-SNP	.											.	ACY3	27	.	0			c.A806G						.						83.0	65.0	71.0					11																	67410349		2200	4294	6494	SO:0001583	missense	91703	exon8			AGCAGGTCCTCCC	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.806A>G	chr11.hg19:g.67410349T>C	ENSP00000255082:p.Asp269Gly	73.0	0.0		91.0	4.0	NM_080658		Missense_Mutation	SNP	ENST00000255082.3	hg19	CCDS8175.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.765609	0.31228	.	.	ENSG00000132744	ENST00000255082;ENST00000529256	D;D	0.97752	-4.52;-4.52	4.36	3.23	0.37069	.	0.262355	0.36628	N	0.002490	D	0.95595	0.8568	M	0.72353	2.195	0.39880	D	0.973625	B	0.20368	0.044	B	0.19391	0.025	D	0.91543	0.5251	10	0.17832	T	0.49	.	9.0536	0.36392	0.0:0.0914:0.0:0.9086	.	269	Q96HD9	ACY3_HUMAN	G	269;148	ENSP00000255082:D269G;ENSP00000434270:D148G	ENSP00000255082:D269G	D	-	2	0	ACY3	67166925	0.167000	0.22975	0.084000	0.20598	0.021000	0.10359	1.494000	0.35616	0.663000	0.31027	0.448000	0.29417	GAC	.	.		0.572	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658	
TCIRG1	10312	hgsc.bcm.edu	37	11	67818045	67818045	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67818045C>A	ENST00000265686.3	+	19	2436	c.2328C>A	c.(2326-2328)atC>atA	p.I776I	TCIRG1_ENST00000532635.1_Silent_p.I560I|RP11-802E16.3_ENST00000526897.1_RNA|TCIRG1_ENST00000530802.1_Intron|CHKA_ENST00000533728.1_5'Flank|RP11-802E16.3_ENST00000534517.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	776					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						TGGTCCCCATCTTTGCCGCCT	0.662																																					p.I776I		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C2328A						.						108.0	118.0	115.0					11																	67818045		2200	4294	6494	SO:0001819	synonymous_variant	10312	exon19			CCCCATCTTTGCC	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.2328C>A	chr11.hg19:g.67818045C>A		433.0	1.0		386.0	167.0	NM_006019	O75877|Q8WVC5	Silent	SNP	ENST00000265686.3	hg19	CCDS8177.1																																																																																			.	.		0.662	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
SHANK2	22941	hgsc.bcm.edu	37	11	70332784	70332784	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:70332784A>G	ENST00000423696.2	-	15	2513	c.2477T>C	c.(2476-2478)cTc>cCc	p.L826P	SHANK2_ENST00000338508.4_Missense_Mutation_p.L1206P|SHANK2_ENST00000409161.1_Missense_Mutation_p.L609P|SHANK2_ENST00000449833.2_Missense_Mutation_p.L610P			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	826					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CCGCCCTGTGAGTGGGTGGAC	0.677																																					p.L617P		Atlas-SNP	.											.	SHANK2	340	.	0			c.T1850C						.						29.0	36.0	34.0					11																	70332784		2199	4294	6493	SO:0001583	missense	22941	exon10			CCTGTGAGTGGGT	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2477T>C	chr11.hg19:g.70332784A>G	ENSP00000394536:p.Leu826Pro	87.0	0.0		101.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.91	1.781106	0.31502	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	4.88	4.88	0.63580	.	0.056200	0.64402	D	0.000001	T	0.76990	0.4065	M	0.78049	2.395	0.80722	D	1	D;D;D	0.67145	0.986;0.992;0.996	P;P;P	0.62089	0.828;0.898;0.898	T	0.81048	-0.1109	10	0.87932	D	0	.	14.486	0.67616	1.0:0.0:0.0:0.0	.	826;1205;610	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	P	610;609;484;1206;826;844;829	ENSP00000399423:L610P;ENSP00000386491:L609P;ENSP00000402944:L484P;ENSP00000345193:L1206P;ENSP00000394536:L826P;ENSP00000294018:L829P	ENSP00000294018:L829P	L	-	2	0	SHANK2	70010432	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	8.722000	0.91452	1.819000	0.53055	0.459000	0.35465	CTC	.	.		0.677	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
P2RY2	5029	hgsc.bcm.edu	37	11	72946264	72946264	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:72946264G>T	ENST00000311131.2	+	3	1527	c.1060G>T	c.(1060-1062)Ggc>Tgc	p.G354C	P2RY2_ENST00000393596.2_Missense_Mutation_p.G354C|P2RY2_ENST00000393597.2_Missense_Mutation_p.G354C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	354					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	AGATGTGTTGGGCAGCAGTGA	0.622																																					p.G354C		Atlas-SNP	.											.	P2RY2	54	.	0			c.G1060T						.						84.0	87.0	86.0					11																	72946264		2191	4272	6463	SO:0001583	missense	5029	exon3			GTGTTGGGCAGCA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1060G>T	chr11.hg19:g.72946264G>T	ENSP00000310305:p.Gly354Cys	127.0	0.0		94.0	4.0	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	hg19	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	G	3.668	-0.068213	0.07228	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.73047	-0.71;-0.71;-0.71	4.43	-0.178	0.13303	.	2.032220	0.03119	N	0.163493	T	0.49167	0.1541	N	0.08118	0	0.09310	N	1	P	0.35527	0.507	B	0.33196	0.159	T	0.46105	-0.9215	10	0.56958	D	0.05	.	4.6964	0.12806	0.2125:0.3375:0.4499:0.0	.	354	P41231	P2RY2_HUMAN	C	354	ENSP00000377222:G354C;ENSP00000310305:G354C;ENSP00000377221:G354C	ENSP00000310305:G354C	G	+	1	0	P2RY2	72623912	0.000000	0.05858	0.013000	0.15412	0.210000	0.24377	0.270000	0.18607	-0.104000	0.12154	0.561000	0.74099	GGC	.	.		0.622	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
C2CD3	26005	hgsc.bcm.edu	37	11	73796884	73796884	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:73796884C>A	ENST00000334126.7	-	21	3915	c.3689G>T	c.(3688-3690)gGg>gTg	p.G1230V	C2CD3_ENST00000313663.7_Missense_Mutation_p.G1230V			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1230	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGCATTGACCCCGACTGTGGC	0.537																																					p.G1230V		Atlas-SNP	.											.	C2CD3	288	.	0			c.G3689T						.						74.0	67.0	69.0					11																	73796884		2200	4293	6493	SO:0001583	missense	26005	exon21			TTGACCCCGACTG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3689G>T	chr11.hg19:g.73796884C>A	ENSP00000334379:p.Gly1230Val	178.0	0.0		116.0	5.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.363126	0.95877	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.59906	0.23;0.36;0.37	5.8	5.8	0.92144	.	0.104717	0.64402	D	0.000004	T	0.75796	0.3898	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73616	-0.3926	9	.	.	.	-14.677	19.6402	0.95754	0.0:1.0:0.0:0.0	.	1230	Q4AC94-1	.	V	1230;1230;1230;38	ENSP00000334379:G1230V;ENSP00000323339:G1230V;ENSP00000388750:G38V	.	G	-	2	0	C2CD3	73474532	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	7.273000	0.78527	2.742000	0.94016	0.655000	0.94253	GGG	.	.		0.537	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
LIPT2	387787	hgsc.bcm.edu	37	11	74203187	74203187	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:74203187G>T	ENST00000310109.4	-	2	718	c.689C>A	c.(688-690)cCc>cAc	p.P230H	AP001372.2_ENST00000526036.1_lincRNA	NM_001144869.1	NP_001138341.1	A6NK58	LIPT2_HUMAN	lipoyl(octanoyl) transferase 2 (putative)	230					cellular protein modification process (GO:0006464)|lipoate biosynthetic process (GO:0009107)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|lipoyl(octanoyl) transferase activity (GO:0033819)|octanoyltransferase activity (GO:0016415)			endometrium(1)|prostate(1)|stomach(1)	3						TCTTCAGTTGGGGCTGTCCTC	0.507																																					p.P230H		Atlas-SNP	.											.	LIPT2	5	.	0			c.C689A						.						140.0	118.0	124.0					11																	74203187		692	1591	2283	SO:0001583	missense	387787	exon2			CAGTTGGGGCTGT		CCDS44679.1	11q13.4	2009-09-09			ENSG00000175536	ENSG00000175536			37216	protein-coding gene	gene with protein product							Standard	NM_001144869		Approved		uc010rrk.2	A6NK58	OTTHUMG00000165646	ENST00000310109.4:c.689C>A	chr11.hg19:g.74203187G>T	ENSP00000309463:p.Pro230His	117.0	0.0		95.0	4.0	NM_001144869		Missense_Mutation	SNP	ENST00000310109.4	hg19	CCDS44679.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.850000	0.32699	.	.	ENSG00000175536	ENST00000310109	.	.	.	4.63	-4.54	0.03452	.	1.685560	0.02861	N	0.130337	T	0.18299	0.0439	N	0.19112	0.55	0.09310	N	1	P	0.50710	0.938	B	0.43360	0.417	T	0.18618	-1.0331	9	0.59425	D	0.04	-4.3503	1.6772	0.02824	0.328:0.2451:0.3137:0.1132	.	230	A6NK58	LIPT2_HUMAN	H	230	.	ENSP00000309463:P230H	P	-	2	0	LIPT2	73880835	0.507000	0.26146	0.001000	0.08648	0.058000	0.15608	0.412000	0.21131	-0.625000	0.05604	-0.311000	0.09066	CCC	.	.		0.507	LIPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385544.1	NM_001144869	
PICALM	8301	hgsc.bcm.edu	37	11	85701369	85701369	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:85701369A>G	ENST00000393346.3	-	13	1480	c.1332T>C	c.(1330-1332)agT>agC	p.S444S	PICALM_ENST00000356360.5_Silent_p.S444S|PICALM_ENST00000526033.1_Silent_p.S437S|PICALM_ENST00000532317.1_Intron|PICALM_ENST00000528398.1_Intron			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	444					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				GAACATCACCACTACTTTTTG	0.363			T	"""MLLT10, MLL"""	"""TALL, AML, """																																p.S444S		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.T1332C						.						129.0	121.0	124.0					11																	85701369		2203	4299	6502	SO:0001819	synonymous_variant	8301	exon13			ATCACCACTACTT	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1332T>C	chr11.hg19:g.85701369A>G		131.0	0.0		100.0	4.0	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	hg19	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	A	9.246	1.039433	0.19669	.	.	ENSG00000073921	ENST00000526961;ENST00000530542	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	T	0.60340	0.2261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60352	-0.7280	4	.	.	.	-10.4418	8.5418	0.33397	0.8543:0.0:0.1457:0.0	.	.	.	.	R	53;147	.	.	W	-	1	0	PICALM	85379017	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.239000	0.43079	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.363	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166	
FAT3	120114	hgsc.bcm.edu	37	11	92616016	92616016	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:92616016T>C	ENST00000298047.6	+	23	12411	c.12394T>C	c.(12394-12396)Tac>Cac	p.Y4132H	FAT3_ENST00000409404.2_Missense_Mutation_p.Y4132H|FAT3_ENST00000533797.1_Missense_Mutation_p.Y467H|FAT3_ENST00000525166.1_Missense_Mutation_p.Y3982H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4132	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CGTGGGCCAGTACTGCGGGCT	0.622										TCGA Ovarian(4;0.039)																											p.Y4132H		Atlas-SNP	.											.	FAT3	1822	.	0			c.T12394C						.						61.0	79.0	73.0					11																	92616016		2093	4213	6306	SO:0001583	missense	120114	exon23			GGCCAGTACTGCG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12394T>C	chr11.hg19:g.92616016T>C	ENSP00000298047:p.Tyr4132His	130.0	0.0		76.0	22.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	0.836	-0.743501	0.03088	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	D;D;D;D	0.91577	-2.24;-2.24;-2.24;-2.87	5.55	-1.56	0.08532	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.75642	0.3877	N	0.10837	0.055	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.09377	0.002;0.004	T	0.62267	-0.6890	9	0.02654	T	1	.	11.637	0.51209	0.0:0.4332:0.0:0.5668	.	4132;4132	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	H	4132;4132;3982;467	ENSP00000298047:Y4132H;ENSP00000387040:Y4132H;ENSP00000432586:Y3982H;ENSP00000436399:Y467H	ENSP00000298047:Y4132H	Y	+	1	0	FAT3	92255664	0.940000	0.31905	0.676000	0.29932	0.598000	0.36846	0.132000	0.15891	-0.451000	0.07097	-0.250000	0.11733	TAC	.	.		0.622	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
HEPHL1	341208	hgsc.bcm.edu	37	11	93844139	93844139	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:93844139C>T	ENST00000315765.9	+	18	3124	c.3116C>T	c.(3115-3117)gCa>gTa	p.A1039V		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1039	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GAACTGTTTGCAGATCACCCA	0.438																																					p.A1039V		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C3116T						.						84.0	84.0	84.0					11																	93844139		2096	4250	6346	SO:0001583	missense	341208	exon18			TGTTTGCAGATCA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3116C>T	chr11.hg19:g.93844139C>T	ENSP00000313699:p.Ala1039Val	112.0	0.0		91.0	4.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.535694	0.85812	.	.	ENSG00000181333	ENST00000315765	D	0.99758	-6.65	5.97	4.1	0.47936	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	M	0.84846	2.72	0.42291	D	0.992134	P	0.48294	0.908	P	0.58391	0.838	D	0.97475	1.0043	10	0.54805	T	0.06	-2.2986	13.3983	0.60868	0.0:0.8701:0.0:0.1299	.	1039	Q6MZM0	HPHL1_HUMAN	V	1039	ENSP00000313699:A1039V	ENSP00000313699:A1039V	A	+	2	0	HEPHL1	93483787	0.997000	0.39634	0.980000	0.43619	0.998000	0.95712	3.633000	0.54295	1.544000	0.49359	0.655000	0.94253	GCA	.	.		0.438	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
CNTN5	53942	hgsc.bcm.edu	37	11	100141826	100141826	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:100141826C>T	ENST00000524871.1	+	18	2457	c.2167C>T	c.(2167-2169)Cca>Tca	p.P723S	CNTN5_ENST00000527185.1_Missense_Mutation_p.P723S|CNTN5_ENST00000418526.2_Missense_Mutation_p.P649S|CNTN5_ENST00000279463.3_Missense_Mutation_p.P723S|CNTN5_ENST00000528682.1_Missense_Mutation_p.P723S|CNTN5_ENST00000524560.1_3'UTR	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	723	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TTCTATAGTCCCAGAAATCAT	0.423																																					p.P723S		Atlas-SNP	.											.	CNTN5	324	.	0			c.C2167T						.						75.0	76.0	76.0					11																	100141826		1909	4134	6043	SO:0001583	missense	53942	exon17			ATAGTCCCAGAAA	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.2167C>T	chr11.hg19:g.100141826C>T	ENSP00000435637:p.Pro723Ser	89.0	0.0		70.0	4.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466543	0.63625	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.59083	0.29;0.33;0.33;0.34;0.33	5.73	5.73	0.89815	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75997	0.3926	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.77278	-0.2647	10	0.87932	D	0	.	18.9016	0.92444	0.0:1.0:0.0:0.0	.	649;723	O94779-2;O94779	.;CNTN5_HUMAN	S	723;723;723;649;723	ENSP00000433575:P723S;ENSP00000436185:P723S;ENSP00000435637:P723S;ENSP00000393229:P649S;ENSP00000279463:P723S	ENSP00000279463:P723S	P	+	1	0	CNTN5	99647036	1.000000	0.71417	0.996000	0.52242	0.210000	0.24377	7.382000	0.79729	2.708000	0.92522	0.467000	0.42956	CCA	.	.		0.423	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
BIRC2	329	hgsc.bcm.edu	37	11	102221307	102221307	+	Missense_Mutation	SNP	G	G	T	rs144530384		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:102221307G>T	ENST00000227758.2	+	2	2121	c.722G>T	c.(721-723)cGg>cTg	p.R241L	BIRC2_ENST00000532672.1_Missense_Mutation_p.R220L|BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.R192L	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	241					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		TCAGAACACCGGAGGCATTTT	0.443																																					p.R241L		Atlas-SNP	.											.	BIRC2	51	.	0			c.G722T						.						91.0	96.0	94.0					11																	102221307		2203	4299	6502	SO:0001583	missense	329	exon2			AACACCGGAGGCA	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	590	protein-coding gene	gene with protein product	"""NFR2-TRAF signalling complex protein"", ""apoptosis inhibitor 1"""	601712	"""baculoviral IAP repeat-containing 2"""	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.722G>T	chr11.hg19:g.102221307G>T	ENSP00000227758:p.Arg241Leu	82.0	0.0		83.0	4.0	NM_001256163	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	hg19	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414163	0.42817	.	.	ENSG00000110330	ENST00000530675;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T	0.70164	-0.46;-0.46;-0.46	5.71	4.8	0.61643	Baculoviral inhibition of apoptosis protein repeat (5);	0.052408	0.85682	D	0.000000	T	0.54111	0.1838	N	0.20483	0.58	0.49130	D	0.999752	B	0.14805	0.011	B	0.24701	0.055	T	0.49854	-0.8895	10	0.39692	T	0.17	-9.9057	14.7345	0.69406	0.0694:0.0:0.9306:0.0	.	241	Q13490	BIRC2_HUMAN	L	192;241;241;220	ENSP00000431723:R192L;ENSP00000227758:R241L;ENSP00000434979:R220L	ENSP00000227758:R241L	R	+	2	0	BIRC2	101726517	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.959000	0.49153	1.427000	0.47276	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.443	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166	
TMEM123	114908	hgsc.bcm.edu	37	11	102272281	102272281	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:102272281C>T	ENST00000398136.2	-	4	1011	c.591G>A	c.(589-591)cgG>cgA	p.R197R	TMEM123_ENST00000532161.1_Silent_p.R109R|TMEM123_ENST00000525577.1_5'Flank|TMEM123_ENST00000361236.3_Silent_p.R178R	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	197					oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		TGGTTCGATACCGAATGCCTC	0.358																																					p.R197R		Atlas-SNP	.											.	TMEM123	16	.	0			c.G591A						.						95.0	91.0	92.0					11																	102272281		1821	4080	5901	SO:0001819	synonymous_variant	114908	exon4			TCGATACCGAATG	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"""pro oncosis receptor inducing membrane injury gene"""	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.591G>A	chr11.hg19:g.102272281C>T		108.0	0.0		90.0	5.0	NM_052932	Q8IWS2|Q96QV2	Silent	SNP	ENST00000398136.2	hg19	CCDS41702.1																																																																																			.	.		0.358	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932	
KBTBD3	143879	hgsc.bcm.edu	37	11	105924774	105924774	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:105924774C>T	ENST00000526793.1	-	3	801	c.642G>A	c.(640-642)atG>atA	p.M214I	KBTBD3_ENST00000534815.1_Missense_Mutation_p.M135I|KBTBD3_ENST00000531837.1_Missense_Mutation_p.M214I	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	210	BACK.									NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		CTTTCAGTACCATTTCTTCTT	0.313																																					p.M214I		Atlas-SNP	.											.	KBTBD3	59	.	0			c.G642A						.						63.0	67.0	66.0					11																	105924774		2201	4298	6499	SO:0001583	missense	143879	exon3			CAGTACCATTTCT	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"""BTB/POZ domain containing"""	22934	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 3"""	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.642G>A	chr11.hg19:g.105924774C>T	ENSP00000436262:p.Met214Ile	88.0	0.0		92.0	4.0	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.256678	0.22965	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.68181	-0.31;-0.31;-0.31	5.71	-7.6	0.01303	BTB/Kelch-associated (2);	0.506452	0.24258	N	0.040120	T	0.31009	0.0783	N	0.08118	0	0.26322	N	0.977669	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04693	-1.0933	10	0.45353	T	0.12	.	1.2847	0.02048	0.2642:0.2301:0.3144:0.1913	.	214;210	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	I	135;214;214	ENSP00000431910:M135I;ENSP00000436262:M214I;ENSP00000432163:M214I	ENSP00000436262:M214I	M	-	3	0	KBTBD3	105429984	0.001000	0.12720	0.536000	0.28039	0.963000	0.63663	-1.398000	0.02509	-1.616000	0.01572	-0.312000	0.09012	ATG	.	.		0.313	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433	
CWF19L2	143884	hgsc.bcm.edu	37	11	107263571	107263571	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:107263571T>C	ENST00000282251.5	-	11	1695	c.1668A>G	c.(1666-1668)agA>agG	p.R556R	CWF19L2_ENST00000433523.1_Silent_p.R556R	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	556							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CAGGCCATACTCTTCCAGACT	0.348																																					p.R556R		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A1668G						.						116.0	111.0	113.0					11																	107263571		2201	4298	6499	SO:0001819	synonymous_variant	143884	exon11			CCATACTCTTCCA	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1668A>G	chr11.hg19:g.107263571T>C		108.0	0.0		86.0	4.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	hg19	CCDS8336.2																																																																																			.	.		0.348	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
C11orf88	399949	hgsc.bcm.edu	37	11	111385715	111385715	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:111385715C>A	ENST00000375618.4	+	1	206	c.206C>A	c.(205-207)cCc>cAc	p.P69H	RP11-794P6.6_ENST00000530283.1_RNA|BTG4_ENST00000525791.1_5'Flank|MIR34B_ENST00000385076.1_RNA|C11orf88_ENST00000529167.1_Missense_Mutation_p.P69H|BTG4_ENST00000356018.2_5'Flank|C11orf88_ENST00000332814.6_Missense_Mutation_p.P69H|MIR34C_ENST00000384831.1_RNA	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	69										endometrium(1)|large_intestine(3)|lung(2)	6						GTGGCGCGGCCCAGGAGGAGC	0.602											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P69H		Atlas-SNP	.											.	C11orf88	37	.	0			c.C206A						.						36.0	42.0	40.0					11																	111385715		2153	4278	6431	SO:0001583	missense	399949	exon1			CGCGGCCCAGGAG	BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"""hypothetical gene supported by BC039505"""					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.206C>A	chr11.hg19:g.111385715C>A	ENSP00000364768:p.Pro69His	74.0	0.0	1434	65.0	5.0	NM_001100388	E9PAN0|Q6ZRL3	Missense_Mutation	SNP	ENST00000375618.4	hg19	CCDS41713.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.309148	0.23821	.	.	ENSG00000183644	ENST00000375618;ENST00000529167;ENST00000332814	.	.	.	5.09	-1.95	0.07548	.	1.790330	0.02949	N	0.141429	T	0.36496	0.0969	L	0.43152	1.355	0.09310	N	1	P;B	0.34780	0.468;0.12	B;B	0.32289	0.143;0.087	T	0.36407	-0.9749	9	0.46703	T	0.11	2.5614	10.6724	0.45766	0.2192:0.3744:0.4064:0.0	.	69;69	E9PAN0;Q6PI97	.;CK088_HUMAN	H	69	.	ENSP00000333845:P69H	P	+	2	0	C11orf88	110890925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.351000	0.20096	-0.880000	0.03997	-2.498000	0.00192	CCC	.	.		0.602	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388	
PTS	5805	hgsc.bcm.edu	37	11	112104184	112104184	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:112104184G>T	ENST00000280362.3	+	6	423	c.344G>T	c.(343-345)tGg>tTg	p.W115L	PTS_ENST00000524931.1_Missense_Mutation_p.W47L|PTS_ENST00000525803.1_3'UTR	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	115					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GTTTATATCTGGGACAACCTC	0.274																																					p.W115L		Atlas-SNP	.											.	PTS	7	.	0			c.G344T						.						41.0	44.0	43.0					11																	112104184		2199	4296	6495	SO:0001583	missense	5805	exon6			ATATCTGGGACAA	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.344G>T	chr11.hg19:g.112104184G>T	ENSP00000280362:p.Trp115Leu	114.0	0.0		93.0	5.0	NM_000317	B0YJ87|Q8WVG8	Missense_Mutation	SNP	ENST00000280362.3	hg19	CCDS8359.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.910445	0.92107	.	.	ENSG00000150787	ENST00000280362;ENST00000524931	D;D	0.99311	-5.73;-5.73	6.01	6.01	0.97437	.	0.054479	0.85682	D	0.000000	D	0.99417	0.9794	M	0.83852	2.665	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.99047	1.0826	10	0.72032	D	0.01	-6.6916	17.2452	0.87026	0.0:0.0:1.0:0.0	.	115	Q03393	PTPS_HUMAN	L	115;47	ENSP00000280362:W115L;ENSP00000434688:W47L	ENSP00000280362:W115L	W	+	2	0	PTS	111609394	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	8.828000	0.92047	2.845000	0.97973	0.643000	0.83706	TGG	.	.		0.274	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317	
USP28	57646	hgsc.bcm.edu	37	11	113694377	113694377	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:113694377A>G	ENST00000003302.4	-	12	1301	c.1233T>C	c.(1231-1233)tgT>tgC	p.C411C	USP28_ENST00000537706.1_Silent_p.C411C|USP28_ENST00000545540.1_Silent_p.C286C|RP11-667M19.10_ENST00000399123.2_RNA|USP28_ENST00000260188.5_Silent_p.C411C|USP28_ENST00000544967.1_Silent_p.C119C	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	411	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		ACTTTCGAATACACTCTCTCT	0.303																																					p.C411C	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.T1233C						.						97.0	90.0	93.0					11																	113694377		2200	4296	6496	SO:0001819	synonymous_variant	57646	exon12			TCGAATACACTCT	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1233T>C	chr11.hg19:g.113694377A>G		92.0	0.0		89.0	4.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Silent	SNP	ENST00000003302.4	hg19	CCDS31680.1																																																																																			.	.		0.303	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		
CADM1	23705	hgsc.bcm.edu	37	11	115109361	115109361	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:115109361T>C	ENST00000452722.3	-	3	303	c.283A>G	c.(283-285)Agc>Ggc	p.S95G	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000537058.1_Missense_Mutation_p.S95G|CADM1_ENST00000542447.2_Missense_Mutation_p.S95G|CADM1_ENST00000536727.1_Missense_Mutation_p.S95G|CADM1_ENST00000331581.6_Missense_Mutation_p.S95G	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TGAAACCTGCTGTCCTTCAAA	0.373																																					p.S95G		Atlas-SNP	.											.	CADM1	74	.	0			c.A283G						.						69.0	69.0	69.0					11																	115109361		2201	4296	6497	SO:0001583	missense	23705	exon3			ACCTGCTGTCCTT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5951	protein-coding gene	gene with protein product	"""nectin-like 2"""	605686	"""tumor suppressor in lung cancer 1"", ""immunoglobulin superfamily, member 4"""	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.283A>G	chr11.hg19:g.115109361T>C	ENSP00000395359:p.Ser95Gly	129.0	0.0		86.0	4.0	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	hg19	CCDS8373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.01|17.01	3.280362|3.280362	0.59758|0.59758	.|.	.|.	ENSG00000182985|ENSG00000182985	ENST00000545380|ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000545094	.|T;T;T;T;T;T	.|0.59364	.|0.27;0.27;0.27;0.27;0.27;0.27	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.173783	.|0.64402	.|D	.|0.000010	T|T	0.62551|0.62551	0.2437|0.2437	M|M	0.62723|0.62723	1.935|1.935	0.51482|0.51482	D|D	0.99992|0.99992	.|P;D;P;B;P	.|0.52996	.|0.942;0.957;0.866;0.447;0.649	.|P;P;P;B;B	.|0.49276	.|0.543;0.57;0.605;0.439;0.222	T|T	0.60058|0.60058	-0.7337|-0.7337	5|10	.|0.22109	.|T	.|0.4	.|.	16.167|16.167	0.81768|0.81768	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|95;95;96;95;95	.|Q9BY67-2;F5H0J4;A4FVB5;Q9BY67;A0A4Z1	.|.;.;.;CADM1_HUMAN;.	R|G	93|95;95;95;95;54;95;62	.|ENSP00000439176:S95G;ENSP00000395359:S95G;ENSP00000439817:S95G;ENSP00000440322:S95G;ENSP00000329797:S95G;ENSP00000439696:S62G	.|ENSP00000329797:S95G	Q|S	-|-	2|1	0|0	CADM1|CADM1	114614571|114614571	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.046000|2.046000	0.41260|0.41260	2.214000|2.214000	0.71695|0.71695	0.528000|0.528000	0.53228|0.53228	CAG|AGC	.	.		0.373	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333	
SIK3	23387	hgsc.bcm.edu	37	11	116746722	116746722	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:116746722A>G	ENST00000292055.4	-	9	960	c.925T>C	c.(925-927)Tta>Cta	p.L309L	SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Intron|SIK3_ENST00000434315.2_Silent_p.L208L|SIK3_ENST00000375300.1_Silent_p.L367L|SIK3_ENST00000446921.2_Intron	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	309	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						TCTGATCTTAATGACTACCAA	0.433																																					p.L309L		Atlas-SNP	.											.	SIK3	112	.	0			c.T925C						.						81.0	75.0	77.0					11																	116746722		2201	4296	6497	SO:0001819	synonymous_variant	23387	exon9			ATCTTAATGACTA	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.925T>C	chr11.hg19:g.116746722A>G		101.0	0.0		76.0	4.0	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Silent	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	9.192	1.026248	0.19512	.	.	ENSG00000160584	ENST00000445177;ENST00000413553	.	.	.	5.45	3.17	0.36434	.	.	.	.	.	T	0.55832	0.1945	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52808	-0.8526	4	.	.	.	.	6.9859	0.24727	0.7012:0.0:0.2988:0.0	.	.	.	.	T	360;269	.	.	I	-	2	0	SIK3	116251932	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	2.547000	0.45786	2.062000	0.61559	0.454000	0.30748	ATT	.	.		0.433	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
DSCAML1	57453	hgsc.bcm.edu	37	11	117374691	117374691	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117374691C>T	ENST00000321322.6	-	11	2409	c.2408G>A	c.(2407-2409)cGc>cAc	p.R803H	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R533H	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	743	Ig-like C2-type 9.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GATCTGGATGCGGCCAGTGAG	0.632																																					p.R803H		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	.	0			c.G2408A						.						104.0	94.0	97.0					11																	117374691		2201	4296	6497	SO:0001583	missense	57453	exon11			TGGATGCGGCCAG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2408G>A	chr11.hg19:g.117374691C>T	ENSP00000315465:p.Arg803His	194.0	0.0		134.0	40.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.619302	0.87460	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	D;D	0.84800	-1.9;-1.9	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.88280	0.6394	L	0.35854	1.095	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.87355	0.2340	9	0.34782	T	0.22	.	16.9369	0.86205	0.0:1.0:0.0:0.0	.	743	Q8TD84	DSCL1_HUMAN	H	533;803;510	ENSP00000434335:R533H;ENSP00000315465:R803H	ENSP00000315465:R803H	R	-	2	0	DSCAML1	116879901	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.605000	0.82844	2.237000	0.73441	0.462000	0.41574	CGC	.	.		0.632	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
DSCAML1	57453	hgsc.bcm.edu	37	11	117392100	117392100	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117392100T>A	ENST00000321322.6	-	6	1139	c.1138A>T	c.(1138-1140)Aca>Tca	p.T380S	DSCAML1_ENST00000527706.1_Missense_Mutation_p.T110S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	320	Ig-like C2-type 4.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TTCTTTGGTGTCAGGGTCACA	0.582																																					p.T380S		Atlas-SNP	.											.	DSCAML1	286	.	0			c.A1138T						.						30.0	30.0	30.0					11																	117392100		2201	4296	6497	SO:0001583	missense	57453	exon6			TTGGTGTCAGGGT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1138A>T	chr11.hg19:g.117392100T>A	ENSP00000315465:p.Thr380Ser	109.0	0.0		80.0	4.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	T	4.454	0.084126	0.08583	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66638	-0.22;-0.22	4.65	4.65	0.58169	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32852	0.0843	N	0.01493	-0.835	0.34265	D	0.680376	B;B	0.06786	0.001;0.001	B;B	0.14023	0.006;0.01	T	0.40496	-0.9560	9	0.02654	T	1	.	9.6215	0.39723	0.1557:0.0:0.0:0.8443	.	110;320	G3V1B5;Q8TD84	.;DSCL1_HUMAN	S	110;380;87	ENSP00000434335:T110S;ENSP00000315465:T380S	ENSP00000315465:T380S	T	-	1	0	DSCAML1	116897310	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.112000	0.50368	1.955000	0.56771	0.496000	0.49642	ACA	.	.		0.582	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117780678	117780678	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117780678C>A	ENST00000430170.2	-	8	1039	c.952G>T	c.(952-954)Gga>Tga	p.G318*	TMPRSS13_ENST00000528626.1_Nonsense_Mutation_p.G283*|TMPRSS13_ENST00000445164.2_Nonsense_Mutation_p.G318*|TMPRSS13_ENST00000524993.1_Nonsense_Mutation_p.G318*|TMPRSS13_ENST00000526090.1_Nonsense_Mutation_p.G318*	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	318	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GCCCTCAGTCCGCAGTCTGGA	0.617																																					p.G318X		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.G952T						.						53.0	57.0	56.0					11																	117780678		2079	4201	6280	SO:0001587	stop_gained	84000	exon8			TCAGTCCGCAGTC	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.952G>T	chr11.hg19:g.117780678C>A	ENSP00000387702:p.Gly318*	97.0	0.0		73.0	5.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Nonsense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405168	0.83230	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.	.	.	4.41	4.41	0.53225	.	0.347098	0.24606	N	0.037092	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.7676	0.85528	0.0:1.0:0.0:0.0	.	.	.	.	X	283;313;318;318;318;318	.	ENSP00000337113:G313X	G	-	1	0	TMPRSS13	117285888	1.000000	0.71417	0.995000	0.50966	0.074000	0.17049	5.332000	0.65911	2.265000	0.75225	0.561000	0.74099	GGA	.	.		0.617	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
KMT2A	4297	hgsc.bcm.edu	37	11	118377325	118377325	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:118377325C>T	ENST00000389506.5	+	27	10709	c.10709C>T	c.(10708-10710)cCa>cTa	p.P3570L	KMT2A_ENST00000354520.4_Missense_Mutation_p.P3532L|KMT2A_ENST00000534358.1_Missense_Mutation_p.P3573L			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3570					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										GCACACATTCCAGACCAAGAA	0.473																																					p.P3573L		Atlas-SNP	.											.	MLL	548	.	0			c.C10718T						.						96.0	93.0	94.0					11																	118377325		2200	4295	6495	SO:0001583	missense	4297	exon27			ACATTCCAGACCA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10709C>T	chr11.hg19:g.118377325C>T	ENSP00000374157:p.Pro3570Leu	104.0	0.0		51.0	4.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004395	0.54254	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.82167	-1.58;-1.58;-1.54	5.85	5.85	0.93711	.	0.117165	0.64402	D	0.000011	D	0.84777	0.5547	L	0.36672	1.1	0.54753	D	0.999987	D;D	0.63880	0.993;0.993	P;P	0.53954	0.738;0.738	D	0.83952	0.0317	10	0.44086	T	0.13	.	20.1663	0.98152	0.0:1.0:0.0:0.0	.	3573;3570	E9PQG7;Q03164	.;MLL1_HUMAN	L	3573;3570;3532;2480	ENSP00000436786:P3573L;ENSP00000374157:P3570L;ENSP00000346516:P3532L	ENSP00000346516:P3532L	P	+	2	0	MLL	117882535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.231000	0.51294	2.773000	0.95371	0.585000	0.79938	CCA	.	.		0.473	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
HSPA8	3312	hgsc.bcm.edu	37	11	122930222	122930222	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:122930222T>C	ENST00000532636.1	-	5	1198	c.1079A>G	c.(1078-1080)aAt>aGt	p.N360S	HSPA8_ENST00000227378.3_Missense_Mutation_p.N360S|HSPA8_ENST00000534624.1_Missense_Mutation_p.N360S|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526862.1_5'UTR|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.N341S|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534319.1_Missense_Mutation_p.N124S|HSPA8_ENST00000533540.1_Missense_Mutation_p.N214S|HSPA8_ENST00000453788.2_Missense_Mutation_p.N360S			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	360	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GATGCTCTTATTCAGTTCTTT	0.448																																					p.N360S	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A1079G						.						113.0	108.0	110.0					11																	122930222		2202	4299	6501	SO:0001583	missense	3312	exon5			CTCTTATTCAGTT	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1079A>G	chr11.hg19:g.122930222T>C	ENSP00000437125:p.Asn360Ser	146.0	0.0		122.0	12.0	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.539880	0.85917	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000528292	T;T;T;T;T;T;T;T	0.00912	5.55;5.55;5.55;5.55;5.55;5.55;5.55;5.55	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.03053	0.0090	L	0.41236	1.265	0.80722	D	1	D;D;D;D	0.58970	0.984;0.966;0.958;0.984	P;D;P;P	0.65684	0.896;0.937;0.896;0.896	T	0.59473	-0.7448	10	0.87932	D	0	-19.7226	14.4185	0.67168	0.0:0.0:0.0:1.0	.	360;360;360;360	Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;HSP7C_HUMAN	S	360;214;360;360;360;124;341;300	ENSP00000437125:N360S;ENSP00000437189:N214S;ENSP00000432083:N360S;ENSP00000404372:N360S;ENSP00000227378:N360S;ENSP00000433316:N124S;ENSP00000433584:N341S;ENSP00000432884:N300S	ENSP00000227378:N360S	N	-	2	0	HSPA8	122435432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.064000	0.71169	1.871000	0.54225	0.454000	0.30748	AAT	.	.		0.448	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
OR10G8	219869	hgsc.bcm.edu	37	11	123901212	123901212	+	Nonsense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:123901212A>T	ENST00000431524.1	+	1	916	c.883A>T	c.(883-885)Aag>Tag	p.K295*		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CAAGGAGGTGAAGAAAGCTCT	0.468																																					p.K295X		Atlas-SNP	.											.	OR10G8	132	.	0			c.A883T						.						102.0	96.0	98.0					11																	123901212		2201	4299	6500	SO:0001587	stop_gained	219869	exon1			GAGGTGAAGAAAG	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.883A>T	chr11.hg19:g.123901212A>T	ENSP00000389072:p.Lys295*	284.0	0.0		201.0	63.0	NM_001004464	B2RNJ3|Q6IEV2	Nonsense_Mutation	SNP	ENST00000431524.1	hg19	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797584	0.31777	.	.	ENSG00000234560	ENST00000431524	.	.	.	2.91	0.326	0.15908	.	0.161493	0.28927	N	0.013682	.	.	.	.	.	.	0.36812	D	0.885947	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.3731	0.16150	0.7224:0.1757:0.1019:0.0	.	.	.	.	X	295	.	ENSP00000389072:K295X	K	+	1	0	OR10G8	123406422	0.044000	0.20184	0.982000	0.44146	0.346000	0.29079	1.529000	0.35996	-0.064000	0.13043	-0.385000	0.06624	AAG	.	.		0.468	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
OR8G5	219865	hgsc.bcm.edu	37	11	124134976	124134976	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:124134976G>A	ENST00000524943.2	+	1	254	c.254G>A	c.(253-255)gGg>gAg	p.G85E	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ACACTGATTGGGCTCAGTTCT	0.507																																					p.G85E	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G254A						.						122.0	114.0	117.0					11																	124134976		2174	4282	6456	SO:0001583	missense	219865	exon1			TGATTGGGCTCAG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.254G>A	chr11.hg19:g.124134976G>A	ENSP00000477014:p.Gly85Glu	137.0	0.0		123.0	34.0	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	hg19																																																																																				.	.		0.507	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
OR8B8	26493	hgsc.bcm.edu	37	11	124310838	124310838	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:124310838C>T	ENST00000328064.2	-	1	216	c.144G>A	c.(142-144)ctG>ctA	p.L48L		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	48					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TGAGCCTTATCAGGGTTATCA	0.483																																					p.L48L		Atlas-SNP	.											.	OR8B8	76	.	0			c.G144A						.						111.0	113.0	112.0					11																	124310838		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			CCTTATCAGGGTT	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"""GPCR / Class A : Olfactory receptors"""	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.144G>A	chr11.hg19:g.124310838C>T		148.0	0.0		84.0	4.0	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.		0.483	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378	
WNK1	65125	hgsc.bcm.edu	37	12	988759	988759	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:988759A>G	ENST00000315939.6	+	11	3037	c.2394A>G	c.(2392-2394)gtA>gtG	p.V798V	WNK1_ENST00000537687.1_Intron|WNK1_ENST00000340908.4_Silent_p.V391V|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Silent_p.V1296V	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	798					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CCCAGCCAGTACCAACTATCC	0.463																																					p.V798V	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1,colon,carcinoma,0,1	WNK1	403	.	0			c.A2394G						.						81.0	76.0	77.0					12																	988759		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon11			GCCAGTACCAACT	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2394A>G	chr12.hg19:g.988759A>G		103.0	0.0		98.0	4.0	NM_018979	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
KCNA5	3741	hgsc.bcm.edu	37	12	5153812	5153812	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:5153812C>T	ENST00000252321.3	+	1	728	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	167					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	CTTCTTCGACCGCAACCGGCC	0.662																																					p.R167C		Atlas-SNP	.											.	KCNA5	138	.	0			c.C499T						.						38.0	41.0	40.0					12																	5153812		2203	4300	6503	SO:0001583	missense	3741	exon1			TTCGACCGCAACC	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.499C>T	chr12.hg19:g.5153812C>T	ENSP00000252321:p.Arg167Cys	98.0	0.0		63.0	26.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.912344	0.72983	.	.	ENSG00000130037	ENST00000252321	D	0.90324	-2.65	4.7	4.7	0.59300	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	U	0.000001	D	0.97729	0.9255	H	0.99650	4.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99564	1.0969	10	0.87932	D	0	.	16.8208	0.85745	0.0:1.0:0.0:0.0	.	167	P22460	KCNA5_HUMAN	C	167	ENSP00000252321:R167C	ENSP00000252321:R167C	R	+	1	0	KCNA5	5024073	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.820000	0.39032	2.443000	0.82685	0.511000	0.50034	CGC	.	.		0.662	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
PIANP	196500	hgsc.bcm.edu	37	12	6804636	6804636	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:6804636T>C	ENST00000540656.1	-	5	1125	c.787A>G	c.(787-789)Atg>Gtg	p.M263V	PIANP_ENST00000320591.5_Missense_Mutation_p.M263V|PIANP_ENST00000534837.1_Missense_Mutation_p.M263V	NM_001244015.1	NP_001230944.1	Q8IYJ0	PIANP_HUMAN	PILR alpha associated neural protein	263						integral component of membrane (GO:0016021)											GGGTGGGGCATCCCAGGCCGG	0.667																																					p.M263V		Atlas-SNP	.											.	.	.	.	0			c.A787G						.						19.0	21.0	20.0					12																	6804636		1851	4075	5926	SO:0001583	missense	196500	exon5			GGGGCATCCCAGG	BC035736	CCDS44818.1, CCDS58205.1	12p13.31	2012-08-17	2012-08-17	2012-08-17	ENSG00000139200	ENSG00000139200			25338	protein-coding gene	gene with protein product	"""PILR-associating neural protein"""		"""chromosome 12 open reading frame 53"""	C12orf53		12975309	Standard	NM_153685		Approved	DKFZp547D2210, PANP	uc001qqf.2	Q8IYJ0	OTTHUMG00000168664	ENST00000540656.1:c.787A>G	chr12.hg19:g.6804636T>C	ENSP00000442157:p.Met263Val	135.0	0.0		84.0	4.0	NM_001244014	A8K0T3|B3KPF7|B3KRI6|Q6UX35	Missense_Mutation	SNP	ENST00000540656.1	hg19	CCDS44818.1	.	.	.	.	.	.	.	.	.	.	T	0.037	-1.304093	0.01353	.	.	ENSG00000139200	ENST00000540656;ENST00000320591;ENST00000534837;ENST00000439553	T;T;T	0.39787	1.06;1.06;1.06	3.73	2.55	0.30701	.	0.399158	0.24178	U	0.040823	T	0.15262	0.0368	N	0.08118	0	0.23468	N	0.997619	B	0.02656	0.0	B	0.06405	0.002	T	0.08700	-1.0709	10	0.14656	T	0.56	-6.8587	0.3592	0.00362	0.1888:0.1829:0.2285:0.3998	.	263	Q8IYJ0	CL053_HUMAN	V	263;263;263;237	ENSP00000442157:M263V;ENSP00000317818:M263V;ENSP00000443919:M263V	ENSP00000317818:M263V	M	-	1	0	C12orf53	6674897	0.999000	0.42202	1.000000	0.80357	0.983000	0.72400	0.285000	0.18883	1.562000	0.49601	0.260000	0.18958	ATG	.	.		0.667	PIANP-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400524.1	NM_153685	
COPS7A	50813	hgsc.bcm.edu	37	12	6833778	6833778	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:6833778A>G	ENST00000543155.1	+	2	439		c.e2-1		COPS7A_ENST00000229251.3_Splice_Site|COPS7A_ENST00000534877.1_Splice_Site|COPS7A_ENST00000539735.1_Splice_Site|COPS7A_ENST00000534947.1_5'UTR|RP4-761J14.9_ENST00000602759.1_RNA|COPS7A_ENST00000538410.1_Splice_Site|COPS7A_ENST00000542150.1_Intron	NM_001164094.1	NP_001157566.1	Q9UBW8	CSN7A_HUMAN	COP9 signalosome subunit 7A						cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	10						CTTTCCTTGCAGCTCTGGACA	0.557																																					.		Atlas-SNP	.											.	COPS7A	26	.	0			.						.						107.0	106.0	106.0					12																	6833778		2203	4300	6503	SO:0001630	splice_region_variant	50813	.			CCTTGCAGCTCTG	AF193844	CCDS8558.1	12p13.31	2013-03-14	2013-03-14		ENSG00000111652	ENSG00000111652			16758	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7A"", ""COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis)"""				Standard	NM_001164093		Approved	CSN7A	uc001qqh.3	Q9UBW8	OTTHUMG00000169182	ENST00000543155.1:c.-43-1A>G	chr12.hg19:g.6833778A>G		49.0	0.0		41.0	4.0	.	A8K9A6|Q9NVX3|Q9UJW4	Splice_Site	SNP	ENST00000543155.1	hg19	CCDS8558.1																																																																																			.	.		0.557	COPS7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402740.1		Intron
USP5	8078	hgsc.bcm.edu	37	12	6968664	6968664	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:6968664G>T	ENST00000229268.8	+	9	1141	c.1089G>T	c.(1087-1089)caG>caT	p.Q363H	USP5_ENST00000389231.5_Missense_Mutation_p.Q363H	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	363	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						AGATCTTCCAGAATGCCCCGA	0.527																																					p.Q363H		Atlas-SNP	.											.	USP5	124	.	0			c.G1089T						.						95.0	86.0	89.0					12																	6968664		2203	4300	6503	SO:0001583	missense	8078	exon9			CTTCCAGAATGCC	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1089G>T	chr12.hg19:g.6968664G>T	ENSP00000229268:p.Gln363His	106.0	0.0		84.0	4.0	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669371	0.47677	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.31769	1.48;1.48	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.105540	0.64402	D	0.000003	T	0.23410	0.0566	L	0.28192	0.835	0.53688	D	0.999978	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.02560	-1.1141	10	0.48119	T	0.1	-7.2631	13.0182	0.58771	0.0826:0.0:0.9174:0.0	.	363;363	P45974;P45974-2	UBP5_HUMAN;.	H	363	ENSP00000229268:Q363H;ENSP00000373883:Q363H	ENSP00000229268:Q363H	Q	+	3	2	USP5	6838925	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.041000	0.49807	2.793000	0.96121	0.655000	0.94253	CAG	.	.		0.527	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1		
AICDA	57379	hgsc.bcm.edu	37	12	8759503	8759503	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:8759503A>G	ENST00000229335.6	-	2	217	c.114T>C	c.(112-114)agT>agC	p.S38S	AICDA_ENST00000537228.1_Silent_p.S38S	NM_020661.2	NP_065712.1	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	38					B cell differentiation (GO:0030183)|cellular response to lipopolysaccharide (GO:0071222)|DNA demethylation (GO:0080111)|isotype switching (GO:0045190)|mRNA processing (GO:0006397)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|somatic diversification of immunoglobulins (GO:0016445)|somatic hypermutation of immunoglobulin genes (GO:0016446)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)	16	Lung SC(5;0.184)					AGGATGTAGCACTGTCACGCC	0.448																																					p.S38S	GBM(62;896 1067 5527 26594 30137)	Atlas-SNP	.											.	AICDA	37	.	0			c.T114C						.						92.0	89.0	90.0					12																	8759503		1988	4152	6140	SO:0001819	synonymous_variant	57379	exon2			TGTAGCACTGTCA	AB040430	CCDS41747.1	12p13	2014-09-17			ENSG00000111732	ENSG00000111732		"""Apolipoprotein B mRNA editing enzymes"""	13203	protein-coding gene	gene with protein product		605257					Standard	NM_020661		Approved	HIGM2, CDA2, ARP2, AID	uc001qur.2	Q9GZX7	OTTHUMG00000168676	ENST00000229335.6:c.114T>C	chr12.hg19:g.8759503A>G		71.0	0.0		57.0	4.0	NM_020661	Q6QJ81|Q8NFC1	Silent	SNP	ENST00000229335.6	hg19	CCDS41747.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.469819	0.26423	.	.	ENSG00000111732	ENST00000543081;ENST00000544516;ENST00000545512	.	.	.	5.36	-4.59	0.03400	.	.	.	.	.	T	0.63010	0.2475	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63395	-0.6647	4	.	.	.	-18.6705	14.4911	0.67651	0.4192:0.0:0.5808:0.0	.	.	.	.	A	37	.	.	V	-	2	0	AICDA	8650770	0.000000	0.05858	0.946000	0.38457	0.880000	0.50808	-2.820000	0.00749	-0.834000	0.04239	0.383000	0.25322	GTG	.	.		0.448	AICDA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400575.1	NM_020661	
PHC1	1911	hgsc.bcm.edu	37	12	9086863	9086863	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:9086863A>G	ENST00000543824.1	+	11	2374	c.2042A>G	c.(2041-2043)gAa>gGa	p.E681G	PHC1_ENST00000544916.1_Splice_Site_p.E681G|PHC1_ENST00000433083.2_Splice_Site_p.E636G|PHC1_ENST00000536844.1_Splice_Site_p.E287G			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	681					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						TGTTTTCCAGAAAAAGCTGAA	0.438																																					p.E681G		Atlas-SNP	.											.	PHC1	67	.	0			c.A2042G						.						68.0	65.0	66.0					12																	9086863		2203	4300	6503	SO:0001630	splice_region_variant	1911	exon10			TTCCAGAAAAAGC	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2042-1A>G	chr12.hg19:g.9086863A>G		58.0	0.0		84.0	4.0	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	hg19	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220598	0.39201	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.7	5.7	0.88788	.	0.215097	0.40728	N	0.001026	T	0.26738	0.0654	N	0.14661	0.345	0.42241	D	0.99193	B	0.17667	0.023	B	0.16289	0.015	T	0.10776	-1.0615	9	.	.	.	.	14.1997	0.65693	1.0:0.0:0.0:0.0	.	681	P78364	PHC1_HUMAN	G	681;681;636;681;287	ENSP00000440674:E681G;ENSP00000251757:E681G;ENSP00000399194:E636G;ENSP00000437659:E681G;ENSP00000440488:E287G	.	E	+	2	0	PHC1	8978130	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	4.639000	0.61361	2.183000	0.69458	0.533000	0.62120	GAA	.	.		0.438	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	Missense_Mutation
TAS2R43	259289	hgsc.bcm.edu	37	12	11244577	11244577	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:11244577A>G	ENST00000531678.1	-	1	335	c.252T>C	c.(250-252)gcT>gcC	p.A84A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	84					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		AGATATTATAAGCAGTAGTTC	0.378																																					p.A84A		Atlas-SNP	.											.	TAS2R43	19	.	0			c.T252C						.						52.0	45.0	48.0					12																	11244577		1879	3859	5738	SO:0001819	synonymous_variant	259289	exon1			ATTATAAGCAGTA	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.252T>C	chr12.hg19:g.11244577A>G		152.0	0.0		107.0	6.0	NM_176884	P59546|Q645X4	Silent	SNP	ENST00000531678.1	hg19	CCDS53749.1																																																																																			.	.		0.378	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
KIAA1467	57613	hgsc.bcm.edu	37	12	13238130	13238130	+	IGR	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:13238130G>A	ENST00000197268.8	+	0	4808				GSG1_ENST00000396310.2_Missense_Mutation_p.T198I|GSG1_ENST00000324458.8_Missense_Mutation_p.T265I|GSG1_ENST00000457134.2_Missense_Mutation_p.T178I|GSG1_ENST00000396302.3_Silent_p.H270H|GSG1_ENST00000537302.1_Missense_Mutation_p.T201I|GSG1_ENST00000351606.6_Silent_p.H306H|GSG1_ENST00000432710.2_Missense_Mutation_p.T242I|GSG1_ENST00000337630.6_Missense_Mutation_p.T229I	NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467							integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		CGTGTTGAAGGTGGTGACAGC	0.493																																					p.T265I		Atlas-SNP	.											.	GSG1	62	.	0			c.C794T						.						93.0	64.0	74.0					12																	13238130		2203	4300	6503	SO:0001628	intergenic_variant	83445	exon7			TTGAAGGTGGTGA	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67			chr12.hg19:g.13238130G>A		172.0	0.0		99.0	4.0	NM_001080555	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	hg19	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983277	0.93044	.	.	ENSG00000111305	ENST00000337630;ENST00000324458;ENST00000396310;ENST00000457134;ENST00000432710;ENST00000537302	T;T;T;T;T;T	0.43294	0.98;0.97;0.98;1.0;0.95;0.98	5.66	5.66	0.87406	.	0.187618	0.32120	U	0.006558	T	0.71533	0.3351	M	0.86651	2.83	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.998	D;D;D;D;D	0.83275	0.995;0.996;0.955;0.974;0.987	T	0.76085	-0.3088	10	0.87932	D	0	.	19.7398	0.96223	0.0:0.0:1.0:0.0	.	242;252;178;201;229	Q2KHT4-6;Q2KHT4;Q2KHT4-5;Q2KHT4-2;F1T0A1	.;GSG1_HUMAN;.;.;.	I	229;265;198;178;242;201	ENSP00000336816:T229I;ENSP00000320838:T265I;ENSP00000379604:T198I;ENSP00000398384:T178I;ENSP00000405032:T242I;ENSP00000441718:T201I	ENSP00000320838:T265I	T	-	2	0	GSG1	13129397	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.980000	0.88113	2.665000	0.90641	0.561000	0.74099	ACC	.	.		0.493	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19489449	19489449	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:19489449G>T	ENST00000299275.6	+	16	2146	c.2140G>T	c.(2140-2142)Gaa>Taa	p.E714*	PLEKHA5_ENST00000429027.2_Splice_Site_p.E817*|PLEKHA5_ENST00000355397.3_Splice_Site_p.E772*|PLEKHA5_ENST00000317589.4_Splice_Site_p.E714*|PLEKHA5_ENST00000539256.1_Splice_Site_p.E472*|PLEKHA5_ENST00000538714.1_Splice_Site_p.E772*|PLEKHA5_ENST00000359180.3_Splice_Site_p.E714*|PLEKHA5_ENST00000424268.1_Splice_Site_p.E645*|PLEKHA5_ENST00000543806.1_Splice_Site_p.E633*	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	714					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTGGTTTTAGGAATTGGAACG	0.353																																					p.E817X	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.G2449T						.						90.0	93.0	92.0					12																	19489449		2203	4300	6503	SO:0001630	splice_region_variant	54477	exon21			TTTTAGGAATTGG	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2140-1G>T	chr12.hg19:g.19489449G>T		72.0	0.0		87.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Nonsense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428455	0.83667	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.8883	17.4031	0.87466	0.0:0.0:1.0:0.0	.	.	.	.	X	714;772;714;818;817;714;472;772;645;633;606;51	.	.	E	+	1	0	PLEKHA5	19380716	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.667000	0.74451	2.204000	0.70986	0.467000	0.42956	GAA	.	.		0.353	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	Nonsense_Mutation
PDE3A	5139	hgsc.bcm.edu	37	12	20769196	20769196	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:20769196G>T	ENST00000359062.3	+	4	1342	c.1302G>T	c.(1300-1302)ttG>ttT	p.L434F	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	434					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CTGGCTTGTTGAGACGAGTTT	0.473																																					p.L434F		Atlas-SNP	.											PDE3A,lower_third,carcinoma,0,1	PDE3A	184	.	0			c.G1302T						.						115.0	109.0	111.0					12																	20769196		2203	4300	6503	SO:0001583	missense	5139	exon4			CTTGTTGAGACGA		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1302G>T	chr12.hg19:g.20769196G>T	ENSP00000351957:p.Leu434Phe	49.0	0.0		39.0	3.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896170	0.72639	.	.	ENSG00000172572	ENST00000359062	T	0.55234	0.53	5.43	3.61	0.41365	.	2.081570	0.02009	N	0.046881	T	0.74313	0.3700	M	0.70595	2.14	0.45227	D	0.998231	D	0.76494	0.999	D	0.87578	0.998	T	0.50389	-0.8834	10	0.72032	D	0.01	.	10.16	0.42847	0.2144:0.0:0.7856:0.0	.	434	Q14432	PDE3A_HUMAN	F	434	ENSP00000351957:L434F	ENSP00000351957:L434F	L	+	3	2	PDE3A	20660463	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.758000	0.26447	0.782000	0.33613	0.655000	0.94253	TTG	.	.		0.473	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
ABCC9	10060	hgsc.bcm.edu	37	12	21962812	21962812	+	Missense_Mutation	SNP	A	A	G	rs144125604		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:21962812A>G	ENST00000261201.4	-	35	4288	c.4289T>C	c.(4288-4290)aTg>aCg	p.M1430T	ABCC9_ENST00000345162.2_Missense_Mutation_p.M1394T|ABCC9_ENST00000261200.4_Missense_Mutation_p.M1430T	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1430	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	AGATTTGACCATATTCTTCAG	0.333																																					p.M1430T		Atlas-SNP	.											.	ABCC9	411	.	0			c.T4289C						.	A	THR/MET,THR/MET	0,4406		0,0,2203	97.0	100.0	99.0		4289,4289	5.3	1.0	12	dbSNP_134	99	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	ABCC9	NM_005691.2,NM_020297.2	81,81	0,1,6501	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	1430/1550,1430/1550	21962812	1,13003	2203	4299	6502	SO:0001583	missense	10060	exon35			TTGACCATATTCT	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4289T>C	chr12.hg19:g.21962812A>G	ENSP00000261201:p.Met1430Thr	60.0	0.0		45.0	4.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636999	0.47049	0.0	1.16E-4	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.29	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.039691	0.85682	D	0.000000	T	0.80899	0.4712	N	0.05031	-0.125	0.58432	D	0.999998	B;B	0.14012	0.004;0.009	B;B	0.20384	0.029;0.013	T	0.76353	-0.2990	10	0.35671	T	0.21	-18.5984	13.954	0.64135	1.0:0.0:0.0:0.0	.	1430;1430	O60706;O60706-2	ABCC9_HUMAN;.	T	1430;1057;1430;1394	ENSP00000261200:M1430T;ENSP00000440521:M1057T;ENSP00000261201:M1430T;ENSP00000261202:M1394T	ENSP00000261200:M1430T	M	-	2	0	ABCC9	21854079	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.688000	0.91260	2.213000	0.71641	0.528000	0.53228	ATG	.	A|1.000;G|0.000		0.333	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	
ITPR2	3709	hgsc.bcm.edu	37	12	26732975	26732975	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:26732975A>T	ENST00000381340.3	-	33	4910	c.4494T>A	c.(4492-4494)aaT>aaA	p.N1498K		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1498					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGCTGGTACTATTGTCTGAAA	0.373																																					p.N1498K		Atlas-SNP	.											.	ITPR2	270	.	0			c.T4494A						.						111.0	100.0	103.0					12																	26732975		1809	4071	5880	SO:0001583	missense	3709	exon33			GGTACTATTGTCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4494T>A	chr12.hg19:g.26732975A>T	ENSP00000370744:p.Asn1498Lys	99.0	0.0		124.0	5.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074147	0.36566	.	.	ENSG00000123104	ENST00000381340	T	0.68331	-0.32	5.17	3.18	0.36537	.	0.042649	0.85682	D	0.000000	T	0.65112	0.2660	M	0.63428	1.95	0.80722	D	1	B	0.27117	0.168	B	0.38842	0.283	T	0.62779	-0.6782	10	0.37606	T	0.19	.	8.009	0.30342	0.0738:0.0:0.6515:0.2747	.	1498	Q14571	ITPR2_HUMAN	K	1498	ENSP00000370744:N1498K	ENSP00000370744:N1498K	N	-	3	2	ITPR2	26624242	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.719000	0.25881	1.394000	0.46624	-0.177000	0.13119	AAT	.	.		0.373	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
STK38L	23012	hgsc.bcm.edu	37	12	27475143	27475143	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:27475143C>T	ENST00000389032.3	+	13	1412	c.1243C>T	c.(1243-1245)Cct>Tct	p.P415S	STK38L_ENST00000539577.1_Missense_Mutation_p.P322S	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TGATGACTTCCCTGAATCTGA	0.328																																					p.P415S		Atlas-SNP	.											.	STK38L	44	.	0			c.C1243T						.						103.0	116.0	112.0					12																	27475143		2203	4299	6502	SO:0001583	missense	23012	exon13			GACTTCCCTGAAT	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.1243C>T	chr12.hg19:g.27475143C>T	ENSP00000373684:p.Pro415Ser	75.0	0.0		58.0	5.0	NM_015000		Missense_Mutation	SNP	ENST00000389032.3	hg19	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509477	0.64522	.	.	ENSG00000211455	ENST00000389032;ENST00000539577	T;T	0.56941	0.43;0.43	4.98	4.98	0.66077	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	M	0.71871	2.18	0.80722	D	1	D;D	0.67145	0.996;0.988	D;P	0.68039	0.955;0.904	T	0.74990	-0.3475	10	0.66056	D	0.02	.	18.6314	0.91361	0.0:1.0:0.0:0.0	.	322;415	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	S	415;322	ENSP00000373684:P415S;ENSP00000446386:P322S	ENSP00000373684:P415S	P	+	1	0	STK38L	27366410	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	5.671000	0.68095	2.477000	0.83638	0.305000	0.20034	CCT	.	.		0.328	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	
SLC2A13	114134	hgsc.bcm.edu	37	12	40158289	40158289	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:40158289G>A	ENST00000280871.4	-	9	1743	c.1693C>T	c.(1693-1695)Cac>Tac	p.H565Y		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	565					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				TCTGCTGTGTGTAAAAATGTT	0.289										HNSCC(50;0.14)																											p.H565Y		Atlas-SNP	.											.	SLC2A13	91	.	0			c.C1693T						.						86.0	86.0	86.0					12																	40158289		2203	4300	6503	SO:0001583	missense	114134	exon9			CTGTGTGTAAAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"""Solute carriers"""	15956	protein-coding gene	gene with protein product	"""H(+)-myo-inositol symporter"""	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1693C>T	chr12.hg19:g.40158289G>A	ENSP00000280871:p.His565Tyr	158.0	0.0		89.0	4.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.545889	0.86022	.	.	ENSG00000151229	ENST00000280871	T	0.72394	-0.65	5.63	5.63	0.86233	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.53916	0.1826	N	0.10707	0.03	0.80722	D	1	D	0.60160	0.987	B	0.41723	0.365	T	0.58042	-0.7706	10	0.29301	T	0.29	-23.9392	19.6978	0.96034	0.0:0.0:1.0:0.0	.	565	Q96QE2	MYCT_HUMAN	Y	565	ENSP00000280871:H565Y	ENSP00000280871:H565Y	H	-	1	0	SLC2A13	38444556	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.389000	0.97243	2.649000	0.89929	0.650000	0.86243	CAC	.	.		0.289	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2		
ANO6	196527	hgsc.bcm.edu	37	12	45742051	45742051	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:45742051A>T	ENST00000320560.8	+	5	788	c.586A>T	c.(586-588)Ata>Tta	p.I196L	ANO6_ENST00000425752.2_Missense_Mutation_p.I196L|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.I178L|ANO6_ENST00000423947.3_Missense_Mutation_p.I217L|ANO6_ENST00000435642.1_Missense_Mutation_p.I196L	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	196					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TGATTTTTACATAGTTGATAG	0.423																																					p.I217L		Atlas-SNP	.											.	ANO6	163	.	0			c.A649T						.						115.0	117.0	116.0					12																	45742051		2203	4300	6503	SO:0001583	missense	196527	exon6			TTTTACATAGTTG	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.586A>T	chr12.hg19:g.45742051A>T	ENSP00000320087:p.Ile196Leu	275.0	0.0		213.0	16.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793353	0.50102	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47	5.3	5.3	0.74995	.	0.109289	0.64402	D	0.000009	T	0.62171	0.2406	L	0.45352	1.415	0.48040	D	0.999571	B;B;B;B	0.33022	0.394;0.013;0.019;0.013	B;B;B;B	0.31245	0.126;0.022;0.017;0.026	T	0.59359	-0.7469	10	0.17832	T	0.49	.	15.9619	0.79936	1.0:0.0:0.0:0.0	.	178;217;196;196	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	L	196;217;196;196;178	ENSP00000391417:I196L;ENSP00000409126:I217L;ENSP00000413840:I196L;ENSP00000320087:I196L;ENSP00000413137:I178L	ENSP00000320087:I196L	I	+	1	0	ANO6	44028318	1.000000	0.71417	0.919000	0.36401	0.787000	0.44495	4.247000	0.58750	2.308000	0.77769	0.533000	0.62120	ATA	.	.		0.423	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	
SENP1	29843	hgsc.bcm.edu	37	12	48491823	48491823	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:48491823G>A	ENST00000004980.5	-	3	567	c.89C>T	c.(88-90)cCa>cTa	p.P30L	SENP1_ENST00000549595.1_Missense_Mutation_p.P30L|SENP1_ENST00000547886.1_5'Flank|SENP1_ENST00000551330.1_Missense_Mutation_p.P30L|SENP1_ENST00000448372.1_Missense_Mutation_p.P30L|SENP1_ENST00000549518.1_Missense_Mutation_p.P30L|SENP1_ENST00000339976.6_Missense_Mutation_p.P62L			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	30					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				ACCTGTTTGTGGCAGGAGGTG	0.433																																					p.P30L		Atlas-SNP	.											.	SENP1	44	.	0			c.C89T						.						83.0	93.0	90.0					12																	48491823		1880	4109	5989	SO:0001583	missense	29843	exon3			GTTTGTGGCAGGA	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.89C>T	chr12.hg19:g.48491823G>A	ENSP00000004980:p.Pro30Leu	106.0	0.0		73.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040593	0.35989	.	.	ENSG00000079387	ENST00000004980;ENST00000339976;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	4.69	1.74	0.24563	.	1.314310	0.05034	N	0.475024	T	0.14657	0.0354	N	0.19112	0.55	0.30326	N	0.787074	B;B	0.11235	0.002;0.004	B;B	0.13407	0.004;0.009	T	0.33979	-0.9847	10	0.56958	D	0.05	3.0118	12.1929	0.54280	0.0:0.0:0.3573:0.6427	.	30;30	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	L	30;62;30;30;30;30;23	ENSP00000004980:P30L;ENSP00000394791:P30L;ENSP00000446681:P30L;ENSP00000450076:P30L;ENSP00000447328:P30L	ENSP00000004980:P30L	P	-	2	0	SENP1	46778090	1.000000	0.71417	0.946000	0.38457	0.795000	0.44927	0.748000	0.26305	0.393000	0.25203	-0.274000	0.10170	CCA	.	.		0.433	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
SENP1	29843	hgsc.bcm.edu	37	12	48491866	48491866	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:48491866T>C	ENST00000004980.5	-	3	524	c.46A>G	c.(46-48)Act>Gct	p.T16A	SENP1_ENST00000549595.1_Missense_Mutation_p.T16A|SENP1_ENST00000547886.1_5'Flank|SENP1_ENST00000551330.1_Missense_Mutation_p.T16A|SENP1_ENST00000448372.1_Missense_Mutation_p.T16A|SENP1_ENST00000549518.1_Missense_Mutation_p.T16A|SENP1_ENST00000339976.6_Missense_Mutation_p.T48A			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	16					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TTCACTAAAGTCACTTCTCCA	0.443																																					p.T16A		Atlas-SNP	.											.	SENP1	44	.	0			c.A46G						.						95.0	102.0	99.0					12																	48491866		1934	4143	6077	SO:0001583	missense	29843	exon3			CTAAAGTCACTTC	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.46A>G	chr12.hg19:g.48491866T>C	ENSP00000004980:p.Thr16Ala	117.0	0.0		81.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	T	16.27	3.074817	0.55646	.	.	ENSG00000079387	ENST00000004980;ENST00000339976;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000005	T	0.11110	0.0271	N	0.19112	0.55	0.20703	N	0.999865	B;B	0.25007	0.071;0.116	B;B	0.26969	0.034;0.075	T	0.15065	-1.0450	10	0.52906	T	0.07	-12.3831	7.7073	0.28657	0.0:0.092:0.0:0.908	.	16;16	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	A	16;48;16;16;16;16;9	ENSP00000004980:T16A;ENSP00000394791:T16A;ENSP00000446681:T16A;ENSP00000450076:T16A;ENSP00000447328:T16A	ENSP00000004980:T16A	T	-	1	0	SENP1	46778133	0.958000	0.32768	0.973000	0.42090	0.992000	0.81027	1.176000	0.31957	2.272000	0.75746	0.460000	0.39030	ACT	.	.		0.443	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
CACNB3	784	hgsc.bcm.edu	37	12	49221409	49221409	+	Silent	SNP	C	C	T	rs191174951	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:49221409C>T	ENST00000301050.2	+	13	1381	c.1182C>T	c.(1180-1182)ccC>ccT	p.P394P	CACNB3_ENST00000540990.1_Silent_p.P381P|CACNB3_ENST00000547230.1_Silent_p.P353P|CACNB3_ENST00000547392.1_Silent_p.P367P|CACNB3_ENST00000536187.2_Silent_p.P393P	NM_000725.3	NP_000716.2	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3 subunit	394					axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1)	12					Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCACTCCCCCCTTGAGCGGG	0.632																																					p.P394P		Atlas-SNP	.											.	CACNB3	51	.	0			c.C1182T						.																																			SO:0001819	synonymous_variant	784	exon13			CTCCCCCCTTGAG		CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1	12q13	2008-05-02				ENSG00000167535		"""Calcium channel subunits"""	1403	protein-coding gene	gene with protein product		601958		CACNLB3		8119293	Standard	NM_000725		Approved		uc010sly.2	P54284		ENST00000301050.2:c.1182C>T	chr12.hg19:g.49221409C>T		91.0	0.0		51.0	4.0	NM_000725	A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913	Silent	SNP	ENST00000301050.2	hg19	CCDS8769.1																																																																																			.	C|1.000;A|0.000		0.632	CACNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408886.1		
SPATS2	65244	hgsc.bcm.edu	37	12	49854820	49854820	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:49854820G>T	ENST00000553127.1	+	4	538	c.25G>T	c.(25-27)Gat>Tat	p.D9Y	SPATS2_ENST00000552918.1_Splice_Site_p.D9Y|SPATS2_ENST00000547865.1_Splice_Site_p.G9*|SPATS2_ENST00000321898.6_Splice_Site_p.D9Y			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	9						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						GAACCAGAAGGGTAAGATTAC	0.338																																					p.D9Y		Atlas-SNP	.											.	SPATS2	43	.	0			c.G25T						.						103.0	102.0	102.0					12																	49854820		2203	4300	6503	SO:0001630	splice_region_variant	65244	exon3			CAGAAGGGTAAGA	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.25+1G>T	chr12.hg19:g.49854820G>T		272.0	0.0		211.0	9.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	hg19	CCDS31794.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.583770|6.583770	0.97684|0.97684	.|.	.|.	ENSG00000123352|ENSG00000123352	ENST00000550997;ENST00000549538;ENST00000550643;ENST00000548710;ENST00000549298;ENST00000553127;ENST00000321898;ENST00000551540;ENST00000552918;ENST00000548777;ENST00000552171|ENST00000547865	.|.	.|.	.|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.70378|.	0.3217|.	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.09377|.	0.004|.	T|.	0.71859|.	-0.4465|.	9|.	0.87932|0.87932	D|D	0|0	-10.8084|-10.8084	15.6543|15.6543	0.77121|0.77121	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	9|.	Q86XZ4|.	SPAS2_HUMAN|.	Y|X	9|9	.|.	ENSP00000326841:D9Y|ENSP00000449615:G9X	D|G	+|+	1|1	0|0	SPATS2|SPATS2	48141087|48141087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	4.219000|4.219000	0.58561|0.58561	2.767000|2.767000	0.95098|0.95098	0.563000|0.563000	0.77884|0.77884	GAT|GGA	.	.		0.338	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071	Missense_Mutation
LARP4	113251	hgsc.bcm.edu	37	12	50822725	50822725	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:50822725A>G	ENST00000398473.2	+	3	286	c.174A>G	c.(172-174)gcA>gcG	p.A58A	LARP4_ENST00000293618.8_Silent_p.A58A|LARP4_ENST00000429001.3_Silent_p.A64A|LARP4_ENST00000518561.1_5'UTR|LARP4_ENST00000522085.1_Silent_p.A58A|LARP4_ENST00000347328.5_Silent_p.A58A|LARP4_ENST00000518444.1_Silent_p.A57A	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	58					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						CAGGTAATGCAGAGCTCTCAG	0.328																																					p.A58A		Atlas-SNP	.											.	LARP4	58	.	0			c.A174G						.						68.0	65.0	66.0					12																	50822725		1813	4064	5877	SO:0001819	synonymous_variant	113251	exon3			TAATGCAGAGCTC	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.174A>G	chr12.hg19:g.50822725A>G		85.0	0.0		86.0	4.0	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.		0.328	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
KRT75	9119	hgsc.bcm.edu	37	12	52826983	52826983	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:52826983C>A	ENST00000252245.5	-	2	772	c.552G>T	c.(550-552)ctG>ctT	p.L184L		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	184	Coil 1A.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CCTGCTCCTGCAGGAGGGCCC	0.562																																					p.L184L		Atlas-SNP	.											.	KRT75	75	.	0			c.G552T						.						77.0	79.0	79.0					12																	52826983		2203	4300	6503	SO:0001819	synonymous_variant	9119	exon2			CTCCTGCAGGAGG	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.552G>T	chr12.hg19:g.52826983C>A		100.0	0.0		69.0	4.0	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	hg19	CCDS8827.1																																																																																			.	.		0.562	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
KRT79	338785	hgsc.bcm.edu	37	12	53217754	53217754	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:53217754G>T	ENST00000330553.5	-	6	1097	c.1063C>A	c.(1063-1065)Ctg>Atg	p.L355M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	355	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTGTCCCGCAGGTTGTCCCCA	0.602																																					p.L355M		Atlas-SNP	.											.	KRT79	78	.	0			c.C1063A						.						87.0	68.0	74.0					12																	53217754		2203	4300	6503	SO:0001583	missense	338785	exon6			CCCGCAGGTTGTC	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1063C>A	chr12.hg19:g.53217754G>T	ENSP00000328358:p.Leu355Met	140.0	0.0		87.0	4.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252877	0.59212	.	.	ENSG00000185640	ENST00000330553	D	0.81908	-1.55	3.9	2.07	0.26955	Filament (1);	0.000000	0.37530	N	0.002059	D	0.89715	0.6795	M	0.84219	2.685	0.37103	D	0.900001	D	0.89917	1.0	D	0.81914	0.995	D	0.90586	0.4533	10	0.87932	D	0	.	9.6816	0.40074	0.1773:0.0:0.8227:0.0	.	355	Q5XKE5	K2C79_HUMAN	M	355	ENSP00000328358:L355M	ENSP00000328358:L355M	L	-	1	2	KRT79	51504021	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.123000	0.77176	0.611000	0.30052	-0.350000	0.07774	CTG	.	.		0.602	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
AAAS	8086	hgsc.bcm.edu	37	12	53701649	53701649	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:53701649T>C	ENST00000209873.4	-	15	1561	c.1396A>G	c.(1396-1398)Aaa>Gaa	p.K466E	AAAS_ENST00000549983.1_5'Flank|AAAS_ENST00000394384.3_Missense_Mutation_p.K433E|AAAS_ENST00000550286.1_Missense_Mutation_p.K342E	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	466					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						AGGGCCCCTTTGTTGAAGGAA	0.597																																					p.K466E		Atlas-SNP	.											.	AAAS	46	.	0			c.A1396G						.						72.0	73.0	73.0					12																	53701649		2203	4300	6503	SO:0001583	missense	8086	exon15			CCCCTTTGTTGAA	AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"""WD repeat domain containing"""	13666	protein-coding gene	gene with protein product	"""aladin"", ""Allgrove, triple-A"""	605378	"""achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"""			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.1396A>G	chr12.hg19:g.53701649T>C	ENSP00000209873:p.Lys466Glu	101.0	0.0		100.0	4.0	NM_015665	Q5JB47|Q9NWI6|Q9UG19	Missense_Mutation	SNP	ENST00000209873.4	hg19	CCDS8856.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.974536	0.53720	.	.	ENSG00000094914	ENST00000209873;ENST00000394384;ENST00000550286	D;D;D	0.95690	-3.78;-3.78;-3.78	4.54	4.54	0.55810	.	0.100290	0.64402	D	0.000002	D	0.88837	0.6545	N	0.14661	0.345	0.39203	D	0.963188	D;B	0.53151	0.958;0.231	B;B	0.44224	0.444;0.039	D	0.87097	0.2176	10	0.10902	T	0.67	-19.0471	10.4798	0.44687	0.0:0.0:0.0:1.0	.	433;466	Q5JB47;Q9NRG9	.;AAAS_HUMAN	E	466;433;342	ENSP00000209873:K466E;ENSP00000377908:K433E;ENSP00000446885:K342E	ENSP00000209873:K466E	K	-	1	0	AAAS	51987916	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.743000	0.55104	2.054000	0.61138	0.533000	0.62120	AAA	.	.		0.597	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405632.1		
NFE2	4778	hgsc.bcm.edu	37	12	54686181	54686181	+	Missense_Mutation	SNP	T	T	C	rs373651500		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:54686181T>C	ENST00000540264.2	-	2	1608	c.1099A>G	c.(1099-1101)Acc>Gcc	p.T367A	NFE2_ENST00000553070.1_Missense_Mutation_p.T367A|RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000435572.2_Missense_Mutation_p.T367A|NFE2_ENST00000312156.4_Missense_Mutation_p.T367A			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	367					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						TCCATCTTGGTCCCCCGGGGC	0.567																																					p.T367A		Atlas-SNP	.											.	NFE2	28	.	0			c.A1099G						.						55.0	52.0	53.0					12																	54686181		2203	4300	6503	SO:0001583	missense	4778	exon4			TCTTGGTCCCCCG	BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"""basic leucine zipper proteins"""	7780	protein-coding gene	gene with protein product		601490	"""nuclear factor (erythroid-derived 2), 45kD"", ""nuclear factor (erythroid-derived 2), 45kDa"""			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.1099A>G	chr12.hg19:g.54686181T>C	ENSP00000439120:p.Thr367Ala	130.0	0.0		121.0	5.0	NM_001261461	Q07720|Q6ICV9	Missense_Mutation	SNP	ENST00000540264.2	hg19	CCDS8876.1	.	.	.	.	.	.	.	.	.	.	t	12.20	1.866560	0.32977	.	.	ENSG00000123405	ENST00000312156;ENST00000435572;ENST00000540264;ENST00000553070	.	.	.	5.27	-6.02	0.02192	.	1.192680	0.06002	N	0.647924	T	0.21718	0.0523	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17592	-1.0364	9	0.36615	T	0.2	-0.6578	2.1584	0.03819	0.105:0.2082:0.3223:0.3645	.	367	Q16621	NFE2_HUMAN	A	367	.	ENSP00000312436:T367A	T	-	1	0	NFE2	52972448	0.000000	0.05858	0.011000	0.14972	0.976000	0.68499	-0.150000	0.10189	-0.814000	0.04352	-1.060000	0.02296	ACC	.	.		0.567	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163	
GPR84	53831	hgsc.bcm.edu	37	12	54757304	54757304	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:54757304A>G	ENST00000551809.1	-	1	967	c.332T>C	c.(331-333)cTc>cCc	p.L111P	RP11-753H16.3_ENST00000550474.1_RNA|GPR84_ENST00000267015.3_Missense_Mutation_p.L111P|RP11-753H16.5_ENST00000552785.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						GATGAGGCAGAGGGTCAGGAT	0.577																																					p.L111P		Atlas-SNP	.											.	GPR84	38	.	0			c.T332C						.						94.0	85.0	88.0					12																	54757304		2203	4300	6503	SO:0001583	missense	53831	exon2			AGGCAGAGGGTCA	AF237762	CCDS8878.1	12q13.13	2012-08-20						"""GPCR / Class A : Fatty acid receptors"""	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.332T>C	chr12.hg19:g.54757304A>G	ENSP00000450310:p.Leu111Pro	96.0	0.0		98.0	4.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928176	0.73327	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	D;D	0.81659	-1.52;-1.52	5.21	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000071	D	0.91226	0.7235	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92965	0.6392	10	0.87932	D	0	-17.6368	13.3521	0.60607	1.0:0.0:0.0:0.0	.	111	Q9NQS5	GPR84_HUMAN	P	111	ENSP00000267015:L111P;ENSP00000450310:L111P	ENSP00000267015:L111P	L	-	2	0	GPR84	53043571	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.700000	0.74619	2.104000	0.64026	0.454000	0.30748	CTC	.	.		0.577	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1		
OR6C4	341418	hgsc.bcm.edu	37	12	55945361	55945361	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:55945361T>C	ENST00000394256.2	+	1	379	c.351T>C	c.(349-351)tcT>tcC	p.S117S	RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						CCTCCATGTCTTATGATCGTT	0.443																																					p.S117S		Atlas-SNP	.											.	OR6C4	34	.	0			c.T351C						.						99.0	102.0	101.0					12																	55945361		2203	4300	6503	SO:0001819	synonymous_variant	341418	exon1			CATGTCTTATGAT	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.351T>C	chr12.hg19:g.55945361T>C		137.0	0.0		120.0	6.0	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Silent	SNP	ENST00000394256.2	hg19	CCDS31827.1																																																																																			.	.		0.443	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
DNAJC14	85406	hgsc.bcm.edu	37	12	56221087	56221087	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56221087G>T	ENST00000357606.3	-	3	1645	c.1356C>A	c.(1354-1356)gcC>gcA	p.A452A	DNAJC14_ENST00000317269.3_Silent_p.A452A|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.H82N|DNAJC14_ENST00000317287.5_Silent_p.A452A|TMEM198B_ENST00000478241.1_RNA			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	452	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						CTGATGCTGTGGCCTCAACCC	0.502																																					p.A452A		Atlas-SNP	.											.	DNAJC14	52	.	0			c.C1356A						.						193.0	174.0	181.0					12																	56221087		2203	4300	6503	SO:0001819	synonymous_variant	85406	exon2			TGCTGTGGCCTCA	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"""Heat shock proteins / DNAJ (HSP40)"""	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1356C>A	chr12.hg19:g.56221087G>T		111.0	0.0		83.0	4.0	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Silent	SNP	ENST00000357606.3	hg19	CCDS8894.1	.	.	.	.	.	.	.	.	.	.	G	6.381	0.438489	0.12104	.	.	ENSG00000257390	ENST00000546837	.	.	.	4.7	2.73	0.32206	.	.	.	.	.	T	0.47173	0.1431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31971	-0.9924	4	.	.	.	-1.7081	4.1991	0.10457	0.2291:0.1879:0.5829:0.0	.	.	.	.	N	82	.	.	H	-	1	0	RP11-762I7.5	54507354	0.998000	0.40836	1.000000	0.80357	0.931000	0.56810	0.515000	0.22801	0.611000	0.30052	-0.367000	0.07326	CAC	.	.		0.502	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364	
MMP19	4327	hgsc.bcm.edu	37	12	56234506	56234506	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56234506G>T	ENST00000322569.4	-	4	556	c.465C>A	c.(463-465)cgC>cgA	p.R155R	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000548629.1_Silent_p.R132R|MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000409200.3_Silent_p.R155R	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	155					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	GGAAGGAGAGGCGGATGTCAG	0.577																																					p.R155R		Atlas-SNP	.											.	MMP19	61	.	0			c.C465A						.						89.0	87.0	88.0					12																	56234506		2203	4300	6503	SO:0001819	synonymous_variant	4327	exon4			GGAGAGGCGGATG	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.465C>A	chr12.hg19:g.56234506G>T		98.0	0.0		89.0	4.0	NM_001272101	B4E030|O15278|O95606|Q99580	Silent	SNP	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.577	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	
ERBB3	2065	hgsc.bcm.edu	37	12	56487950	56487950	+	Missense_Mutation	SNP	G	G	T	rs202048840		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56487950G>T	ENST00000267101.3	+	14	2121	c.1681G>T	c.(1681-1683)Ggc>Tgc	p.G561C	ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Missense_Mutation_p.G502C|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	561					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			ACCCATGGAGGGCACTGCCAC	0.562																																					p.G561C		Atlas-SNP	.											.	ERBB3	350	.	0			c.G1681T						.						65.0	63.0	63.0					12																	56487950		2203	4300	6503	SO:0001583	missense	2065	exon14			ATGGAGGGCACTG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1681G>T	chr12.hg19:g.56487950G>T	ENSP00000267101:p.Gly561Cys	68.0	0.0		52.0	4.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586656	0.86851	.	.	ENSG00000065361	ENST00000267101;ENST00000415288	T;T	0.45276	0.9;0.9	5.48	5.48	0.80851	Growth factor, receptor (1);	0.000000	0.64402	D	0.000004	T	0.67970	0.2950	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.968;0.995	T	0.72171	-0.4371	10	0.87932	D	0	.	18.1181	0.89563	0.0:0.0:1.0:0.0	.	502;561	P21860-4;P21860	.;ERBB3_HUMAN	C	561;502	ENSP00000267101:G561C;ENSP00000408340:G502C	ENSP00000267101:G561C	G	+	1	0	ERBB3	54774217	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	5.651000	0.67951	2.570000	0.86706	0.561000	0.74099	GGC	.	G|0.999;A|0.001		0.562	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
LRP1	4035	hgsc.bcm.edu	37	12	57573622	57573622	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57573622C>G	ENST00000243077.3	+	30	5490	c.5024C>G	c.(5023-5025)aCa>aGa	p.T1675R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1675					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)	CTGTTCTGGACAAGCTATGAC	0.587																																					p.T1675R		Atlas-SNP	.											.	LRP1	428	.	0			c.C5024G						.						127.0	128.0	127.0					12																	57573622		2203	4300	6503	SO:0001583	missense	4035	exon30			TCTGGACAAGCTA	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.5024C>G	chr12.hg19:g.57573622C>G	ENSP00000243077:p.Thr1675Arg	89.0	0.0		72.0	16.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.020624	0.54576	.	.	ENSG00000123384	ENST00000243077	D	0.92446	-3.04	4.57	4.57	0.56435	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.96867	0.8977	M	0.93106	3.38	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	D	0.97868	1.0284	10	0.87932	D	0	.	16.2887	0.82737	0.0:1.0:0.0:0.0	.	1675	Q07954	LRP1_HUMAN	R	1675	ENSP00000243077:T1675R	ENSP00000243077:T1675R	T	+	2	0	LRP1	55859889	0.998000	0.40836	0.941000	0.38009	0.983000	0.72400	3.928000	0.56506	2.383000	0.81215	0.655000	0.94253	ACA	.	.		0.587	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
LRP1	4035	hgsc.bcm.edu	37	12	57592334	57592334	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57592334C>A	ENST00000243077.3	+	60	10023	c.9557C>A	c.(9556-9558)aCc>aAc	p.T3186N		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3186					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)	ATCGTGGACACCAAGATCACA	0.592																																					p.T3186N		Atlas-SNP	.											.	LRP1	428	.	0			c.C9557A						.						99.0	72.0	81.0					12																	57592334		2203	4300	6503	SO:0001583	missense	4035	exon60			TGGACACCAAGAT	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.9557C>A	chr12.hg19:g.57592334C>A	ENSP00000243077:p.Thr3186Asn	65.0	0.0		84.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.906710	0.52333	.	.	ENSG00000123384	ENST00000243077	D	0.95554	-3.74	4.39	4.39	0.52855	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.149041	0.44688	D	0.000432	D	0.91526	0.7324	L	0.28192	0.835	0.80722	D	1	B	0.27013	0.166	B	0.31946	0.138	D	0.88543	0.3111	10	0.20046	T	0.44	.	16.2482	0.82460	0.0:1.0:0.0:0.0	.	3186	Q07954	LRP1_HUMAN	N	3186	ENSP00000243077:T3186N	ENSP00000243077:T3186N	T	+	2	0	LRP1	55878601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.782000	0.55401	2.434000	0.82447	0.561000	0.74099	ACC	.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
SHMT2	6472	hgsc.bcm.edu	37	12	57627867	57627867	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57627867T>C	ENST00000328923.3	+	11	1813	c.1361T>C	c.(1360-1362)aTt>aCt	p.I454T	SHMT2_ENST00000449049.3_Missense_Mutation_p.I433T|SHMT2_ENST00000553474.1_Missense_Mutation_p.I433T|SHMT2_ENST00000557487.1_Missense_Mutation_p.I444T|SHMT2_ENST00000414700.3_Missense_Mutation_p.I433T|SHMT2_ENST00000393827.4_Missense_Mutation_p.I358T	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	454					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	GGGGTCAACATTGGCTTAGAG	0.567																																					p.I454T	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.T1361C						.						88.0	92.0	91.0					12																	57627867		2203	4300	6503	SO:0001583	missense	6472	exon11			TCAACATTGGCTT	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.1361T>C	chr12.hg19:g.57627867T>C	ENSP00000333667:p.Ile454Thr	98.0	0.0		94.0	5.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287601	0.80803	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000414700;ENST00000553474;ENST00000449049;ENST00000393827	T;T;T;T;T;T	0.35421	1.52;1.38;1.52;1.52;1.52;1.31	4.98	4.98	0.66077	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.67832	0.2935	M	0.93150	3.385	0.80722	D	1	P;P;D;D;D	0.76494	0.944;0.895;0.999;0.972;0.996	P;P;D;P;P	0.73380	0.696;0.652;0.98;0.778;0.894	T	0.77035	-0.2737	10	0.87932	D	0	-12.3206	12.9362	0.58316	0.0:0.0:0.0:1.0	.	463;444;358;385;454	B4DWA7;Q8N1A5;B4DLV4;B4DP88;P34897	.;.;.;.;GLYM_HUMAN	T	454;444;433;433;433;358	ENSP00000333667:I454T;ENSP00000452315:I444T;ENSP00000406881:I433T;ENSP00000452419:I433T;ENSP00000413770:I433T;ENSP00000377413:I358T	ENSP00000333667:I454T	I	+	2	0	SHMT2	55914134	0.999000	0.42202	0.588000	0.28705	0.936000	0.57629	4.989000	0.63870	2.011000	0.59026	0.533000	0.62120	ATT	.	.		0.567	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
HELB	92797	hgsc.bcm.edu	37	12	66698763	66698763	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66698763G>T	ENST00000247815.4	+	2	499	c.440G>T	c.(439-441)tGg>tTg	p.W147L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	147					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TTTTTAACATGGGTAAAGGAG	0.353																																					p.W147L		Atlas-SNP	.											.	HELB	90	.	0			c.G440T						.						75.0	74.0	74.0					12																	66698763		2203	4300	6503	SO:0001583	missense	92797	exon2			TAACATGGGTAAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.440G>T	chr12.hg19:g.66698763G>T	ENSP00000247815:p.Trp147Leu	164.0	0.0		100.0	5.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.926937	0.73327	.	.	ENSG00000127311	ENST00000247815	T	0.15372	2.43	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.40909	0.1136	M	0.68593	2.085	0.49687	D	0.999811	D	0.89917	1.0	D	0.66716	0.946	T	0.10941	-1.0608	9	.	.	.	-9.7652	18.835	0.92159	0.0:0.0:1.0:0.0	.	147	Q8NG08	HELB_HUMAN	L	147	ENSP00000247815:W147L	.	W	+	2	0	HELB	64985030	1.000000	0.71417	0.670000	0.29842	0.015000	0.08874	5.458000	0.66679	2.438000	0.82558	0.455000	0.32223	TGG	.	.		0.353	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
HELB	92797	hgsc.bcm.edu	37	12	66725244	66725244	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66725244T>C	ENST00000247815.4	+	12	3040	c.2981T>C	c.(2980-2982)aTg>aCg	p.M994T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	994					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GACCACGCCATGACAAATGAT	0.537																																					p.M994T		Atlas-SNP	.											.	HELB	90	.	0			c.T2981C						.						88.0	66.0	73.0					12																	66725244		2203	4300	6503	SO:0001583	missense	92797	exon12			ACGCCATGACAAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2981T>C	chr12.hg19:g.66725244T>C	ENSP00000247815:p.Met994Thr	81.0	0.0		85.0	4.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	T	5.190	0.220595	0.09863	.	.	ENSG00000127311	ENST00000247815	T	0.10763	2.84	4.6	-9.2	0.00682	.	2.051000	0.02191	N	0.061329	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.32534	-0.9903	9	.	.	.	1.0983	2.6293	0.04939	0.1254:0.3382:0.3622:0.1741	.	994	Q8NG08	HELB_HUMAN	T	994	ENSP00000247815:M994T	.	M	+	2	0	HELB	65011511	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.082000	0.03400	-2.008000	0.00955	-0.366000	0.07423	ATG	.	.		0.537	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
HELB	92797	hgsc.bcm.edu	37	12	66731843	66731843	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66731843C>A	ENST00000247815.4	+	13	3284	c.3225C>A	c.(3223-3225)ccC>ccA	p.P1075P		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1075					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		ATTTAATTCCCAGGCAACTTT	0.323																																					p.P1075P		Atlas-SNP	.											.	HELB	90	.	0			c.C3225A						.						68.0	72.0	70.0					12																	66731843		2203	4299	6502	SO:0001819	synonymous_variant	92797	exon13			AATTCCCAGGCAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.3225C>A	chr12.hg19:g.66731843C>A		140.0	0.0		98.0	4.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	hg19	CCDS8976.1																																																																																			.	.		0.323	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
LGR5	8549	hgsc.bcm.edu	37	12	71976289	71976289	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:71976289C>A	ENST00000266674.5	+	17	1917	c.1606C>A	c.(1606-1608)Ctt>Att	p.L536I	LGR5_ENST00000540815.2_Missense_Mutation_p.L512I|LGR5_ENST00000536515.1_Missense_Mutation_p.L464I|RP11-186F10.2_ENST00000546601.1_RNA			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	536					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						CCTGAAAGCCCTTCATTCAGT	0.443																																					p.L536I		Atlas-SNP	.											.	LGR5	103	.	0			c.C1606A						.						149.0	123.0	132.0					12																	71976289		2203	4300	6503	SO:0001583	missense	8549	exon17			AAAGCCCTTCATT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1606C>A	chr12.hg19:g.71976289C>A	ENSP00000266674:p.Leu536Ile	161.0	0.0		114.0	5.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	hg19	CCDS9000.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851439	0.51270	.	.	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	T;T;T	0.22134	1.97;1.97;1.97	5.36	4.41	0.53225	.	0.209998	0.33057	N	0.005322	T	0.20820	0.0501	L	0.47716	1.5	0.28130	N	0.93022	P;P	0.40875	0.731;0.592	B;B	0.39660	0.306;0.162	T	0.09079	-1.0691	10	0.22109	T	0.4	.	15.8484	0.78907	0.0:0.8643:0.1357:0.0	.	512;536	O75473-2;O75473	.;LGR5_HUMAN	I	536;536;464;512	ENSP00000266674:L536I;ENSP00000443033:L464I;ENSP00000441035:L512I	ENSP00000266674:L536I	L	+	1	0	LGR5	70262556	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	3.410000	0.52664	2.668000	0.90789	0.650000	0.86243	CTT	.	.		0.443	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72057219	72057219	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:72057219G>T	ENST00000378743.3	-	1	530	c.172C>A	c.(172-174)Cct>Act	p.P58T	ZFC3H1_ENST00000552037.1_Missense_Mutation_p.P58T|THAP2_ENST00000547843.1_5'Flank|THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000549407.1_5'Flank|ZFC3H1_ENST00000548100.1_Missense_Mutation_p.P58T	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	58	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P58S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GCCGAGTGAGGAGGCCTTCGC	0.632											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P58T		Atlas-SNP	.											ZFC3H1,NS,carcinoma,0,1	ZFC3H1	172	.	1	Substitution - Missense(1)	lung(1)	c.C172A						.						41.0	51.0	48.0					12																	72057219		2042	4188	6230	SO:0001583	missense	196441	exon1			AGTGAGGAGGCCT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.172C>A	chr12.hg19:g.72057219G>T	ENSP00000368017:p.Pro58Thr	70.0	0.0	1134	43.0	2.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.452917	0.63290	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.33654	1.4	4.66	4.66	0.58398	.	0.310293	0.23694	N	0.045485	T	0.27241	0.0668	N	0.14661	0.345	0.80722	D	1	P;P;P	0.44946	0.846;0.603;0.535	B;B;B	0.42738	0.396;0.396;0.151	T	0.12116	-1.0560	10	0.52906	T	0.07	.	15.8933	0.79318	0.0:0.0:1.0:0.0	.	58;58;58	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	T	58	ENSP00000368017:P58T	ENSP00000368017:P58T	P	-	1	0	ZFC3H1	70343486	0.999000	0.42202	0.995000	0.50966	0.977000	0.68977	2.343000	0.44001	2.427000	0.82271	0.455000	0.32223	CCT	.	.		0.632	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
TPH2	121278	hgsc.bcm.edu	37	12	72416258	72416258	+	Missense_Mutation	SNP	C	C	A	rs371065822		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:72416258C>A	ENST00000333850.3	+	9	1289	c.1148C>A	c.(1147-1149)tCc>tAc	p.S383Y		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	383					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CTCCTTTCCTCCATTGGAGAA	0.418																																					p.S383Y		Atlas-SNP	.											.	TPH2	81	.	0			c.C1148A						.						101.0	95.0	97.0					12																	72416258		2203	4300	6503	SO:0001583	missense	121278	exon9			TTTCCTCCATTGG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1148C>A	chr12.hg19:g.72416258C>A	ENSP00000329093:p.Ser383Tyr	111.0	0.0		74.0	4.0	NM_173353	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	hg19	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690515	0.88735	.	.	ENSG00000139287	ENST00000333850	D	0.99801	-6.81	5.98	5.98	0.97165	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99891	0.9948	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96636	0.9470	10	0.87932	D	0	-25.8637	20.452	0.99131	0.0:1.0:0.0:0.0	.	383	Q8IWU9	TPH2_HUMAN	Y	383	ENSP00000329093:S383Y	ENSP00000329093:S383Y	S	+	2	0	TPH2	70702525	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.838000	0.97847	0.591000	0.81541	TCC	.	.		0.418	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353	
CAPS2	84698	hgsc.bcm.edu	37	12	75683540	75683540	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:75683540T>C	ENST00000409445.3	-	15	1509	c.1313A>G	c.(1312-1314)aAa>aGa	p.K438R	CAPS2_ENST00000393284.3_Missense_Mutation_p.K206R|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.K356R|CAPS2_ENST00000442339.2_Missense_Mutation_p.K28R|RP11-560G2.1_ENST00000549953.1_RNA	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	438							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TTTATGTAGTTTTTCTTTTAG	0.313																																					p.K438R		Atlas-SNP	.											.	CAPS2	96	.	0			c.A1313G						.						98.0	99.0	99.0					12																	75683540		2201	4299	6500	SO:0001583	missense	84698	exon15			TGTAGTTTTTCTT	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"""EF-hand domain containing"""	16471	protein-coding gene	gene with protein product		607724	"""calcyphosphine 2"""			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1313A>G	chr12.hg19:g.75683540T>C	ENSP00000386959:p.Lys438Arg	107.0	0.0		98.0	4.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	T	12.25	1.880475	0.33255	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284;ENST00000442339	T;T;T;T	0.24908	1.91;1.88;1.88;1.83	5.58	5.58	0.84498	.	0.373187	0.26995	N	0.021444	T	0.16811	0.0404	N	0.15975	0.35	0.24863	N	0.992339	B;B;B;B;B	0.17852	0.002;0.004;0.016;0.008;0.024	B;B;B;B;B	0.29077	0.021;0.025;0.02;0.046;0.098	T	0.24512	-1.0158	10	0.16420	T	0.52	-1.8459	12.507	0.55987	0.0:0.0:0.1486:0.8513	.	28;206;174;438;356	A2RRN2;Q9BXY5-2;Q9BXY5-3;Q9BXY5;B9A061	.;.;.;CAYP2_HUMAN;.	R	356;438;174;206;28	ENSP00000386977:K356R;ENSP00000386959:K438R;ENSP00000376963:K206R;ENSP00000389633:K28R	ENSP00000367975:K174R	K	-	2	0	CAPS2	73969807	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	2.585000	0.46111	2.120000	0.65058	0.533000	0.62120	AAA	.	.		0.313	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2		
NAV3	89795	hgsc.bcm.edu	37	12	78513068	78513068	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:78513068G>T	ENST00000397909.2	+	15	3265	c.3092G>T	c.(3091-3093)gGa>gTa	p.G1031V	NAV3_ENST00000228327.6_Missense_Mutation_p.G1031V|NAV3_ENST00000536525.2_Missense_Mutation_p.G1031V|NAV3_ENST00000266692.7_Missense_Mutation_p.G1031V			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1031						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CCCCTAAAAGGATCATCTCTA	0.443										HNSCC(70;0.22)																											p.G1031V		Atlas-SNP	.											.	NAV3	506	.	0			c.G3092T						.						120.0	115.0	116.0					12																	78513068		1859	4096	5955	SO:0001583	missense	89795	exon15			TAAAAGGATCATC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3092G>T	chr12.hg19:g.78513068G>T	ENSP00000381007:p.Gly1031Val	98.0	0.0		83.0	4.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.63|19.63	3.864159|3.864159	0.71949|0.71949	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000552895	T;T;T;T|.	0.29142|.	1.58;1.58;1.58;1.58|.	6.0|6.0	5.09|5.09	0.68999|0.68999	.|.	0.000000|.	0.39341|.	U|.	0.001388|.	T|T	0.59404|0.59404	0.2191|0.2191	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	P;D;D;B|.	0.89917|.	0.895;1.0;0.998;0.328|.	B;D;P;B|.	0.74348|.	0.392;0.983;0.859;0.155|.	T|T	0.55742|0.55742	-0.8093|-0.8093	10|5	0.52906|.	T|.	0.07|.	-10.147|-10.147	17.1406|17.1406	0.86752|0.86752	0.0:0.1265:0.8735:0.0|0.0:0.1265:0.8735:0.0	.|.	1031;1031;1031;1031|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	V|S	1031|102	ENSP00000446132:G1031V;ENSP00000381007:G1031V;ENSP00000228327:G1031V;ENSP00000266692:G1031V|.	ENSP00000228327:G1031V|.	G|R	+|+	2|3	0|2	NAV3|NAV3	77037199|77037199	1.000000|1.000000	0.71417|0.71417	0.915000|0.915000	0.36163|0.36163	0.982000|0.982000	0.71751|0.71751	7.597000|7.597000	0.82733|0.82733	1.496000|1.496000	0.48567|0.48567	0.655000|0.655000	0.94253|0.94253	GGA|AGG	.	.		0.443	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
PAWR	5074	hgsc.bcm.edu	37	12	80007382	80007382	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:80007382G>T	ENST00000328827.4	-	4	1028	c.656C>A	c.(655-657)cCt>cAt	p.P219H		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	219					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						AACTGTTCTAGGTGGCTCCTG	0.289																																					p.P219H		Atlas-SNP	.											.	PAWR	14	.	0			c.C656A						.						113.0	116.0	115.0					12																	80007382		2203	4299	6502	SO:0001583	missense	5074	exon4			GTTCTAGGTGGCT	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"""prostate apoptosis response-4"""	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.656C>A	chr12.hg19:g.80007382G>T	ENSP00000328088:p.Pro219His	137.0	0.0		98.0	6.0	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	G	9.493	1.101312	0.20632	.	.	ENSG00000177425	ENST00000328827	T	0.18016	2.24	4.68	4.68	0.58851	.	1.160130	0.06516	N	0.738775	T	0.15565	0.0375	N	0.14661	0.345	0.25000	N	0.991474	P	0.36249	0.545	B	0.41236	0.351	T	0.23261	-1.0193	9	.	.	.	0.4321	13.2844	0.60235	0.0:0.0:1.0:0.0	.	219	Q96IZ0	PAWR_HUMAN	H	219	ENSP00000328088:P219H	.	P	-	2	0	PAWR	78531513	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	4.020000	0.57189	2.587000	0.87381	0.655000	0.94253	CCT	.	.		0.289	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583	
TMTC2	160335	hgsc.bcm.edu	37	12	83526015	83526015	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:83526015A>G	ENST00000321196.3	+	12	3065	c.2358A>G	c.(2356-2358)ggA>ggG	p.G786G	TMTC2_ENST00000549919.1_Silent_p.G780G	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	786					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TGAACCTGGGAGCCATTCTGC	0.498																																					p.G786G		Atlas-SNP	.											.	TMTC2	100	.	0			c.A2358G						.						97.0	87.0	91.0					12																	83526015		2203	4300	6503	SO:0001819	synonymous_variant	160335	exon12			CCTGGGAGCCATT	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2358A>G	chr12.hg19:g.83526015A>G		139.0	0.0		124.0	5.0	NM_152588	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	hg19	CCDS9025.1																																																																																			.	.		0.498	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
ATP2B1	490	hgsc.bcm.edu	37	12	90015326	90015326	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:90015326C>A	ENST00000428670.3	-	10	2043	c.1587G>T	c.(1585-1587)ttG>ttT	p.L529F	ATP2B1_ENST00000261173.2_Splice_Site_p.L529F|ATP2B1_ENST00000359142.3_Splice_Site_p.L529F|ATP2B1_ENST00000348959.3_Splice_Site_p.L529F|ATP2B1_ENST00000393164.2_Splice_Site_p.L272F			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	529					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AAAACCTTACCAATATTTTTG	0.279																																					p.L529F		Atlas-SNP	.											.	ATP2B1	191	.	0			c.G1587T						.						33.0	33.0	33.0					12																	90015326		2181	4276	6457	SO:0001630	splice_region_variant	490	exon9			CCTTACCAATATT	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1587+1G>T	chr12.hg19:g.90015326C>A		115.0	0.0		81.0	4.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.618329	0.66787	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.85	4.96	0.65561	.	0.054532	0.64402	D	0.000001	T	0.69387	0.3105	L	0.28054	0.825	0.80722	D	1	P;P;P	0.46512	0.879;0.855;0.486	B;P;B	0.53809	0.408;0.735;0.347	T	0.67715	-0.5599	9	.	.	.	-13.6016	15.0228	0.71643	0.0:0.9319:0.0:0.0681	.	529;529;529	P20020-3;P20020-2;P20020-6	.;.;.	F	529;529;529;529;272	ENSP00000261173:L529F;ENSP00000343599:L529F;ENSP00000352054:L529F;ENSP00000392043:L529F;ENSP00000376869:L272F	.	L	-	3	2	ATP2B1	88539457	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.487000	0.81328	1.487000	0.48415	0.563000	0.77884	TTG	.	.		0.279	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	Missense_Mutation
APAF1	317	hgsc.bcm.edu	37	12	99056270	99056270	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:99056270G>T	ENST00000551964.1	+	6	1483	c.747G>T	c.(745-747)tgG>tgT	p.W249C	APAF1_ENST00000357310.1_Missense_Mutation_p.W249C|APAF1_ENST00000333991.1_Missense_Mutation_p.W249C|APAF1_ENST00000552268.1_Missense_Mutation_p.W249C|APAF1_ENST00000339433.3_Missense_Mutation_p.W249C|APAF1_ENST00000550527.1_Missense_Mutation_p.W238C|APAF1_ENST00000549007.1_Missense_Mutation_p.W249C|APAF1_ENST00000547045.1_Missense_Mutation_p.W249C|APAF1_ENST00000359972.2_Missense_Mutation_p.W238C	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	249	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GGGACTCTTGGGTGTTGAAAG	0.323																																					p.W249C		Atlas-SNP	.											.	APAF1	111	.	0			c.G747T						.						118.0	114.0	115.0					12																	99056270		2203	4299	6502	SO:0001583	missense	317	exon6			CTCTTGGGTGTTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.747G>T	chr12.hg19:g.99056270G>T	ENSP00000448165:p.Trp249Cys	173.0	0.0		122.0	5.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881118	0.51801	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	5.77	5.77	0.91146	NB-ARC (1);	0.159535	0.64402	D	0.000019	D	0.87912	0.6297	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;0.999	D;D;D;D;P	0.78314	0.945;0.977;0.945;0.991;0.871	D	0.87585	0.2487	10	0.59425	D	0.04	-15.6004	19.9859	0.97351	0.0:0.0:1.0:0.0	.	249;249;238;249;238	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	C	249;238;249;249;249;249;238;249;249	ENSP00000448165:W249C;ENSP00000353059:W238C;ENSP00000349862:W249C;ENSP00000341830:W249C;ENSP00000334558:W249C;ENSP00000448826:W249C;ENSP00000448449:W238C;ENSP00000449791:W249C;ENSP00000448161:W249C	ENSP00000334558:W249C	W	+	3	0	APAF1	97580401	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.509000	0.53386	2.729000	0.93468	0.655000	0.94253	TGG	.	.		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
MYBPC1	4604	hgsc.bcm.edu	37	12	102067212	102067212	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:102067212C>T	ENST00000550270.1	+	24	2600	c.2600C>T	c.(2599-2601)cCa>cTa	p.P867L	MYBPC1_ENST00000547509.1_Missense_Mutation_p.P835L|MYBPC1_ENST00000452455.2_Missense_Mutation_p.P867L|MYBPC1_ENST00000360610.2_Missense_Mutation_p.P867L|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000361466.2_Missense_Mutation_p.P874L|MYBPC1_ENST00000545503.2_Missense_Mutation_p.P849L|MYBPC1_ENST00000541119.1_Missense_Mutation_p.P837L|MYBPC1_ENST00000549145.1_Missense_Mutation_p.P880L|MYBPC1_ENST00000392934.3_Missense_Mutation_p.P836L|MYBPC1_ENST00000361685.2_Missense_Mutation_p.P874L|MYBPC1_ENST00000441232.1_Missense_Mutation_p.P867L|MYBPC1_ENST00000536007.1_Missense_Mutation_p.P830L|MYBPC1_ENST00000553190.1_Missense_Mutation_p.P849L|MYBPC1_ENST00000547405.1_Missense_Mutation_p.P823L|MYBPC1_ENST00000551300.1_Missense_Mutation_p.P750L			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	867	Ig-like C2-type 6.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						TAGGGAAAACCAAGACCAGAA	0.343																																					p.P874L		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C2621T						.						103.0	108.0	106.0					12																	102067212		2203	4300	6503	SO:0001583	missense	4604	exon25			GAAAACCAAGACC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.2600C>T	chr12.hg19:g.102067212C>T	ENSP00000449702:p.Pro867Leu	113.0	0.0		92.0	4.0	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995554	0.93167	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	5.75	5.75	0.90469	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000140	D	0.91036	0.7180	H	0.95816	3.725	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.996;0.999;1.0;1.0;1.0;0.999;1.0	D	0.93019	0.6438	10	0.87932	D	0	.	19.9379	0.97147	0.0:1.0:0.0:0.0	.	830;837;867;849;836;823;849;867;874;874	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.	L	823;867;867;867;836;835;874;880;849;849;830;837;874;750;867	ENSP00000448175:P823L;ENSP00000400908:P867L;ENSP00000388989:P867L;ENSP00000353822:P867L;ENSP00000376665:P836L;ENSP00000447362:P835L;ENSP00000354845:P874L;ENSP00000447660:P880L;ENSP00000447900:P849L;ENSP00000440034:P849L;ENSP00000446128:P830L;ENSP00000442847:P837L;ENSP00000354849:P874L;ENSP00000447116:P750L;ENSP00000449702:P867L	ENSP00000353822:P867L	P	+	2	0	MYBPC1	100591343	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.400000	0.79949	2.710000	0.92621	0.555000	0.69702	CCA	.	.		0.343	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
KIAA1033	23325	hgsc.bcm.edu	37	12	105534742	105534742	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:105534742G>T	ENST00000332180.5	+	17	1713	c.1626G>T	c.(1624-1626)ttG>ttT	p.L542F		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTCTAGTTTTGGCTGAAAACA	0.373																																					p.L542F		Atlas-SNP	.											.	KIAA1033	83	.	0			c.G1626T						.						167.0	157.0	160.0					12																	105534742		1889	4129	6018	SO:0001583	missense	23325	exon17			AGTTTTGGCTGAA	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.1626G>T	chr12.hg19:g.105534742G>T	ENSP00000328062:p.Leu542Phe	162.0	0.0		103.0	5.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.145255	0.77888	.	.	ENSG00000136051	ENST00000332180	T	0.51325	0.71	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.68677	0.3027	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	T	0.70597	-0.4828	10	0.72032	D	0.01	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	543;542	B7ZKT9;Q2M389	.;WASH7_HUMAN	F	542	ENSP00000328062:L542F	ENSP00000328062:L542F	L	+	3	2	KIAA1033	104058872	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.275000	0.51639	2.668000	0.90789	0.650000	0.86243	TTG	.	.		0.373	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
TCP11L2	255394	hgsc.bcm.edu	37	12	106740234	106740234	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:106740234G>T	ENST00000299045.3	+	10	1660	c.1486G>T	c.(1486-1488)Gca>Tca	p.A496S		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	496										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						ACCATTTTATGCAAATATACT	0.443																																					p.A496S		Atlas-SNP	.											.	TCP11L2	59	.	0			c.G1486T						.						88.0	82.0	84.0					12																	106740234		2203	4300	6503	SO:0001583	missense	255394	exon10			TTTTATGCAAATA	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 2"", ""t-complex 11 (mouse)-like 2"""				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.1486G>T	chr12.hg19:g.106740234G>T	ENSP00000299045:p.Ala496Ser	109.0	0.0		69.0	4.0	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774837	0.49786	.	.	ENSG00000166046	ENST00000299045	T	0.11385	2.78	5.69	5.69	0.88448	.	0.108901	0.64402	D	0.000008	T	0.28200	0.0696	M	0.64170	1.965	0.80722	D	1	D	0.56521	0.976	D	0.65140	0.932	T	0.02893	-1.1097	10	0.10377	T	0.69	-13.0341	19.812	0.96551	0.0:0.0:1.0:0.0	.	496	Q8N4U5	T11L2_HUMAN	S	496	ENSP00000299045:A496S	ENSP00000299045:A496S	A	+	1	0	TCP11L2	105264364	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.423000	0.66458	2.685000	0.91497	0.655000	0.94253	GCA	.	.		0.443	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772	
RIC8B	55188	hgsc.bcm.edu	37	12	107209055	107209055	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:107209055G>T	ENST00000392839.2	+	3	820	c.714G>T	c.(712-714)acG>acT	p.T238T	RIC8B_ENST00000355478.2_Silent_p.T198T|RIC8B_ENST00000392837.4_Silent_p.T238T|RIC8B_ENST00000549643.1_Intron	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	238					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.T238T(1)		kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TCAATGTGACGGTAGACAGTT	0.473																																					p.T238T		Atlas-SNP	.											RIC8B_ENST00000355478,NS,carcinoma,0,2	RIC8B	51	.	1	Substitution - coding silent(1)	lung(1)	c.G714T						.						122.0	118.0	120.0					12																	107209055		2203	4300	6503	SO:0001819	synonymous_variant	55188	exon3			TGTGACGGTAGAC	AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"""resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"""				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.714G>T	chr12.hg19:g.107209055G>T		90.0	0.0		45.0	3.0	NM_018157	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Silent	SNP	ENST00000392839.2	hg19	CCDS9109.2																																																																																			.	.		0.473	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157	
DAO	1610	hgsc.bcm.edu	37	12	109278816	109278816	+	Missense_Mutation	SNP	G	G	T	rs373913310		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:109278816G>T	ENST00000228476.3	+	2	238	c.34G>T	c.(34-36)Ggg>Tgg	p.G12W	DAO_ENST00000551281.1_Missense_Mutation_p.G12W	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	12					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	AGGAGTCATCGGGCTGTCCAC	0.577																																					p.G12W		Atlas-SNP	.											DAO,caecum,carcinoma,0,2	DAO	58	.	0			c.G34T						.	G	TRP/GLY	0,4406		0,0,2203	154.0	115.0	128.0		34	5.4	1.0	12		128	1,8599	1.2+/-3.3	0,1,4299	no	missense	DAO	NM_001917.4	184	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	12/348	109278816	1,13005	2203	4300	6503	SO:0001583	missense	1610	exon2			GTCATCGGGCTGT	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.34G>T	chr12.hg19:g.109278816G>T	ENSP00000228476:p.Gly12Trp	54.0	0.0		86.0	4.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990236	0.74589	0.0	1.16E-4	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547166	D;D;D	0.98400	-3.55;-3.55;-4.91	5.44	5.44	0.79542	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99366	0.9777	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98614	1.0664	10	0.87932	D	0	-23.0601	17.8335	0.88689	0.0:0.0:1.0:0.0	.	12;12	P14920;Q7Z312	OXDA_HUMAN;.	W	12	ENSP00000446853:G12W;ENSP00000228476:G12W;ENSP00000447104:G12W	ENSP00000228476:G12W	G	+	1	0	DAO	107802945	1.000000	0.71417	0.965000	0.40720	0.534000	0.34807	9.777000	0.99008	2.541000	0.85698	0.591000	0.81541	GGG	.	.		0.577	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1		
ACACB	32	hgsc.bcm.edu	37	12	109660331	109660331	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:109660331A>G	ENST00000338432.7	+	25	3703	c.3584A>G	c.(3583-3585)gAc>gGc	p.D1195G	ACACB_ENST00000377854.5_Missense_Mutation_p.D1125G|ACACB_ENST00000377848.3_Missense_Mutation_p.D1195G			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1195					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TGTGGCCCAGACCCTTCCCTG	0.572																																					p.D1195G		Atlas-SNP	.											.	ACACB	330	.	0			c.A3584G						.						95.0	91.0	92.0					12																	109660331		2203	4300	6503	SO:0001583	missense	32	exon24			GCCCAGACCCTTC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3584A>G	chr12.hg19:g.109660331A>G	ENSP00000341044:p.Asp1195Gly	132.0	0.0		88.0	4.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935008	0.52866	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.17	5.17	0.71159	Acetyl-CoA carboxylase, central domain (1);	0.046636	0.85682	D	0.000000	T	0.42268	0.1195	L	0.59436	1.845	0.80722	D	1	B	0.14805	0.011	B	0.20577	0.03	T	0.27606	-1.0069	10	0.36615	T	0.2	.	15.2981	0.73925	1.0:0.0:0.0:0.0	.	1195	O00763	ACACB_HUMAN	G	1195;1195;1125;426	ENSP00000341044:D1195G;ENSP00000367079:D1195G;ENSP00000367085:D1125G	ENSP00000341044:D1195G	D	+	2	0	ACACB	108144714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.172000	0.94808	2.074000	0.62210	0.528000	0.53228	GAC	.	.		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
TCHP	84260	hgsc.bcm.edu	37	12	110340853	110340853	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:110340853T>C	ENST00000312777.5	+	2	236	c.22T>C	c.(22-24)Tcc>Ccc	p.S8P	TCHP_ENST00000405876.4_Missense_Mutation_p.S8P	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						GACGCTGCCGTCCTACTGGTG	0.602																																					p.S8P		Atlas-SNP	.											.	TCHP	45	.	0			c.T22C						.						49.0	51.0	50.0					12																	110340853		2203	4300	6503	SO:0001583	missense	84260	exon2			CTGCCGTCCTACT	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.22T>C	chr12.hg19:g.110340853T>C	ENSP00000324404:p.Ser8Pro	149.0	0.0		87.0	4.0	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	hg19	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.411064	0.25465	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.51071	1.37;1.37;0.72	4.81	3.66	0.41972	.	0.317802	0.34245	N	0.004123	T	0.39172	0.1068	L	0.55103	1.725	0.40394	D	0.979571	B	0.09022	0.002	B	0.06405	0.002	T	0.18650	-1.0330	10	0.25751	T	0.34	-0.7753	8.5903	0.33684	0.0:0.093:0.0:0.907	.	8	Q9BT92	TCHP_HUMAN	P	8	ENSP00000384520:S8P;ENSP00000324404:S8P;ENSP00000441835:S8P	ENSP00000324404:S8P	S	+	1	0	TCHP	108825236	0.010000	0.17322	0.930000	0.37139	0.076000	0.17211	1.235000	0.32671	0.710000	0.31997	0.369000	0.22263	TCC	.	.		0.602	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
OAS1	4938	hgsc.bcm.edu	37	12	113357204	113357204	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:113357204A>G	ENST00000202917.5	+	6	1312	c.1049A>G	c.(1048-1050)aAc>aGc	p.N350S	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	350					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GCTGAAAGCAACAGTGCAGAC	0.483																																					p.N350S		Atlas-SNP	.											.	OAS1	128	.	0			c.A1049G						.						83.0	82.0	83.0					12																	113357204		2203	4300	6503	SO:0001583	missense	4938	exon6			AAAGCAACAGTGC	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1049A>G	chr12.hg19:g.113357204A>G	ENSP00000202917:p.Asn350Ser	93.0	0.0		92.0	5.0	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	A	2.929	-0.221556	0.06061	.	.	ENSG00000089127	ENST00000202917	T	0.04502	3.61	1.9	1.9	0.25705	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.48031	-0.9070	9	0.09590	T	0.72	.	5.8476	0.18675	1.0:0.0:0.0:0.0	.	350	P00973	OAS1_HUMAN	S	350	ENSP00000202917:N350S	ENSP00000202917:N350S	N	+	2	0	OAS1	111841587	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.024000	0.12435	1.136000	0.42199	0.455000	0.32223	AAC	.	.		0.483	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
LHX5	64211	hgsc.bcm.edu	37	12	113901182	113901182	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:113901182A>G	ENST00000261731.3	-	5	1595	c.1022T>C	c.(1021-1023)tTc>tCc	p.F341S		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	341					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						CATGTCGGTGAACCTGGGGTT	0.751																																					p.F341S		Atlas-SNP	.											.	LHX5	39	.	0			c.T1022C						.						11.0	14.0	13.0					12																	113901182		2037	3996	6033	SO:0001583	missense	64211	exon5			TCGGTGAACCTGG	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"""Homeoboxes / LIM class"""	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.1022T>C	chr12.hg19:g.113901182A>G	ENSP00000261731:p.Phe341Ser	118.0	0.0		88.0	6.0	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	hg19	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.223565	0.58668	.	.	ENSG00000089116	ENST00000261731	D	0.91407	-2.84	4.08	1.05	0.20165	.	0.279818	0.24983	N	0.034052	D	0.86896	0.6043	L	0.57536	1.79	0.40601	D	0.981589	P	0.43938	0.822	B	0.43809	0.432	T	0.81355	-0.0970	10	0.22706	T	0.39	.	8.4052	0.32610	0.3463:0.0:0.0:0.6537	.	341	Q9H2C1	LHX5_HUMAN	S	341	ENSP00000261731:F341S	ENSP00000261731:F341S	F	-	2	0	LHX5	112385565	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	1.711000	0.37930	0.538000	0.28769	0.459000	0.35465	TTC	.	.		0.751	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363	
CIT	11113	hgsc.bcm.edu	37	12	120151337	120151337	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120151337G>T	ENST00000261833.7	-	33	4349	c.4297C>A	c.(4297-4299)Cca>Aca	p.P1433T	CIT_ENST00000392521.2_Missense_Mutation_p.P1475T|CIT_ENST00000537607.1_5'UTR|MIR1178_ENST00000408396.1_RNA	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1433					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)		TGGAGACCTGGGGAGTTCATT	0.607																																					p.P1475T		Atlas-SNP	.											.	CIT	535	.	0			c.C4423A						.						73.0	62.0	66.0					12																	120151337		2203	4300	6503	SO:0001583	missense	11113	exon34			GACCTGGGGAGTT	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.4297C>A	chr12.hg19:g.120151337G>T	ENSP00000261833:p.Pro1433Thr	149.0	0.0		119.0	5.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796029	0.50208	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.65178	-0.12;-0.14	6.07	6.07	0.98685	.	0.059274	0.64402	D	0.000002	T	0.55752	0.1940	L	0.43152	1.355	0.58432	D	0.999998	P;P;B	0.45126	0.851;0.851;0.148	B;B;B	0.37550	0.162;0.253;0.033	T	0.52631	-0.8550	10	0.24483	T	0.36	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1475;1433;951	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	T	1475;1433	ENSP00000376306:P1475T;ENSP00000261833:P1433T	ENSP00000261833:P1433T	P	-	1	0	CIT	118635720	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.443000	0.73447	2.884000	0.98904	0.655000	0.94253	CCA	.	.		0.607	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
GCN1L1	10985	hgsc.bcm.edu	37	12	120572406	120572406	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120572406T>C	ENST00000300648.6	-	52	7145	c.7133A>G	c.(7132-7134)cAc>cGc	p.H2378R		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2378					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACCTTAATGTGGATGGAAAT	0.622																																					p.H2378R		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A7133G						.						75.0	79.0	78.0					12																	120572406		1972	4157	6129	SO:0001583	missense	10985	exon52			TTAATGTGGATGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7133A>G	chr12.hg19:g.120572406T>C	ENSP00000300648:p.His2378Arg	145.0	0.0		95.0	5.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905149	0.92035	.	.	ENSG00000089154	ENST00000300648	T	0.63255	-0.03	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81721	0.4882	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.84824	0.0798	10	0.62326	D	0.03	-18.4244	15.8461	0.78890	0.0:0.0:0.0:1.0	.	2378	Q92616	GCN1L_HUMAN	R	2378	ENSP00000300648:H2378R	ENSP00000300648:H2378R	H	-	2	0	GCN1L1	119056789	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.490000	0.81461	2.151000	0.67156	0.496000	0.49642	CAC	.	.		0.622	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
GCN1L1	10985	hgsc.bcm.edu	37	12	120600885	120600885	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120600885T>C	ENST00000300648.6	-	19	2039	c.2027A>G	c.(2026-2028)cAc>cGc	p.H676R		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	676					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAAGGATGGGTGGTGGGAGAT	0.597																																					p.H676R		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A2027G						.						90.0	88.0	89.0					12																	120600885		2070	4198	6268	SO:0001583	missense	10985	exon19			GATGGGTGGTGGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.2027A>G	chr12.hg19:g.120600885T>C	ENSP00000300648:p.His676Arg	108.0	0.0		92.0	4.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505128	0.85282	.	.	ENSG00000089154	ENST00000300648	T	0.04654	3.58	5.71	5.71	0.89125	Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	M	0.65975	2.015	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.00109	-1.2049	10	0.72032	D	0.01	.	15.9958	0.80243	0.0:0.0:0.0:1.0	.	676	Q92616	GCN1L_HUMAN	R	676	ENSP00000300648:H676R	ENSP00000300648:H676R	H	-	2	0	GCN1L1	119085268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.249000	0.78278	2.188000	0.69820	0.533000	0.62120	CAC	.	.		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
MSI1	4440	hgsc.bcm.edu	37	12	120795696	120795696	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120795696C>A	ENST00000257552.2	-	8	545	c.457G>T	c.(457-459)Ggg>Tgg	p.G153W	MSI1_ENST00000546622.1_5'UTR	NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	153	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTGACAAACCCGAACCCTAGA	0.493																																					p.G153W		Atlas-SNP	.											MSI1,NS,carcinoma,0,1	MSI1	40	.	0			c.G457T						.						107.0	86.0	93.0					12																	120795696		2203	4300	6503	SO:0001583	missense	4440	exon8			CAAACCCGAACCC	AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	7330	protein-coding gene	gene with protein product		603328	"""Musashi (Drosophila) homolog 1"", ""musashi homolog 1 (Drosophila)"""			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.457G>T	chr12.hg19:g.120795696C>A	ENSP00000257552:p.Gly153Trp	140.0	1.0		85.0	5.0	NM_002442	Q96PU0|Q96PU1|Q96PU2|Q96PU3	Missense_Mutation	SNP	ENST00000257552.2	hg19	CCDS9196.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483654	0.84854	.	.	ENSG00000135097	ENST00000257552	T	0.80480	-1.38	5.27	5.27	0.74061	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000001	D	0.94679	0.8284	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96861	0.9632	10	0.87932	D	0	.	19.2695	0.94003	0.0:1.0:0.0:0.0	.	153	O43347	MSI1H_HUMAN	W	153	ENSP00000257552:G153W	ENSP00000257552:G153W	G	-	1	0	MSI1	119280079	1.000000	0.71417	0.998000	0.56505	0.818000	0.46254	7.455000	0.80726	2.637000	0.89404	0.462000	0.41574	GGG	.	.		0.493	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1	NM_002442	
P2RX4	5025	hgsc.bcm.edu	37	12	121648016	121648016	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:121648016A>G	ENST00000337233.4	+	1	357	c.49A>G	c.(49-51)Acg>Gcg	p.T17A	P2RX4_ENST00000359949.7_Missense_Mutation_p.T17A|P2RX4_ENST00000543171.1_5'UTR|P2RX4_ENST00000541532.1_Missense_Mutation_p.T17A|P2RX4_ENST00000540930.1_3'UTR	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	17					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGAGTACGACACGCCGCGCAT	0.711																																					p.T17A		Atlas-SNP	.											.	P2RX4	27	.	0			c.A49G						.						20.0	19.0	20.0					12																	121648016		2197	4295	6492	SO:0001583	missense	5025	exon1			TACGACACGCCGC	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.49A>G	chr12.hg19:g.121648016A>G	ENSP00000336607:p.Thr17Ala	72.0	0.0		93.0	4.0	NM_001261398	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Missense_Mutation	SNP	ENST00000337233.4	hg19	CCDS9214.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753047	0.69648	.	.	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000541532;ENST00000538701;ENST00000542067	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	3.78	2.62	0.31277	.	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	M	0.93678	3.445	0.43399	D	0.995524	D;P;D	0.76494	0.999;0.929;0.999	D;P;D	0.81914	0.991;0.803;0.995	T	0.32402	-0.9908	10	0.87932	D	0	-18.2534	8.4382	0.32799	0.904:0.0:0.096:0.0	.	17;17;17	F6RU17;E7EPF7;Q99571	.;.;P2RX4_HUMAN	A	17	ENSP00000336607:T17A;ENSP00000353032:T17A;ENSP00000443115:T17A;ENSP00000444033:T17A;ENSP00000438329:T17A	ENSP00000336607:T17A	T	+	1	0	P2RX4	120132399	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.154000	0.64894	0.629000	0.30376	0.172000	0.16884	ACG	.	.		0.711	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567	
CAMKK2	10645	hgsc.bcm.edu	37	12	121701741	121701741	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:121701741A>G	ENST00000324774.5	-	6	1455	c.627T>C	c.(625-627)cgT>cgC	p.R209R	CAMKK2_ENST00000392473.2_Splice_Site_p.R209R|CAMKK2_ENST00000404169.3_Splice_Site_p.R209R|CAMKK2_ENST00000392474.2_Splice_Site_p.R209R|CAMKK2_ENST00000538733.1_Splice_Site_p.R209R|CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000337174.3_Splice_Site_p.R209R|CAMKK2_ENST00000412367.2_Splice_Site_p.R209R|CAMKK2_ENST00000347034.2_Splice_Site_p.R209R|CAMKK2_ENST00000446440.2_Splice_Site_p.R209R|CAMKK2_ENST00000402834.4_Splice_Site_p.R209R	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|RP domain.				calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGGAGGGCGACCTGAAGGAA	0.602																																					p.R209R		Atlas-SNP	.											.	CAMKK2	87	.	0			c.T627C						.						20.0	19.0	19.0					12																	121701741		2203	4297	6500	SO:0001630	splice_region_variant	10645	exon6			AGGGCGACCTGAA	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.626-1T>C	chr12.hg19:g.121701741A>G		62.0	0.0		76.0	4.0	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Silent	SNP	ENST00000324774.5	hg19	CCDS9216.1																																																																																			.	.		0.602	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	Silent
SETD1B	23067	hgsc.bcm.edu	37	12	122257551	122257551	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:122257551G>T	ENST00000604567.1	+	11	3728	c.3660G>T	c.(3658-3660)ccG>ccT	p.P1220P	SETD1B_ENST00000267197.5_Silent_p.P1177P|SETD1B_ENST00000542440.1_Silent_p.P1177P			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1220	Glu-rich.|Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						CTCTGGCCCCGGGGGCACCTG	0.652																																					p.P1177P		Atlas-SNP	.											.	SETD1B	105	.	0			c.G3531T						.						75.0	102.0	94.0					12																	122257551		692	1591	2283	SO:0001819	synonymous_variant	23067	exon11			GGCCCCGGGGGCA	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.3660G>T	chr12.hg19:g.122257551G>T		106.0	0.0		79.0	4.0	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	hg19																																																																																				.	.		0.652	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
SETD1B	23067	hgsc.bcm.edu	37	12	122261465	122261465	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:122261465C>A	ENST00000604567.1	+	12	5048	c.4980C>A	c.(4978-4980)ccC>ccA	p.P1660P	SETD1B_ENST00000267197.5_Silent_p.P1617P|SETD1B_ENST00000542440.1_Silent_p.P1617P			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1660	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						CGGGCTCGCCCGAACTCTCGC	0.637																																					p.P1617P		Atlas-SNP	.											.	SETD1B	105	.	0			c.C4851A						.						36.0	40.0	39.0					12																	122261465		692	1591	2283	SO:0001819	synonymous_variant	23067	exon12			CTCGCCCGAACTC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.4980C>A	chr12.hg19:g.122261465C>A		68.0	0.0		81.0	4.0	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	hg19																																																																																				.	.		0.637	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
LRRC43	254050	hgsc.bcm.edu	37	12	122669301	122669301	+	Missense_Mutation	SNP	G	G	T	rs372181783		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:122669301G>T	ENST00000339777.4	+	2	414	c.386G>T	c.(385-387)cGg>cTg	p.R129L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	129										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		TCCTACTTCCGGTCCCTGCGG	0.562																																					p.R129L		Atlas-SNP	.											.	LRRC43	105	.	0			c.G386T						.	G	LEU/ARG,	0,3986		0,0,1993	25.0	26.0	26.0		386,	1.3	1.0	12		26	1,8349		0,1,4174	no	missense,utr-5	LRRC43	NM_001098519.1,NM_152759.4	102,	0,1,6167	TT,TG,GG		0.012,0.0,0.0081	possibly-damaging,	129/657,	122669301	1,12335	1993	4175	6168	SO:0001583	missense	254050	exon2			ACTTCCGGTCCCT	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.386G>T	chr12.hg19:g.122669301G>T	ENSP00000344233:p.Arg129Leu	192.0	0.0		144.0	6.0	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.892321	0.72524	0.0	1.2E-4	ENSG00000158113	ENST00000339777	T	0.58358	0.34	4.9	1.34	0.21922	.	.	.	.	.	T	0.60209	0.2251	M	0.62723	1.935	0.39919	D	0.974138	D	0.65815	0.995	P	0.60682	0.878	T	0.62779	-0.6782	9	0.66056	D	0.02	-19.8237	6.3874	0.21568	0.2552:0.1498:0.595:0.0	.	129	Q8N309	LRC43_HUMAN	L	129	ENSP00000344233:R129L	ENSP00000344233:R129L	R	+	2	0	LRRC43	121235254	0.937000	0.31787	0.983000	0.44433	0.867000	0.49689	0.382000	0.20635	1.069000	0.40788	0.462000	0.41574	CGG	.	.		0.562	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
SFSWAP	6433	hgsc.bcm.edu	37	12	132283969	132283969	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:132283969A>G	ENST00000261674.4	+	18	2933	c.2792A>G	c.(2791-2793)gAt>gGt	p.D931G	SFSWAP_ENST00000539506.1_3'UTR|RNA5SP378_ENST00000363646.1_RNA|SFSWAP_ENST00000541286.1_Splice_Site_p.D983G	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	931	Arg/Ser-rich (RS domain).				mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CCTGCACAGGATCTCATGGCC	0.577																																					p.D983G		Atlas-SNP	.											.	SFSWAP	69	.	0			c.A2948G						.						61.0	54.0	57.0					12																	132283969		2203	4300	6503	SO:0001630	splice_region_variant	6433	exon19			CACAGGATCTCAT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.2791-1A>G	chr12.hg19:g.132283969A>G		140.0	0.0		81.0	4.0	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	hg19	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.975453	0.53720	.	.	ENSG00000061936	ENST00000261674;ENST00000541286	T;T	0.20332	2.25;2.08	5.14	5.14	0.70334	.	0.140754	0.64402	D	0.000006	T	0.42562	0.1208	L	0.56769	1.78	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.79784	0.993;0.984	T	0.33317	-0.9873	10	0.72032	D	0.01	-32.0351	14.2322	0.65901	1.0:0.0:0.0:0.0	.	983;931	F5H6B8;Q12872	.;SFSWA_HUMAN	G	931;983	ENSP00000261674:D931G;ENSP00000437738:D983G	ENSP00000261674:D931G	D	+	2	0	SFSWAP	130849922	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.904000	0.69886	2.064000	0.61679	0.454000	0.30748	GAT	.	.		0.577	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	Missense_Mutation
EP400	57634	hgsc.bcm.edu	37	12	132549272	132549272	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:132549272A>G	ENST00000333577.4	+	49	8611	c.8502A>G	c.(8500-8502)ccA>ccG	p.P2834P	EP400_ENST00000389561.2_Silent_p.P2798P|EP400_ENST00000389562.2_Silent_p.P2797P|EP400_ENST00000330386.6_Silent_p.P2717P|EP400_ENST00000332482.4_Silent_p.P2761P			Q96L91	EP400_HUMAN	E1A binding protein p400	2834	Poly-Pro.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCCACCGCCACAGGCCCAGT	0.592																																					p.P2798P		Atlas-SNP	.											.	EP400	370	.	0			c.A8394G						.						32.0	47.0	42.0					12																	132549272		2200	4298	6498	SO:0001819	synonymous_variant	57634	exon48			ACCGCCACAGGCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8502A>G	chr12.hg19:g.132549272A>G		100.0	0.0		73.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.592	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
ZNF10	7556	hgsc.bcm.edu	37	12	133732852	133732852	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:133732852G>T	ENST00000248211.6	+	5	1242	c.1020G>T	c.(1018-1020)caG>caT	p.Q340H	CTD-2140B24.4_ENST00000540096.2_Intron|ZNF268_ENST00000416488.1_Intron|ZNF10_ENST00000426665.2_Missense_Mutation_p.Q340H|ZNF10_ENST00000402932.2_Missense_Mutation_p.Q206H	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	340					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(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TTACTCATCAGAGAACTCATA	0.418																																					p.Q340H		Atlas-SNP	.											.	ZNF10	58	.	0			c.G1020T						.						114.0	122.0	119.0					12																	133732852		2203	4300	6503	SO:0001583	missense	7556	exon5			TCATCAGAGAACT	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"""Zinc fingers, C2H2-type"", ""-"""	12879	protein-coding gene	gene with protein product		194538	"""zinc finger protein 10 (KOX 1)"""			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.1020G>T	chr12.hg19:g.133732852G>T	ENSP00000248211:p.Gln340His	100.0	0.0		75.0	4.0	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.550609	0.27739	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000402932	T;T;T	0.18502	3.18;3.18;2.21	3.6	2.69	0.31865	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.314161	0.18298	N	0.145506	T	0.12518	0.0304	L	0.44542	1.39	0.80722	D	1	B	0.20164	0.042	B	0.17433	0.018	T	0.08086	-1.0739	9	.	.	.	.	6.506	0.22196	0.1092:0.1899:0.7009:0.0	.	340	P21506	ZNF10_HUMAN	H	340;340;206	ENSP00000248211:Q340H;ENSP00000393814:Q340H;ENSP00000384893:Q206H	.	Q	+	3	2	ZNF10	132242925	0.291000	0.24352	1.000000	0.80357	0.996000	0.88848	0.875000	0.28079	2.012000	0.59069	0.655000	0.94253	CAG	.	.		0.418	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394	
SACS	26278	hgsc.bcm.edu	37	13	23908202	23908202	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:23908202A>G	ENST00000382292.3	-	9	10086	c.9813T>C	c.(9811-9813)gtT>gtC	p.V3271V	SACS_ENST00000382298.3_Silent_p.V3271V|SACS_ENST00000402364.1_Silent_p.V2521V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3271					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAGTATCAACAACAATGTCAA	0.398																																					p.V3271V		Atlas-SNP	.											.	SACS	871	.	0			c.T9813C						.						107.0	99.0	102.0					13																	23908202		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			ATCAACAACAATG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9813T>C	chr13.hg19:g.23908202A>G		98.0	0.0		84.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SLC46A3	283537	hgsc.bcm.edu	37	13	29286871	29286871	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:29286871T>C	ENST00000266943.6	-	3	1375	c.1006A>G	c.(1006-1008)Atg>Gtg	p.M336V	SLC46A3_ENST00000380814.4_Missense_Mutation_p.M336V	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	336					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		ATTCCTGTCATCGTGGTAAAA	0.373																																					p.M336V		Atlas-SNP	.											.	SLC46A3	86	.	0			c.A1006G						.						89.0	86.0	87.0					13																	29286871		2203	4300	6503	SO:0001583	missense	283537	exon3			CTGTCATCGTGGT		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.1006A>G	chr13.hg19:g.29286871T>C	ENSP00000266943:p.Met336Val	154.0	0.0		112.0	5.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	T	3.555	-0.090823	0.07053	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.56103	0.48;0.48	5.43	4.23	0.50019	Major facilitator superfamily domain, general substrate transporter (1);	0.578774	0.20321	N	0.094629	T	0.41166	0.1147	L	0.44542	1.39	0.28488	N	0.914614	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.28776	-1.0033	10	0.10111	T	0.7	-16.2244	11.7366	0.51769	0.0:0.0699:0.0:0.9301	.	261;336;336	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	V	336	ENSP00000266943:M336V;ENSP00000370192:M336V	ENSP00000266943:M336V	M	-	1	0	SLC46A3	28184871	0.511000	0.26179	0.958000	0.39756	0.526000	0.34562	0.376000	0.20535	0.982000	0.38575	0.533000	0.62120	ATG	.	.		0.373	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
STARD13	90627	hgsc.bcm.edu	37	13	33681005	33681005	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:33681005T>C	ENST00000336934.5	-	13	3230	c.3114A>G	c.(3112-3114)gaA>gaG	p.E1038E	STARD13_ENST00000255486.4_Silent_p.E1030E|STARD13_ENST00000399365.3_Silent_p.E920E	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	1038	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGAGCTGGGCTTCCTCATGCT	0.532																																					p.E1038E		Atlas-SNP	.											.	STARD13	100	.	0			c.A3114G						.						134.0	123.0	127.0					13																	33681005		2203	4300	6503	SO:0001819	synonymous_variant	90627	exon13			CTGGGCTTCCTCA	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.3114A>G	chr13.hg19:g.33681005T>C		132.0	0.0		97.0	4.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	hg19	CCDS9348.1																																																																																			.	.		0.532	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
NBEA	26960	hgsc.bcm.edu	37	13	36239245	36239245	+	Missense_Mutation	SNP	G	G	A	rs368581341		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:36239245G>A	ENST00000400445.3	+	55	8857	c.8323G>A	c.(8323-8325)Gtc>Atc	p.V2775I	NBEA_ENST00000537702.1_Missense_Mutation_p.V568I|NBEA_ENST00000310336.4_Missense_Mutation_p.V2775I|NBEA_ENST00000540320.1_Missense_Mutation_p.V2775I|NBEA_ENST00000379922.3_Missense_Mutation_p.V353I|NBEA_ENST00000379939.2_Missense_Mutation_p.V2772I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2775					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ACCAAGAGCCGTCCTCACAGG	0.483																																					p.V2775I		Atlas-SNP	.											.	NBEA	340	.	0			c.G8323A						.	G	ILE/VAL,ILE/VAL	0,4088		0,0,2044	83.0	83.0	83.0		1702,8323	4.7	1.0	13		83	1,8379		0,1,4189	no	missense,missense	NBEA	NM_001204197.1,NM_015678.4	29,29	0,1,6233	AA,AG,GG		0.0119,0.0,0.0080	benign,benign	568/740,2775/2947	36239245	1,12467	2044	4190	6234	SO:0001583	missense	26960	exon55			AGAGCCGTCCTCA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8323G>A	chr13.hg19:g.36239245G>A	ENSP00000383295:p.Val2775Ile	282.0	0.0		177.0	53.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	6.332	0.429400	0.11987	0.0	1.19E-4	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.52	4.66	0.58398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.08044	0.0201	N	0.00427	-1.505	0.54753	D	0.999987	B;B;B	0.21905	0.062;0.006;0.038	B;B;B	0.16289	0.015;0.004;0.005	T	0.33137	-0.9880	10	0.02654	T	1	.	14.7267	0.69349	0.0709:0.0:0.9291:0.0	.	2775;353;2772	Q8NFP9;Q8NFP9-2;Q5T321	NBEA_HUMAN;.;.	I	2775;2775;2772;2775;1404;353;568;353	ENSP00000440951:V2775I;ENSP00000383295:V2775I;ENSP00000369271:V2772I;ENSP00000308534:V2775I;ENSP00000440233:V568I;ENSP00000369254:V353I	ENSP00000308534:V2775I	V	+	1	0	NBEA	35137245	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	7.210000	0.77924	2.582000	0.87167	0.655000	0.94253	GTC	.	.		0.483	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
KBTBD7	84078	hgsc.bcm.edu	37	13	41768100	41768100	+	Missense_Mutation	SNP	G	G	T	rs138677495		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:41768100G>T	ENST00000379483.3	-	1	602	c.294C>A	c.(292-294)agC>agA	p.S98R		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	98	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		CTGTGAACATGCTCTTGAAGT	0.607																																					p.S98R		Atlas-SNP	.											.	KBTBD7	60	.	0			c.C294A						.						83.0	55.0	64.0					13																	41768100		2203	4300	6503	SO:0001583	missense	84078	exon1			GAACATGCTCTTG	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"""BTB/POZ domain containing"""	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.294C>A	chr13.hg19:g.41768100G>T	ENSP00000368797:p.Ser98Arg	153.0	0.0		99.0	4.0	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	hg19	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221378	0.58560	.	.	ENSG00000120696	ENST00000379483	T	0.68025	-0.3	4.79	3.04	0.35103	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	U	0.000000	T	0.78033	0.4220	M	0.72894	2.215	0.45979	D	0.99879	D	0.89917	1.0	D	0.91635	0.999	T	0.77490	-0.2568	10	0.87932	D	0	.	9.5678	0.39409	0.178:0.0:0.822:0.0	.	98	Q8WVZ9	KBTB7_HUMAN	R	98	ENSP00000368797:S98R	ENSP00000368797:S98R	S	-	3	2	KBTBD7	40666100	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.262000	0.58847	0.534000	0.28695	0.563000	0.77884	AGC	.	G|1.000;A|0.000		0.607	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138	
COG3	83548	hgsc.bcm.edu	37	13	46085936	46085936	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:46085936T>C	ENST00000349995.5	+	16	1868	c.1756T>C	c.(1756-1758)Tct>Cct	p.S586P	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	586					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GGAAGCATTGTCTGCCTGCAT	0.398																																					p.S586P	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.T1756C						.						136.0	122.0	127.0					13																	46085936		2203	4300	6503	SO:0001583	missense	83548	exon16			GCATTGTCTGCCT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1756T>C	chr13.hg19:g.46085936T>C	ENSP00000258654:p.Ser586Pro	105.0	0.0		91.0	5.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.030526	0.75504	.	.	ENSG00000136152	ENST00000349995	T	0.46819	0.86	5.41	4.22	0.49857	.	0.110324	0.64402	D	0.000004	T	0.59046	0.2165	M	0.79475	2.455	0.80722	D	1	P;D	0.67145	0.653;0.996	B;P	0.53912	0.243;0.737	T	0.59606	-0.7423	10	0.31617	T	0.26	-10.3941	12.056	0.53536	0.0:0.0:0.144:0.8559	.	423;586	B4E2F3;Q96JB2	.;COG3_HUMAN	P	586	ENSP00000258654:S586P	ENSP00000258654:S586P	S	+	1	0	COG3	44983937	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.814000	0.69208	1.058000	0.40530	0.482000	0.46254	TCT	.	.		0.398	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
INTS6	26512	hgsc.bcm.edu	37	13	51961531	51961531	+	Silent	SNP	C	C	A	rs142545429		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:51961531C>A	ENST00000311234.4	-	7	1357	c.885G>T	c.(883-885)tcG>tcT	p.S295S	INTS6_ENST00000425000.1_5'UTR|INTS6_ENST00000490542.1_5'Flank|INTS6_ENST00000420668.2_3'UTR|INTS6_ENST00000497989.1_Silent_p.S117S|INTS6_ENST00000398119.2_Silent_p.S282S|INTS6_ENST00000463928.1_Intron	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	295					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.S295S(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		CTAGTGTTGGCGAATTTTGAT	0.378																																					p.S295S		Atlas-SNP	.											INTS6,NS,carcinoma,-1,1	INTS6	72	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G885T						.						95.0	87.0	90.0					13																	51961531		2203	4300	6503	SO:0001819	synonymous_variant	26512	exon7			TGTTGGCGAATTT	AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"""DEAD-boxes"""	14879	protein-coding gene	gene with protein product		604331	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"""	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.885G>T	chr13.hg19:g.51961531C>A		68.0	0.0		57.0	3.0	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Silent	SNP	ENST00000311234.4	hg19	CCDS9428.1																																																																																			.	C|1.000;T|0.000		0.378	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141	
ATP7B	540	hgsc.bcm.edu	37	13	52539142	52539142	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:52539142C>T	ENST00000242839.4	-	5	1891	c.1735G>A	c.(1735-1737)Gtc>Atc	p.V579I	ATP7B_ENST00000542656.1_Intron|ATP7B_ENST00000448424.2_Missense_Mutation_p.V579I|ATP7B_ENST00000400366.3_Missense_Mutation_p.V468I|ATP7B_ENST00000344297.5_Missense_Mutation_p.V579I|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000418097.2_Missense_Mutation_p.V579I	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	579	HMA 6. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATGTTGTGGACACAGGACGCG	0.527									Wilson disease																												p.V579I		Atlas-SNP	.											.	ATP7B	123	.	0			c.G1735A						.						87.0	89.0	89.0					13																	52539142		2064	4209	6273	SO:0001583	missense	540	exon5	Familial Cancer Database		TGTGGACACAGGA	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1735G>A	chr13.hg19:g.52539142C>T	ENSP00000242839:p.Val579Ile	108.0	0.0		88.0	4.0	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.761702	0.89932	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	5.95	5.95	0.96441	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);Heavy-metal-associated, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94578	0.8253	M	0.85630	2.765	0.80722	D	1	B;B;D;P;P;B	0.76494	0.016;0.407;0.999;0.937;0.868;0.037	B;B;D;P;P;B	0.85130	0.013;0.33;0.997;0.72;0.513;0.174	D	0.94398	0.7620	10	0.72032	D	0.01	-29.5788	20.3932	0.98965	0.0:1.0:0.0:0.0	.	579;579;579;468;579;579	E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;ATP7B_HUMAN	I	579;468;579;579;579	ENSP00000242839:V579I;ENSP00000383217:V468I;ENSP00000342559:V579I;ENSP00000416738:V579I;ENSP00000393343:V579I	ENSP00000242839:V579I	V	-	1	0	ATP7B	51437143	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.735000	0.68587	2.824000	0.97209	0.655000	0.94253	GTC	.	.		0.527	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
PCDH20	64881	hgsc.bcm.edu	37	13	61987996	61987996	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:61987996C>A	ENST00000409186.1	-	5	2341	c.236G>T	c.(235-237)gGg>gTg	p.G79V	PCDH20_ENST00000409204.4_Missense_Mutation_p.G79V			Q8N6Y1	PCD20_HUMAN	protocadherin 20	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GATGAGCACCCCCGCGGGTAG	0.662																																					p.G79V		Atlas-SNP	.											.	PCDH20	265	.	0			c.G236T						.						14.0	15.0	14.0					13																	61987996		2195	4289	6484	SO:0001583	missense	64881	exon2			AGCACCCCCGCGG	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.236G>T	chr13.hg19:g.61987996C>A	ENSP00000386653:p.Gly79Val	102.0	0.0		83.0	4.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	hg19	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	c	29.1	4.976742	0.92982	.	.	ENSG00000197991	ENST00000409204;ENST00000409186	T;T	0.60548	0.18;0.18	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000015	D	0.83830	0.5339	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89023	0.3436	10	0.87932	D	0	.	18.6958	0.91600	0.0:1.0:0.0:0.0	.	79	A8K1K9	.	V	79	ENSP00000387250:G79V;ENSP00000386653:G79V	ENSP00000386653:G79V	G	-	2	0	PCDH20	60885997	1.000000	0.71417	0.906000	0.35671	0.982000	0.71751	7.507000	0.81676	2.413000	0.81919	0.591000	0.81541	GGG	.	.		0.662	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
KLF12	11278	hgsc.bcm.edu	37	13	74420058	74420058	+	Silent	SNP	C	C	A	rs200955639		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:74420058C>A	ENST00000377669.2	-	3	602	c.576G>T	c.(574-576)tcG>tcT	p.S192S	KLF12_ENST00000377666.4_Silent_p.S192S|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	192					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S192S(1)		central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		CAACAGGCACCGACTGTACCA	0.488																																					p.S192S		Atlas-SNP	.											.	KLF12	42	.	1	Substitution - coding silent(1)	lung(1)	c.G576T						.						122.0	101.0	108.0					13																	74420058		2203	4300	6503	SO:0001819	synonymous_variant	11278	exon4			AGGCACCGACTGT	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.576G>T	chr13.hg19:g.74420058C>A		166.0	0.0		137.0	7.0	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	hg19	CCDS9449.1																																																																																			.	C|1.000;T|0.000		0.488	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
POU4F1	5457	hgsc.bcm.edu	37	13	79175920	79175920	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:79175920T>C	ENST00000377208.5	-	2	1101	c.890A>G	c.(889-891)aAg>aGg	p.K297R	RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606429.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	297	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	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 (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		GCCCGGGATCTTGAGGTTGGC	0.667																																					p.K297R	Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	Atlas-SNP	.											.	POU4F1	43	.	0			c.A890G						.						33.0	30.0	31.0					13																	79175920		2202	4300	6502	SO:0001583	missense	5457	exon2			GGGATCTTGAGGT	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"""Homeoboxes / POU class"""	9218	protein-coding gene	gene with protein product		601632	"""POU domain class 4, transcription factor 1"""	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.890A>G	chr13.hg19:g.79175920T>C	ENSP00000366413:p.Lys297Arg	126.0	0.0		91.0	4.0	NM_006237	Q14986|Q15318|Q5T227	Missense_Mutation	SNP	ENST00000377208.5	hg19	CCDS31996.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.381290	0.42207	.	.	ENSG00000152192	ENST00000377208	D	0.83673	-1.75	3.21	3.21	0.36854	POU-specific (3);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	U	0.000000	D	0.86965	0.6060	L	0.59912	1.85	0.53688	D	0.999971	D	0.65815	0.995	D	0.64410	0.925	D	0.87137	0.2200	10	0.59425	D	0.04	.	10.9225	0.47174	0.0:0.0:0.0:1.0	.	297	Q01851	PO4F1_HUMAN	R	297	ENSP00000366413:K297R	ENSP00000366413:K297R	K	-	2	0	POU4F1	78073921	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.606000	0.82863	1.473000	0.48159	0.323000	0.21402	AAG	.	.		0.667	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3		
DOCK9	23348	hgsc.bcm.edu	37	13	99536145	99536145	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:99536145A>G	ENST00000376460.1	-	22	2471	c.2391T>C	c.(2389-2391)ggT>ggC	p.G797G	DOCK9_ENST00000448493.2_Silent_p.G809G|DOCK9_ENST00000442173.1_Silent_p.G797G|DOCK9_ENST00000339416.2_Silent_p.G798G	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	798	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TAATTTCCGGACCATAATGCT	0.373																																					p.G798G		Atlas-SNP	.											.	DOCK9	311	.	0			c.T2394C						.						56.0	55.0	55.0					13																	99536145		1846	4090	5936	SO:0001819	synonymous_variant	23348	exon22			TTCCGGACCATAA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2391T>C	chr13.hg19:g.99536145A>G		73.0	0.0		72.0	4.0	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	hg19	CCDS45062.1																																																																																			.	.		0.373	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
COL4A1	1282	hgsc.bcm.edu	37	13	110831299	110831299	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:110831299G>T	ENST00000375820.4	-	31	2550	c.2429C>A	c.(2428-2430)cCt>cAt	p.P810H		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	810	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CTGTCCTCCAGGGGGACCCCT	0.572																																					p.P810H		Atlas-SNP	.											.	COL4A1	372	.	0			c.C2429A						.						15.0	17.0	16.0					13																	110831299		2202	4298	6500	SO:0001583	missense	1282	exon31			CCTCCAGGGGGAC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2429C>A	chr13.hg19:g.110831299G>T	ENSP00000364979:p.Pro810His	69.0	0.0		52.0	4.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480937	0.84747	.	.	ENSG00000187498	ENST00000375820	D	0.98701	-5.08	4.89	4.89	0.63831	.	0.206902	0.43260	D	0.000594	D	0.99312	0.9759	M	0.92219	3.285	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.98931	1.0787	10	0.54805	T	0.06	.	17.4237	0.87521	0.0:0.0:1.0:0.0	.	810	P02462	CO4A1_HUMAN	H	810	ENSP00000364979:P810H	ENSP00000364979:P810H	P	-	2	0	COL4A1	109629300	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	5.705000	0.68355	2.431000	0.82371	0.655000	0.94253	CCT	.	.		0.572	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
COL4A2	1284	hgsc.bcm.edu	37	13	111144454	111144454	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:111144454A>G	ENST00000360467.5	+	38	3798	c.3492A>G	c.(3490-3492)ggA>ggG	p.G1164G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1164	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGTCGCAGGGAGAGCTGGGGC	0.612																																					p.G1164G		Atlas-SNP	.											.	COL4A2	178	.	0			c.A3492G						.						28.0	38.0	34.0					13																	111144454		1946	4068	6014	SO:0001819	synonymous_variant	1284	exon38			GCAGGGAGAGCTG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3492A>G	chr13.hg19:g.111144454A>G		84.0	0.0		57.0	4.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	hg19	CCDS41907.1																																																																																			.	.		0.612	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
TUBGCP3	10426	hgsc.bcm.edu	37	13	113174218	113174218	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:113174218C>T	ENST00000261965.3	-	15	2049	c.1863G>A	c.(1861-1863)ctG>ctA	p.L621L	TUBGCP3_ENST00000462580.1_5'Flank|TUBGCP3_ENST00000375669.3_Silent_p.L621L	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	621					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					GCCGCACGTCCAGCCTTCGCA	0.582																																					p.L621L		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.G1863A						.						92.0	92.0	92.0					13																	113174218		2203	4300	6503	SO:0001819	synonymous_variant	10426	exon15			CACGTCCAGCCTT	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"""spindle pole body protein"""					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.1863G>A	chr13.hg19:g.113174218C>T		97.0	0.0		92.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Silent	SNP	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.		0.582	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322	
ATP11A	23250	hgsc.bcm.edu	37	13	113512575	113512575	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:113512575T>C	ENST00000487903.1	+	22	2726	c.2638T>C	c.(2638-2640)Tct>Cct	p.S880P	ATP11A_ENST00000375630.2_Missense_Mutation_p.S880P|ATP11A_ENST00000375645.3_Missense_Mutation_p.S880P|ATP11A_ENST00000283558.8_Missense_Mutation_p.S880P			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	880					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				CATTAGGATCTCTGAGCTCGT	0.522																																					p.S880P		Atlas-SNP	.											.	ATP11A	225	.	0			c.T2638C						.						94.0	92.0	93.0					13																	113512575		2203	4300	6503	SO:0001583	missense	23250	exon22			AGGATCTCTGAGC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2638T>C	chr13.hg19:g.113512575T>C	ENSP00000420387:p.Ser880Pro	168.0	0.0		121.0	5.0	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907221	0.52333	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000432166	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.62	-2.64	0.06114	.	0.220919	0.47852	D	0.000217	T	0.70413	0.3221	M	0.91090	3.175	0.45390	D	0.998376	P;P;B	0.45715	0.865;0.559;0.18	P;P;P	0.49192	0.544;0.602;0.474	T	0.81446	-0.0929	10	0.66056	D	0.02	.	16.7801	0.85561	0.0:0.0:0.5845:0.4155	.	880;880;880	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	P	880;880;880;880;321	ENSP00000420387:S880P;ENSP00000364781:S880P;ENSP00000364796:S880P;ENSP00000283558:S880P	ENSP00000283558:S880P	S	+	1	0	ATP11A	112560576	0.991000	0.36638	0.003000	0.11579	0.294000	0.27393	1.459000	0.35234	-0.241000	0.09681	0.533000	0.62120	TCT	.	.		0.522	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
RASA3	22821	hgsc.bcm.edu	37	13	114780788	114780788	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:114780788C>T	ENST00000334062.7	-	14	1423	c.1302G>A	c.(1300-1302)gtG>gtA	p.V434V	RASA3_ENST00000389544.4_Silent_p.V402V	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	434	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			AGACGCGGTCCACATACTGCC	0.662																																					p.V434V		Atlas-SNP	.											.	RASA3	83	.	0			c.G1302A						.						109.0	91.0	97.0					13																	114780788		2203	4299	6502	SO:0001819	synonymous_variant	22821	exon14			GCGGTCCACATAC		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1302G>A	chr13.hg19:g.114780788C>T		81.0	0.0		59.0	4.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	hg19	CCDS32016.1																																																																																			.	.		0.662	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
CDC16	8881	hgsc.bcm.edu	37	13	115002339	115002339	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:115002339G>T	ENST00000356221.3	+	3	277	c.169G>T	c.(169-171)Gcc>Tcc	p.A57S	CDC16_ENST00000375308.1_5'UTR|CDC16_ENST00000375312.3_5'UTR|CDC16_ENST00000375310.1_5'UTR|CDC16_ENST00000252458.6_5'UTR|CDC16_ENST00000252457.5_Missense_Mutation_p.A56S|CDC16_ENST00000360383.3_Missense_Mutation_p.A57S			Q13042	CDC16_HUMAN	cell division cycle 16	57					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TCACAGAGCCGCCCATGCACT	0.453																																					p.A57S		Atlas-SNP	.											.	CDC16	50	.	0			c.G169T						.						83.0	80.0	81.0					13																	115002339		2203	4300	6503	SO:0001583	missense	8881	exon3			AGAGCCGCCCATG	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.169G>T	chr13.hg19:g.115002339G>T	ENSP00000348554:p.Ala57Ser	116.0	0.0		90.0	4.0	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	hg19	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	G	5.183	0.219273	0.09863	.	.	ENSG00000130177	ENST00000360383;ENST00000356221;ENST00000252457	T;T;T	0.38240	1.15;1.15;1.15	5.29	5.29	0.74685	Tetratricopeptide-like helical (1);	0.050215	0.85682	D	0.000000	T	0.20941	0.0504	N	0.10972	0.075	0.80722	D	1	B;B;B;B	0.19445	0.036;0.005;0.002;0.009	B;B;B;B	0.25506	0.058;0.026;0.026;0.061	T	0.09509	-1.0671	9	.	.	.	-4.5644	13.1066	0.59252	0.0:0.0:0.84:0.1599	.	57;56;56;57	B4DK74;Q13042-3;Q13042-2;Q13042	.;.;.;CDC16_HUMAN	S	57;57;56	ENSP00000353549:A57S;ENSP00000348554:A57S;ENSP00000252457:A56S	.	A	+	1	0	CDC16	114020441	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	4.801000	0.62532	2.756000	0.94617	0.561000	0.74099	GCC	.	.		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
OR4K14	122740	hgsc.bcm.edu	37	14	20483233	20483233	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20483233C>A	ENST00000305045.2	-	1	119	c.120G>T	c.(118-120)ctG>ctT	p.L40L		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GAAGGTTACCCAGCATAATGG	0.448																																					p.L40L		Atlas-SNP	.											.	OR4K14	86	.	0			c.G120T						.						73.0	68.0	70.0					14																	20483233		2203	4300	6503	SO:0001819	synonymous_variant	122740	exon1			GTTACCCAGCATA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"""GPCR / Class A : Olfactory receptors"""	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.120G>T	chr14.hg19:g.20483233C>A		296.0	0.0		224.0	78.0	NM_001004712	Q6IEU1|Q96R71	Silent	SNP	ENST00000305045.2	hg19	CCDS32027.1																																																																																			.	.		0.448	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1		
TEP1	7011	hgsc.bcm.edu	37	14	20848600	20848600	+	Silent	SNP	G	G	T	rs200043242		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20848600G>T	ENST00000262715.5	-	34	4837	c.4797C>A	c.(4795-4797)ccC>ccA	p.P1599P	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Silent_p.P1491P	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1599					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CGTCAGCCTCGGGGAGCTTTT	0.587																																					p.P1599P		Atlas-SNP	.											TEP1,bladder,carcinoma,0,1	TEP1	224	.	0			c.C4797A						.						50.0	51.0	51.0					14																	20848600		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon34			AGCCTCGGGGAGC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.4797C>A	chr14.hg19:g.20848600G>T		70.0	0.0		54.0	4.0	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	G|1.000;A|0.000		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
TEP1	7011	hgsc.bcm.edu	37	14	20872802	20872802	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20872802A>G	ENST00000262715.5	-	5	1040	c.1000T>C	c.(1000-1002)Tct>Cct	p.S334P	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	334	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		ATCCAGTCAGAAGGCAGCTGG	0.537																																					p.S334P		Atlas-SNP	.											.	TEP1	224	.	0			c.T1000C						.						72.0	65.0	67.0					14																	20872802		2203	4300	6503	SO:0001583	missense	7011	exon5			AGTCAGAAGGCAG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1000T>C	chr14.hg19:g.20872802A>G	ENSP00000262715:p.Ser334Pro	114.0	0.0		92.0	4.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.532968	0.85812	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.16073	2.37	5.55	5.55	0.83447	TROVE (2);	0.066420	0.64402	D	0.000010	T	0.43612	0.1255	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44937	-0.9295	10	0.87932	D	0	-18.4815	10.8794	0.46929	0.8425:0.1575:0.0:0.0	.	334	Q99973	TEP1_HUMAN	P	334	ENSP00000262715:S334P	ENSP00000262715:S334P	S	-	1	0	TEP1	19942642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.952000	0.63618	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
KLHL33	123103	hgsc.bcm.edu	37	14	20898426	20898426	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20898426A>G	ENST00000344581.4	-	2	631	c.409T>C	c.(409-411)Ttt>Ctt	p.F137L		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	137												all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		GCAGCCACAAAGGCCTCAAAC	0.597																																					p.F137L		Atlas-SNP	.											.	KLHL33	37	.	0			c.T409C						.						43.0	44.0	43.0					14																	20898426		692	1591	2283	SO:0001583	missense	123103	exon2			CCACAAAGGCCTC		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.409T>C	chr14.hg19:g.20898426A>G	ENSP00000341549:p.Phe137Leu	116.0	0.0		95.0	4.0	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	hg19	CCDS53882.1	.	.	.	.	.	.	.	.	.	.	A	18.19	3.569692	0.65765	.	.	ENSG00000185271	ENST00000344581	T	0.70749	-0.51	4.75	4.75	0.60458	BTB/Kelch-associated (2);	0.059847	0.64402	D	0.000002	T	0.67757	0.2927	L	0.42581	1.335	0.35511	D	0.800599	P	0.46784	0.884	P	0.48227	0.571	T	0.73880	-0.3843	10	0.33141	T	0.24	.	11.8692	0.52511	1.0:0.0:0.0:0.0	.	137	A6NCF5	KLH33_HUMAN	L	137	ENSP00000341549:F137L	ENSP00000341549:F137L	F	-	1	0	KLHL33	19968266	1.000000	0.71417	0.956000	0.39512	0.991000	0.79684	5.076000	0.64413	1.978000	0.57642	0.533000	0.62120	TTT	.	.		0.597	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
RNASE1	6035	hgsc.bcm.edu	37	14	21270132	21270132	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:21270132C>A	ENST00000397967.4	-	2	602	c.96G>T	c.(94-96)cgG>cgT	p.R32R	RNASE1_ENST00000555698.1_5'UTR|RNASE1_ENST00000397970.4_Silent_p.R32R|RNASE1_ENST00000340900.3_Silent_p.R32R|RNASE1_ENST00000412779.2_Silent_p.R32R	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	32					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATTTCTTGGCCCGGGATTCCT	0.577																																					p.R32R		Atlas-SNP	.											.	RNASE1	14	.	0			c.G96T						.						43.0	44.0	44.0					14																	21270132		2203	4300	6503	SO:0001819	synonymous_variant	6035	exon3			CTTGGCCCGGGAT	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.96G>T	chr14.hg19:g.21270132C>A		92.0	0.0		96.0	4.0	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	hg19	CCDS9559.1																																																																																			.	.		0.577	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21547122	21547122	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:21547122C>A	ENST00000298694.4	+	11	2453	c.2326C>A	c.(2326-2328)Cac>Aac	p.H776N	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.H776N			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	776						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.H776N(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CTCCAACCTGCACGTGCAGCA	0.627																																					p.H776N		Atlas-SNP	.											ARHGEF40,NS,carcinoma,0,1	ARHGEF40	84	.	1	Substitution - Missense(1)	ovary(1)	c.C2326A						.						61.0	55.0	57.0					14																	21547122		2203	4300	6503	SO:0001583	missense	55701	exon11			AACCTGCACGTGC		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.2326C>A	chr14.hg19:g.21547122C>A	ENSP00000298694:p.His776Asn	60.0	0.0		56.0	3.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.770771	0.31320	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02216	4.45;4.39	5.3	4.33	0.51752	.	0.411593	0.21075	N	0.080583	T	0.02193	0.0068	L	0.36672	1.1	0.09310	N	1	B;B	0.18310	0.027;0.009	B;B	0.16289	0.015;0.007	T	0.43245	-0.9403	10	0.27785	T	0.31	.	7.9979	0.30280	0.0:0.8892:0.0:0.1108	.	776;776	Q8TER5-4;Q8TER5	.;ARH40_HUMAN	N	776	ENSP00000298694:H776N;ENSP00000298693:H776N	ENSP00000298693:H776N	H	+	1	0	ARHGEF40	20616962	0.020000	0.18652	0.398000	0.26321	0.969000	0.65631	0.979000	0.29500	2.756000	0.94617	0.563000	0.77884	CAC	.	.		0.627	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
OXA1L	5018	hgsc.bcm.edu	37	14	23237290	23237290	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23237290G>T	ENST00000604262.1	+	3	372	c.349G>T	c.(349-351)Ggg>Tgg	p.G117W	OXA1L_ENST00000412791.1_Missense_Mutation_p.G117W|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000285848.5_Missense_Mutation_p.G177W|OXA1L_ENST00000358043.5_Missense_Mutation_p.G101W			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	117					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		ACTGGGGCTGGGGTCATACAC	0.542																																					p.G177W		Atlas-SNP	.											.	OXA1L	49	.	0			c.G529T						.						56.0	53.0	54.0					14																	23237290		2203	4300	6503	SO:0001583	missense	5018	exon3			GGGCTGGGGTCAT		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.349G>T	chr14.hg19:g.23237290G>T	ENSP00000474623:p.Gly117Trp	113.0	0.0		68.0	4.0	NM_005015	B4DPA2	Missense_Mutation	SNP	ENST00000604262.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.53	3.644409	0.67244	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.35048	1.33;1.38;1.36	5.76	4.87	0.63330	.	0.208448	0.49305	D	0.000155	T	0.62563	0.2438	M	0.83953	2.67	0.50313	D	0.999866	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.999;0.998	T	0.68025	-0.5518	10	0.62326	D	0.03	-11.0391	13.612	0.62086	0.0757:0.0:0.9243:0.0	.	117;117;117;177	B4DGZ2;E7EVY0;Q15070;Q2M1J6	.;.;OXA1L_HUMAN;.	W	177;117;101	ENSP00000285848:G177W;ENSP00000387601:G117W;ENSP00000350740:G101W	ENSP00000285848:G177W	G	+	1	0	OXA1L	22307130	1.000000	0.71417	0.815000	0.32552	0.641000	0.38312	6.169000	0.71913	1.432000	0.47375	0.655000	0.94253	GGG	.	.		0.542	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468876.1	NM_005015	
MMP14	4323	hgsc.bcm.edu	37	14	23314461	23314461	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23314461T>C	ENST00000311852.6	+	9	1564	c.1303T>C	c.(1303-1305)Tac>Cac	p.Y435H	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	435					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	CTTCCCCAGGTACTACCGTTT	0.572																																					p.Y435H		Atlas-SNP	.											.	MMP14	40	.	0			c.T1303C						.						56.0	45.0	49.0					14																	23314461		2203	4299	6502	SO:0001630	splice_region_variant	4323	exon9			CCCAGGTACTACC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1302-1T>C	chr14.hg19:g.23314461T>C		40.0	0.0		49.0	4.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	hg19	CCDS9577.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.423028	0.83559	.	.	ENSG00000157227	ENST00000311852	T	0.06849	3.25	5.45	5.45	0.79879	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.39384	0.1076	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53229	-0.8468	10	0.87932	D	0	.	14.4911	0.67651	0.0:0.0:0.0:1.0	.	435	P50281	MMP14_HUMAN	H	435	ENSP00000308208:Y435H	ENSP00000308208:Y435H	Y	+	1	0	MMP14	22384301	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.944000	0.87722	2.076000	0.62316	0.455000	0.32223	TAC	.	.		0.572	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	Missense_Mutation
SLC7A8	23428	hgsc.bcm.edu	37	14	23598939	23598939	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23598939T>C	ENST00000316902.7	-	9	1908	c.1183A>G	c.(1183-1185)Aac>Gac	p.N395D	SLC7A8_ENST00000422941.2_Missense_Mutation_p.N171D|SLC7A8_ENST00000529705.2_Missense_Mutation_p.N290D|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000453702.1_Missense_Mutation_p.N192D	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	395					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	AAGAGGTAGTTGATGAAGCCC	0.532																																					p.N395D		Atlas-SNP	.											.	SLC7A8	54	.	0			c.A1183G						.						250.0	215.0	227.0					14																	23598939		2203	4300	6503	SO:0001583	missense	23428	exon9			GGTAGTTGATGAA	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1183A>G	chr14.hg19:g.23598939T>C	ENSP00000320378:p.Asn395Asp	165.0	0.0		80.0	4.0	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.9|24.9	4.583889|4.583889	0.86748|0.86748	.|.	.|.	ENSG00000092068|ENSG00000092068	ENST00000316902;ENST00000453702;ENST00000529705;ENST00000422941;ENST00000206514|ENST00000334354	D;D;D;D|.	0.89939|.	-2.59;-2.59;-2.59;-2.59|.	5.86|5.86	5.86|5.86	0.93980|0.93980	Amino acid permease domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70263|0.70263	0.3204|0.3204	L|L	0.55103|0.55103	1.725|1.725	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;0.999;1.0|.	D;D;D|.	0.77557|.	0.988;0.984;0.99|.	T|T	0.71293|0.71293	-0.4636|-0.4636	10|6	0.21540|0.52906	T|T	0.41|0.07	.|.	15.2376|15.2376	0.73443|0.73443	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	290;171;395|.	B4DKT4;B4DTV6;Q9UHI5|.	.;.;LAT2_HUMAN|.	D|R	395;192;290;171;192|191	ENSP00000320378:N395D;ENSP00000391577:N192D;ENSP00000434345:N290D;ENSP00000416398:N171D|.	ENSP00000206514:N192D|ENSP00000334744:Q191R	N|Q	-|-	1|2	0|0	SLC7A8|SLC7A8	22668779|22668779	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.767000|7.767000	0.85331|0.85331	2.240000|2.240000	0.73641|0.73641	0.533000|0.533000	0.62120|0.62120	AAC|CAA	.	.		0.532	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
PABPN1	8106	hgsc.bcm.edu	37	14	23790983	23790983	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23790983C>T	ENST00000216727.4	+	1	486	c.305C>T	c.(304-306)cCg>cTg	p.P102L	PABPN1_ENST00000557702.1_5'Flank|BCL2L2-PABPN1_ENST00000553781.1_Intron|BCL2L2-PABPN1_ENST00000557008.1_Intron|PABPN1_ENST00000556821.1_5'UTR|AL049829.1_ENST00000594872.1_Silent_p.P45P|PABPN1_ENST00000397276.2_Missense_Mutation_p.P102L	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	102	Interacts with SKIP.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GAGGAGGAGCCGGGACTGGTC	0.781																																					p.P102L		Atlas-SNP	.											.	PABPN1	18	.	0			c.C305T						.						5.0	6.0	6.0					14																	23790983		1931	3826	5757	SO:0001583	missense	8106	exon1			AGGAGCCGGGACT	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"""RNA binding motif (RRM) containing"""	8565	protein-coding gene	gene with protein product		602279	"""poly(A)-binding protein, nuclear 1"""	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.305C>T	chr14.hg19:g.23790983C>T	ENSP00000216727:p.Pro102Leu	176.0	0.0		102.0	5.0	NM_004643	D3DS49|O43484	Missense_Mutation	SNP	ENST00000216727.4	hg19	CCDS9592.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.970224	0.53614	.	.	ENSG00000100836	ENST00000216727;ENST00000397276	T;T	0.57436	0.4;0.81	3.65	3.65	0.41850	.	0.000000	0.44902	U	0.000406	T	0.31796	0.0808	.	.	.	0.80722	D	1	P;P	0.40197	0.581;0.706	B;B	0.20384	0.013;0.029	T	0.24728	-1.0152	9	0.40728	T	0.16	-8.0E-4	10.1285	0.42665	0.2006:0.7994:0.0:0.0	.	102;102	Q86U42;Q86U42-2	PABP2_HUMAN;.	L	102	ENSP00000216727:P102L;ENSP00000380446:P102L	ENSP00000216727:P102L	P	+	2	0	PABPN1	22860823	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.852000	0.39348	2.049000	0.60858	0.456000	0.33151	CCG	.	.		0.781	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643	
MYH6	4624	hgsc.bcm.edu	37	14	23866382	23866382	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23866382G>T	ENST00000356287.3	-	16	2076	c.2047C>A	c.(2047-2049)Cca>Aca	p.P683T	MYH6_ENST00000405093.3_Missense_Mutation_p.P683T			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	683	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGCTCACCTGGAGCCTTCCGC	0.547																																					p.P683T		Atlas-SNP	.											.	MYH6	274	.	0			c.C2047A						.						143.0	141.0	141.0					14																	23866382		2203	4300	6503	SO:0001583	missense	4624	exon17			CACCTGGAGCCTT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2047C>A	chr14.hg19:g.23866382G>T	ENSP00000348634:p.Pro683Thr	110.0	0.0		93.0	4.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	17.87	3.494992	0.64186	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.74526	-0.85;-0.85	4.14	3.25	0.37280	Myosin head, motor domain (2);	.	.	.	.	D	0.89093	0.6617	H	0.98802	4.335	0.58432	D	0.999998	P	0.38420	0.63	P	0.51135	0.66	D	0.91006	0.4846	9	0.62326	D	0.03	.	12.3534	0.55161	0.0837:0.0:0.9163:0.0	.	683	P13533	MYH6_HUMAN	T	683	ENSP00000386041:P683T;ENSP00000348634:P683T	ENSP00000348634:P683T	P	-	1	0	MYH6	22936222	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.819000	0.91997	1.094000	0.41399	-0.157000	0.13467	CCA	.	.		0.547	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
MYH7	4625	hgsc.bcm.edu	37	14	23890225	23890225	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23890225C>A	ENST00000355349.3	-	26	3440	c.3278G>T	c.(3277-3279)aGg>aTg	p.R1093M	MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1093					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ATCCTCAATCCTTGCGTTGAG	0.587																																					p.R1093M		Atlas-SNP	.											.	MYH7	349	.	0			c.G3278T						.						94.0	86.0	89.0					14																	23890225		2203	4300	6503	SO:0001583	missense	4625	exon26			TCAATCCTTGCGT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3278G>T	chr14.hg19:g.23890225C>A	ENSP00000347507:p.Arg1093Met	160.0	0.0		100.0	5.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783576	0.70222	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.83591	-1.74	5.55	4.66	0.58398	Myosin tail (1);	.	.	.	.	D	0.89928	0.6857	M	0.87547	2.89	0.46849	D	0.999221	P	0.40266	0.71	P	0.55455	0.776	D	0.90717	0.4632	9	0.87932	D	0	.	9.774	0.40607	0.0:0.7863:0.0:0.2137	.	1093	P12883	MYH7_HUMAN	M	1093	ENSP00000347507:R1093M	ENSP00000347507:R1093M	R	-	2	0	MYH7	22960065	0.199000	0.23386	0.995000	0.50966	0.932000	0.56968	0.984000	0.29565	1.575000	0.49775	0.655000	0.94253	AGG	.	.		0.587	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
TM9SF1	10548	hgsc.bcm.edu	37	14	24662037	24662037	+	Silent	SNP	G	G	T	rs533902919		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:24662037G>T	ENST00000261789.4	-	3	1142	c.784C>A	c.(784-786)Cgg>Agg	p.R262R	TM9SF1_ENST00000396854.4_Silent_p.R262R|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000556387.1_Silent_p.R471R|TM9SF1_ENST00000528669.1_Silent_p.R262R|TM9SF1_ENST00000524835.1_Silent_p.R175R|TM9SF1_ENST00000530611.1_Silent_p.R471R	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	262					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AGGTCATTCCGAAGCACACGC	0.473																																					p.R262R		Atlas-SNP	.											.	TM9SF1	58	.	0			c.C784A						.						126.0	111.0	116.0					14																	24662037		2203	4300	6503	SO:0001819	synonymous_variant	10548	exon3			CATTCCGAAGCAC	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.784C>A	chr14.hg19:g.24662037G>T		144.0	0.0		100.0	4.0	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Silent	SNP	ENST00000261789.4	hg19	CCDS9617.1																																																																																			.	.		0.473	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
RIPK3	11035	hgsc.bcm.edu	37	14	24808320	24808320	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:24808320C>A	ENST00000216274.5	-	3	590	c.372G>T	c.(370-372)gtG>gtT	p.V124V	RIPK3_ENST00000554338.1_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	124	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TCCCAAGCACCACTTCTTTCA	0.612																																					p.V124V	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.G372T						.						60.0	66.0	64.0					14																	24808320		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon3			AAGCACCACTTCT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.372G>T	chr14.hg19:g.24808320C>A		103.0	0.0		67.0	4.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.612	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
PRKD1	5587	hgsc.bcm.edu	37	14	30066937	30066937	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:30066937G>A	ENST00000331968.5	-	16	2423	c.2194C>T	c.(2194-2196)Cgg>Tgg	p.R732W	PRKD1_ENST00000415220.2_Missense_Mutation_p.R740W	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	732	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CCAATGATCCGGGCAAAACCA	0.473																																					p.R732W		Atlas-SNP	.											PRKD1_ENST00000331968,right_upper_lobe,carcinoma,0,4	PRKD1	316	.	0			c.C2194T						.						50.0	55.0	53.0					14																	30066937		2203	4300	6503	SO:0001583	missense	5587	exon16			TGATCCGGGCAAA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2194C>T	chr14.hg19:g.30066937G>A	ENSP00000333568:p.Arg732Trp	34.0	0.0		24.0	2.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454641	0.84209	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.84873	-1.91;-1.91	5.72	3.76	0.43208	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.92286	0.7553	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93616	0.6943	10	0.87932	D	0	-11.0088	14.7829	0.69779	0.0:0.0:0.7372:0.2628	.	732	Q15139	KPCD1_HUMAN	W	732;740	ENSP00000333568:R732W;ENSP00000390535:R740W	ENSP00000333568:R732W	R	-	1	2	PRKD1	29136688	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.632000	0.67819	1.523000	0.49018	0.650000	0.86243	CGG	.	.		0.473	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
PRKD1	5587	hgsc.bcm.edu	37	14	30068321	30068321	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:30068321G>A	ENST00000331968.5	-	15	2307	c.2078C>T	c.(2077-2079)gCt>gTt	p.A693V	PRKD1_ENST00000415220.2_Missense_Mutation_p.A701V	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GTGCCGCAAAGCCACGAGTAT	0.358																																					p.A693V		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2078T						.						90.0	89.0	89.0					14																	30068321		2203	4300	6503	SO:0001583	missense	5587	exon15			CGCAAAGCCACGA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2078C>T	chr14.hg19:g.30068321G>A	ENSP00000333568:p.Ala693Val	101.0	0.0		70.0	4.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352183	0.95830	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.88124	-2.34;-2.34	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94618	0.8265	M	0.87269	2.87	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.94831	0.7996	10	0.87932	D	0	-15.3433	19.9348	0.97133	0.0:0.0:1.0:0.0	.	693	Q15139	KPCD1_HUMAN	V	693;701	ENSP00000333568:A693V;ENSP00000390535:A701V	ENSP00000333568:A693V	A	-	2	0	PRKD1	29138072	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.740000	0.98839	2.789000	0.95967	0.591000	0.81541	GCT	.	.		0.358	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
FBXO33	254170	hgsc.bcm.edu	37	14	39900875	39900875	+	Silent	SNP	A	A	G	rs377484603		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:39900875A>G	ENST00000298097.7	-	1	829	c.492T>C	c.(490-492)acT>acC	p.T164T	FBXO33_ENST00000554190.1_Silent_p.T36T	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	164					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		CCTCCCCTCCAGTCCCGGTGT	0.652																																					p.T164T		Atlas-SNP	.											.	FBXO33	21	.	0			c.T492C						.						38.0	42.0	41.0					14																	39900875		2203	4300	6503	SO:0001819	synonymous_variant	254170	exon1			CCCTCCAGTCCCG	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.492T>C	chr14.hg19:g.39900875A>G		94.0	0.0		70.0	4.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	hg19	CCDS9677.1																																																																																			.	.		0.652	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
FBXO33	254170	hgsc.bcm.edu	37	14	39900902	39900902	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:39900902C>T	ENST00000298097.7	-	1	802	c.465G>A	c.(463-465)ggG>ggA	p.G155G	FBXO33_ENST00000554190.1_Silent_p.G27G	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	155					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		CACCTCCGTCCCCTGGGCCAC	0.652																																					p.G155G		Atlas-SNP	.											.	FBXO33	21	.	0			c.G465A						.						33.0	39.0	37.0					14																	39900902		2201	4300	6501	SO:0001819	synonymous_variant	254170	exon1			TCCGTCCCCTGGG	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.465G>A	chr14.hg19:g.39900902C>T		110.0	0.0		83.0	4.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	hg19	CCDS9677.1																																																																																			.	.		0.652	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
FAM179B	23116	hgsc.bcm.edu	37	14	45465036	45465036	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:45465036A>G	ENST00000361577.3	+	2	2348	c.2134A>G	c.(2134-2136)Aga>Gga	p.R712G	FAM179B_ENST00000382233.2_Missense_Mutation_p.R712G|FAM179B_ENST00000361462.2_Missense_Mutation_p.R712G|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	712										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TAGCAGAAAAAGAGTATCAAG	0.343																																					p.R712G		Atlas-SNP	.											.	FAM179B	115	.	0			c.A2134G						.						102.0	99.0	100.0					14																	45465036		2203	4300	6503	SO:0001583	missense	23116	exon2			AGAAAAAGAGTAT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2134A>G	chr14.hg19:g.45465036A>G	ENSP00000355045:p.Arg712Gly	148.0	0.0		110.0	5.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629626	0.67015	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	5.42	5.42	0.78866	Armadillo-type fold (1);	0.174903	0.39687	N	0.001294	T	0.09642	0.0237	L	0.27053	0.805	0.37052	D	0.897644	D;D;D;D	0.67145	0.991;0.974;0.996;0.991	P;P;P;P	0.61874	0.801;0.731;0.895;0.801	T	0.15065	-1.0450	10	0.87932	D	0	-18.5762	9.6499	0.39890	0.8249:0.1751:0.0:0.0	.	712;712;712;712	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	G	712;712;712;712;31	ENSP00000355045:R712G;ENSP00000354917:R712G;ENSP00000371668:R712G;ENSP00000451141:R31G	ENSP00000354917:R712G	R	+	1	2	FAM179B	44534786	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.163000	0.64948	2.064000	0.61679	0.477000	0.44152	AGA	.	.		0.343	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
FANCM	57697	hgsc.bcm.edu	37	14	45633698	45633698	+	Missense_Mutation	SNP	G	G	T	rs550238354		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:45633698G>T	ENST00000267430.5	+	10	1803	c.1718G>T	c.(1717-1719)cGa>cTa	p.R573L	FANCM_ENST00000556036.1_Missense_Mutation_p.R573L|FANCM_ENST00000542564.2_Missense_Mutation_p.R547L	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	573	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CTTGTACAACGAATGGGTAGA	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R573L		Atlas-SNP	.											.	FANCM	225	.	0			c.G1718T						.						76.0	74.0	74.0					14																	45633698		2203	4300	6503	SO:0001583	missense	57697	exon10	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACAACGAATGGG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.1718G>T	chr14.hg19:g.45633698G>T	ENSP00000267430:p.Arg573Leu	128.0	0.0		80.0	4.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	34	5.394071	0.96009	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	D;D;D	0.81908	-1.55;-1.55;-1.55	6.07	6.07	0.98685	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.95677	0.8594	H	0.99325	4.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96905	0.9663	10	0.87932	D	0	.	20.2544	0.98414	0.0:0.0:1.0:0.0	.	547;573;573	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	L	573;573;547	ENSP00000450596:R573L;ENSP00000267430:R573L;ENSP00000442493:R547L	ENSP00000267430:R573L	R	+	2	0	FANCM	44703448	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.432000	0.97498	2.885000	0.99019	0.655000	0.94253	CGA	.	.		0.423	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
MDGA2	161357	hgsc.bcm.edu	37	14	47613426	47613426	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:47613426T>C	ENST00000399232.2	-	4	804	c.440A>G	c.(439-441)gAa>gGa	p.E147G	MDGA2_ENST00000439988.3_Missense_Mutation_p.E216G|MDGA2_ENST00000426342.1_5'UTR|MDGA2_ENST00000357362.3_5'UTR	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	147	Ig-like 2.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						GTAAAATTGTTCTTTAGCTTC	0.408																																					p.E216G		Atlas-SNP	.											.	MDGA2	470	.	0			c.A647G						.						147.0	132.0	136.0					14																	47613426		692	1591	2283	SO:0001583	missense	161357	exon4			AATTGTTCTTTAG	AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19835	protein-coding gene	gene with protein product		611128	"""MAM domain containing 1"""	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.440A>G	chr14.hg19:g.47613426T>C	ENSP00000382178:p.Glu147Gly	146.0	0.0		112.0	5.0	NM_001113498	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.63	3.175804	0.57692	.	.	ENSG00000139915	ENST00000439988;ENST00000399232	T;T	0.42900	0.96;0.96	5.52	5.52	0.82312	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.52532	U	0.000071	T	0.28599	0.0708	N	0.17474	0.49	0.80722	D	1	B	0.14012	0.009	B	0.22880	0.042	T	0.09509	-1.0671	10	0.17832	T	0.49	.	14.4758	0.67546	0.0:0.0:0.0:1.0	.	147	Q7Z553	MDGA2_HUMAN	G	147;216	ENSP00000400011:E147G;ENSP00000382178:E216G	ENSP00000382178:E216G	E	-	2	0	MDGA2	46683176	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.621000	0.83083	2.108000	0.64289	0.477000	0.44152	GAA	.	.		0.408	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830	
NID2	22795	hgsc.bcm.edu	37	14	52509008	52509008	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:52509008A>G	ENST00000216286.5	-	7	1639	c.1640T>C	c.(1639-1641)gTg>gCg	p.V547A	NID2_ENST00000541773.1_Missense_Mutation_p.V494A	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	547	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					AGTGAAGTGCACGGGTGTATG	0.577																																					p.V547A		Atlas-SNP	.											.	NID2	201	.	0			c.T1640C						.						139.0	141.0	140.0					14																	52509008		2203	4300	6503	SO:0001583	missense	22795	exon7			AAGTGCACGGGTG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1640T>C	chr14.hg19:g.52509008A>G	ENSP00000216286:p.Val547Ala	137.0	0.0		82.0	5.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155519	0.57259	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.35236	1.32;1.32	6.17	6.17	0.99709	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.052456	0.85682	D	0.000000	T	0.64918	0.2642	M	0.84326	2.69	0.42283	D	0.992109	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.995;0.992;1.0;0.998	T	0.69892	-0.5022	10	0.72032	D	0.01	.	16.4837	0.84171	1.0:0.0:0.0:0.0	.	141;494;549;547	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	A	547;141;494;549	ENSP00000216286:V547A;ENSP00000443730:V494A	ENSP00000216286:V547A	V	-	2	0	NID2	51578758	1.000000	0.71417	0.990000	0.47175	0.009000	0.06853	8.901000	0.92560	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
WDHD1	11169	hgsc.bcm.edu	37	14	55434060	55434060	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:55434060C>T	ENST00000360586.3	-	17	2181	c.2116G>A	c.(2116-2118)Gtt>Att	p.V706I	WDHD1_ENST00000421192.1_Missense_Mutation_p.V583I|WDHD1_ENST00000359167.4_Missense_Mutation_p.V224I|WDHD1_ENST00000420358.2_Missense_Mutation_p.V583I	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	706					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						AATATAGCAACAGCAGGGCGT	0.388																																					p.V706I		Atlas-SNP	.											.	WDHD1	82	.	0			c.G2116A						.						96.0	94.0	95.0					14																	55434060		2203	4300	6503	SO:0001583	missense	11169	exon17			TAGCAACAGCAGG	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2116G>A	chr14.hg19:g.55434060C>T	ENSP00000353793:p.Val706Ile	101.0	0.0		82.0	4.0	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	hg19	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815286	0.32053	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.62232	0.42;0.83;0.04	5.34	3.54	0.40534	.	0.137252	0.48286	N	0.000181	T	0.52125	0.1715	L	0.40543	1.245	0.54753	D	0.999984	B;B	0.22414	0.069;0.006	B;B	0.27715	0.082;0.006	T	0.40590	-0.9555	10	0.27082	T	0.32	.	11.7104	0.51623	0.0:0.8575:0.0:0.1425	.	224;706	F8W7P7;O75717	.;WDHD1_HUMAN	I	706;224;583	ENSP00000353793:V706I;ENSP00000352085:V224I;ENSP00000391049:V583I	ENSP00000352085:V224I	V	-	1	0	WDHD1	54503810	0.996000	0.38824	0.679000	0.29978	0.438000	0.31896	2.338000	0.43957	0.643000	0.30638	0.655000	0.94253	GTT	.	.		0.388	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
SLC38A6	145389	hgsc.bcm.edu	37	14	61550393	61550393	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550393T>C	ENST00000354886.2	+	17	1693	c.1529T>C	c.(1528-1530)aTc>aCc	p.I510T	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	346					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		cacaccttgatcttgcacttc	0.463																																					p.I510T		Atlas-SNP	.											.	SLC38A6	87	.	0			c.T1529C						.																																			SO:0001583	missense	145389	exon17			CCTTGATCTTGCA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1529T>C	chr14.hg19:g.61550393T>C	ENSP00000346959:p.Ile510Thr	99.0	0.0		92.0	4.0	NM_001172702	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000354886.2	hg19	CCDS53900.1	.	.	.	.	.	.	.	.	.	.	T	5.651	0.304812	0.10678	.	.	ENSG00000139974	ENST00000354886;ENST00000451406	T;T	0.06142	3.34;3.34	2.8	-2.93	0.05598	.	.	.	.	.	T	0.04634	0.0126	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	8	0.87932	D	0	.	4.0768	0.09908	0.1611:0.3483:0.0:0.4905	.	510	Q8IZM9-2	.	T	510;505	ENSP00000346959:I510T;ENSP00000395851:I505T	ENSP00000346959:I510T	I	+	2	0	SLC38A6	60620146	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.840000	0.04363	-1.120000	0.02953	-1.162000	0.01777	ATC	.	.		0.463	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
SLC38A6	145389	hgsc.bcm.edu	37	14	61550399	61550399	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550399A>G	ENST00000354886.2	+	17	1699	c.1535A>G	c.(1534-1536)cAc>cGc	p.H512R	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	348					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ttgatcttgcacttcccaacc	0.458																																					p.H512R		Atlas-SNP	.											.	SLC38A6	87	.	0			c.A1535G						.																																			SO:0001583	missense	145389	exon17			TCTTGCACTTCCC	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1535A>G	chr14.hg19:g.61550399A>G	ENSP00000346959:p.His512Arg	96.0	0.0		84.0	5.0	NM_001172702	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000354886.2	hg19	CCDS53900.1	.	.	.	.	.	.	.	.	.	.	A	8.343	0.829158	0.16749	.	.	ENSG00000139974	ENST00000354886;ENST00000451406	T;T	0.05139	3.49;3.49	2.9	-0.921	0.10472	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.09310	N	1	B	0.25169	0.119	B	0.23574	0.047	T	0.40961	-0.9535	8	0.87932	D	0	.	3.0296	0.06102	0.5001:0.2305:0.2694:0.0	.	512	Q8IZM9-2	.	R	512;507	ENSP00000346959:H512R;ENSP00000395851:H507R	ENSP00000346959:H512R	H	+	2	0	SLC38A6	60620152	0.000000	0.05858	0.003000	0.11579	0.032000	0.12392	-0.124000	0.10595	-0.173000	0.10761	0.528000	0.53228	CAC	.	.		0.458	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
SLC38A6	145389	hgsc.bcm.edu	37	14	61550409	61550409	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550409C>A	ENST00000354886.2	+	17	1709	c.1545C>A	c.(1543-1545)acC>acA	p.T515T	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	351					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		acttcccaacctccagaactg	0.448																																					p.T515T		Atlas-SNP	.											.	SLC38A6	87	.	0			c.C1545A						.																																			SO:0001819	synonymous_variant	145389	exon17			CCCAACCTCCAGA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1545C>A	chr14.hg19:g.61550409C>A		87.0	0.0		79.0	4.0	NM_001172702	C9JWA6|Q86SY5	Silent	SNP	ENST00000354886.2	hg19	CCDS53900.1																																																																																			.	.		0.448	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
PRKCH	5583	hgsc.bcm.edu	37	14	61920071	61920071	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61920071G>T	ENST00000332981.5	+	7	1345	c.960G>T	c.(958-960)tcG>tcT	p.S320S	PRKCH_ENST00000555082.1_Splice_Site_p.S159S	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	320					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CTCCAACCTCGGTGAGACTTT	0.483																																					p.S320S	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.G960T						.						76.0	64.0	68.0					14																	61920071		2203	4300	6503	SO:0001630	splice_region_variant	5583	exon7			AACCTCGGTGAGA	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.960+1G>T	chr14.hg19:g.61920071G>T		114.0	0.0		112.0	5.0	NM_006255	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	hg19	CCDS9752.1																																																																																			.	.		0.483	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255	Silent
SYNE2	23224	hgsc.bcm.edu	37	14	64641845	64641845	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:64641845A>G	ENST00000344113.4	+	95	17631	c.17419A>G	c.(17419-17421)Agc>Ggc	p.S5807G	SYNE2_ENST00000358025.3_Missense_Mutation_p.S5807G|SYNE2_ENST00000357395.3_Missense_Mutation_p.S2192G|SYNE2_ENST00000394768.2_Missense_Mutation_p.S2192G|SYNE2_ENST00000555002.1_Missense_Mutation_p.S2441G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Missense_Mutation_p.S5672G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5807					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCAGTTCCAGAGCACTGTAGA	0.413																																					p.S5807G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A17419G						.						71.0	73.0	72.0					14																	64641845		2203	4300	6503	SO:0001583	missense	23224	exon95			TTCCAGAGCACTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17419A>G	chr14.hg19:g.64641845A>G	ENSP00000341781:p.Ser5807Gly	88.0	0.0		113.0	5.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	9.500	1.103026	0.20632	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.75589	1.31;1.31;1.31;-0.95;1.31;1.31	5.46	3.09	0.35607	.	0.395446	0.23847	N	0.043988	T	0.60143	0.2246	L	0.52364	1.645	0.41980	D	0.990793	B;B;B;B;B	0.18310	0.003;0.001;0.004;0.004;0.027	B;B;B;B;B	0.15484	0.011;0.003;0.006;0.005;0.013	T	0.49244	-0.8960	10	0.02654	T	1	.	7.6073	0.28110	0.8192:0.0:0.1808:0.0	.	2192;195;5672;5807;5807	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	G	5807;2192;5807;5672;5678;2441;2192	ENSP00000350719:S5807G;ENSP00000349969:S2192G;ENSP00000341781:S5807G;ENSP00000452570:S5672G;ENSP00000450831:S2441G;ENSP00000378249:S2192G	ENSP00000261678:S5678G	S	+	1	0	SYNE2	63711598	0.975000	0.34042	0.703000	0.30354	0.173000	0.22820	1.135000	0.31454	0.446000	0.26666	0.482000	0.46254	AGC	.	.		0.413	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
RAB15	376267	hgsc.bcm.edu	37	14	65417736	65417736	+	Intron	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:65417736G>T	ENST00000533601.2	-	4	662				FNTB_ENST00000542227.1_Intron|RAB15_ENST00000267512.5_Missense_Mutation_p.A127E|RAB15_ENST00000426039.3_Intron|RAB15_ENST00000436278.2_Missense_Mutation_p.A81E|CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000447296.2_Intron			P59190	RAB15_HUMAN	RAB15, member RAS oncogene family						protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	8				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		CCCTCGCCTTGCCTTCCCCGG	0.582																																					p.A127E		Atlas-SNP	.											.	RAB15	23	.	0			c.C380A						.						68.0	61.0	63.0					14																	65417736		2203	4300	6503	SO:0001627	intron_variant	376267	exon4			CGCCTTGCCTTCC	BC014511	CCDS9768.1	14q23.2	2012-02-28	2012-02-28		ENSG00000139998	ENSG00000139998		"""RAB, member RAS oncogene"""	20150	protein-coding gene	gene with protein product						11697911	Standard	NM_198686		Approved		uc001xhz.2	P59190	OTTHUMG00000142810	ENST00000533601.2:c.324+55C>A	chr14.hg19:g.65417736G>T		31.0	0.0		35.0	5.0	NM_198686	G5EMR7|Q86TX7|Q8IW89	Missense_Mutation	SNP	ENST00000533601.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.336	1.061676	0.19987	.	.	ENSG00000139998	ENST00000267512	T	0.66099	-0.19	4.44	0.293	0.15742	.	0.752556	0.10886	N	0.623228	T	0.29976	0.0750	N	0.04768	-0.165	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.17289	-1.0374	10	0.10636	T	0.68	.	0.8357	0.01140	0.262:0.1695:0.395:0.1735	.	127	P59190-2	.	E	127	ENSP00000267512:A127E	ENSP00000267512:A127E	A	-	2	0	RAB15	64487489	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	-0.067000	0.11579	0.066000	0.16515	0.462000	0.41574	GCA	.	.		0.582	RAB15-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000390443.2	NM_198686	
FUT8	2530	hgsc.bcm.edu	37	14	66083023	66083023	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:66083023G>T	ENST00000360689.5	+	5	2141	c.414G>T	c.(412-414)aaG>aaT	p.K138N	FUT8_ENST00000394585.1_Missense_Mutation_p.K138N|FUT8_ENST00000358307.2_5'UTR|FUT8_ENST00000394586.2_Missense_Mutation_p.K138N|FUT8_ENST00000557164.1_5'UTR	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	138					cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		AGAAATTAAAGAACTTAGAAG	0.378																																					p.K138N		Atlas-SNP	.											FUT8_ENST00000360689,NS,carcinoma,0,4	FUT8	101	.	0			c.G414T						.						66.0	72.0	70.0					14																	66083023		2203	4299	6502	SO:0001583	missense	2530	exon5			ATTAAAGAACTTA	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"""Fucosyltransferases"""	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.414G>T	chr14.hg19:g.66083023G>T	ENSP00000353910:p.Lys138Asn	115.0	0.0		86.0	4.0	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	hg19	CCDS9775.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120068	0.37436	.	.	ENSG00000033170	ENST00000360689;ENST00000394586;ENST00000394585	T;T;T	0.21031	2.03;2.03;2.03	5.81	1.49	0.22878	.	0.315147	0.38111	N	0.001818	T	0.14874	0.0359	L	0.35854	1.095	0.80722	D	1	B	0.25719	0.132	B	0.21546	0.035	T	0.06881	-1.0802	10	0.62326	D	0.03	-12.1693	7.9475	0.29995	0.4102:0.0:0.5898:0.0	.	138	Q9BYC5	FUT8_HUMAN	N	138	ENSP00000353910:K138N;ENSP00000378087:K138N;ENSP00000378086:K138N	ENSP00000345865:K138N	K	+	3	2	FUT8	65152776	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	1.151000	0.31651	0.393000	0.25203	0.557000	0.71058	AAG	.	.		0.378	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480	
RDH11	51109	hgsc.bcm.edu	37	14	68157901	68157901	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:68157901T>C	ENST00000381346.4	-	4	520	c.410A>G	c.(409-411)aAg>aGg	p.K137R	RDH11_ENST00000428130.2_Missense_Mutation_p.K137R|RDH11_ENST00000553384.1_Missense_Mutation_p.K124R|RP11-1012A1.4_ENST00000553306.1_5'Flank|RP11-1012A1.4_ENST00000554493.1_5'Flank	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	137					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	ATCTGCTGTCTTCGAGTACGG	0.478																																					p.K137R		Atlas-SNP	.											.	RDH11	21	.	0			c.A410G						.						271.0	252.0	258.0					14																	68157901		2203	4300	6503	SO:0001583	missense	51109	exon4			GCTGTCTTCGAGT	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	17964	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 1"", ""androgen-regulated short-chain dehydrogenase/reductase 1"""	607849	"""retinol dehydrogenase 11 (all-trans and 9-cis)"""			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.410A>G	chr14.hg19:g.68157901T>C	ENSP00000370750:p.Lys137Arg	129.0	0.0		89.0	4.0	NM_001252650	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	hg19	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.082882	0.55861	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000554035;ENST00000557726	D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26	5.85	5.85	0.93711	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.83524	0.5273	N	0.14661	0.345	0.48632	D	0.999686	P;P;P	0.51240	0.943;0.889;0.91	P;P;P	0.53912	0.733;0.618;0.737	T	0.80832	-0.1206	10	0.12766	T	0.61	.	16.2365	0.82377	0.0:0.0:0.0:1.0	.	137;124;137	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	R	137;124;137;36;85	ENSP00000370750:K137R;ENSP00000452079:K124R;ENSP00000416395:K137R;ENSP00000450802:K36R;ENSP00000450435:K85R	ENSP00000370750:K137R	K	-	2	0	RDH11	67227654	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.054000	0.64275	2.238000	0.73509	0.477000	0.44152	AAG	.	.		0.478	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3		
PLEKHD1	400224	hgsc.bcm.edu	37	14	69967627	69967627	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:69967627A>G	ENST00000322564.7	+	4	585	c.373A>G	c.(373-375)Acc>Gcc	p.T125A		NM_001161498.1	NP_001154970.1	A6NEE1	PLHD1_HUMAN	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	125	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(1)|endometrium(1)|kidney(2)	4						GTTTGAGCAGACCCAGTGGCT	0.632																																					p.T125A		Atlas-SNP	.											.	PLEKHD1	24	.	0			c.A373G						.						72.0	66.0	68.0					14																	69967627		692	1591	2283	SO:0001583	missense	400224	exon4			GAGCAGACCCAGT	AK126770	CCDS53903.1	14q24.1	2013-01-10	2011-05-04		ENSG00000175985	ENSG00000175985		"""Pleckstrin homology (PH) domain containing"""	20148	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family D (with M protein repeats) member 1"""				Standard	NM_001161498		Approved	UPF0639	uc010ttf.1	A6NEE1		ENST00000322564.7:c.373A>G	chr14.hg19:g.69967627A>G	ENSP00000317175:p.Thr125Ala	64.0	0.0		60.0	4.0	NM_001161498	B9EJC2	Missense_Mutation	SNP	ENST00000322564.7	hg19	CCDS53903.1	.	.	.	.	.	.	.	.	.	.	A	3.643	-0.073041	0.07228	.	.	ENSG00000175985	ENST00000322564	T	0.74947	-0.89	4.56	2.13	0.27403	.	.	.	.	.	T	0.55449	0.1921	N	0.19112	0.55	0.25436	N	0.988134	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	8	.	.	.	.	7.5933	0.28033	0.7438:0.0:0.2562:0.0	.	125	B9EJC2	.	A	125	ENSP00000317175:T125A	.	T	+	1	0	PLEKHD1	69037380	0.984000	0.35163	0.995000	0.50966	0.614000	0.37383	1.559000	0.36320	0.792000	0.33850	0.459000	0.35465	ACC	.	.		0.632	PLEKHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412451.2	NM_001161498	
PAPLN	89932	hgsc.bcm.edu	37	14	73720573	73720573	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:73720573G>T	ENST00000554301.1	+	11	1369	c.1206G>T	c.(1204-1206)gaG>gaT	p.E402D	PAPLN_ENST00000555445.1_Missense_Mutation_p.E402D|PAPLN_ENST00000340738.5_Missense_Mutation_p.E375D|PAPLN_ENST00000427855.1_Missense_Mutation_p.E402D|PAPLN_ENST00000381166.3_Missense_Mutation_p.E402D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	402	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AGGCCGTGGAGGAGGCTGAGT	0.692																																					p.E375D		Atlas-SNP	.											.	PAPLN	180	.	0			c.G1125T						.						35.0	37.0	36.0					14																	73720573		2202	4300	6502	SO:0001583	missense	89932	exon11			CGTGGAGGAGGCT	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1206G>T	chr14.hg19:g.73720573G>T	ENSP00000451803:p.Glu402Asp	145.0	0.0		94.0	4.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	hg19		.	.	.	.	.	.	.	.	.	.	G	1.192	-0.634944	0.03584	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22	5.1	-3.13	0.05266	.	.	.	.	.	T	0.22666	0.0547	N	0.04320	-0.23	0.20196	N	0.999923	B;B;B	0.28933	0.011;0.014;0.228	B;B;B	0.24541	0.006;0.01;0.054	T	0.20773	-1.0265	9	0.10111	T	0.7	.	2.3034	0.04168	0.1429:0.3301:0.2631:0.2639	.	402;402;375	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	D	375;402;402;402;402	ENSP00000345395:E375D;ENSP00000403403:E402D;ENSP00000370558:E402D;ENSP00000451803:E402D;ENSP00000451729:E402D	ENSP00000216658:E402D	E	+	3	2	PAPLN	72790326	0.978000	0.34361	0.016000	0.15963	0.099000	0.18886	0.119000	0.15626	-0.359000	0.08150	-0.379000	0.06801	GAG	.	.		0.692	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
HEATR4	399671	hgsc.bcm.edu	37	14	73969702	73969702	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:73969702A>G	ENST00000553558.1	-	11	2323	c.2002T>C	c.(2002-2004)Ttg>Ctg	p.L668L	HEATR4_ENST00000560393.1_Silent_p.L621L|HEATR4_ENST00000334988.2_Silent_p.L668L	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	668										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		AGCTGGATCAACTTATGTTTC	0.403																																					p.L668L		Atlas-SNP	.											.	HEATR4	126	.	0			c.T2002C						.						109.0	98.0	101.0					14																	73969702		2203	4300	6503	SO:0001819	synonymous_variant	399671	exon10			GGATCAACTTATG	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2002T>C	chr14.hg19:g.73969702A>G		84.0	0.0		88.0	4.0	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	.		0.403	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
ALDH6A1	4329	hgsc.bcm.edu	37	14	74534081	74534081	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:74534081A>G	ENST00000553458.1	-	8	1141		c.e8+1		ALDH6A1_ENST00000555126.1_Splice_Site|CCDC176_ENST00000553773.1_Intron|AC005484.5_ENST00000492026.1_RNA|ALDH6A1_ENST00000350259.4_Splice_Site	NM_001278593.1|NM_005589.2	NP_001265522.1|NP_005580.1	Q02252	MMSA_HUMAN	aldehyde dehydrogenase 6 family, member A1						branched-chain amino acid catabolic process (GO:0009083)|brown fat cell differentiation (GO:0050873)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|thymine metabolic process (GO:0019859)|valine catabolic process (GO:0006574)|valine metabolic process (GO:0006573)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fatty-acyl-CoA binding (GO:0000062)|malonate-semialdehyde dehydrogenase (acetylating) activity (GO:0018478)|methylmalonate-semialdehyde dehydrogenase (acylating) activity (GO:0004491)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(3)|skin(3)	21				BRCA - Breast invasive adenocarcinoma(234;0.00354)		GTGATTGATTACCTGCATTGA	0.507																																					.		Atlas-SNP	.											.	ALDH6A1	42	.	0			c.1042+2T>C						.						72.0	71.0	71.0					14																	74534081		2203	4300	6503	SO:0001630	splice_region_variant	4329	exon9			TTGATTACCTGCA	M93405	CCDS9826.1, CCDS61501.1	14q24.3	2014-02-03			ENSG00000119711	ENSG00000119711	1.2.1.27	"""Aldehyde dehydrogenases"""	7179	protein-coding gene	gene with protein product		603178		MMSDH		1527093	Standard	NM_005589		Approved		uc001xpo.3	Q02252	OTTHUMG00000171203	ENST00000553458.1:c.1042+1T>C	chr14.hg19:g.74534081A>G		63.0	0.0		73.0	4.0	NM_005589	B2R609|B4DFS8|J3KNU8|Q9UKM8	Splice_Site	SNP	ENST00000553458.1	hg19	CCDS9826.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.007886	0.75046	.	.	ENSG00000119711	ENST00000553458;ENST00000350259;ENST00000555126	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9558	0.71113	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ALDH6A1	73603834	1.000000	0.71417	0.935000	0.37517	0.955000	0.61496	9.084000	0.94076	2.270000	0.75569	0.482000	0.46254	.	.	.		0.507	ALDH6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412309.1		Intron
ADCK1	57143	hgsc.bcm.edu	37	14	78374194	78374194	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:78374194G>T	ENST00000238561.5	+	7	889	c.790G>T	c.(790-792)Gag>Tag	p.E264*	ADCK1_ENST00000341211.5_Nonsense_Mutation_p.E196*	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	271	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		CCTCCTGATGGAGTTTGTGGA	0.592																																					p.E264X		Atlas-SNP	.											.	ADCK1	81	.	0			c.G790T						.						104.0	90.0	95.0					14																	78374194		2203	4300	6503	SO:0001587	stop_gained	57143	exon7			CTGATGGAGTTTG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.790G>T	chr14.hg19:g.78374194G>T	ENSP00000238561:p.Glu264*	147.0	0.0		71.0	5.0	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Nonsense_Mutation	SNP	ENST00000238561.5	hg19	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	G	39	7.883161	0.98542	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	.	.	.	4.76	4.76	0.60689	.	0.048925	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-40.5031	17.9868	0.89158	0.0:0.0:1.0:0.0	.	.	.	.	X	264;196	.	ENSP00000238561:E264X	E	+	1	0	ADCK1	77443947	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.411000	0.97342	2.473000	0.83533	0.561000	0.74099	GAG	.	.		0.592	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
NRXN3	9369	hgsc.bcm.edu	37	14	80130289	80130289	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:80130289A>G	ENST00000557594.1	+	3	1551	c.598A>G	c.(598-600)Aca>Gca	p.T200A	NRXN3_ENST00000554719.1_Missense_Mutation_p.T832A|RP11-242P2.1_ENST00000553322.1_RNA|NRXN3_ENST00000556003.1_3'UTR|NRXN3_ENST00000281127.7_Missense_Mutation_p.T200A|NRXN3_ENST00000335750.5_Missense_Mutation_p.T832A|NRXN3_ENST00000428277.2_Missense_Mutation_p.T200A	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	200	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ACATTATCCTACAGGTACATG	0.478																																					p.T832A		Atlas-SNP	.											.	NRXN3	342	.	0			c.A2494G						.						120.0	109.0	113.0					14																	80130289		2203	4300	6503	SO:0001583	missense	9369	exon14			TATCCTACAGGTA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.598A>G	chr14.hg19:g.80130289A>G	ENSP00000451672:p.Thr200Ala	115.0	0.0		93.0	4.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	hg19		.	.	.	.	.	.	.	.	.	.	A	3.606	-0.080515	0.07141	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.77877	-1.13;-1.13;-1.05;-1.05;-1.05	5.38	4.1	0.47936	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.270973	0.35013	N	0.003515	T	0.52256	0.1723	N	0.04335	-0.225	0.27521	N	0.951405	B;B;B;B	0.15473	0.013;0.0;0.0;0.0	B;B;B;B	0.24701	0.055;0.0;0.001;0.0	T	0.37220	-0.9715	9	.	.	.	.	5.9111	0.19029	0.6982:0.0:0.0813:0.2204	.	200;200;200;832	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	A	1205;1194;832;832;200;200;200	ENSP00000451648:T832A;ENSP00000338349:T832A;ENSP00000451672:T200A;ENSP00000281127:T200A;ENSP00000394426:T200A	.	T	+	1	0	NRXN3	79200042	0.492000	0.26027	1.000000	0.80357	0.861000	0.49209	1.248000	0.32827	2.159000	0.67721	0.379000	0.24179	ACA	.	.		0.478	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250	
CEP128	145508	hgsc.bcm.edu	37	14	80971326	80971326	+	Missense_Mutation	SNP	C	C	A	rs377362585		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:80971326C>A	ENST00000555265.1	-	24	3485	c.3110G>T	c.(3109-3111)gGg>gTg	p.G1037V	CEP128_ENST00000553717.1_5'UTR|CEP128_ENST00000281129.3_Missense_Mutation_p.G1037V			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	1037						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						GTGATCTAACCCACGAGTGTG	0.423																																					p.G1037V		Atlas-SNP	.											.	CEP128	146	.	0			c.G3110T						.	C	VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	68.0	65.0	66.0		3110	3.4	0.0	14		66	0,8600		0,0,4300	no	missense	CEP128	NM_152446.3	109	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	benign	1037/1095	80971326	1,13005	2203	4300	6503	SO:0001583	missense	145508	exon23			TCTAACCCACGAG	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.3110G>T	chr14.hg19:g.80971326C>A	ENSP00000451162:p.Gly1037Val	78.0	0.0		60.0	4.0	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.36|11.36	1.615669|1.615669	0.28801|0.28801	2.27E-4|2.27E-4	0.0|0.0	ENSG00000100629|ENSG00000100629	ENST00000281129;ENST00000555265|ENST00000556061	T;T|.	0.33216|.	1.42;1.42|.	5.32|5.32	3.38|3.38	0.38709|0.38709	.|.	0.718872|.	0.12773|.	N|.	0.440346|.	T|T	0.23965|0.23965	0.0580|0.0580	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999999|0.999999	B|.	0.16603|.	0.018|.	B|.	0.19946|.	0.027|.	T|T	0.19386|0.19386	-1.0307|-1.0307	10|5	0.37606|.	T|.	0.19|.	.|.	5.7203|5.7203	0.17982|0.17982	0.187:0.7092:0.0:0.1037|0.187:0.7092:0.0:0.1037	.|.	1037|.	Q6ZU80|.	CE128_HUMAN|.	V|C	1037|102	ENSP00000281129:G1037V;ENSP00000451162:G1037V|.	ENSP00000281129:G1037V|.	G|W	-|-	2|3	0|0	CEP128|CEP128	80041079|80041079	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.167000|0.167000	0.22549|0.22549	0.136000|0.136000	0.15974|0.15974	0.708000|0.708000	0.31955|0.31955	-0.355000|-0.355000	0.07637|0.07637	GGG|TGG	.	.		0.423	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
PTPN21	11099	hgsc.bcm.edu	37	14	88974267	88974267	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:88974267C>T	ENST00000556564.1	-	4	732	c.448G>A	c.(448-450)Gcg>Acg	p.A150T	RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000554628.1_5'UTR|PTPN21_ENST00000328736.3_Splice_Site_p.A150T	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	150	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCTTATTTACCTTGAACAGCT	0.313																																					p.A150T		Atlas-SNP	.											.	PTPN21	113	.	0			c.G448A						.						73.0	68.0	70.0					14																	88974267		2202	4299	6501	SO:0001630	splice_region_variant	11099	exon4			ATTTACCTTGAAC	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.448+1G>A	chr14.hg19:g.88974267C>T		95.0	0.0		79.0	4.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	35	5.508892	0.96386	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000555243	T;T;T	0.79554	-1.28;-1.28;-1.28	5.36	5.36	0.76844	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.137638	0.48767	D	0.000178	D	0.92080	0.7490	M	0.91510	3.215	0.53005	D	0.999963	D;P	0.89917	1.0;0.875	D;P	0.78314	0.991;0.672	D	0.93399	0.6758	9	.	.	.	.	19.0908	0.93225	0.0:1.0:0.0:0.0	.	150;150	G3V3S6;Q16825	.;PTN21_HUMAN	T	150	ENSP00000330276:A150T;ENSP00000452414:A150T;ENSP00000451401:A150T	.	A	-	1	0	PTPN21	88044020	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.818000	0.86416	2.498000	0.84270	0.591000	0.81541	GCG	.	.		0.313	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		Missense_Mutation
GPR68	8111	hgsc.bcm.edu	37	14	91700499	91700499	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:91700499C>T	ENST00000531499.2	-	2	1235	c.896G>A	c.(895-897)cGc>cAc	p.R299H	GPR68_ENST00000238699.3_Missense_Mutation_p.R309H|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.R299H			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	299					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		CCCGCGGAGGCGGGCCAGGTC	0.711																																					p.R299H		Atlas-SNP	.											GPR68,colon,carcinoma,0,1	GPR68	32	.	0			c.G896A						.						8.0	12.0	11.0					14																	91700499		2110	4150	6260	SO:0001583	missense	8111	exon2			CGGAGGCGGGCCA	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.896G>A	chr14.hg19:g.91700499C>T	ENSP00000434045:p.Arg299His	40.0	0.0		32.0	11.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728328	0.69074	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.26	5.26	0.73747	.	0.226361	0.35739	N	0.003009	T	0.45915	0.1366	L	0.27053	0.805	0.30915	N	0.728668	D;D	0.89917	1.0;1.0	D;D	0.65443	0.935;0.935	T	0.51474	-0.8701	10	0.66056	D	0.02	.	8.091	0.30801	0.0:0.8617:0.0:0.1383	.	299;299	Q6NWR5;Q15743	.;OGR1_HUMAN	H	299;309;299;299	ENSP00000434045:R299H;ENSP00000238699:R309H;ENSP00000440797:R299H;ENSP00000432740:R299H	ENSP00000238699:R309H	R	-	2	0	GPR68	90770252	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.952000	0.63618	2.457000	0.83068	0.555000	0.69702	CGC	.	.		0.711	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
UNC79	57578	hgsc.bcm.edu	37	14	94158258	94158258	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:94158258C>A	ENST00000393151.2	+	47	7553	c.7553C>A	c.(7552-7554)cCc>cAc	p.P2518H	UNC79_ENST00000553484.1_Missense_Mutation_p.P2540H|UNC79_ENST00000555664.1_Missense_Mutation_p.P2479H|UNC79_ENST00000256339.4_Missense_Mutation_p.P2341H			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2518					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGGGTGACACCCAGCATCCTT	0.463																																					p.P2341H		Atlas-SNP	.											.	UNC79	366	.	0			c.C7022A						.						139.0	126.0	130.0					14																	94158258		2203	4300	6503	SO:0001583	missense	57578	exon47			TGACACCCAGCAT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7553C>A	chr14.hg19:g.94158258C>A	ENSP00000376858:p.Pro2518His	173.0	0.0		138.0	8.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	C	26.9	4.783060	0.90282	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.33438	1.42;1.47;1.41;1.42	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.59662	0.2210	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60984	-0.7154	10	0.87932	D	0	-20.8729	20.0784	0.97758	0.0:1.0:0.0:0.0	.	2540	C9JQL1	.	H	2341;2479;2540;2518;2540	ENSP00000256339:P2341H;ENSP00000450868:P2479H;ENSP00000451360:P2540H;ENSP00000376858:P2518H	ENSP00000256339:P2341H	P	+	2	0	KIAA1409	93228011	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	7.818000	0.86416	2.736000	0.93811	0.655000	0.94253	CCC	.	.		0.463	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
EVL	51466	hgsc.bcm.edu	37	14	100613207	100613207	+	IGR	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:100613207G>T	ENST00000402714.2	+	0	2353				DEGS2_ENST00000305631.5_Missense_Mutation_p.P288Q|DEGS2_ENST00000557117.1_5'Flank|DEGS2_ENST00000553834.1_Silent_p.A40A			Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				GTGGTGCTGCGGCAGGTGGTC	0.637																																					p.P288Q		Atlas-SNP	.											.	DEGS2	25	.	0			c.C863A						.						105.0	103.0	104.0					14																	100613207		2203	4300	6503	SO:0001628	intergenic_variant	123099	exon3			TGCTGCGGCAGGT	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530		chr14.hg19:g.100613207G>T		114.0	0.0		75.0	4.0	NM_206918	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Missense_Mutation	SNP	ENST00000402714.2	hg19		.	.	.	.	.	.	.	.	.	.	G	27.1	4.802559	0.90623	.	.	ENSG00000168350	ENST00000305631	T	0.33216	1.42	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.66858	0.2832	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76841	-0.2810	10	0.56958	D	0.05	-8.3096	17.986	0.89156	0.0:0.0:1.0:0.0	.	288	Q6QHC5	DEGS2_HUMAN	Q	288	ENSP00000307126:P288Q	ENSP00000307126:P288Q	P	-	2	0	DEGS2	99682960	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.714000	0.98744	2.251000	0.74343	0.561000	0.74099	CCG	.	.		0.637	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446804	102446804	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102446804A>G	ENST00000360184.4	+	5	1042	c.878A>G	c.(877-879)gAg>gGg	p.E293G		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	293	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGAAACGGGAGAGCCCGGAA	0.473																																					p.E293G		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A878G						.						81.0	81.0	81.0					14																	102446804		2203	4300	6503	SO:0001583	missense	1778	exon5			AACGGGAGAGCCC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.878A>G	chr14.hg19:g.102446804A>G	ENSP00000348965:p.Glu293Gly	113.0	0.0		102.0	6.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398526	0.62177	.	.	ENSG00000197102	ENST00000360184	T	0.56941	0.43	5.24	5.24	0.73138	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.63379	0.2506	M	0.69248	2.105	0.80722	D	1	P	0.46020	0.871	P	0.52343	0.696	T	0.62774	-0.6783	10	0.35671	T	0.21	.	15.421	0.75011	1.0:0.0:0.0:0.0	.	293	Q14204	DYHC1_HUMAN	G	293	ENSP00000348965:E293G	ENSP00000348965:E293G	E	+	2	0	DYNC1H1	101516557	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.833000	0.92089	2.102000	0.63906	0.482000	0.46254	GAG	.	.		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102494143	102494143	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102494143C>A	ENST00000360184.4	+	47	9400	c.9236C>A	c.(9235-9237)gCa>gAa	p.A3079E		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3079	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AAGGACCGGGCAGCTACATCA	0.562																																					p.A3079E		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C9236A						.						130.0	124.0	126.0					14																	102494143		2203	4300	6503	SO:0001583	missense	1778	exon47			ACCGGGCAGCTAC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.9236C>A	chr14.hg19:g.102494143C>A	ENSP00000348965:p.Ala3079Glu	88.0	0.0		59.0	14.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721168	0.89205	.	.	ENSG00000197102	ENST00000360184	T	0.49139	0.79	5.78	5.78	0.91487	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	0.112123	0.64402	D	0.000011	T	0.79100	0.4389	H	0.96943	3.91	0.80722	D	1	D	0.63046	0.992	P	0.61275	0.886	D	0.85690	0.1306	10	0.72032	D	0.01	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	3079	Q14204	DYHC1_HUMAN	E	3079	ENSP00000348965:A3079E	ENSP00000348965:A3079E	A	+	2	0	DYNC1H1	101563896	1.000000	0.71417	0.944000	0.38274	0.889000	0.51656	7.554000	0.82212	2.730000	0.93505	0.655000	0.94253	GCA	.	.		0.562	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ZNF839	55778	hgsc.bcm.edu	37	14	102805186	102805186	+	Silent	SNP	C	C	A	rs535523717		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102805186C>A	ENST00000558850.1	+	6	1695	c.1345C>A	c.(1345-1347)Cgg>Agg	p.R449R	AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000559185.1_Silent_p.R449R|ZNF839_ENST00000442396.2_Silent_p.R565R|ZNF839_ENST00000262236.5_Silent_p.R449R	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	449							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAATTCCTACGGAAGAAAGA	0.502																																					p.R565R		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1693A						.						95.0	93.0	94.0					14																	102805186		1960	4144	6104	SO:0001819	synonymous_variant	55778	exon6			TTCCTACGGAAGA	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1345C>A	chr14.hg19:g.102805186C>A		217.0	0.0		149.0	35.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.502	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
AMN	81693	hgsc.bcm.edu	37	14	103396365	103396365	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:103396365C>A	ENST00000299155.5	+	9	981	c.948C>A	c.(946-948)ccC>ccA	p.P316P		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	316					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGAATGGGCCCGAGACAGGCG	0.746																																					p.P316P		Atlas-SNP	.											.	AMN	13	.	0			c.C948A						.						9.0	10.0	10.0					14																	103396365		2102	4163	6265	SO:0001819	synonymous_variant	81693	exon9			TGGGCCCGAGACA	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"""amnionless homolog (mouse)"""			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.948C>A	chr14.hg19:g.103396365C>A		114.0	0.0		76.0	4.0	NM_030943	Q6UX83	Silent	SNP	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.746	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		
C14orf2	9556	hgsc.bcm.edu	37	14	104379023	104379023	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:104379023G>A	ENST00000554880.1	-	4	310	c.157C>T	c.(157-159)Cct>Tct	p.P53S	C14orf2_ENST00000286953.3_Missense_Mutation_p.P53S|C14orf2_ENST00000555030.1_3'UTR|C14orf2_ENST00000557040.1_Missense_Mutation_p.P53S|C14orf2_ENST00000553430.1_3'UTR|C14orf2_ENST00000414262.2_Missense_Mutation_p.P70S|C14orf2_ENST00000553449.1_5'UTR			P56378	68MP_HUMAN	chromosome 14 open reading frame 2	53						integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)				kidney(1)	1				Epithelial(152;0.223)		CCAGGAGCAGGCGCTGAAGCT	0.378																																					p.P70S		Atlas-SNP	.											.	C14orf2	7	.	0			c.C208T						.						146.0	140.0	142.0					14																	104379023		2203	4300	6503	SO:0001583	missense	9556	exon5			GAGCAGGCGCTGA	AF054175	CCDS9986.1, CCDS45169.1	14q32.33	2013-02-18			ENSG00000156411	ENSG00000156411			1188	protein-coding gene	gene with protein product	"""6.8 kDa mitochondrial proteolipid"""	604573				9653160	Standard	NM_001127393		Approved	MP68	uc001yoi.4	P56378	OTTHUMG00000171601	ENST00000554880.1:c.157C>T	chr14.hg19:g.104379023G>A	ENSP00000452133:p.Pro53Ser	72.0	0.0		66.0	4.0	NM_001127393	B2R588|G3V5Q3|Q86TT7	Missense_Mutation	SNP	ENST00000554880.1	hg19	CCDS9986.1	.	.	.	.	.	.	.	.	.	.	G	9.555	1.117061	0.20795	.	.	ENSG00000156411	ENST00000286953;ENST00000554880;ENST00000414262;ENST00000557040	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	3.8	1.9	0.25705	.	0.301114	0.23838	N	0.044066	T	0.25865	0.0630	.	.	.	0.09310	N	0.999999	B	0.16166	0.016	B	0.12837	0.008	T	0.13176	-1.0519	9	0.38643	T	0.18	.	5.3066	0.15807	0.1167:0.2081:0.6752:0.0	.	53	P56378	68MP_HUMAN	S	53;53;70;53	ENSP00000286953:P53S;ENSP00000452133:P53S;ENSP00000401770:P70S;ENSP00000450894:P53S	ENSP00000286953:P53S	P	-	1	0	C14orf2	103448776	0.872000	0.30054	0.002000	0.10522	0.228000	0.25075	0.895000	0.28363	0.377000	0.24735	0.655000	0.94253	CCT	.	.		0.378	C14orf2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414398.1	NM_001127393	
TDRD9	122402	hgsc.bcm.edu	37	14	104470585	104470585	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:104470585A>G	ENST00000409874.4	+	14	1542	c.1494A>G	c.(1492-1494)ggA>ggG	p.G498G	TDRD9_ENST00000339063.5_Silent_p.G498G	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	498	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GCCGTGCTGGACGAGTGTCTA	0.408																																					p.G498G		Atlas-SNP	.											.	TDRD9	175	.	0			c.A1494G						.						112.0	86.0	95.0					14																	104470585		2203	4300	6503	SO:0001819	synonymous_variant	122402	exon14			TGCTGGACGAGTG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1494A>G	chr14.hg19:g.104470585A>G		137.0	0.0		91.0	4.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	A	10.50	1.368680	0.24771	.	.	ENSG00000156414	ENST00000557332	.	.	.	5.87	-2.58	0.06228	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47736	-0.9094	4	.	.	.	.	8.437	0.32793	0.4929:0.107:0.4001:0.0	.	.	.	.	A	225	.	.	T	+	1	0	TDRD9	103540338	0.281000	0.24258	0.963000	0.40424	0.943000	0.58893	-0.382000	0.07408	-0.394000	0.07727	-0.250000	0.11733	ACG	.	.		0.408	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
GPR132	29933	hgsc.bcm.edu	37	14	105517772	105517772	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:105517772A>G	ENST00000329797.3	-	4	1613	c.702T>C	c.(700-702)gcT>gcC	p.A234A	GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Silent_p.A225A|GPR132_ENST00000539291.2_Silent_p.A234A	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	234					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		CCTTCTGGGCAGCGCTTAAGC	0.582																																					p.A234A		Atlas-SNP	.											.	GPR132	40	.	0			c.T702C						.						97.0	89.0	91.0					14																	105517772		2203	4300	6503	SO:0001819	synonymous_variant	29933	exon4			CTGGGCAGCGCTT	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"""GPCR / Class A : Orphans"""	17482	protein-coding gene	gene with protein product	"""G2 accumulation"""	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.702T>C	chr14.hg19:g.105517772A>G		152.0	0.0		99.0	4.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Silent	SNP	ENST00000329797.3	hg19	CCDS9997.1																																																																																			.	.		0.582	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22873209	22873209	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:22873209T>C	ENST00000283645.4	+	23	3166	c.3036T>C	c.(3034-3036)tcT>tcC	p.S1012S		NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	1012					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGTGGAATCTCTAGCGTTGT	0.373																																					p.S1012S		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.T3036C						.						130.0	130.0	130.0					15																	22873209		2203	4300	6503	SO:0001819	synonymous_variant	114791	exon23			GGAATCTCTAGCG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.3036T>C	chr15.hg19:g.22873209T>C		100.0	0.0		100.0	4.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	hg19	CCDS10008.1																																																																																			.	.		0.373	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
GABRB3	2562	hgsc.bcm.edu	37	15	26812847	26812847	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:26812847A>G	ENST00000311550.5	-	7	827	c.716T>C	c.(715-717)tTg>tCg	p.L239S	GABRB3_ENST00000400188.3_Missense_Mutation_p.L168S|GABRB3_ENST00000545868.1_Missense_Mutation_p.L154S|GABRB3_ENST00000541819.2_Missense_Mutation_p.L295S|GABRB3_ENST00000299267.4_Missense_Mutation_p.L239S	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	239					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTTCCTCTTCAACCGAAAGCT	0.423																																					p.L239S		Atlas-SNP	.											.	GABRB3	338	.	0			c.T716C						.						127.0	108.0	115.0					15																	26812847		2203	4300	6503	SO:0001583	missense	2562	exon7			CTCTTCAACCGAA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.716T>C	chr15.hg19:g.26812847A>G	ENSP00000308725:p.Leu239Ser	103.0	0.0		80.0	4.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	hg19	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677285	0.88445	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	6.06	6.06	0.98353	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.94218	0.8144	H	0.96833	3.89	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.988;0.991;0.995	D	0.95891	0.8907	10	0.87932	D	0	.	15.7938	0.78394	1.0:0.0:0.0:0.0	.	295;239;239	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	S	239;295;239;168;154	ENSP00000308725:L239S;ENSP00000442408:L295S;ENSP00000299267:L239S;ENSP00000383049:L168S;ENSP00000439169:L154S	ENSP00000299267:L239S	L	-	2	0	GABRB3	24363940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.204000	0.95041	2.322000	0.78497	0.528000	0.53228	TTG	.	.		0.423	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
TRPM1	4308	hgsc.bcm.edu	37	15	31360167	31360167	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:31360167G>A	ENST00000256552.6	-	5	555	c.408C>T	c.(406-408)ccC>ccT	p.P136P	MIR211_ENST00000384969.1_RNA|TRPM1_ENST00000397795.2_Silent_p.P114P|TRPM1_ENST00000542188.1_Silent_p.P153P	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GTTTCAGCTTGGGCTGCATCT	0.542																																					p.P153P		Atlas-SNP	.											.	TRPM1	183	.	0			c.C459T						.						119.0	118.0	118.0					15																	31360167		1898	4128	6026	SO:0001819	synonymous_variant	4308	exon4			CAGCTTGGGCTGC	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.408C>T	chr15.hg19:g.31360167G>A		101.0	0.0		99.0	4.0	NM_001252020		Silent	SNP	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
RYR3	6263	hgsc.bcm.edu	37	15	33855056	33855056	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:33855056G>T	ENST00000389232.4	+	11	1061	c.991G>T	c.(991-993)Gac>Tac	p.D331Y	RYR3_ENST00000415757.3_Missense_Mutation_p.D331Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	331	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GGAGAAATTAGACTCCAGTCA	0.393																																					p.D331Y		Atlas-SNP	.											.	RYR3	760	.	0			c.G991T						.						66.0	65.0	65.0					15																	33855056		1862	4106	5968	SO:0001583	missense	6263	exon11			AAATTAGACTCCA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.991G>T	chr15.hg19:g.33855056G>T	ENSP00000373884:p.Asp331Tyr	120.0	0.0		86.0	30.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335986	0.81801	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.93953	-3.32;-3.32	5.27	5.27	0.74061	MIR motif (2);MIR (2);	0.118731	0.56097	D	0.000026	D	0.95573	0.8561	L	0.54323	1.7	0.58432	D	0.999998	D;D	0.67145	0.996;0.989	D;P	0.65874	0.939;0.883	D	0.95691	0.8740	10	0.72032	D	0.01	.	18.6774	0.91534	0.0:0.0:1.0:0.0	.	331;331	Q15413-2;Q15413	.;RYR3_HUMAN	Y	331	ENSP00000373884:D331Y;ENSP00000399610:D331Y	ENSP00000354735:D331Y	D	+	1	0	RYR3	31642348	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.491000	0.97954	2.748000	0.94277	0.655000	0.94253	GAC	.	.		0.393	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
AQR	9716	hgsc.bcm.edu	37	15	35182513	35182513	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:35182513A>G	ENST00000156471.5	-	24	2809	c.2584T>C	c.(2584-2586)Ttg>Ctg	p.L862L		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	862					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTCTCAAACAACTGGTTTAGG	0.423																																					p.L862L		Atlas-SNP	.											.	AQR	139	.	0			c.T2584C						.						155.0	145.0	148.0					15																	35182513		1901	4121	6022	SO:0001819	synonymous_variant	9716	exon24			CAAACAACTGGTT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2584T>C	chr15.hg19:g.35182513A>G		147.0	0.0		97.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.423	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
AQR	9716	hgsc.bcm.edu	37	15	35212582	35212582	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:35212582G>T	ENST00000156471.5	-	14	1397	c.1172C>A	c.(1171-1173)cCt>cAt	p.P391H		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	391					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTCATTTTTAGGAAGAGTTGG	0.338																																					p.P391H		Atlas-SNP	.											.	AQR	139	.	0			c.C1172A						.						77.0	74.0	75.0					15																	35212582		1819	4083	5902	SO:0001583	missense	9716	exon14			TTTTTAGGAAGAG	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1172C>A	chr15.hg19:g.35212582G>T	ENSP00000156471:p.Pro391His	92.0	0.0		88.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685655	0.68157	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94138	-3.36	5.16	5.16	0.70880	.	0.097095	0.64402	D	0.000001	D	0.94404	0.8200	M	0.87097	2.86	0.49798	D	0.999827	P	0.44344	0.833	B	0.40659	0.336	D	0.95277	0.8382	10	0.62326	D	0.03	-17.0567	18.8265	0.92121	0.0:0.0:1.0:0.0	.	391	O60306	AQR_HUMAN	H	391	ENSP00000156471:P391H	ENSP00000156471:P391H	P	-	2	0	AQR	32999874	1.000000	0.71417	0.998000	0.56505	0.599000	0.36880	7.335000	0.79234	2.688000	0.91661	0.563000	0.77884	CCT	.	.		0.338	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
EIF2AK4	440275	hgsc.bcm.edu	37	15	40301931	40301931	+	Splice_Site	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:40301931G>A	ENST00000263791.5	+	26	3736	c.3693G>A	c.(3691-3693)gtG>gtA	p.V1231V	EIF2AK4_ENST00000382727.2_Splice_Site_p.V1203V	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1231	Histidyl-tRNA synthetase-like.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATGATGCTGTGGTAAGCATTT	0.323																																					p.V1231V		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.G3693A						.						92.0	89.0	90.0					15																	40301931		1857	4097	5954	SO:0001630	splice_region_variant	440275	exon26			TGCTGTGGTAAGC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.3693+1G>A	chr15.hg19:g.40301931G>A		138.0	0.0		96.0	4.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	hg19	CCDS42016.1																																																																																			.	.		0.323	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		Silent
PAK6	56924	hgsc.bcm.edu	37	15	40565184	40565184	+	Missense_Mutation	SNP	A	A	G	rs140245743		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:40565184A>G	ENST00000542403.2	+	5	1585	c.1474A>G	c.(1474-1476)Atc>Gtc	p.I492V	PAK6_ENST00000453867.1_Missense_Mutation_p.I492V|PAK6_ENST00000260404.4_Missense_Mutation_p.I492V|PAK6_ENST00000455577.2_Missense_Mutation_p.I492V|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000560346.1_Missense_Mutation_p.I492V|PAK6_ENST00000441369.1_Missense_Mutation_p.I492V	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	492	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CCTCACAGACATCGTCTCCCA	0.622																																					p.I492V		Atlas-SNP	.											.	PAK6	49	.	0			c.A1474G						.	A	VAL/ILE,VAL/ILE,VAL/ILE	0,4406		0,0,2203	129.0	114.0	119.0		1474,1474,1474	4.7	1.0	15	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	29,29,29	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	492/682,492/682,492/682	40565184	1,13005	2203	4300	6503	SO:0001583	missense	56924	exon6			ACAGACATCGTCT	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"""p21(CDKN1A)-activated kinase 6"""			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1474A>G	chr15.hg19:g.40565184A>G	ENSP00000439597:p.Ile492Val	66.0	0.0		70.0	4.0	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	hg19	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535649	0.64972	0.0	1.16E-4	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	4.69	4.69	0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.052324	0.85682	D	0.000000	T	0.62708	0.2450	N	0.11892	0.195	0.80722	D	1	P;P	0.46656	0.882;0.639	D;B	0.68765	0.96;0.172	T	0.63363	-0.6654	10	0.30854	T	0.27	.	14.342	0.66633	1.0:0.0:0.0:0.0	.	492;492	Q9NQU5;G5E9R2	PAK6_HUMAN;.	V	492	ENSP00000406873:I492V;ENSP00000401153:I492V;ENSP00000409465:I492V;ENSP00000260404:I492V;ENSP00000439597:I492V	ENSP00000260404:I492V	I	+	1	0	PAK6	38352476	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.139000	0.94554	1.974000	0.57490	0.533000	0.62120	ATC	.	A|1.000;G|0.000		0.622	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1		
VPS18	57617	hgsc.bcm.edu	37	15	41187016	41187016	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41187016T>C	ENST00000220509.5	+	1	389	c.50T>C	c.(49-51)gTc>gCc	p.V17A	VPS18_ENST00000558474.1_Missense_Mutation_p.V17A	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	17					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CGCTCGGCCGTCTTGCAGCCC	0.652											OREG0023068	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V17A		Atlas-SNP	.											.	VPS18	67	.	0			c.T50C						.						21.0	19.0	20.0					15																	41187016		2169	4246	6415	SO:0001583	missense	57617	exon1			CGGCCGTCTTGCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.50T>C	chr15.hg19:g.41187016T>C	ENSP00000220509:p.Val17Ala	127.0	0.0	899	48.0	4.0	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	hg19	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	T	7.813	0.716130	0.15306	.	.	ENSG00000104142	ENST00000220509	T	0.41758	0.99	4.68	3.56	0.40772	.	0.384243	0.29972	N	0.010740	T	0.18467	0.0443	N	0.08118	0	0.26613	N	0.972797	B	0.10296	0.003	B	0.08055	0.003	T	0.16276	-1.0408	10	0.16896	T	0.51	-51.0287	5.667	0.17700	0.0:0.254:0.0:0.746	.	17	Q9P253	VPS18_HUMAN	A	17	ENSP00000220509:V17A	ENSP00000220509:V17A	V	+	2	0	VPS18	38974308	0.874000	0.30092	1.000000	0.80357	0.181000	0.23173	1.022000	0.30052	0.941000	0.37499	0.402000	0.26972	GTC	.	.		0.652	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
NDUFAF1	51103	hgsc.bcm.edu	37	15	41687071	41687071	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41687071A>G	ENST00000260361.4	-	3	1126	c.745T>C	c.(745-747)Tgg>Cgg	p.W249R		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	249					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ACCTCCTGCCAGTAGGGTCCC	0.478																																					p.W249R		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.T745C						.						76.0	73.0	74.0					15																	41687071		2203	4300	6503	SO:0001583	missense	51103	exon3			CCTGCCAGTAGGG	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.745T>C	chr15.hg19:g.41687071A>G	ENSP00000260361:p.Trp249Arg	95.0	0.0		71.0	4.0	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	hg19	CCDS10075.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522096	0.85600	.	.	ENSG00000137806	ENST00000260361	D	0.82619	-1.63	5.52	5.52	0.82312	NADH:ubiquinone oxidoreductase intermediate-associated protein 30 (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.93344	0.7878	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94959	0.8106	10	0.87932	D	0	-20.7997	15.9772	0.80079	1.0:0.0:0.0:0.0	.	249	Q9Y375	CIA30_HUMAN	R	249	ENSP00000260361:W249R	ENSP00000260361:W249R	W	-	1	0	NDUFAF1	39474363	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.047000	0.93823	2.235000	0.73313	0.451000	0.29950	TGG	.	.		0.478	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
LTK	4058	hgsc.bcm.edu	37	15	41801262	41801262	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41801262G>T	ENST00000263800.6	-	8	1159	c.1063C>A	c.(1063-1065)Ccc>Acc	p.P355T	LTK_ENST00000561619.1_Missense_Mutation_p.P37T|LTK_ENST00000453182.2_Missense_Mutation_p.P294T|LTK_ENST00000355166.5_Missense_Mutation_p.P294T	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	355					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TCGCTGCTGGGGTGTATGAAG	0.587										TSP Lung(18;0.14)																											p.P355T		Atlas-SNP	.											.	LTK	117	.	0			c.C1063A						.						95.0	92.0	93.0					15																	41801262		2203	4300	6503	SO:0001583	missense	4058	exon8			TGCTGGGGTGTAT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1063C>A	chr15.hg19:g.41801262G>T	ENSP00000263800:p.Pro355Thr	238.0	0.0		163.0	7.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253548	0.80135	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;D	0.81659	-1.07;1.2;-1.52	5.33	4.42	0.53409	.	0.000000	0.33364	U	0.004998	D	0.87807	0.6270	M	0.72118	2.19	0.28559	N	0.911205	P;D;D;D	0.89917	0.915;0.999;1.0;1.0	P;D;D;D	0.87578	0.468;0.921;0.996;0.998	T	0.82552	-0.0400	10	0.48119	T	0.1	.	12.4858	0.55872	0.0816:0.0:0.9184:0.0	.	294;294;294;355	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	T	355;294;355;294	ENSP00000347293:P294T;ENSP00000263800:P355T;ENSP00000392196:P294T	ENSP00000263800:P355T	P	-	1	0	LTK	39588554	1.000000	0.71417	0.603000	0.28903	0.989000	0.77384	6.530000	0.73816	1.233000	0.43693	0.491000	0.48974	CCC	.	.		0.587	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
MGA	23269	hgsc.bcm.edu	37	15	41989188	41989188	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41989188G>T	ENST00000570161.1	+	2	1980	c.1980G>T	c.(1978-1980)gtG>gtT	p.V660V	MGA_ENST00000389936.4_Silent_p.V660V|MGA_ENST00000545763.1_Silent_p.V660V|MGA_ENST00000219905.7_Silent_p.V660V|MGA_ENST00000566586.1_Silent_p.V660V			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGGAAGATGTGGATGGTGTTC	0.378																																					p.V660V		Atlas-SNP	.											.	MGA	264	.	0			c.G1980T						.						16.0	15.0	16.0					15																	41989188		1840	4001	5841	SO:0001819	synonymous_variant	23269	exon3			AGATGTGGATGGT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1980G>T	chr15.hg19:g.41989188G>T		88.0	0.0		86.0	4.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.378	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
SPTBN5	51332	hgsc.bcm.edu	37	15	42182404	42182404	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:42182404C>A	ENST00000320955.6	-	4	612		c.e4-1		RP11-23P13.6_ENST00000309874.2_RNA|RP11-23P13.6_ENST00000564432.2_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GTACTGGCACCTGTGGGCACA	0.577																																					.		Atlas-SNP	.											.	SPTBN5	171	.	0			c.280-1G>T						.						93.0	94.0	93.0					15																	42182404		2058	4200	6258	SO:0001630	splice_region_variant	51332	exon5			TGGCACCTGTGGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.385-1G>T	chr15.hg19:g.42182404C>A		147.0	0.0		90.0	4.0	NM_016642		Splice_Site	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	C	19.25	3.790500	0.70337	.	.	ENSG00000137877	ENST00000320955	.	.	.	4.89	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5858	0.56416	0.0:0.9188:0.0:0.0812	.	.	.	.	.	-1	.	.	.	-	.	.	SPTBN5	39969696	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.357000	0.73051	1.048000	0.40298	0.655000	0.94253	.	.	.		0.577	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	Intron
TMEM87A	25963	hgsc.bcm.edu	37	15	42529654	42529654	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:42529654T>C	ENST00000389834.4	-	9	1108	c.844A>G	c.(844-846)Aat>Gat	p.N282D	TMEM87A_ENST00000448392.1_Missense_Mutation_p.N221D	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	282						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		TATCGGATATTCTGAAATTCC	0.428																																					p.N282D		Atlas-SNP	.											.	TMEM87A	56	.	0			c.A844G						.						105.0	98.0	100.0					15																	42529654		2203	4299	6502	SO:0001583	missense	25963	exon9			GGATATTCTGAAA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.844A>G	chr15.hg19:g.42529654T>C	ENSP00000374484:p.Asn282Asp	101.0	0.0		89.0	4.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	T	33	5.205764	0.95033	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.8	5.8	0.92144	.	0.047282	0.85682	D	0.000000	T	0.66386	0.2784	M	0.63428	1.95	0.50171	D	0.999859	D;P	0.53312	0.959;0.544	P;B	0.52343	0.696;0.341	T	0.65817	-0.6076	9	0.37606	T	0.19	-16.717	16.1464	0.81575	0.0:0.0:0.0:1.0	.	282;221	Q8NBN3;Q8NBN3-3	TM87A_HUMAN;.	D	282;221;258	.	ENSP00000374484:N282D	N	-	1	0	TMEM87A	40316946	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	8.040000	0.89188	2.220000	0.72140	0.383000	0.25322	AAT	.	.		0.428	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	
SERINC4	619189	hgsc.bcm.edu	37	15	44089116	44089116	+	Silent	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:44089116T>A	ENST00000319327.6	-	7	1101	c.867A>T	c.(865-867)ctA>ctT	p.L289L	SERF2_ENST00000594896.1_Intron|HYPK_ENST00000406925.1_5'UTR|SERINC4_ENST00000249714.3_Silent_p.L45L|SERF2_ENST00000409646.1_Intron|SERF2_ENST00000409291.1_Intron|SERINC4_ENST00000299969.6_Intron|RP11-296A16.1_ENST00000417761.2_Missense_Mutation_p.T98S	NM_001258031.1	NP_001244960.1	A6NH21	SERC4_HUMAN	serine incorporator 4	289					phospholipid biosynthetic process (GO:0008654)	integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	6		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;7.81e-07)		CAGAAGCTTGTAGGAGGCCAG	0.493																																					p.L289L		Atlas-SNP	.											.	SERINC4	18	.	0			c.A867T						.						133.0	137.0	136.0					15																	44089116		2198	4298	6496	SO:0001819	synonymous_variant	619189	exon7			AGCTTGTAGGAGG	DQ103711	CCDS58360.1	15q15.3	2013-09-25			ENSG00000184716	ENSG00000184716			32237	protein-coding gene	gene with protein product		614550					Standard	NM_001258031		Approved	FLJ40363	uc031qrp.1	A6NH21	OTTHUMG00000060144	ENST00000319327.6:c.867A>T	chr15.hg19:g.44089116T>A		175.0	0.0		121.0	5.0	NM_001258031	B2RN41|Q3YL75	Silent	SNP	ENST00000319327.6	hg19	CCDS58360.1																																																																																			.	.		0.493	SERINC4-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133485.2		
SPG11	80208	hgsc.bcm.edu	37	15	44876208	44876208	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:44876208A>G	ENST00000261866.7	-	30	5686	c.5670T>C	c.(5668-5670)tgT>tgC	p.C1890C	SPG11_ENST00000558253.1_5'Flank|SPG11_ENST00000427534.2_Silent_p.C1890C|SPG11_ENST00000535302.2_Silent_p.C1890C|SPG11_ENST00000558319.1_Silent_p.C1890C	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1890					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CTTCATGCACACAGCCATCAT	0.453																																					p.C1890C		Atlas-SNP	.											.	SPG11	207	.	0			c.T5670C						.						120.0	99.0	106.0					15																	44876208		2198	4298	6496	SO:0001819	synonymous_variant	80208	exon30			ATGCACACAGCCA		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.5670T>C	chr15.hg19:g.44876208A>G		102.0	0.0		98.0	5.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	hg19	CCDS10112.1																																																																																			.	.		0.453	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
SPATA5L1	79029	hgsc.bcm.edu	37	15	45713246	45713246	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:45713246T>C	ENST00000305560.6	+	8	2199	c.2100T>C	c.(2098-2100)gcT>gcC	p.A700A	SPATA5L1_ENST00000533841.1_3'UTR	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	700						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		AATAGGCTGCTTTGCTGGCTC	0.403																																					p.A700A		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.T2100C						.						52.0	53.0	53.0					15																	45713246		2198	4298	6496	SO:0001819	synonymous_variant	79029	exon8			GGCTGCTTTGCTG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.2100T>C	chr15.hg19:g.45713246T>C		43.0	0.0		60.0	4.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	T	9.528	1.110046	0.20714	.	.	ENSG00000171763	ENST00000531624	.	.	.	5.6	2.22	0.28083	.	.	.	.	.	T	0.58264	0.2110	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53143	-0.8480	4	.	.	.	-26.8576	9.1663	0.37054	0.0:0.6612:0.0:0.3388	.	.	.	.	P	205	.	.	L	+	2	0	SPATA5L1	43500538	0.966000	0.33281	1.000000	0.80357	0.980000	0.70556	-0.056000	0.11787	0.705000	0.31890	-0.366000	0.07423	CTT	.	.		0.403	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
SLC12A1	6557	hgsc.bcm.edu	37	15	48519318	48519318	+	Intron	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:48519318C>T	ENST00000558405.1	+	4	738				SLC12A1_ENST00000396577.3_Missense_Mutation_p.T224I|SLC12A1_ENST00000380993.3_Intron|SLC12A1_ENST00000330289.6_Intron|SLC12A1_ENST00000559723.1_Intron			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1						cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GTAGTAACGACACTCACAGGT	0.418																																					p.T224I		Atlas-SNP	.											.	SLC12A1	243	.	0			c.C671T						.						255.0	210.0	223.0					15																	48519318		687	1588	2275	SO:0001627	intron_variant	6557	exon5			TAACGACACTCAC		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.724+550C>T	chr15.hg19:g.48519318C>T		155.0	0.0		99.0	4.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	17.66	3.443428	0.63067	.	.	ENSG00000074803	ENST00000396577	D	0.98617	-5.03	5.77	5.77	0.91146	.	0.212326	0.49916	D	0.000122	D	0.98701	0.9564	L	0.57130	1.785	0.80722	D	1	.	.	.	.	.	.	D	0.99709	1.1006	8	0.72032	D	0.01	.	20.3473	0.98799	0.0:1.0:0.0:0.0	.	.	.	.	I	224	ENSP00000379822:T224I	ENSP00000379822:T224I	T	+	2	0	SLC12A1	46306610	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.428000	0.52792	2.884000	0.98904	0.655000	0.94253	ACA	.	.		0.418	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
SLC12A1	6557	hgsc.bcm.edu	37	15	48539187	48539187	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:48539187C>T	ENST00000558405.1	+	11	1548	c.1534C>T	c.(1534-1536)Ctt>Ttt	p.L512F	SLC12A1_ENST00000396577.3_Missense_Mutation_p.L512F|SLC12A1_ENST00000380993.3_Missense_Mutation_p.L512F			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	512					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CCTGGCCTCCCTTGTCAGCGC	0.498																																					p.L512F		Atlas-SNP	.											.	SLC12A1	243	.	0			c.C1534T						.						220.0	203.0	209.0					15																	48539187		2198	4297	6495	SO:0001583	missense	6557	exon12			GCCTCCCTTGTCA		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1534C>T	chr15.hg19:g.48539187C>T	ENSP00000453409:p.Leu512Phe	138.0	0.0		98.0	4.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	26.1	4.707984	0.89018	.	.	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000396577	D;D	0.99129	-5.46;-5.46	4.98	4.98	0.66077	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99429	1.0935	10	0.87932	D	0	.	18.4428	0.90673	0.0:1.0:0.0:0.0	.	512;512	E9PDW4;Q13621	.;S12A1_HUMAN	F	325;512;512	ENSP00000370381:L512F;ENSP00000379822:L512F	ENSP00000370381:L512F	L	+	1	0	SLC12A1	46326479	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.890000	0.69774	2.582000	0.87167	0.655000	0.94253	CTT	.	.		0.498	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
SECISBP2L	9728	hgsc.bcm.edu	37	15	49320786	49320786	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:49320786G>C	ENST00000559471.1	-	5	1021	c.758C>G	c.(757-759)cCt>cGt	p.P253R	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.P253R	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	253							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTCAGCAGTAGGGTGGGATGC	0.498																																					p.P253R		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.C758G						.						144.0	129.0	134.0					15																	49320786		2197	4295	6492	SO:0001583	missense	9728	exon5			GCAGTAGGGTGGG	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.758C>G	chr15.hg19:g.49320786G>C	ENSP00000453854:p.Pro253Arg	218.0	0.0		140.0	51.0	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	hg19	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.900694	0.52227	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.88741	-2.42	5.78	5.78	0.91487	.	0.062479	0.64402	D	0.000004	D	0.91057	0.7186	L	0.29908	0.895	0.45295	D	0.998295	D;D	0.71674	0.998;0.996	P;P	0.62813	0.873;0.907	D	0.91760	0.5419	10	0.72032	D	0.01	.	20.0278	0.97529	0.0:0.0:1.0:0.0	.	253;253	Q93073;Q93073-2	SBP2L_HUMAN;.	R	253	ENSP00000261847:P253R	ENSP00000261847:P253R	P	-	2	0	SECISBP2L	47108078	1.000000	0.71417	0.959000	0.39883	0.299000	0.27559	5.734000	0.68580	2.732000	0.93576	0.655000	0.94253	CCT	.	.		0.498	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
GALK2	2585	hgsc.bcm.edu	37	15	49611880	49611880	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:49611880T>C	ENST00000560031.1	+	9	1354	c.1047T>C	c.(1045-1047)tgT>tgC	p.C349C	GALK2_ENST00000327171.3_Silent_p.C338C|GALK2_ENST00000544523.1_Silent_p.C325C|GALK2_ENST00000543495.1_3'UTR|GALK2_ENST00000559454.1_Silent_p.C325C|GALK2_ENST00000396509.2_Silent_p.C325C|GALK2_ENST00000561014.1_3'UTR			Q01415	GALK2_HUMAN	galactokinase 2	349					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		AGAAGATATGTGAAGAAGCAC	0.537																																					p.C349C		Atlas-SNP	.											.	GALK2	78	.	0			c.T1047C						.						87.0	79.0	82.0					15																	49611880		2196	4295	6491	SO:0001819	synonymous_variant	2585	exon9			GATATGTGAAGAA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.1047T>C	chr15.hg19:g.49611880T>C		135.0	0.0		100.0	4.0	NM_002044	Q7Z4Q4	Silent	SNP	ENST00000560031.1	hg19	CCDS42034.1																																																																																			.	.		0.537	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
UNC13C	440279	hgsc.bcm.edu	37	15	54307628	54307628	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:54307628A>G	ENST00000260323.11	+	1	2528	c.2528A>G	c.(2527-2529)gAg>gGg	p.E843G	UNC13C_ENST00000537900.1_Missense_Mutation_p.E843G|UNC13C_ENST00000545554.1_Missense_Mutation_p.E843G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	843					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACTGCAAATGAGTCAAGTACC	0.428																																					p.E843G		Atlas-SNP	.											UNC13C_ENST00000260323,colon,carcinoma,0,2	UNC13C	674	.	0			c.A2528G						.						79.0	77.0	78.0					15																	54307628		1954	4144	6098	SO:0001583	missense	440279	exon1			CAAATGAGTCAAG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.2528A>G	chr15.hg19:g.54307628A>G	ENSP00000260323:p.Glu843Gly	76.0	1.0		69.0	3.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597578	0.46318	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.80653	-1.4;-1.4;-1.4	5.42	5.42	0.78866	.	.	.	.	.	T	0.70727	0.3257	L	0.29908	0.895	0.30377	N	0.78235	P	0.35844	0.524	B	0.28849	0.095	T	0.73119	-0.4083	9	0.59425	D	0.04	.	14.6463	0.68764	1.0:0.0:0.0:0.0	.	843	Q8NB66	UN13C_HUMAN	G	843	ENSP00000260323:E843G;ENSP00000438156:E843G;ENSP00000442569:E843G	ENSP00000260323:E843G	E	+	2	0	UNC13C	52094920	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	3.973000	0.56845	2.047000	0.60756	0.528000	0.53228	GAG	.	.		0.428	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
CCPG1	9236	hgsc.bcm.edu	37	15	55664085	55664085	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:55664085C>T	ENST00000310958.6	-	6	910	c.612G>A	c.(610-612)aaG>aaA	p.K204K	CCPG1_ENST00000569205.1_Silent_p.K204K|CCPG1_ENST00000425574.3_Silent_p.K204K|MIR628_ENST00000385229.1_RNA|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Silent_p.K204K	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	204	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TACTCAACTCCTTAGAAGGTT	0.448																																					p.K204K		Atlas-SNP	.											.	CCPG1	74	.	0			c.G612A						.						114.0	103.0	106.0					15																	55664085		1876	4107	5983	SO:0001819	synonymous_variant	9236	exon6			CAACTCCTTAGAA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.612G>A	chr15.hg19:g.55664085C>T		271.0	0.0		204.0	34.0	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Silent	SNP	ENST00000310958.6	hg19	CCDS42039.1																																																																																			.	.		0.448	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
VPS13C	54832	hgsc.bcm.edu	37	15	62202491	62202491	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:62202491C>A	ENST00000261517.5	-	64	8802	c.8729G>T	c.(8728-8730)tGg>tTg	p.W2910L	VPS13C_ENST00000395896.4_Missense_Mutation_p.W2910L|VPS13C_ENST00000395898.3_Missense_Mutation_p.W2867L|VPS13C_ENST00000249837.3_Missense_Mutation_p.W2867L	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACTTTCTGGCCAAAATGGAAG	0.333																																					p.W2910L		Atlas-SNP	.											.	VPS13C	506	.	0			c.G8729T						.						48.0	50.0	49.0					15																	62202491		2203	4300	6503	SO:0001583	missense	54832	exon64			TCTGGCCAAAATG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.8729G>T	chr15.hg19:g.62202491C>A	ENSP00000261517:p.Trp2910Leu	100.0	0.0		78.0	4.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.903713	0.92035	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.30448	1.53;1.53;1.53	5.85	5.85	0.93711	Vacuolar protein sorting-associated protein (1);	0.000000	0.85682	D	0.000000	T	0.64114	0.2569	M	0.88310	2.945	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.998;0.999	T	0.63576	-0.6606	10	0.33940	T	0.23	.	20.1649	0.98147	0.0:1.0:0.0:0.0	.	2910;2867;2910;2867;2910	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	L	2867;2910;2910;2910	ENSP00000249837:W2867L;ENSP00000261517:W2910L;ENSP00000379233:W2910L	ENSP00000249837:W2867L	W	-	2	0	VPS13C	59989783	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.766000	0.74970	2.753000	0.94483	0.655000	0.94253	TGG	.	.		0.333	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
FBXL22	283807	hgsc.bcm.edu	37	15	63889776	63889776	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:63889776A>G	ENST00000360587.2	+	1	225	c.185A>G	c.(184-186)aAg>aGg	p.K62R	USP3-AS1_ENST00000560622.1_RNA|FBXL22_ENST00000534939.1_Missense_Mutation_p.K62R|FBXL22_ENST00000539570.3_Missense_Mutation_p.K56R|USP3-AS1_ENST00000559861.1_RNA|USP3-AS1_ENST00000561191.1_RNA|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000559737.1_RNA|USP3-AS1_ENST00000561256.1_RNA|USP3-AS1_ENST00000558831.1_RNA	NM_203373.2	NP_976307.2	Q6P050	FXL22_HUMAN	F-box and leucine-rich repeat protein 22	62					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(4)	4						GAACTCCAGAAGGACAACTTC	0.627																																					p.K62R		Atlas-SNP	.											.	FBXL22	4	.	0			c.A185G						.						62.0	50.0	54.0					15																	63889776		2203	4300	6503	SO:0001583	missense	283807	exon1			TCCAGAAGGACAA	BC065833	CCDS10187.1, CCDS10187.2	15q22.1	2012-04-05			ENSG00000197361	ENSG00000197361		"""F-boxes / Leucine-rich repeats"""	27537	protein-coding gene	gene with protein product		609088				12477932	Standard	NM_203373		Approved	Fbl22, FLJ39626	uc002amn.4	Q6P050	OTTHUMG00000132905	ENST00000360587.2:c.185A>G	chr15.hg19:g.63889776A>G	ENSP00000353794:p.Lys62Arg	80.0	0.0		83.0	4.0	NM_203373		Missense_Mutation	SNP	ENST00000360587.2	hg19	CCDS10187.2	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138354	0.77775	.	.	ENSG00000197361	ENST00000360587;ENST00000539570	T;T	0.39056	1.1;1.1	5.49	5.49	0.81192	.	0.158011	0.56097	D	0.000032	T	0.29684	0.0741	L	0.41824	1.3	0.33837	D	0.630966	P	0.43750	0.816	B	0.32762	0.152	T	0.52290	-0.8595	10	0.52906	T	0.07	-11.311	10.7624	0.46272	0.9261:0.0:0.0739:0.0	.	56	Q6P050	FXL22_HUMAN	R	62;56	ENSP00000353794:K62R;ENSP00000442112:K56R	ENSP00000353794:K62R	K	+	2	0	FBXL22	61676829	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.369000	0.44231	2.090000	0.63153	0.460000	0.39030	AAG	.	.		0.627	FBXL22-001	KNOWN	downstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256412.4	NM_203373	
PARP16	54956	hgsc.bcm.edu	37	15	65578651	65578651	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:65578651C>A	ENST00000444347.2	-	1	530	c.114G>T	c.(112-114)tcG>tcT	p.S38S	PARP16_ENST00000261888.6_Silent_p.S38S|SNORA24_ENST00000384176.1_RNA|PARP16_ENST00000558873.1_Intron			Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	38	PARP alpha-helical.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						GCCGCAGCACCGAGTCGCGCT	0.716																																					p.S38S	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.G114T						.						15.0	17.0	16.0					15																	65578651		2197	4295	6492	SO:0001819	synonymous_variant	54956	exon1			CAGCACCGAGTCG	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"""Poly (ADP-ribose) polymerases"""	26040	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 30"""	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000444347.2:c.114G>T	chr15.hg19:g.65578651C>A		68.0	0.0		78.0	4.0	NM_017851	Q6PK64|Q9NX03	Silent	SNP	ENST00000444347.2	hg19																																																																																				.	.		0.716	PARP16-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000418174.1	NM_017851	
IGDCC3	9543	hgsc.bcm.edu	37	15	65621487	65621487	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:65621487C>A	ENST00000327987.4	-	14	2457		c.e14-1		IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3						neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGGATCCTGCTGGGGAAAGA	0.667																																					.		Atlas-SNP	.											.	IGDCC3	82	.	0			c.2206-1G>T						.						14.0	17.0	16.0					15																	65621487		2201	4297	6498	SO:0001630	splice_region_variant	9543	exon15			ATCCTGCTGGGGA	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2206-1G>T	chr15.hg19:g.65621487C>A		51.0	0.0		46.0	16.0	NM_004884	O95215	Splice_Site	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.743246	0.30865	.	.	ENSG00000174498	ENST00000327987	.	.	.	5.45	2.48	0.30137	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.3969	0.16275	0.1661:0.6644:0.0:0.1695	.	.	.	.	.	-1	.	.	.	-	.	.	IGDCC3	63408540	0.073000	0.21202	0.343000	0.25615	0.045000	0.14185	0.301000	0.19174	0.242000	0.21303	0.555000	0.69702	.	.	.		0.667	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	Intron
ARIH1	25820	hgsc.bcm.edu	37	15	72767267	72767267	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:72767267A>G	ENST00000379887.4	+	1	601	c.287A>G	c.(286-288)gAg>gGg	p.E96G	RP11-1007O24.3_ENST00000565181.1_lincRNA	NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	96					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						CATGAGCAGGAGGAGGATTAC	0.711																																					p.E96G		Atlas-SNP	.											.	ARIH1	42	.	0			c.A287G						.						19.0	13.0	15.0					15																	72767267		2072	4097	6169	SO:0001583	missense	25820	exon1			AGCAGGAGGAGGA	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"""ariadne, Drosophila, homolog of"""	605624	"""ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1"", ""ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"""			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.287A>G	chr15.hg19:g.72767267A>G	ENSP00000369217:p.Glu96Gly	86.0	0.0		79.0	4.0	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.291195	0.59976	.	.	ENSG00000166233	ENST00000379887	D	0.88664	-2.41	4.06	4.06	0.47325	.	0.157254	0.39274	N	0.001416	T	0.77260	0.4104	N	0.19112	0.55	0.44762	D	0.997764	P	0.36199	0.543	B	0.25987	0.065	T	0.76410	-0.2969	10	0.33940	T	0.23	.	11.2844	0.49214	1.0:0.0:0.0:0.0	.	96	Q9Y4X5	ARI1_HUMAN	G	96	ENSP00000369217:E96G	ENSP00000369217:E96G	E	+	2	0	ARIH1	70554321	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.672000	0.68102	1.603000	0.50134	0.459000	0.35465	GAG	.	.		0.711	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744	
PML	5371	hgsc.bcm.edu	37	15	74327563	74327563	+	Intron	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:74327563C>A	ENST00000268058.3	+	7	1806				PML_ENST00000565898.1_Intron|PML_ENST00000268059.6_Silent_p.S587S|PML_ENST00000563500.1_3'UTR|PML_ENST00000569477.1_Missense_Mutation_p.L601I|PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Silent_p.S539S|PML_ENST00000436891.3_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000435786.2_3'UTR	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CAGCCCACTCCTCGCCAGCCC	0.647			T	"""RARA, PAX5"""	"""APL, ALL"""																																p.S587S		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.C1761A						.						100.0	116.0	110.0					15																	74327563		2198	4297	6495	SO:0001627	intron_variant	5371	exon8			CCACTCCTCGCCA	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+692C>A	chr15.hg19:g.74327563C>A		159.0	0.0		94.0	4.0	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.		0.647	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
CYP1A1	1543	hgsc.bcm.edu	37	15	75015213	75015213	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:75015213T>C	ENST00000379727.3	-	2	424	c.226A>G	c.(226-228)Atc>Gtc	p.I76V	CYP1A1_ENST00000564596.1_Intron|CYP1A1_ENST00000395049.4_Missense_Mutation_p.I76V|CYP1A1_ENST00000567032.1_Missense_Mutation_p.I76V|CYP1A1_ENST00000395048.2_Missense_Mutation_p.I76V			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	76					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	CCAATTCGGATCTGCAGCACG	0.647									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.I76V		Atlas-SNP	.											.	CYP1A1	60	.	0			c.A226G						.						64.0	54.0	57.0					15																	75015213		2197	4296	6493	SO:0001583	missense	1543	exon2	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	TTCGGATCTGCAG	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"""Cytochrome P450s"""	2595	protein-coding gene	gene with protein product		108330	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"""	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.226A>G	chr15.hg19:g.75015213T>C	ENSP00000369050:p.Ile76Val	142.0	0.0		99.0	5.0	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	hg19	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	T	9.329	1.060079	0.19987	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.68181	-0.31;-0.31;-0.31	5.23	2.95	0.34219	.	0.157502	0.56097	N	0.000024	T	0.50292	0.1607	N	0.24115	0.695	0.50171	D	0.999851	B;B	0.24368	0.102;0.012	B;B	0.30495	0.116;0.048	T	0.42068	-0.9473	10	0.40728	T	0.16	.	7.5077	0.27555	0.0:0.2876:0.0:0.7124	.	76;76	E7EMT5;P04798	.;CP1A1_HUMAN	V	76	ENSP00000369050:I76V;ENSP00000378488:I76V;ENSP00000378489:I76V	ENSP00000268062:I76V	I	-	1	0	CYP1A1	72802266	1.000000	0.71417	0.998000	0.56505	0.333000	0.28666	3.388000	0.52509	0.833000	0.34828	0.379000	0.24179	ATC	.	.		0.647	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499	
NEIL1	79661	hgsc.bcm.edu	37	15	75647049	75647049	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:75647049T>C	ENST00000564784.1	+	10	1621	c.992T>C	c.(991-993)cTt>cCt	p.L331P	NEIL1_ENST00000569035.1_Missense_Mutation_p.L331P|MIR631_ENST00000384904.1_RNA|RP11-817O13.6_ENST00000563660.1_lincRNA|NEIL1_ENST00000355059.4_Missense_Mutation_p.L331P			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	331					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						AAGAGAGACCTTCCTAAGAGG	0.622								Base excision repair (BER), DNA glycosylases																													p.L417P		Atlas-SNP	.											.	NEIL1	36	.	0			c.T1250C						.						50.0	55.0	53.0					15																	75647049		2197	4294	6491	SO:0001583	missense	79661	exon9			GAGACCTTCCTAA	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.992T>C	chr15.hg19:g.75647049T>C	ENSP00000457352:p.Leu331Pro	82.0	0.0		66.0	4.0	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	hg19	CCDS10278.1	.	.	.	.	.	.	.	.	.	.	T	6.154	0.396553	0.11638	.	.	ENSG00000140398	ENST00000355059	T	0.12672	2.66	3.65	-0.0446	0.13855	.	1.484880	0.03689	N	0.246787	T	0.09949	0.0244	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32981	-0.9886	10	0.44086	T	0.13	-2.4153	3.3161	0.07034	0.0:0.2306:0.2096:0.5598	.	331	Q96FI4	NEIL1_HUMAN	P	331	ENSP00000347170:L331P	ENSP00000347170:L331P	L	+	2	0	NEIL1	73434102	0.000000	0.05858	0.001000	0.08648	0.098000	0.18820	-0.118000	0.10692	-0.015000	0.14150	0.454000	0.30748	CTT	.	.		0.622	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
ACSBG1	23205	hgsc.bcm.edu	37	15	78474373	78474373	+	Missense_Mutation	SNP	C	C	A	rs372447099		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:78474373C>A	ENST00000258873.4	-	8	1214	c.1009G>T	c.(1009-1011)Gac>Tac	p.D337Y	ACSBG1_ENST00000560817.1_Missense_Mutation_p.D95Y|ACSBG1_ENST00000541759.1_Missense_Mutation_p.D95Y	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	337					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						GTCCACAGGTCGTAGATCTGG	0.637																																					p.D337Y		Atlas-SNP	.											.	ACSBG1	79	.	0			c.G1009T						.						83.0	69.0	74.0					15																	78474373		2196	4293	6489	SO:0001583	missense	23205	exon8			ACAGGTCGTAGAT	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1009G>T	chr15.hg19:g.78474373C>A	ENSP00000258873:p.Asp337Tyr	70.0	0.0		48.0	4.0	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	hg19	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922995	0.92319	.	.	ENSG00000103740	ENST00000258873;ENST00000541759	T;T	0.42131	0.98;0.98	5.32	5.32	0.75619	AMP-dependent synthetase/ligase (1);	0.117935	0.53938	D	0.000044	T	0.71099	0.3300	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.77004	0.989;0.974	T	0.77453	-0.2582	10	0.87932	D	0	-46.0626	18.0808	0.89440	0.0:1.0:0.0:0.0	.	333;337	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	Y	337;95	ENSP00000258873:D337Y;ENSP00000439955:D95Y	ENSP00000258873:D337Y	D	-	1	0	ACSBG1	76261428	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	7.736000	0.84948	2.512000	0.84698	0.650000	0.86243	GAC	.	.		0.637	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84561455	84561455	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:84561455A>G	ENST00000286744.5	+	13	1506	c.1282A>G	c.(1282-1284)Act>Gct	p.T428A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.T428A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	428	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TAATCCTTGGACTGCATGTTC	0.408																																					p.T428A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A1282G						.						131.0	117.0	122.0					15																	84561455		2203	4300	6503	SO:0001583	missense	57188	exon13			CCTTGGACTGCAT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1282A>G	chr15.hg19:g.84561455A>G	ENSP00000286744:p.Thr428Ala	120.0	0.0		91.0	4.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.448979	0.84101	.	.	ENSG00000156218	ENST00000286744	T	0.53423	0.62	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66297	0.2775	M	0.62088	1.915	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.996	T	0.69723	-0.5068	10	0.72032	D	0.01	.	15.2316	0.73395	1.0:0.0:0.0:0.0	.	428;428	P82987-2;P82987	.;ATL3_HUMAN	A	428	ENSP00000286744:T428A	ENSP00000286744:T428A	T	+	1	0	ADAMTSL3	82352459	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.858000	0.92256	1.994000	0.58287	0.533000	0.62120	ACT	.	.		0.408	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
NTRK3	4916	hgsc.bcm.edu	37	15	88679734	88679734	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:88679734C>G	ENST00000360948.2	-	7	890	c.729G>C	c.(727-729)tgG>tgC	p.W243C	NTRK3_ENST00000317501.3_Missense_Mutation_p.W243C|NTRK3_ENST00000394480.2_Missense_Mutation_p.W243C|NTRK3_ENST00000557856.1_Missense_Mutation_p.W243C|NTRK3_ENST00000540489.2_Missense_Mutation_p.W243C|NTRK3_ENST00000357724.2_Missense_Mutation_p.W243C|NTRK3_ENST00000558676.1_Missense_Mutation_p.W243C|NTRK3_ENST00000355254.2_Missense_Mutation_p.W243C|NTRK3_ENST00000542733.2_Missense_Mutation_p.W145C	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	243	Ig-like C2-type 1.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.W243C(3)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CAGTGACTATCCAGTCCACAT	0.547			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																											p.W243C		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	.	3	Substitution - Missense(3)	lung(3)	c.G729C						.						151.0	97.0	115.0					15																	88679734		2201	4299	6500	SO:0001583	missense	4916	exon8			GACTATCCAGTCC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.729G>C	chr15.hg19:g.88679734C>G	ENSP00000354207:p.Trp243Cys	134.0	0.0		75.0	4.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440008	0.83993	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	D;D;D;D;D;D;D	0.96300	-3.97;-3.97;-3.97;-3.97;-3.97;-3.97;-3.97	5.64	5.64	0.86602	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.98566	0.9521	M	0.91354	3.2	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.996;1.0	D	0.99461	1.0943	10	0.87932	D	0	.	18.6884	0.91574	0.0:1.0:0.0:0.0	.	145;243;243;243;243;243	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	C	243;243;243;243;145;243;243	ENSP00000377990:W243C;ENSP00000354207:W243C;ENSP00000350356:W243C;ENSP00000347397:W243C;ENSP00000437773:W145C;ENSP00000444673:W243C;ENSP00000318328:W243C	ENSP00000318328:W243C	W	-	3	0	NTRK3	86480738	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.359000	0.79477	2.657000	0.90304	0.655000	0.94253	TGG	.	.		0.547	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
MFGE8	4240	hgsc.bcm.edu	37	15	89442944	89442944	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:89442944G>T	ENST00000566497.1	-	7	1030	c.969C>A	c.(967-969)taC>taA	p.Y323*	MFGE8_ENST00000268150.8_Nonsense_Mutation_p.Y323*|MFGE8_ENST00000539437.1_Nonsense_Mutation_p.Y315*|MFGE8_ENST00000542878.1_Nonsense_Mutation_p.Y279*|MFGE8_ENST00000268151.7_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	323	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					TGTCATTACTGTAGGCAACCT	0.567																																					p.Y323X		Atlas-SNP	.											.	MFGE8	60	.	0			c.C969A						.						106.0	87.0	93.0					15																	89442944		2200	4299	6499	SO:0001587	stop_gained	4240	exon7			ATTACTGTAGGCA	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.969C>A	chr15.hg19:g.89442944G>T	ENSP00000456281:p.Tyr323*	125.0	0.0		97.0	4.0	NM_005928	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Nonsense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922032	0.92319	.	.	ENSG00000140545	ENST00000268150;ENST00000539437;ENST00000542878	.	.	.	5.03	2.04	0.26737	.	0.437377	0.27315	N	0.019926	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.7146	8.9969	0.36059	0.2572:0.0:0.7428:0.0	.	.	.	.	X	323;315;279	.	ENSP00000268150:Y323X	Y	-	3	2	MFGE8	87243948	1.000000	0.71417	0.989000	0.46669	0.888000	0.51559	2.796000	0.47869	0.524000	0.28502	0.485000	0.47835	TAC	.	.		0.567	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
RLBP1	6017	hgsc.bcm.edu	37	15	89760380	89760380	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:89760380T>C	ENST00000268125.5	-	5	756	c.317A>G	c.(316-318)aAc>aGc	p.N106S		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	106					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.N106S(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	ACGGCCCACGTTGAACTTCCG	0.657																																					p.N106S		Atlas-SNP	.											RLBP1,face,carcinoma,0,1	RLBP1	34	.	1	Substitution - Missense(1)	skin(1)	c.A317G						.						42.0	43.0	43.0					15																	89760380		2200	4299	6499	SO:0001583	missense	6017	exon5			CCCACGTTGAACT	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.317A>G	chr15.hg19:g.89760380T>C	ENSP00000268125:p.Asn106Ser	108.0	0.0		74.0	3.0	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	hg19	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.159036	0.57368	.	.	ENSG00000140522	ENST00000268125	D	0.87179	-2.22	5.03	5.03	0.67393	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.208161	0.49305	D	0.000145	T	0.74435	0.3716	N	0.10837	0.055	0.28284	N	0.923864	B	0.12630	0.006	B	0.08055	0.003	T	0.58956	-0.7544	10	0.13853	T	0.58	-20.6791	14.7632	0.69619	0.0:0.0:0.0:1.0	.	106	P12271	RLBP1_HUMAN	S	106	ENSP00000268125:N106S	ENSP00000268125:N106S	N	-	2	0	RLBP1	87561384	0.987000	0.35691	0.890000	0.34922	0.832000	0.47134	7.419000	0.80179	1.898000	0.54952	0.459000	0.35465	AAC	.	.		0.657	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
TICRR	90381	hgsc.bcm.edu	37	15	90142664	90142664	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:90142664C>A	ENST00000268138.7	+	8	2115	c.2010C>A	c.(2008-2010)acC>acA	p.T670T	TICRR_ENST00000560985.1_Silent_p.T669T			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	670					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TGATCTCAACCGTTAAAATGT	0.403																																					p.T670T		Atlas-SNP	.											.	.	.	.	0			c.C2010A						.						102.0	94.0	96.0					15																	90142664		1867	4112	5979	SO:0001819	synonymous_variant	90381	exon8			CTCAACCGTTAAA	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2010C>A	chr15.hg19:g.90142664C>A		144.0	0.0		92.0	4.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.		0.403	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
VPS33B	26276	hgsc.bcm.edu	37	15	91549273	91549273	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:91549273C>T	ENST00000333371.3	-	12	1222	c.869G>A	c.(868-870)cGg>cAg	p.R290Q	VPS33B_ENST00000535906.1_Missense_Mutation_p.R263Q|VPS33B_ENST00000535843.1_Missense_Mutation_p.R199Q	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	290					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					GTGCTCGTTCCGAATCTCATT	0.483																																					p.R290Q		Atlas-SNP	.											.	VPS33B	42	.	0			c.G869A						.						59.0	55.0	56.0					15																	91549273		2198	4298	6496	SO:0001583	missense	26276	exon12			TCGTTCCGAATCT	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.869G>A	chr15.hg19:g.91549273C>T	ENSP00000327650:p.Arg290Gln	113.0	0.0		110.0	5.0	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	hg19	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	C	32	5.134609	0.94517	.	.	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.80909	-1.43;-1.43;-1.43	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.92057	0.7483	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	D	0.93060	0.6473	10	0.87932	D	0	-10.9832	19.2714	0.94011	0.0:1.0:0.0:0.0	.	263;290	F5H008;Q9H267	.;VP33B_HUMAN	Q	290;263;199;245	ENSP00000327650:R290Q;ENSP00000444053:R263Q;ENSP00000446267:R199Q	ENSP00000327650:R290Q	R	-	2	0	VPS33B	89350277	1.000000	0.71417	0.971000	0.41717	0.575000	0.36095	6.684000	0.74538	2.884000	0.98904	0.655000	0.94253	CGG	.	.		0.483	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
NR2F2	7026	hgsc.bcm.edu	37	15	96877485	96877485	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:96877485G>T	ENST00000394166.3	+	2	2012	c.623G>T	c.(622-624)gGt>gTt	p.G208V	NR2F2_ENST00000421109.2_Missense_Mutation_p.G75V|NR2F2_ENST00000453270.2_Missense_Mutation_p.G55V|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000394171.2_Missense_Mutation_p.G55V	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	208	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			AACATCATGGGTATCGAGAAC	0.602																																					p.G208V		Atlas-SNP	.											.	NR2F2	35	.	0			c.G623T						.						166.0	159.0	162.0					15																	96877485		2197	4298	6495	SO:0001583	missense	7026	exon2			TCATGGGTATCGA	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"""Nuclear hormone receptors"""	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.623G>T	chr15.hg19:g.96877485G>T	ENSP00000377721:p.Gly208Val	135.0	0.0		112.0	5.0	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089585	0.94149	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	D;D;D;D	0.96992	-4.2;-4.2;-4.2;-4.2	4.96	4.96	0.65561	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.97723	0.9253	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.97110	1.0;0.948	D	0.98080	1.0403	10	0.51188	T	0.08	.	18.1811	0.89779	0.0:0.0:1.0:0.0	.	208;75	P24468;Q3KQR7	COT2_HUMAN;.	V	75;208;55;55	ENSP00000401674:G75V;ENSP00000377721:G208V;ENSP00000377726:G55V;ENSP00000389853:G55V	ENSP00000377721:G208V	G	+	2	0	NR2F2	94678489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.866000	0.99616	2.306000	0.77630	0.561000	0.74099	GGT	.	.		0.602	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1261545	1261545	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:1261545A>G	ENST00000348261.5	+	23	4663	c.4415A>G	c.(4414-4416)cAg>cGg	p.Q1472R	CACNA1H_ENST00000358590.4_Missense_Mutation_p.Q1472R|CACNA1H_ENST00000565831.1_Missense_Mutation_p.Q1472R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1472					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	ACCAAGGCACAGTGCCGGGCC	0.682																																					p.Q1472R		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A4415G						.						33.0	39.0	37.0					16																	1261545		2017	4161	6178	SO:0001583	missense	8912	exon23			AGGCACAGTGCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4415A>G	chr16.hg19:g.1261545A>G	ENSP00000334198:p.Gln1472Arg	137.0	0.0		89.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154628	0.57259	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-4.01	3.99	3.99	0.46301	Ion transport (1);	0.333388	0.30686	N	0.009086	D	0.93367	0.7885	L	0.48218	1.51	0.29692	N	0.840876	B;B;B;B;B	0.32031	0.174;0.095;0.352;0.072;0.101	B;B;B;B;B	0.29440	0.042;0.102;0.102;0.062;0.102	D	0.91848	0.5489	10	0.87932	D	0	.	12.4821	0.55850	1.0:0.0:0.0:0.0	.	213;213;213;1472;1472	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	R	1472	ENSP00000334198:Q1472R;ENSP00000351401:Q1472R	ENSP00000334198:Q1472R	Q	+	2	0	CACNA1H	1201546	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	7.127000	0.77210	1.789000	0.52484	0.402000	0.26972	CAG	.	.		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
CACNA1H	8912	hgsc.bcm.edu	37	16	1270004	1270004	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:1270004G>A	ENST00000348261.5	+	35	6320	c.6072G>A	c.(6070-6072)ttG>ttA	p.L2024L	CACNA1H_ENST00000358590.4_Silent_p.L2018L|CACNA1H_ENST00000565831.1_Silent_p.L2018L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2024					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGATTCCTTGGAAGGGAAGA	0.662																																					p.L2024L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G6072A						.						16.0	19.0	18.0					16																	1270004		1916	4114	6030	SO:0001819	synonymous_variant	8912	exon35			TTCCTTGGAAGGG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6072G>A	chr16.hg19:g.1270004G>A		118.0	0.0		99.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.662	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TBL3	10607	hgsc.bcm.edu	37	16	2024958	2024958	+	Missense_Mutation	SNP	G	G	T	rs541759826		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2024958G>T	ENST00000568546.1	+	7	622	c.494G>T	c.(493-495)cGc>cTc	p.R165L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	165					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)	p.R165H(1)		breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GACCCTACACGCCTGCTGCTC	0.677																																					p.R165L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											TBL3,NS,carcinoma,0,1	TBL3	54	.	1	Substitution - Missense(1)	lung(1)	c.G494T						.						69.0	53.0	59.0					16																	2024958		2197	4299	6496	SO:0001583	missense	10607	exon7			CTACACGCCTGCT	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.494G>T	chr16.hg19:g.2024958G>T	ENSP00000454836:p.Arg165Leu	109.0	1.0		56.0	3.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.912003	0.52439	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.32	4.15	0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.547110	0.03341	N	0.194821	T	0.65913	0.2737	M	0.63208	1.945	0.54753	D	0.999985	B	0.20780	0.048	B	0.22753	0.041	T	0.47368	-0.9123	9	0.42905	T	0.14	-25.763	13.9416	0.64059	0.0875:0.0:0.9125:0.0	.	165	Q12788	TBL3_HUMAN	L	165	.	ENSP00000331815:R165L	R	+	2	0	TBL3	1964959	0.990000	0.36364	0.993000	0.49108	0.690000	0.40134	1.546000	0.36179	2.484000	0.83849	0.561000	0.74099	CGC	.	.		0.677	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
TBL3	10607	hgsc.bcm.edu	37	16	2027159	2027159	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2027159T>C	ENST00000568546.1	+	15	1673	c.1545T>C	c.(1543-1545)ggT>ggC	p.G515G		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	515					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AGCTGCTGGGTGTCTTCTCAG	0.652																																					p.G515G	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.T1545C						.						41.0	41.0	41.0					16																	2027159		2198	4300	6498	SO:0001819	synonymous_variant	10607	exon15			GCTGGGTGTCTTC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1545T>C	chr16.hg19:g.2027159T>C		57.0	0.0		40.0	4.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	hg19	CCDS10453.1																																																																																			.	.		0.652	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
ABCA3	21	hgsc.bcm.edu	37	16	2339468	2339468	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2339468C>T	ENST00000301732.5	-	20	3367	c.2667G>A	c.(2665-2667)gaG>gaA	p.E889E	ABCA3_ENST00000382381.3_Silent_p.E831E	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	889					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	TGCGCTCCTCCTCGATGAGGG	0.677																																					p.E889E		Atlas-SNP	.											.	ABCA3	176	.	0			c.G2667A						.						29.0	27.0	28.0					16																	2339468		2195	4298	6493	SO:0001819	synonymous_variant	21	exon20			CTCCTCCTCGATG	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2667G>A	chr16.hg19:g.2339468C>T		110.0	0.0		67.0	16.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	hg19	CCDS10466.1																																																																																			.	.		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
SRRM2	23524	hgsc.bcm.edu	37	16	2812361	2812361	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2812361G>T	ENST00000301740.8	+	11	2381	c.1832G>T	c.(1831-1833)cGg>cTg	p.R611L		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	611	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ACACCAGCCCGGAGGGGCAGG	0.622																																					p.R611L		Atlas-SNP	.											.	SRRM2	263	.	0			c.G1832T						.						57.0	59.0	58.0					16																	2812361		2198	4300	6498	SO:0001583	missense	23524	exon11			CAGCCCGGAGGGG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.1832G>T	chr16.hg19:g.2812361G>T	ENSP00000301740:p.Arg611Leu	89.0	0.0		54.0	5.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536390	0.27475	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000426305	T	0.26223	1.75	5.91	5.91	0.95273	.	0.000000	0.56097	D	0.000031	T	0.35248	0.0925	L	0.27053	0.805	0.36903	D	0.890505	D	0.63880	0.993	D	0.74023	0.982	T	0.23619	-1.0183	10	0.44086	T	0.13	-8.1276	11.1017	0.48179	0.0836:0.0:0.9164:0.0	.	611	Q9UQ35	SRRM2_HUMAN	L	611;611;576	ENSP00000301740:R611L	ENSP00000301740:R611L	R	+	2	0	SRRM2	2752362	0.139000	0.22563	0.924000	0.36721	0.284000	0.27059	3.181000	0.50903	2.801000	0.96364	0.655000	0.94253	CGG	.	.		0.622	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
CCDC64B	146439	hgsc.bcm.edu	37	16	3078749	3078749	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3078749C>A	ENST00000572449.1	-	8	1252	c.1190G>T	c.(1189-1191)gGg>gTg	p.G397V	CCDC64B_ENST00000573514.1_Missense_Mutation_p.G190V|CCDC64B_ENST00000389347.4_Missense_Mutation_p.G397V			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	397										breast(1)|endometrium(2)|large_intestine(1)	4						CAGGGCCTCCCCAGGGTCTTC	0.672																																					p.G397V		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G1190T						.						28.0	38.0	35.0					16																	3078749		2037	4159	6196	SO:0001583	missense	146439	exon7			GCCTCCCCAGGGT	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1190G>T	chr16.hg19:g.3078749C>A	ENSP00000459043:p.Gly397Val	143.0	0.0		118.0	6.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	C	8.389	0.839369	0.16891	.	.	ENSG00000162069	ENST00000389347	T	0.30981	1.51	4.81	-1.42	0.08913	.	0.734974	0.12341	N	0.477507	T	0.18299	0.0439	N	0.24115	0.695	0.09310	N	0.999993	B	0.26195	0.144	B	0.29942	0.109	T	0.24621	-1.0155	10	0.56958	D	0.05	-3.5455	5.365	0.16109	0.0:0.3698:0.1541:0.4762	.	397	A1A5D9	BICR2_HUMAN	V	397	ENSP00000373998:G397V	ENSP00000373998:G397V	G	-	2	0	CCDC64B	3018750	0.000000	0.05858	0.031000	0.17742	0.014000	0.08584	0.335000	0.19806	-0.324000	0.08589	-0.367000	0.07326	GGG	.	.		0.672	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
ZNF75A	7627	hgsc.bcm.edu	37	16	3367499	3367499	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3367499C>G	ENST00000574298.1	+	6	994	c.521C>G	c.(520-522)tCt>tGt	p.S174C	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	174					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(1)|large_intestine(3)|lung(7)|prostate(1)	12						AGAGTTAGCTCTGACCTTATT	0.383																																					p.S174C		Atlas-SNP	.											.	ZNF75A	34	.	0			c.C521G						.						81.0	79.0	79.0					16																	3367499		2197	4300	6497	SO:0001583	missense	7627	exon6			TTAGCTCTGACCT	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"""Zinc fingers, C2H2-type"", ""-"""	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.521C>G	chr16.hg19:g.3367499C>G	ENSP00000459566:p.Ser174Cys	220.0	0.0		199.0	62.0	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	hg19	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.202946	0.58234	.	.	ENSG00000162086	ENST00000293995	.	.	.	4.57	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44285	D	0.000464	T	0.54775	0.1879	M	0.80028	2.48	0.26965	N	0.96573	B	0.22414	0.069	B	0.19946	0.027	T	0.56649	-0.7944	9	0.66056	D	0.02	.	12.5959	0.56470	0.0:0.8312:0.1688:0.0	.	174	Q96N20	ZN75A_HUMAN	C	174	.	ENSP00000293995:S174C	S	+	2	0	ZNF75A	3307500	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.207000	0.17395	1.253000	0.44018	0.557000	0.71058	TCT	.	.		0.383	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028	
CREBBP	1387	hgsc.bcm.edu	37	16	3778391	3778391	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3778391G>T	ENST00000262367.5	-	31	7466	c.6657C>A	c.(6655-6657)gcC>gcA	p.A2219A	CREBBP_ENST00000382070.3_Silent_p.A2181A	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2219					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CAGCCATGCCGGCACTCCCTt	0.642			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.A2219A		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C6657A						.						33.0	30.0	31.0					16																	3778391		2196	4300	6496	SO:0001819	synonymous_variant	1387	exon31			CATGCCGGCACTC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6657C>A	chr16.hg19:g.3778391G>T		82.0	0.0		76.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.642	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
DNAJA3	9093	hgsc.bcm.edu	37	16	4500484	4500484	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:4500484C>T	ENST00000262375.6	+	10	1402	c.1325C>T	c.(1324-1326)aCc>aTc	p.T442I	DNAJA3_ENST00000431375.2_Missense_Mutation_p.T289I|DNAJA3_ENST00000355296.4_Missense_Mutation_p.T442I	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	442					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|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 I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						AACGGCGTCACCCTCACCAGC	0.612																																					p.T442I		Atlas-SNP	.											.	DNAJA3	52	.	0			c.C1325T						.						45.0	35.0	38.0					16																	4500484		2197	4296	6493	SO:0001583	missense	9093	exon10			GCGTCACCCTCAC	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1325C>T	chr16.hg19:g.4500484C>T	ENSP00000262375:p.Thr442Ile	72.0	0.0		66.0	4.0	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Missense_Mutation	SNP	ENST00000262375.6	hg19	CCDS10515.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633660	0.67015	.	.	ENSG00000103423	ENST00000262375;ENST00000355296;ENST00000431375	T;T;T	0.65364	-0.11;-0.15;0.84	5.63	5.63	0.86233	.	0.046583	0.85682	D	0.000000	T	0.71921	0.3397	M	0.62723	1.935	0.80722	D	1	D;D;D	0.62365	0.991;0.963;0.967	P;P;P	0.52672	0.606;0.706;0.606	T	0.75082	-0.3443	10	0.87932	D	0	-26.8186	18.6707	0.91510	0.0:1.0:0.0:0.0	.	289;442;442	E7ES32;Q96EY1-2;Q96EY1	.;.;DNJA3_HUMAN	I	442;442;289	ENSP00000262375:T442I;ENSP00000347445:T442I;ENSP00000393970:T289I	ENSP00000262375:T442I	T	+	2	0	DNAJA3	4440485	1.000000	0.71417	0.999000	0.59377	0.683000	0.39861	4.787000	0.62432	2.659000	0.90383	0.561000	0.74099	ACC	.	.		0.612	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1		
ABAT	18	hgsc.bcm.edu	37	16	8866644	8866644	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:8866644A>G	ENST00000396600.2	+	12	1762	c.824A>G	c.(823-825)gAt>gGt	p.D275G	ABAT_ENST00000425191.2_Missense_Mutation_p.D275G|ABAT_ENST00000268251.8_Missense_Mutation_p.D275G|ABAT_ENST00000567812.1_Missense_Mutation_p.D290G|ABAT_ENST00000569156.1_Missense_Mutation_p.D275G	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	275					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	CAGGTGGAGGATCTGATTGTG	0.552																																					p.D275G		Atlas-SNP	.											.	ABAT	46	.	0			c.A824G						.						77.0	71.0	73.0					16																	8866644		2197	4300	6497	SO:0001583	missense	18	exon12			TGGAGGATCTGAT	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.824A>G	chr16.hg19:g.8866644A>G	ENSP00000379845:p.Asp275Gly	103.0	0.0		100.0	4.0	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.956399	0.34565	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	T;T;T	0.77229	-1.08;-1.08;-1.08	4.94	4.94	0.65067	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.74581	0.3735	L	0.53780	1.695	0.80722	D	1	B	0.22146	0.065	B	0.28232	0.087	T	0.71974	-0.4430	10	0.41790	T	0.15	.	13.7814	0.63085	1.0:0.0:0.0:0.0	.	275	P80404	GABT_HUMAN	G	275	ENSP00000268251:D275G;ENSP00000379845:D275G;ENSP00000411916:D275G	ENSP00000268251:D275G	D	+	2	0	ABAT	8774145	1.000000	0.71417	0.999000	0.59377	0.253000	0.25986	9.083000	0.94067	1.847000	0.53656	0.459000	0.35465	GAT	.	.		0.552	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686	
USP7	7874	hgsc.bcm.edu	37	16	9015082	9015082	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:9015082G>T	ENST00000344836.4	-	4	652	c.454C>A	c.(454-456)Cgt>Agt	p.R152S	USP7_ENST00000566224.1_5'Flank|USP7_ENST00000535863.1_Missense_Mutation_p.R53S|USP7_ENST00000381886.4_Missense_Mutation_p.R136S	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	152	Interaction with TSPYL5.|Interaction with p53/TP53, MDM2 and EBNA1.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Necessary for nuclear localization.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CTAATACGACGACTGAACGAC	0.358																																					p.R152S		Atlas-SNP	.											.	USP7	116	.	0			c.C454A						.						95.0	86.0	89.0					16																	9015082		2197	4300	6497	SO:0001583	missense	7874	exon4			TACGACGACTGAA	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.454C>A	chr16.hg19:g.9015082G>T	ENSP00000343535:p.Arg152Ser	148.0	0.0		135.0	8.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	hg19	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179091	0.57692	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	T;T;T	0.42131	0.98;0.98;0.98	5.9	5.9	0.94986	TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.63570	0.2522	M	0.86420	2.815	0.80722	D	1	P;P	0.44946	0.846;0.846	P;P	0.51550	0.673;0.673	T	0.61466	-0.7057	10	0.29301	T	0.29	.	20.3398	0.98759	0.0:0.0:1.0:0.0	.	152;136	Q93009;B7Z815	UBP7_HUMAN;.	S	152;160;53;53;94	ENSP00000343535:R152S;ENSP00000443646:R53S;ENSP00000439272:R94S	ENSP00000343535:R152S	R	-	1	0	USP7	8922583	1.000000	0.71417	0.801000	0.32222	0.921000	0.55340	9.509000	0.98002	2.817000	0.96982	0.552000	0.68991	CGT	.	.		0.358	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		
GRIN2A	2903	hgsc.bcm.edu	37	16	9934644	9934644	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:9934644C>A	ENST00000396573.2	-	8	1820	c.1511G>T	c.(1510-1512)cGg>cTg	p.R504L	GRIN2A_ENST00000396575.2_Missense_Mutation_p.R504L|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R504L|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R347L|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R504L|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R504L	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	504			R -> W (in FESD). {ECO:0000269|PubMed:23933820}.		directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CATGACTGCCCGTTGATAGAC	0.448																																					p.R504L		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G1511T						.						80.0	63.0	69.0					16																	9934644		2197	4300	6497	SO:0001583	missense	2903	exon8			ACTGCCCGTTGAT		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1511G>T	chr16.hg19:g.9934644C>A	ENSP00000379818:p.Arg504Leu	109.0	0.0		72.0	4.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.322313	0.41096	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54	5.3	5.3	0.74995	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.126603	0.53938	D	0.000051	T	0.54806	0.1881	M	0.66560	2.04	0.49687	D	0.999818	B;P;P	0.41710	0.307;0.76;0.758	B;B;B	0.40228	0.071;0.187;0.323	T	0.57015	-0.7883	9	.	.	.	.	17.9735	0.89120	0.0:1.0:0.0:0.0	.	347;504;504	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	L	504;504;347;504;504	ENSP00000379818:R504L;ENSP00000385872:R504L;ENSP00000441572:R347L;ENSP00000332549:R504L;ENSP00000379820:R504L	.	R	-	2	0	GRIN2A	9842145	1.000000	0.71417	0.610000	0.28997	0.282000	0.26991	4.425000	0.59875	2.469000	0.83416	0.655000	0.94253	CGG	.	.		0.448	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
PDXDC1	23042	hgsc.bcm.edu	37	16	15127208	15127208	+	Silent	SNP	C	C	A	rs151129728	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:15127208C>A	ENST00000396410.4	+	19	1861	c.1764C>A	c.(1762-1764)ctC>ctA	p.L588L	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000325823.7_Silent_p.L573L|PDXDC1_ENST00000450288.2_Silent_p.L560L|PDXDC1_ENST00000569715.1_Silent_p.L561L|PDXDC1_ENST00000563679.1_Silent_p.L606L|PDXDC1_ENST00000447912.2_Silent_p.L497L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	588					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCTGAGCTCGTGGAGACCA	0.537																																					p.L588L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C1764A						.						145.0	130.0	135.0					16																	15127208		2197	4300	6497	SO:0001819	synonymous_variant	23042	exon19			TGAGCTCGTGGAG	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1764C>A	chr16.hg19:g.15127208C>A		86.0	0.0		72.0	4.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	hg19	CCDS32393.1																																																																																			.	C|1.000;T|0.000		0.537	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
USP31	57478	hgsc.bcm.edu	37	16	23080459	23080459	+	Silent	SNP	G	G	T	rs201814190		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23080459G>T	ENST00000219689.7	-	16	2966	c.2967C>A	c.(2965-2967)atC>atA	p.I989I	USP31_ENST00000567975.1_Silent_p.I282I	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.I989I(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCACATAAGCGATCTGATTAT	0.522																																					p.I989I		Atlas-SNP	.											USP31,leg,malignant_melanoma,0,1	USP31	122	.	1	Substitution - coding silent(1)	skin(1)	c.C2967A						.						78.0	82.0	81.0					16																	23080459		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon16			ATAAGCGATCTGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2967C>A	chr16.hg19:g.23080459G>T		50.0	0.0		27.0	4.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	G|1.000;A|0.000		0.522	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
USP31	57478	hgsc.bcm.edu	37	16	23080589	23080589	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23080589T>C	ENST00000219689.7	-	16	2836	c.2837A>G	c.(2836-2838)gAa>gGa	p.E946G	USP31_ENST00000567975.1_Missense_Mutation_p.E239G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GAACACGCCTTCCATGACAGC	0.577																																					p.E946G		Atlas-SNP	.											.	USP31	122	.	0			c.A2837G						.						85.0	87.0	86.0					16																	23080589		2197	4300	6497	SO:0001583	missense	57478	exon16			ACGCCTTCCATGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2837A>G	chr16.hg19:g.23080589T>C	ENSP00000219689:p.Glu946Gly	103.0	0.0		96.0	5.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.672299	0.67928	.	.	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.12039	2.72	6.16	6.16	0.99307	.	0.649429	0.13781	N	0.363238	T	0.35480	0.0933	L	0.56769	1.78	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.994;0.986;0.995	T	0.00484	-1.1712	10	0.37606	T	0.19	-15.1034	15.9872	0.80168	0.0:0.0:0.0:1.0	.	249;946;239	Q70CQ4-2;Q70CQ4;B3KS48	.;UBP31_HUMAN;.	G	946;249	ENSP00000219689:E946G	ENSP00000219689:E946G	E	-	2	0	USP31	22988090	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.665000	0.83852	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
USP31	57478	hgsc.bcm.edu	37	16	23091273	23091273	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23091273A>G	ENST00000219689.7	-	13	2169	c.2170T>C	c.(2170-2172)Tac>Cac	p.Y724H		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	354	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGACCTGTGTAGTGCCCCCCT	0.577																																					p.Y724H		Atlas-SNP	.											.	USP31	122	.	0			c.T2170C						.						84.0	66.0	72.0					16																	23091273		2197	4300	6497	SO:0001583	missense	57478	exon13			CTGTGTAGTGCCC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2170T>C	chr16.hg19:g.23091273A>G	ENSP00000219689:p.Tyr724His	116.0	0.0		75.0	4.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.602357	0.87157	.	.	ENSG00000103404	ENST00000219689	T	0.21361	2.01	5.11	5.11	0.69529	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000001	T	0.60741	0.2292	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75260	-0.3380	10	0.87932	D	0	-13.1175	14.0861	0.64957	1.0:0.0:0.0:0.0	.	724	Q70CQ4	UBP31_HUMAN	H	724	ENSP00000219689:Y724H	ENSP00000219689:Y724H	Y	-	1	0	USP31	22998774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.958000	0.93099	1.917000	0.55516	0.455000	0.32223	TAC	.	.		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
XPO6	23214	hgsc.bcm.edu	37	16	28167437	28167437	+	Missense_Mutation	SNP	T	T	A	rs369899782		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:28167437T>A	ENST00000304658.5	-	7	1555	c.1055A>T	c.(1054-1056)aAt>aTt	p.N352I	XPO6_ENST00000565698.1_Missense_Mutation_p.N338I|XPO6_ENST00000561488.1_5'UTR	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	352					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						TGTGTGGGCATTGTTATCCTT	0.478																																					p.N352I		Atlas-SNP	.											.	XPO6	177	.	0			c.A1055T						.						108.0	95.0	100.0					16																	28167437		1963	4151	6114	SO:0001583	missense	23214	exon7			TGGGCATTGTTAT	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"""Exportins"""	19733	protein-coding gene	gene with protein product		608411	"""RAN binding protein 20"""	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.1055A>T	chr16.hg19:g.28167437T>A	ENSP00000302790:p.Asn352Ile	773.0	0.0		544.0	173.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.500126	0.44455	.	.	ENSG00000169180	ENST00000304658	T	0.51071	0.72	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	L	0.46157	1.445	0.80722	D	1	P;P	0.51933	0.949;0.893	B;B	0.40901	0.343;0.343	T	0.48969	-0.8987	10	0.72032	D	0.01	-17.8237	14.5226	0.67863	0.0:0.0:0.0:1.0	.	352;352	B7ZM10;Q96QU8	.;XPO6_HUMAN	I	352	ENSP00000302790:N352I	ENSP00000302790:N352I	N	-	2	0	XPO6	28074938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.478	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195	
SH2B1	25970	hgsc.bcm.edu	37	16	28856082	28856082	+	5'Flank	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:28856082G>T	ENST00000322610.8	+	0	0				TUFM_ENST00000313511.3_Silent_p.T207T|MIR4721_ENST00000577590.1_RNA			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						AGCCAAACTCGGTGAGCAGCT	0.592																																					p.T207T		Atlas-SNP	.											TUFM,rectum,carcinoma,0,1	TUFM	33	.	0			c.C621A						.						110.0	103.0	106.0					16																	28856082		2197	4300	6497	SO:0001631	upstream_gene_variant	7284	exon5			AAACTCGGTGAGC	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2			chr16.hg19:g.28856082G>T	Exception_encountered	126.0	0.0		100.0	4.0	NM_003321	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Silent	SNP	ENST00000322610.8	hg19	CCDS53996.1																																																																																			.	.		0.592	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503	
SPN	6693	hgsc.bcm.edu	37	16	29675060	29675060	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:29675060T>C	ENST00000360121.3	+	2	103	c.11T>C	c.(10-12)cTt>cCt	p.L4P	SPN_ENST00000395389.2_Missense_Mutation_p.L4P	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						ATGGCCACGCTTCTCCTTCTC	0.627																																					p.L4P		Atlas-SNP	.											.	SPN	44	.	0			c.T11C						.						118.0	129.0	125.0					16																	29675060		2197	4300	6497	SO:0001583	missense	6693	exon2			CCACGCTTCTCCT	J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"""CD molecules"""	11249	protein-coding gene	gene with protein product	"""leukosialin"""	182160	"""sialophorin (gpL115, leukosialin, CD43)"""			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.11T>C	chr16.hg19:g.29675060T>C	ENSP00000353238:p.Leu4Pro	122.0	0.0		104.0	5.0	NM_001030288	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000360121.3	hg19	CCDS10650.1	.	.	.	.	.	.	.	.	.	.	.	13.37	2.217088	0.39201	.	.	ENSG00000197471	ENST00000395389;ENST00000436527;ENST00000360121	T;T;T	0.47869	0.87;0.83;0.87	4.51	3.42	0.39159	.	0.203527	0.24481	N	0.038145	T	0.34978	0.0916	L	0.39898	1.24	0.20638	N	0.999877	B	0.31931	0.347	B	0.29176	0.099	T	0.32107	-0.9919	10	0.87932	D	0	-6.7037	7.0944	0.25301	0.0:0.1065:0.0:0.8935	.	4	P16150	LEUK_HUMAN	P	4	ENSP00000378787:L4P;ENSP00000412907:L4P;ENSP00000353238:L4P	ENSP00000353238:L4P	L	+	2	0	SPN	29582561	0.012000	0.17670	0.124000	0.21820	0.011000	0.07611	1.911000	0.39937	0.839000	0.34971	0.459000	0.35465	CTT	.	.		0.627	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2		
MAZ	4150	hgsc.bcm.edu	37	16	29820871	29820871	+	Intron	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:29820871G>T	ENST00000322945.6	+	5	1444				AC009133.20_ENST00000569039.1_RNA|AC009133.15_ENST00000566537.1_RNA|PRRT2_ENST00000358758.7_5'Flank|PRRT2_ENST00000300797.6_5'Flank|MAZ_ENST00000563402.1_Intron|AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000562337.1_Intron|MAZ_ENST00000568544.1_Intron|PRRT2_ENST00000567659.1_5'Flank|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000219782.6_Silent_p.T430T|MAZ_ENST00000568282.1_Silent_p.T31T|MAZ_ENST00000545521.1_Intron|MAZ_ENST00000566906.2_Intron	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						GCTTCACCACGGCAGCATACC	0.682																																					p.T430T	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.	MAZ	48	.	0			c.G1290T						.						22.0	23.0	22.0					16																	29820871		1987	4123	6110	SO:0001627	intron_variant	4150	exon5			CACCACGGCAGCA	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"""Zinc fingers, C2H2-type"""	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1280-527G>T	chr16.hg19:g.29820871G>T		141.0	0.0		125.0	5.0	NM_001042539	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Silent	SNP	ENST00000322945.6	hg19	CCDS42143.1																																																																																			.	.		0.682	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383	
HIRIP3	8479	hgsc.bcm.edu	37	16	30002499	30002499	+	IGR	SNP	G	G	T	rs138517482		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30002499G>T	ENST00000279392.3	-	0	3385				TAOK2_ENST00000279394.3_Silent_p.L920L	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3						chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						GCATGGCTCTGGGGGGCATCC	0.677																																					p.L920L		Atlas-SNP	.											.	TAOK2	142	.	0			c.G2760T						.						57.0	61.0	59.0					16																	30002499		2197	4300	6497	SO:0001628	intergenic_variant	9344	exon19			GGCTCTGGGGGGC	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118		chr16.hg19:g.30002499G>T		97.0	0.0		79.0	4.0	NM_004783	H3BSR3|O75707|O75708	Silent	SNP	ENST00000279392.3	hg19	CCDS10664.1																																																																																			.	G|1.000;C|0.000		0.677	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609	
DOC2A	8448	hgsc.bcm.edu	37	16	30020840	30020840	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30020840G>T	ENST00000350119.4	-	3	491	c.301C>A	c.(301-303)Cgg>Agg	p.R101R	DOC2A_ENST00000564944.1_Silent_p.R101R|DOC2A_ENST00000564979.1_Silent_p.R101R|DOC2A_ENST00000567824.1_5'Flank	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	101	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CAGGAGGCCCGGTCGTAGAGA	0.657																																					p.R101R		Atlas-SNP	.											.	DOC2A	40	.	0			c.C301A						.						47.0	40.0	42.0					16																	30020840		1910	3689	5599	SO:0001819	synonymous_variant	8448	exon3			AGGCCCGGTCGTA	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.301C>A	chr16.hg19:g.30020840G>T		58.0	0.0		57.0	4.0	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	hg19	CCDS10666.1																																																																																			.	.		0.657	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
GDPD3	79153	hgsc.bcm.edu	37	16	30124047	30124047	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30124047C>T	ENST00000406256.3	-	3	627	c.250G>A	c.(250-252)Gtg>Atg	p.V84M	RP11-455F5.4_ENST00000566190.1_RNA|MAPK3_ENST00000494643.1_5'Flank	NM_024307.2	NP_077283.2	Q7L5L3	GDPD3_HUMAN	glycerophosphodiester phosphodiesterase domain containing 3	84	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)	11						TCATGTGACACCACCACCACT	0.667											OREG0023731	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V84M		Atlas-SNP	.											.	GDPD3	23	.	0			c.G250A						.						69.0	61.0	64.0					16																	30124047		2197	4300	6497	SO:0001583	missense	79153	exon3			GTGACACCACCAC	AK026256	CCDS10671.2	16p11.2	2008-02-05			ENSG00000102886	ENSG00000102886			28638	protein-coding gene	gene with protein product							Standard	NM_024307		Approved	MGC4171	uc002dwp.3	Q7L5L3	OTTHUMG00000132106	ENST00000406256.3:c.250G>A	chr16.hg19:g.30124047C>T	ENSP00000384363:p.Val84Met	52.0	0.0	814	40.0	13.0	NM_024307	Q9H652	Missense_Mutation	SNP	ENST00000406256.3	hg19	CCDS10671.2	.	.	.	.	.	.	.	.	.	.	C	18.59	3.655806	0.67586	.	.	ENSG00000102886	ENST00000406256;ENST00000360688	T	0.19532	2.14	5.57	4.61	0.57282	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.059458	0.64402	D	0.000003	T	0.51702	0.1690	M	0.91196	3.185	0.48571	D	0.999676	D	0.76494	0.999	D	0.66602	0.945	T	0.62765	-0.6785	10	0.87932	D	0	.	12.4157	0.55492	0.0:0.8309:0.1691:0.0	.	84	Q7L5L3	GDPD3_HUMAN	M	84;22	ENSP00000384363:V84M	ENSP00000353909:V22M	V	-	1	0	GDPD3	30031548	0.999000	0.42202	0.998000	0.56505	0.529000	0.34654	4.175000	0.58263	1.318000	0.45170	0.563000	0.77884	GTG	.	.		0.667	GDPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255144.1	NM_024307	
ZNF629	23361	hgsc.bcm.edu	37	16	30793344	30793344	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30793344G>T	ENST00000262525.4	-	3	2512	c.2305C>A	c.(2305-2307)Cgc>Agc	p.R769S	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	769					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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			TCTGAGCAGCGGTAGGGTCTG	0.657																																					p.R769S		Atlas-SNP	.											.	ZNF629	44	.	0			c.C2305A						.						63.0	74.0	71.0					16																	30793344		1896	4104	6000	SO:0001583	missense	23361	exon3			AGCAGCGGTAGGG	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.2305C>A	chr16.hg19:g.30793344G>T	ENSP00000262525:p.Arg769Ser	89.0	0.0		89.0	4.0	NM_001080417	Q15938	Missense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	g	3.042	-0.197282	0.06259	.	.	ENSG00000102870	ENST00000262525	T	0.14893	2.47	5.65	4.56	0.56223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.126886	0.35970	N	0.002877	T	0.09468	0.0233	N	0.11255	0.115	0.21802	N	0.999535	B	0.02656	0.0	B	0.01281	0.0	T	0.26677	-1.0096	10	0.29301	T	0.29	-18.3376	11.3261	0.49450	0.0:0.0:0.1532:0.8468	.	769	Q9UEG4	ZN629_HUMAN	S	769	ENSP00000262525:R769S	ENSP00000262525:R769S	R	-	1	0	ZNF629	30700845	0.583000	0.26757	1.000000	0.80357	0.938000	0.57974	0.401000	0.20948	0.984000	0.38629	-0.367000	0.07326	CGC	.	.		0.657	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
SETD1A	9739	hgsc.bcm.edu	37	16	30976649	30976649	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30976649A>G	ENST00000262519.8	+	7	2272	c.1586A>G	c.(1585-1587)gAg>gGg	p.E529G		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	529	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ACAGGGAGTGAGGTGCCTTCT	0.612																																					p.E529G		Atlas-SNP	.											.	SETD1A	143	.	0			c.A1586G						.						58.0	63.0	61.0					16																	30976649		2197	4300	6497	SO:0001583	missense	9739	exon7			GGAGTGAGGTGCC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1586A>G	chr16.hg19:g.30976649A>G	ENSP00000262519:p.Glu529Gly	133.0	0.0		101.0	5.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	A	12.51	1.960356	0.34565	.	.	ENSG00000099381	ENST00000262519	D	0.94862	-3.54	5.53	5.53	0.82687	.	0.282904	0.32161	N	0.006486	D	0.87981	0.6315	N	0.11427	0.14	0.36161	D	0.848091	B	0.18610	0.029	B	0.17433	0.018	D	0.86817	0.2002	10	0.48119	T	0.1	.	13.5996	0.62011	1.0:0.0:0.0:0.0	.	529	O15047	SET1A_HUMAN	G	529	ENSP00000262519:E529G	ENSP00000262519:E529G	E	+	2	0	SETD1A	30884150	0.998000	0.40836	0.997000	0.53966	0.637000	0.38172	2.181000	0.42547	2.100000	0.63781	0.459000	0.35465	GAG	.	.		0.612	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
HSD3B7	80270	hgsc.bcm.edu	37	16	30997766	30997766	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30997766T>C	ENST00000297679.5	+	4	438	c.345T>C	c.(343-345)gcT>gcC	p.A115A	AC135048.1_ENST00000602217.1_5'Flank|HSD3B7_ENST00000262520.6_Silent_p.A115A|HSD3B7_ENST00000353250.5_Silent_p.A115A	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	115					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						TGATCGAGGCTTGTGTGCAGA	0.597																																					p.A115A		Atlas-SNP	.											.	HSD3B7	33	.	0			c.T345C						.						96.0	81.0	86.0					16																	30997766		2197	4300	6497	SO:0001819	synonymous_variant	80270	exon4			CGAGGCTTGTGTG	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	18324	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 3"""	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.345T>C	chr16.hg19:g.30997766T>C		96.0	0.0		123.0	6.0	NM_025193	Q96M28|Q9BSN9	Silent	SNP	ENST00000297679.5	hg19	CCDS10698.1																																																																																			.	.		0.597	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2		
BCKDK	10295	hgsc.bcm.edu	37	16	31123498	31123498	+	Missense_Mutation	SNP	T	T	C	rs398124213		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:31123498T>C	ENST00000394951.1	+	13	1774	c.1151T>C	c.(1150-1152)cTg>cCg	p.L384P	BCKDK_ENST00000394950.3_3'UTR|BCKDK_ENST00000219794.6_Missense_Mutation_p.L384P|BCKDK_ENST00000287507.3_3'UTR|AC135050.1_ENST00000517000.2_RNA			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	384	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						GGTGGGTCTCTGCAGCTGCAG	0.657																																					p.L384P		Atlas-SNP	.											.	BCKDK	52	.	0			c.T1151C						.						68.0	65.0	66.0					16																	31123498		2197	4300	6497	SO:0001583	missense	10295	exon12			GGTCTCTGCAGCT	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.1151T>C	chr16.hg19:g.31123498T>C	ENSP00000378405:p.Leu384Pro	90.0	0.0		90.0	4.0	NM_005881	A8MY43|Q6FGL4|Q96G95|Q96IN5	Missense_Mutation	SNP	ENST00000394951.1	hg19	CCDS10705.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.848931	0.91277	.	.	ENSG00000103507	ENST00000394951;ENST00000219794	D;D	0.81739	-1.53;-1.53	5.66	5.66	0.87406	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.91499	0.7316	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.93269	0.6650	10	0.87932	D	0	-19.1152	14.8634	0.70397	0.0:0.0:0.0:1.0	.	384	O14874	BCKD_HUMAN	P	384	ENSP00000378405:L384P;ENSP00000219794:L384P	ENSP00000219794:L384P	L	+	2	0	BCKDK	31030999	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.682000	0.84083	2.158000	0.67659	0.482000	0.46254	CTG	.	.		0.657	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881	
ZNF267	10308	hgsc.bcm.edu	37	16	31926476	31926476	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:31926476A>G	ENST00000300870.10	+	4	1115	c.906A>G	c.(904-906)aaA>aaG	p.K302K		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	302					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AATATGATAAAGATCTTAGTC	0.313																																					p.K302K		Atlas-SNP	.											ZNF267,right_upper_lobe,carcinoma,0,1	ZNF267	94	.	0			c.A906G						.						63.0	67.0	65.0					16																	31926476		2197	4297	6494	SO:0001819	synonymous_variant	10308	exon4			TGATAAAGATCTT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"""Zinc fingers, C2H2-type"", ""-"""	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.906A>G	chr16.hg19:g.31926476A>G		99.0	0.0		72.0	3.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.313	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414	
SHCBP1	79801	hgsc.bcm.edu	37	16	46633834	46633834	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:46633834G>T	ENST00000303383.3	-	9	1520	c.1254C>A	c.(1252-1254)ggC>ggA	p.G418G		NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	418					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				TGTCGCCTTTGCCCCTCTTTT	0.413																																					p.G418G		Atlas-SNP	.											.	SHCBP1	54	.	0			c.C1254A						.						91.0	84.0	86.0					16																	46633834		2203	4300	6503	SO:0001819	synonymous_variant	79801	exon9			GCCTTTGCCCCTC	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.1254C>A	chr16.hg19:g.46633834G>T		110.0	0.0		70.0	4.0	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Silent	SNP	ENST00000303383.3	hg19	CCDS10720.1																																																																																			.	.		0.413	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745	
NLRC5	84166	hgsc.bcm.edu	37	16	57113154	57113154	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:57113154T>C	ENST00000262510.6	+	45	5412	c.5187T>C	c.(5185-5187)gcT>gcC	p.A1729A	NLRC5_ENST00000436936.1_3'UTR|NLRC5_ENST00000539144.1_Silent_p.A1700A|NLRC5_ENST00000308149.7_Silent_p.A1700A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1729					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				ACAACCTGGCTGGAGGGGTCC	0.642																																					p.A1729A		Atlas-SNP	.											.	NLRC5	186	.	0			c.T5187C						.						52.0	53.0	53.0					16																	57113154		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon44			CCTGGCTGGAGGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.5187T>C	chr16.hg19:g.57113154T>C		142.0	0.0		100.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1																																																																																			.	.		0.642	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CFAP20	29105	hgsc.bcm.edu	37	16	58150036	58150036	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:58150036G>T	ENST00000262498.3	-	3	519	c.185C>A	c.(184-186)cCt>cAt	p.P62H	C16orf80_ENST00000562443.1_5'Flank|CTB-134F13.1_ENST00000564672.1_RNA	NM_013242.2	NP_037374.1														kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						GGGGTCTGCAGGGCATGTGAT	0.418																																					p.P62H	Pancreas(103;1212 1612 18629 30162 52390)	Atlas-SNP	.											.	C16orf80	17	.	0			c.C185A						.						116.0	113.0	114.0					16																	58150036		2198	4300	6498	SO:0001583	missense	29105	exon3			TCTGCAGGGCATG																												ENST00000262498.3:c.185C>A	chr16.hg19:g.58150036G>T	ENSP00000262498:p.Pro62His	170.0	0.0		96.0	4.0	NM_013242		Missense_Mutation	SNP	ENST00000262498.3	hg19	CCDS10793.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970315	0.92919	.	.	ENSG00000070761	ENST00000262498	T	0.56275	0.47	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.81927	0.4926	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87069	0.2158	10	0.87932	D	0	-10.1419	17.3425	0.87301	0.0:0.0:1.0:0.0	.	62	Q9Y6A4	CP080_HUMAN	H	62	ENSP00000262498:P62H	ENSP00000262498:P62H	P	-	2	0	C16orf80	56707537	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.226000	0.95229	2.775000	0.95449	0.655000	0.94253	CCT	.	.		0.418	C16orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257388.2		
DYNC1LI2	1783	hgsc.bcm.edu	37	16	66764024	66764024	+	Silent	SNP	G	G	T	rs145562779		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:66764024G>T	ENST00000258198.2	-	8	1238	c.1032C>A	c.(1030-1032)ccC>ccA	p.P344P	DYNC1LI2_ENST00000379482.2_Intron|DYNC1LI2_ENST00000443351.2_Silent_p.P267P|DYNC1LI2_ENST00000570201.1_5'UTR|RP11-63M22.2_ENST00000569274.1_RNA	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	344					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.P344P(1)		central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		CCTTTCTCACGGGAGGTTTCA	0.468																																					p.P344P		Atlas-SNP	.											.	DYNC1LI2	37	.	1	Substitution - coding silent(1)	lung(1)	c.C1032A						.						72.0	66.0	68.0					16																	66764024		2200	4300	6500	SO:0001819	synonymous_variant	1783	exon8			TCTCACGGGAGGT	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"""Cytoplasmic dyneins"""	2966	protein-coding gene	gene with protein product		611406	"""dynein, cytoplasmic, light intermediate polypeptide 2"""	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.1032C>A	chr16.hg19:g.66764024G>T		105.0	0.0		79.0	4.0	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Silent	SNP	ENST00000258198.2	hg19	CCDS10818.1																																																																																			.	G|1.000;A|0.000		0.468	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141	
ZDHHC1	29800	hgsc.bcm.edu	37	16	67432186	67432186	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67432186G>T	ENST00000348579.2	-	8	1197	c.856C>A	c.(856-858)Cgc>Agc	p.R286S	ZDHHC1_ENST00000566075.1_5'Flank	NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	286					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		TGTGGTGGGCGGTGCTGCACG	0.622																																					p.R286S		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.C856A						.						119.0	100.0	107.0					16																	67432186		2198	4300	6498	SO:0001583	missense	29800	exon8			GTGGGCGGTGCTG	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.856C>A	chr16.hg19:g.67432186G>T	ENSP00000340299:p.Arg286Ser	78.0	0.0		61.0	4.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262895	0.95399	.	.	ENSG00000159714	ENST00000348579	T	0.42513	0.97	5.46	5.46	0.80206	.	0.682773	0.14213	N	0.333908	T	0.56093	0.1962	L	0.29908	0.895	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.54741	-0.8248	10	0.51188	T	0.08	.	18.2808	0.90097	0.0:0.0:1.0:0.0	.	286	Q8WTX9	ZDHC1_HUMAN	S	286	ENSP00000340299:R286S	ENSP00000340299:R286S	R	-	1	0	ZDHHC1	65989687	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	5.438000	0.66550	2.563000	0.86464	0.407000	0.27541	CGC	.	.		0.622	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
RLTPR	146206	hgsc.bcm.edu	37	16	67679452	67679452	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67679452C>T	ENST00000334583.6	+	2	378	c.50C>T	c.(49-51)aCc>aTc	p.T17I	RLTPR_ENST00000545661.1_Missense_Mutation_p.T17I	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	17					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GGCGAGATCACCAGGTTCCTG	0.622																																					p.T17I		Atlas-SNP	.											.	RLTPR	124	.	0			c.C50T						.																																			SO:0001583	missense	146206	exon2			AGATCACCAGGTT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.50C>T	chr16.hg19:g.67679452C>T	ENSP00000334958:p.Thr17Ile	109.0	0.0		75.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	c	20.2	3.951096	0.73787	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.16324	2.35;2.38	4.5	3.55	0.40652	.	1.135210	0.06547	N	0.744305	T	0.13841	0.0335	N	0.22421	0.69	0.32048	N	0.597355	B;P	0.43477	0.007;0.808	B;B	0.39590	0.007;0.304	T	0.14282	-1.0478	10	0.45353	T	0.12	-8.4582	9.8859	0.41262	0.0:0.9031:0.0:0.0969	.	17;17	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	I	17	ENSP00000334958:T17I;ENSP00000441481:T17I	ENSP00000334958:T17I	T	+	2	0	RLTPR	66236953	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.862000	0.48388	1.253000	0.44018	0.556000	0.70494	ACC	.	.		0.622	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
CENPT	80152	hgsc.bcm.edu	37	16	67859899	67859899	+	IGR	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67859899A>G	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.K355R|TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.K301R|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.K286R	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		AGCACGCTGAAGGAACGGGAC	0.612																																					p.K301R		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.A902G						.						62.0	51.0	55.0					16																	67859899		2198	4300	6498	SO:0001628	intergenic_variant	55815	exon9			CGCTGAAGGAACG	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"""chromosome 16 open reading frame 56"""	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67859899A>G		94.0	0.0		64.0	4.0	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.757646	0.49468	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.8	3.53	0.40419	.	0.312152	0.31233	N	0.008006	T	0.52289	0.1725	L	0.60455	1.87	0.28676	N	0.9054	B;B;B;B;B;D	0.63880	0.037;0.037;0.02;0.197;0.02;0.993	B;B;B;B;B;P	0.60789	0.039;0.027;0.016;0.062;0.027;0.879	T	0.46735	-0.9170	9	0.46703	T	0.11	-33.0536	9.0471	0.36354	0.8511:0.0:0.1489:0.0	.	286;355;91;9;301;286	E7ENJ7;B4DXD0;B4DY78;Q2TAA8-2;Q2TAA8;B4E1H3	.;.;.;.;TXIP1_HUMAN;.	R	286;301;91	.	ENSP00000373485:K301R	K	+	2	0	TSNAXIP1	66417400	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	1.883000	0.39658	1.018000	0.39521	0.533000	0.62120	AAG	.	.		0.612	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082	
ESRP2	80004	hgsc.bcm.edu	37	16	68269764	68269764	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:68269764G>T	ENST00000565858.1	-	1	271	c.185C>A	c.(184-186)cCg>cAg	p.P62Q	ESRP2_ENST00000473183.2_Missense_Mutation_p.P62Q|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	62					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						GCGGCTCCGCGGCTCAACCAC	0.672																																					p.P62Q		Atlas-SNP	.											.	ESRP2	118	.	0			c.C185A						.						22.0	18.0	20.0					16																	68269764		2184	4274	6458	SO:0001583	missense	80004	exon1			CTCCGCGGCTCAA	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"""RNA binding motif (RRM) containing"""	26152	protein-coding gene	gene with protein product		612960	"""RNA binding motif protein 35B"""	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.185C>A	chr16.hg19:g.68269764G>T	ENSP00000454554:p.Pro62Gln	138.0	0.0		85.0	4.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Missense_Mutation	SNP	ENST00000565858.1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.1	3.937974	0.73557	.	.	ENSG00000103067	ENST00000473183	T	0.44482	0.92	4.26	2.29	0.28610	.	0.068424	0.64402	D	0.000008	T	0.30293	0.0760	N	0.22421	0.69	0.29787	N	0.833503	P;P	0.49447	0.924;0.908	B;P	0.47206	0.339;0.541	T	0.16571	-1.0398	10	0.59425	D	0.04	-12.6571	5.9021	0.18972	0.2339:0.0:0.7661:0.0	.	62;62	Q9H6T0;Q9H6T0-2	ESRP2_HUMAN;.	Q	62	ENSP00000418748:P62Q	ENSP00000418748:P62Q	P	-	2	0	ESRP2	66827265	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.212000	0.65225	1.160000	0.42584	0.555000	0.69702	CCG	.	.		0.672	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	
MTSS1L	92154	hgsc.bcm.edu	37	16	70698860	70698860	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:70698860G>T	ENST00000338779.6	-	13	1542	c.1268C>A	c.(1267-1269)cCg>cAg	p.P423Q	FLJ00418_ENST00000597002.1_Missense_Mutation_p.G57C	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	423					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CCGGGGTCGCGGTGCCTCTTC	0.716																																					p.P423Q		Atlas-SNP	.											MTSS1L,NS,carcinoma,0,1	MTSS1L	22	.	0			c.C1268A						.						11.0	12.0	12.0					16																	70698860		2181	4287	6468	SO:0001583	missense	92154	exon13			GGTCGCGGTGCCT		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"""actin-bundling protein with BAIAP2 homology"""					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1268C>A	chr16.hg19:g.70698860G>T	ENSP00000341171:p.Pro423Gln	93.0	0.0		62.0	3.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	G	1.520	-0.547286	0.04024	.	.	ENSG00000132613	ENST00000338779	T	0.28069	1.63	4.87	4.87	0.63330	.	0.134525	0.50627	D	0.000117	T	0.18002	0.0432	N	0.17082	0.46	0.35561	D	0.80467	B	0.18610	0.029	B	0.11329	0.006	T	0.17349	-1.0372	10	0.13108	T	0.6	-12.5589	12.6841	0.56938	0.0:0.0:0.8346:0.1654	.	423	Q765P7	MTSSL_HUMAN	Q	423	ENSP00000341171:P423Q	ENSP00000341171:P423Q	P	-	2	0	MTSS1L	69256361	1.000000	0.71417	0.047000	0.18901	0.286000	0.27126	5.692000	0.68256	2.233000	0.73108	0.313000	0.20887	CCG	.	.		0.716	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383	
PMFBP1	83449	hgsc.bcm.edu	37	16	72163129	72163129	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:72163129T>C	ENST00000237353.10	-	13	2047	c.1786A>G	c.(1786-1788)Agg>Ggg	p.R596G	PMFBP1_ENST00000355636.6_Missense_Mutation_p.R451G|PMFBP1_ENST00000537465.1_Missense_Mutation_p.R601G	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	601						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				CCTTGCTCCCTGTGCTGAAAA	0.433																																					p.R596G		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A1786G						.						167.0	173.0	171.0					16																	72163129		2198	4300	6498	SO:0001583	missense	83449	exon13			GCTCCCTGTGCTG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.1786A>G	chr16.hg19:g.72163129T>C	ENSP00000237353:p.Arg596Gly	103.0	0.0		84.0	4.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	hg19	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211638	0.39102	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.12984	2.63;2.64;2.63	4.31	4.31	0.51392	.	0.382752	0.22695	N	0.056780	T	0.14874	0.0359	L	0.34521	1.04	0.09310	N	1	P;P;P	0.40731	0.728;0.728;0.728	B;P;B	0.46076	0.297;0.503;0.297	T	0.06972	-1.0797	10	0.59425	D	0.04	-14.5575	10.1548	0.42816	0.0:0.0:0.0:1.0	rs34703574	601;596;601	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	G	601;596;451	ENSP00000443817:R601G;ENSP00000237353:R596G;ENSP00000347854:R451G	ENSP00000237353:R596G	R	-	1	2	PMFBP1	70720630	0.351000	0.24887	0.090000	0.20809	0.145000	0.21501	1.818000	0.39012	2.175000	0.68902	0.533000	0.62120	AGG	.	.		0.433	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184647	72184647	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:72184647A>G	ENST00000237353.10	-	5	757	c.496T>C	c.(496-498)Ttg>Ctg	p.L166L	PMFBP1_ENST00000355636.6_Silent_p.L21L|PMFBP1_ENST00000537465.1_Silent_p.L166L	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	166						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCCCCGGCCAAGGCGAGTTGC	0.488																																					p.L166L		Atlas-SNP	.											.	PMFBP1	101	.	0			c.T496C						.						119.0	110.0	113.0					16																	72184647		2198	4300	6498	SO:0001819	synonymous_variant	83449	exon5			CGGCCAAGGCGAG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.496T>C	chr16.hg19:g.72184647A>G		111.0	0.0		94.0	4.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Silent	SNP	ENST00000237353.10	hg19	CCDS32483.1																																																																																			.	.		0.488	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
CMIP	80790	hgsc.bcm.edu	37	16	81654516	81654516	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:81654516T>C	ENST00000537098.3	+	3	534	c.462T>C	c.(460-462)caT>caC	p.H154H	CMIP_ENST00000539778.2_Silent_p.H60H|CMIP_ENST00000566513.1_3'UTR	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	154	PH.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						AGTGGTTCCATTCTCTGCAAT	0.512																																					p.H154H		Atlas-SNP	.											.	CMIP	37	.	0			c.T462C						.						118.0	115.0	116.0					16																	81654516		2031	4208	6239	SO:0001819	synonymous_variant	80790	exon3			GTTCCATTCTCTG	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.462T>C	chr16.hg19:g.81654516T>C		125.0	0.0		98.0	4.0	NM_198390	Q9C0G9	Silent	SNP	ENST00000537098.3	hg19	CCDS54044.1																																																																																			.	.		0.512	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629	
MBTPS1	8720	hgsc.bcm.edu	37	16	84097002	84097002	+	Missense_Mutation	SNP	A	A	G	rs138967616		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:84097002A>G	ENST00000343411.3	-	19	2975	c.2480T>C	c.(2479-2481)aTt>aCt	p.I827T		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	827					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AAGTCCCAAAATGGGGACGTT	0.463											OREG0023981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I827T		Atlas-SNP	.											.	MBTPS1	85	.	0			c.T2480C						.	A	THR/ILE	1,4399	2.1+/-5.4	0,1,2199	85.0	81.0	82.0		2480	5.4	1.0	16	dbSNP_134	82	0,8600		0,0,4300	no	missense	MBTPS1	NM_003791.2	89	0,1,6499	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging	827/1053	84097002	1,12999	2200	4300	6500	SO:0001583	missense	8720	exon19			CCCAAAATGGGGA	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.2480T>C	chr16.hg19:g.84097002A>G	ENSP00000344223:p.Ile827Thr	143.0	0.0	1226	121.0	5.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	hg19	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.410106	0.83340	2.27E-4	0.0	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.35236	1.32	5.44	5.44	0.79542	.	0.201589	0.52532	D	0.000064	T	0.43986	0.1272	M	0.67569	2.06	0.58432	D	0.999991	P	0.43938	0.822	B	0.43575	0.424	T	0.49799	-0.8901	10	0.87932	D	0	-16.8187	15.7875	0.78319	1.0:0.0:0.0:0.0	.	827	Q14703	MBTP1_HUMAN	T	827;272	ENSP00000344223:I827T	ENSP00000344223:I827T	I	-	2	0	MBTPS1	82654503	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.275000	0.95738	2.197000	0.70478	0.402000	0.26972	ATT	.	A|1.000;G|0.000		0.463	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
TAF1C	9013	hgsc.bcm.edu	37	16	84212983	84212983	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:84212983C>T	ENST00000567759.1	-	14	2356	c.2174G>A	c.(2173-2175)tGg>tAg	p.W725*	TAF1C_ENST00000570117.1_Nonsense_Mutation_p.W393*|TAF1C_ENST00000566732.1_Nonsense_Mutation_p.W699*|TAF1C_ENST00000378541.4_Nonsense_Mutation_p.W725*|TAF1C_ENST00000341690.6_Nonsense_Mutation_p.W631*|TAF1C_ENST00000541676.1_Nonsense_Mutation_p.W632*	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	725					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TCGGCCTGCCCAGGCTTCCCC	0.716																																					p.W725X		Atlas-SNP	.											.	TAF1C	60	.	0			c.G2174A						.						17.0	21.0	20.0					16																	84212983		2198	4292	6490	SO:0001587	stop_gained	9013	exon14			CCTGCCCAGGCTT	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2174G>A	chr16.hg19:g.84212983C>T	ENSP00000455265:p.Trp725*	122.0	0.0		84.0	4.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Nonsense_Mutation	SNP	ENST00000567759.1	hg19	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274598	0.95459	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	.	.	.	5.14	5.14	0.70334	.	0.101272	0.43579	D	0.000553	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.0209	14.0909	0.64990	0.0:1.0:0.0:0.0	.	.	.	.	X	725;632;631;248	.	ENSP00000345305:W631X	W	-	2	0	TAF1C	82770484	0.533000	0.26354	1.000000	0.80357	0.981000	0.71138	1.161000	0.31773	2.390000	0.81377	0.561000	0.74099	TGG	.	.		0.716	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
GALNS	2588	hgsc.bcm.edu	37	16	88909227	88909227	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:88909227C>T	ENST00000268695.5	-	2	219	c.131G>A	c.(130-132)gGt>gAt	p.G44D	GALNS_ENST00000542788.1_Intron|GALNS_ENST00000565364.1_5'UTR	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	44	Catalytic domain.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		CCCGAGGTCACCCCATCCCAT	0.607																																					p.G44D	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.G131A						.						49.0	45.0	47.0					16																	88909227		2197	4300	6497	SO:0001583	missense	2588	exon2			AGGTCACCCCATC	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.131G>A	chr16.hg19:g.88909227C>T	ENSP00000268695:p.Gly44Asp	92.0	0.0		84.0	4.0	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	hg19	CCDS10970.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545763	0.86022	.	.	ENSG00000141012	ENST00000268695	D	0.92911	-3.13	4.8	4.8	0.61643	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96827	0.8964	M	0.90595	3.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97729	1.0201	10	0.87932	D	0	.	18.2008	0.89838	0.0:1.0:0.0:0.0	.	44;44	B2R6P1;P34059	.;GALNS_HUMAN	D	44	ENSP00000268695:G44D	ENSP00000268695:G44D	G	-	2	0	GALNS	87436728	1.000000	0.71417	0.955000	0.39395	0.615000	0.37417	7.383000	0.79741	2.388000	0.81334	0.561000	0.74099	GGT	.	.		0.607	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
METTL16	79066	hgsc.bcm.edu	37	17	2323799	2323799	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2323799T>C	ENST00000263092.6	-	10	1281	c.1154A>G	c.(1153-1155)aAa>aGa	p.K385R	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.K167R	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	385							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						ACGCTCTCTTTTCTTTCTCCT	0.488																																					p.K385R		Atlas-SNP	.											.	METTL16	75	.	0			c.A1154G						.						78.0	82.0	80.0					17																	2323799		1867	4100	5967	SO:0001583	missense	79066	exon10			TCTCTTTTCTTTC	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1154A>G	chr17.hg19:g.2323799T>C	ENSP00000263092:p.Lys385Arg	50.0	0.0		74.0	4.0	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	T	3.059	-0.193714	0.06259	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.38077	1.16;1.36	5.75	2.37	0.29283	.	0.182120	0.64402	N	0.000015	T	0.15696	0.0378	N	0.13235	0.315	0.28140	N	0.929833	B	0.06786	0.001	B	0.06405	0.002	T	0.34378	-0.9831	10	0.02654	T	1	-0.1836	7.5271	0.27662	0.0:0.3501:0.0:0.6498	.	385	Q86W50	MET16_HUMAN	R	385;65;167	ENSP00000263092:K385R;ENSP00000443633:K167R	ENSP00000263092:K385R	K	-	2	0	METTL16	2270549	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.049000	0.41288	0.131000	0.18576	-0.256000	0.11100	AAA	.	.		0.488	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	
CLUH	23277	hgsc.bcm.edu	37	17	2599486	2599486	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2599486A>G	ENST00000570628.2	-	13	2346	c.2241T>C	c.(2239-2241)gcT>gcC	p.A747A	CLUH_ENST00000538975.1_Silent_p.A747A|CLUH_ENST00000435359.1_Silent_p.A747A			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	747					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GCAGGAAGGCAGCCGCGTCCT	0.647																																					p.A747A		Atlas-SNP	.											.	.	.	.	0			c.T2241C						.						22.0	26.0	25.0					17																	2599486		1985	4147	6132	SO:0001819	synonymous_variant	23277	exon13			GAAGGCAGCCGCG	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.2241T>C	chr17.hg19:g.2599486A>G		158.0	0.0		99.0	6.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.		0.647	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2921396	2921396	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2921396G>A	ENST00000254695.8	+	18	1626	c.1536G>A	c.(1534-1536)gtG>gtA	p.V512V	RAP1GAP2_ENST00000540393.2_Silent_p.V493V|RAP1GAP2_ENST00000366401.4_Silent_p.V497V|RAP1GAP2_ENST00000542807.1_Silent_p.V512V	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	512					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AGACCATGGTGGGCGGCCAGA	0.637																																					p.V512V		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.G1536A						.						17.0	21.0	20.0					17																	2921396		2075	4190	6265	SO:0001819	synonymous_variant	23108	exon18			CATGGTGGGCGGC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1536G>A	chr17.hg19:g.2921396G>A		77.0	0.0		54.0	4.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	hg19	CCDS45573.1																																																																																			.	.		0.637	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
GSG2	83903	hgsc.bcm.edu	37	17	3628016	3628016	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:3628016G>T	ENST00000325418.4	+	1	806	c.787G>T	c.(787-789)Ggg>Tgg	p.G263W	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	263					histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										TCGGGCAGATGGGAAGAATAT	0.552																																					p.G263W		Atlas-SNP	.											.	GSG2	48	.	0			c.G787T						.						61.0	71.0	68.0					17																	3628016		2203	4300	6503	SO:0001583	missense	83903	exon1			GCAGATGGGAAGA	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.787G>T	chr17.hg19:g.3628016G>T	ENSP00000325290:p.Gly263Trp	110.0	0.0		75.0	4.0	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	hg19	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.042756	0.75732	.	.	ENSG00000177602	ENST00000325418	T	0.08282	3.11	3.95	3.95	0.45737	.	0.196377	0.25194	N	0.032424	T	0.17023	0.0409	L	0.27053	0.805	0.26655	N	0.972021	D	0.89917	1.0	D	0.85130	0.997	T	0.01583	-1.1319	10	0.87932	D	0	-50.6244	13.7897	0.63133	0.0:0.0:1.0:0.0	.	263	Q8TF76	HASP_HUMAN	W	263	ENSP00000325290:G263W	ENSP00000325290:G263W	G	+	1	0	GSG2	3574765	0.558000	0.26554	0.239000	0.24122	0.277000	0.26821	0.708000	0.25719	2.470000	0.83445	0.655000	0.94253	GGG	.	.		0.552	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458458	4458458	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4458458C>T	ENST00000254718.4	-	1	468	c.162G>A	c.(160-162)acG>acA	p.T54T	MYBBP1A_ENST00000381556.2_Silent_p.T54T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	54	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GCAGCTTCTCCGTGGCCGCAA	0.647																																					p.T54T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G162A						.						19.0	18.0	19.0					17																	4458458		2197	4299	6496	SO:0001819	synonymous_variant	10514	exon1			CTTCTCCGTGGCC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.162G>A	chr17.hg19:g.4458458C>T		82.0	0.0		77.0	4.0	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.		0.647	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
MINK1	50488	hgsc.bcm.edu	37	17	4793904	4793904	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4793904G>T	ENST00000355280.6	+	14	1636	c.1440G>T	c.(1438-1440)caG>caT	p.Q480H	MINK1_ENST00000453408.3_Missense_Mutation_p.Q480H|MINK1_ENST00000347992.7_Missense_Mutation_p.Q480H	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGTCCCTgcagcagcagcaac	0.612																																					p.Q480H		Atlas-SNP	.											.	MINK1	110	.	0			c.G1440T						.						16.0	21.0	19.0					17																	4793904		2177	4255	6432	SO:0001583	missense	50488	exon14			CCTGCAGCAGCAG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1440G>T	chr17.hg19:g.4793904G>T	ENSP00000347427:p.Gln480His	72.0	0.0		64.0	4.0	NM_170663		Missense_Mutation	SNP	ENST00000355280.6	hg19	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.427383	0.43122	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.52057	0.68;0.68;0.68	4.89	3.93	0.45458	.	0.068143	0.64402	D	0.000015	T	0.64616	0.2614	M	0.70842	2.15	0.49051	D	0.999743	D;D;D;D	0.60575	0.988;0.988;0.98;0.988	D;D;D;D	0.72338	0.977;0.977;0.948;0.977	T	0.67296	-0.5706	10	0.66056	D	0.02	.	11.0187	0.47705	0.0906:0.0:0.9094:0.0	.	480;480;480;480	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	H	480	ENSP00000347427:Q480H;ENSP00000406487:Q480H;ENSP00000269296:Q480H	ENSP00000269296:Q480H	Q	+	3	2	MINK1	4734686	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.607000	0.61133	1.293000	0.44690	-0.258000	0.10820	CAG	.	.		0.612	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936582	4936582	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4936582C>A	ENST00000424747.1	-	4	1820	c.1108G>T	c.(1108-1110)Ggc>Tgc	p.G370C	SLC52A1_ENST00000512825.2_Intron|SLC52A1_ENST00000254853.5_Missense_Mutation_p.G370C	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	370					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										GCAGTGGTGCCCACCAGGGGT	0.627																																					p.G370C		Atlas-SNP	.											.	.	.	.	0			c.G1108T						.						74.0	86.0	82.0					17																	4936582		2203	4300	6503	SO:0001583	missense	55065	exon4			TGGTGCCCACCAG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.1108G>T	chr17.hg19:g.4936582C>A	ENSP00000399979:p.Gly370Cys	105.0	0.0		88.0	4.0	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	hg19	CCDS11066.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.815482	0.70912	.	.	ENSG00000132517	ENST00000254853;ENST00000424747	T;T	0.72615	-0.67;-0.67	0.913	-0.217	0.13149	.	0.000000	0.85682	D	0.000000	T	0.80149	0.4570	M	0.83603	2.65	0.58432	D	0.999995	D	0.89917	1.0	D	0.80764	0.994	T	0.76350	-0.2991	10	0.66056	D	0.02	.	5.7669	0.18231	0.3146:0.6853:0.0:0.0	.	370	Q9NWF4	RFT_HUMAN	C	370	ENSP00000254853:G370C;ENSP00000399979:G370C	ENSP00000254853:G370C	G	-	1	0	GPR172B	4877306	0.599000	0.26891	0.766000	0.31476	0.882000	0.50991	2.005000	0.40864	-0.059000	0.13154	-0.181000	0.13052	GGC	.	.		0.627	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
RABEP1	9135	hgsc.bcm.edu	37	17	5283729	5283729	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:5283729A>G	ENST00000546142.2	+	16	2529	c.2342A>G	c.(2341-2343)gAg>gGg	p.E781G	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000341923.6_Intron|RABEP1_ENST00000262477.6_Missense_Mutation_p.E781G|RABEP1_ENST00000537505.1_Missense_Mutation_p.E738G|RABEP1_ENST00000408982.2_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	781					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AGTTTGGAAGAGCAGTTAAAG	0.373																																					p.E781G		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2342G						.						68.0	61.0	63.0					17																	5283729		1822	4078	5900	SO:0001583	missense	9135	exon16			TGGAAGAGCAGTT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2342A>G	chr17.hg19:g.5283729A>G	ENSP00000437701:p.Glu781Gly	107.0	0.0		75.0	4.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.078022	0.55753	.	.	ENSG00000029725	ENST00000262477;ENST00000546142;ENST00000537505	T;T;T	0.46451	0.87;0.87;0.87	5.21	5.21	0.72293	Rabaptin, GTPase-Rab5 binding (1);	0.273852	0.40640	N	0.001049	T	0.29126	0.0724	N	0.19112	0.55	0.80722	D	1	B;B	0.24823	0.112;0.029	B;B	0.20955	0.032;0.017	T	0.06698	-1.0812	10	0.32370	T	0.25	-10.4351	14.3671	0.66812	1.0:0.0:0.0:0.0	.	738;781	F5H355;Q15276	.;RABE1_HUMAN	G	781;781;738	ENSP00000262477:E781G;ENSP00000437701:E781G;ENSP00000445408:E738G	ENSP00000262477:E781G	E	+	2	0	RABEP1	5224453	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.114000	0.77103	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.373	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
NUP88	4927	hgsc.bcm.edu	37	17	5317451	5317451	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:5317451G>T	ENST00000573584.1	-	3	980	c.471C>A	c.(469-471)acC>acA	p.T157T		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	157					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CAACTGGAGTGGTACTAAAAT	0.383																																					p.T157T		Atlas-SNP	.											.	NUP88	47	.	0			c.C471A						.						56.0	53.0	54.0					17																	5317451		2203	4300	6503	SO:0001819	synonymous_variant	4927	exon3			TGGAGTGGTACTA	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.471C>A	chr17.hg19:g.5317451G>T		62.0	0.0		66.0	4.0	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	hg19	CCDS11070.1																																																																																			.	.		0.383	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
TEKT1	83659	hgsc.bcm.edu	37	17	6716342	6716342	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:6716342G>T	ENST00000338694.2	-	6	789	c.660C>A	c.(658-660)ttC>ttA	p.F220L	TEKT1_ENST00000535086.1_Missense_Mutation_p.F74L	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	220						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TGGTGCTGGAGAAGTCCAACC	0.547																																					p.F220L		Atlas-SNP	.											.	TEKT1	49	.	0			c.C660A						.						76.0	68.0	71.0					17																	6716342		2203	4300	6503	SO:0001583	missense	83659	exon6			GCTGGAGAAGTCC		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.660C>A	chr17.hg19:g.6716342G>T	ENSP00000341346:p.Phe220Leu	95.0	0.0		65.0	4.0	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	hg19	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311936	0.81358	.	.	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.02916	4.11;4.11	4.96	4.96	0.65561	.	0.237839	0.43747	D	0.000533	T	0.09730	0.0239	M	0.87900	2.915	0.34957	D	0.751854	B	0.24576	0.106	B	0.34452	0.183	T	0.02546	-1.1143	10	0.44086	T	0.13	.	16.0725	0.80946	0.0:0.0:1.0:0.0	.	220	Q969V4	TEKT1_HUMAN	L	220;74	ENSP00000341346:F220L;ENSP00000444142:F74L	ENSP00000341346:F220L	F	-	3	2	TEKT1	6657066	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.093000	0.57714	2.458000	0.83093	0.591000	0.81541	TTC	.	.		0.547	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
DVL2	1856	hgsc.bcm.edu	37	17	7132581	7132581	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7132581A>G	ENST00000005340.5	-	8	1112	c.830T>C	c.(829-831)tTc>tCc	p.F277S	DVL2_ENST00000575458.1_Missense_Mutation_p.F271S|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	277	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GATACCCAGGAAGTTGTACTT	0.622																																					p.F277S		Atlas-SNP	.											.	DVL2	49	.	0			c.T830C						.						81.0	85.0	84.0					17																	7132581		2203	4300	6503	SO:0001583	missense	1856	exon8			CCCAGGAAGTTGT	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.830T>C	chr17.hg19:g.7132581A>G	ENSP00000005340:p.Phe277Ser	115.0	0.0		79.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060179	0.76074	.	.	ENSG00000004975	ENST00000005340	T	0.14640	2.49	5.11	5.11	0.69529	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	N	0.16233	0.39	0.80722	D	1	P;D	0.89917	0.946;1.0	P;D	0.87578	0.869;0.998	T	0.05920	-1.0856	10	0.87932	D	0	-17.7532	12.856	0.57886	1.0:0.0:0.0:0.0	.	271;277	B4DLQ0;O14641	.;DVL2_HUMAN	S	277	ENSP00000005340:F277S	ENSP00000005340:F277S	F	-	2	0	DVL2	7073305	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	9.307000	0.96226	1.938000	0.56188	0.459000	0.35465	TTC	.	.		0.622	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
DVL2	1856	hgsc.bcm.edu	37	17	7133190	7133190	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7133190A>G	ENST00000005340.5	-	5	875	c.593T>C	c.(592-594)cTc>cCc	p.L198P	DVL2_ENST00000575458.1_Missense_Mutation_p.L192P|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	198					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GCTGGTCATGAGGGTAGAGGA	0.647																																					p.L198P		Atlas-SNP	.											.	DVL2	49	.	0			c.T593C						.						69.0	72.0	71.0					17																	7133190		2203	4300	6503	SO:0001583	missense	1856	exon5			GTCATGAGGGTAG	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.593T>C	chr17.hg19:g.7133190A>G	ENSP00000005340:p.Leu198Pro	93.0	0.0		50.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.864584	0.71949	.	.	ENSG00000004975	ENST00000005340	T	0.04917	3.53	5.18	5.18	0.71444	Dishevelled protein domain (1);	0.137790	0.49305	D	0.000146	T	0.23410	0.0566	M	0.74881	2.28	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.994	D;D;D	0.71184	0.972;0.961;0.961	T	0.00557	-1.1672	10	0.72032	D	0.01	-21.0209	12.972	0.58517	1.0:0.0:0.0:0.0	.	105;192;198	B4DM44;B4DLQ0;O14641	.;.;DVL2_HUMAN	P	198	ENSP00000005340:L198P	ENSP00000005340:L198P	L	-	2	0	DVL2	7073914	1.000000	0.71417	0.998000	0.56505	0.807000	0.45602	8.930000	0.92872	1.961000	0.56991	0.418000	0.28097	CTC	.	.		0.647	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
TNK1	8711	hgsc.bcm.edu	37	17	7290400	7290400	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7290400G>T	ENST00000576812.1	+	9	1708	c.1339G>T	c.(1339-1341)Ggc>Tgc	p.G447C	TNK1_ENST00000570896.1_Missense_Mutation_p.G442C|TNK1_ENST00000311668.2_Missense_Mutation_p.G442C	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				AGATGCGGGGGGCTTGCCAGC	0.632																																					p.G447C		Atlas-SNP	.											.	TNK1	31	.	0			c.G1339T						.						24.0	24.0	24.0					17																	7290400		1934	4122	6056	SO:0001583	missense	8711	exon9			GCGGGGGGCTTGC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1339G>T	chr17.hg19:g.7290400G>T	ENSP00000459799:p.Gly447Cys	97.0	0.0		67.0	4.0	NM_001251902		Missense_Mutation	SNP	ENST00000576812.1	hg19	CCDS58510.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628971	0.46944	.	.	ENSG00000174292	ENST00000311668	T	0.76709	-1.04	4.2	3.21	0.36854	.	0.174595	0.27851	N	0.017593	T	0.68988	0.3061	L	0.29908	0.895	0.21445	N	0.999684	P;P	0.48407	0.91;0.855	P;B	0.46758	0.526;0.326	T	0.61466	-0.7057	10	0.54805	T	0.06	.	8.5117	0.33222	0.1142:0.0:0.8858:0.0	.	442;447	Q13470-2;Q13470	.;TNK1_HUMAN	C	442	ENSP00000312309:G442C	ENSP00000312309:G442C	G	+	1	0	TNK1	7231124	0.104000	0.21937	0.330000	0.25442	0.325000	0.28411	0.758000	0.26447	1.100000	0.41517	0.313000	0.20887	GGC	.	.		0.632	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
ZBTB4	57659	hgsc.bcm.edu	37	17	7370026	7370026	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7370026A>G	ENST00000311403.4	-	3	434	c.95T>C	c.(94-96)gTc>gCc	p.V32A	ZBTB4_ENST00000380599.4_Missense_Mutation_p.V32A	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	32	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		TATGAGGGTGACGTCACAGAA	0.647																																					p.V32A		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T95C						.						47.0	36.0	40.0					17																	7370026		2203	4300	6503	SO:0001583	missense	57659	exon3			AGGGTGACGTCAC	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.95T>C	chr17.hg19:g.7370026A>G	ENSP00000307858:p.Val32Ala	113.0	0.0		67.0	4.0	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	hg19	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.628141	0.66901	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.77750	-1.12;-1.12	4.91	4.91	0.64330	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.086330	0.44483	D	0.000452	D	0.83741	0.5320	L	0.49699	1.58	0.44129	D	0.996917	D	0.71674	0.998	D	0.69654	0.965	D	0.85411	0.1137	10	0.72032	D	0.01	-22.8599	13.6415	0.62253	1.0:0.0:0.0:0.0	.	32	Q9P1Z0	ZBTB4_HUMAN	A	32	ENSP00000307858:V32A;ENSP00000369973:V32A	ENSP00000307858:V32A	V	-	2	0	ZBTB4	7310750	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.423000	0.90264	2.060000	0.61445	0.459000	0.35465	GTC	.	.		0.647	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
SENP3	26168	hgsc.bcm.edu	37	17	7466514	7466514	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7466514C>A	ENST00000429205.2	+	2	170	c.121C>A	c.(121-123)Cga>Aga	p.R41R	SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.R41R			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	41	Pro-rich.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCCCAAACCCCGACTCAAGTC	0.662																																					p.R41R		Atlas-SNP	.											.	SENP3	18	.	0			c.C121A						.						11.0	14.0	13.0					17																	7466514		1972	4133	6105	SO:0001819	synonymous_variant	26168	exon2			AAACCCCGACTCA	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.121C>A	chr17.hg19:g.7466514C>A		91.0	0.0		83.0	4.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	hg19																																																																																				.	.		0.662	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
KDM6B	23135	hgsc.bcm.edu	37	17	7749921	7749921	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7749921C>T	ENST00000448097.2	+	8	905	c.574C>T	c.(574-576)Cgg>Tgg	p.R192W	KDM6B_ENST00000254846.5_Missense_Mutation_p.R192W			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	192					cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						TGGAGCCAAGCGGGGAGGTCC	0.627																																					p.R192W		Atlas-SNP	.											.	KDM6B	95	.	0			c.C574T						.						67.0	78.0	74.0					17																	7749921		2203	4297	6500	SO:0001583	missense	23135	exon8			GCCAAGCGGGGAG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.574C>T	chr17.hg19:g.7749921C>T	ENSP00000412513:p.Arg192Trp	73.0	0.0		63.0	26.0	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.36	3.370768	0.61624	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.08458	3.09;3.09	5.17	5.17	0.71159	.	0.255620	0.32055	N	0.006647	T	0.15565	0.0375	N	0.14661	0.345	0.45806	D	0.998682	D	0.89917	1.0	D	0.72338	0.977	T	0.10019	-1.0648	10	0.72032	D	0.01	-12.7822	16.5365	0.84373	0.0:1.0:0.0:0.0	.	192	O15054-1	.	W	192	ENSP00000254846:R192W;ENSP00000412513:R192W	ENSP00000254846:R192W	R	+	1	2	KDM6B	7690646	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.104000	0.41815	2.579000	0.87056	0.650000	0.86243	CGG	.	.		0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
CTC1	80169	hgsc.bcm.edu	37	17	8138160	8138160	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8138160A>G	ENST00000315684.8	-	9	1531	c.1524T>C	c.(1522-1524)gcT>gcC	p.A508A	CTC1_ENST00000581671.1_5'Flank	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	508					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CCAGGGTAGGAGCCAGGAGTT	0.572																																					p.A508A		Atlas-SNP	.											.	CTC1	75	.	0			c.T1524C						.						91.0	97.0	95.0					17																	8138160		1973	4150	6123	SO:0001819	synonymous_variant	80169	exon9			GGTAGGAGCCAGG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.1524T>C	chr17.hg19:g.8138160A>G		208.0	0.0		130.0	6.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.572	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
ARHGEF15	22899	hgsc.bcm.edu	37	17	8221748	8221748	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8221748A>G	ENST00000361926.3	+	10	1858	c.1748A>G	c.(1747-1749)aAt>aGt	p.N583S	AC135178.7_ENST00000458568.1_RNA|ARHGEF15_ENST00000421050.1_Missense_Mutation_p.N583S	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	583	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CGTCAGGAGAATGCCCAGAAG	0.617																																					p.N583S		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.A1748G						.						78.0	86.0	83.0					17																	8221748		2203	4300	6503	SO:0001583	missense	22899	exon10			AGGAGAATGCCCA	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.1748A>G	chr17.hg19:g.8221748A>G	ENSP00000355026:p.Asn583Ser	105.0	0.0		56.0	5.0	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	hg19	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	a	15.03	2.713359	0.48517	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.63417	-0.04;-0.04	5.29	5.29	0.74685	Dbl homology (DH) domain (5);	0.318671	0.31734	N	0.007150	T	0.42585	0.1209	N	0.01188	-0.97	0.32048	N	0.597275	P;P	0.48162	0.906;0.906	P;P	0.52109	0.69;0.69	T	0.53229	-0.8468	10	0.24483	T	0.36	-13.5783	11.6242	0.51136	1.0:0.0:0.0:0.0	.	583;583	D3DTR7;O94989	.;ARHGF_HUMAN	S	583;373;583	ENSP00000355026:N583S;ENSP00000412505:N583S	ENSP00000355026:N583S	N	+	2	0	ARHGEF15	8162473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.286000	0.51724	1.999000	0.58509	0.454000	0.30748	AAT	.	.		0.617	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
NDEL1	81565	hgsc.bcm.edu	37	17	8347657	8347657	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8347657C>A	ENST00000334527.7	+	2	265	c.68C>A	c.(67-69)tCc>tAc	p.S23Y	NDEL1_ENST00000380025.4_Missense_Mutation_p.S23Y|NDEL1_ENST00000585098.1_Missense_Mutation_p.S23Y|NDEL1_ENST00000402554.3_Missense_Mutation_p.S23Y|NDEL1_ENST00000583066.1_3'UTR|NDEL1_ENST00000299734.7_Missense_Mutation_p.S23Y	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	23					activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						AAGGAACTTTCCTTGAAGTAT	0.353																																					p.S23Y		Atlas-SNP	.											.	NDEL1	47	.	0			c.C68A						.						88.0	87.0	87.0					17																	8347657		2203	4300	6503	SO:0001583	missense	81565	exon2			AACTTTCCTTGAA	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"""nudE nuclear distribution gene E homolog (A. nidulans)-like 1"", ""nudE nuclear distribution E homolog (A. nidulans)-like 1"""			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.68C>A	chr17.hg19:g.8347657C>A	ENSP00000333982:p.Ser23Tyr	120.0	0.0		88.0	4.0	NM_001025579	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	hg19	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169783	0.78452	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	4.18	4.18	0.49190	.	0.126774	0.56097	D	0.000036	T	0.59810	0.2221	L	0.34521	1.04	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.59487	0.858;0.726	T	0.53450	-0.8437	9	0.11485	T	0.65	-1.654	16.7216	0.85411	0.0:1.0:0.0:0.0	.	23;23	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	Y	23;23;78;23	.	ENSP00000299734:S23Y	S	+	2	0	NDEL1	8288382	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.405000	0.80007	2.152000	0.67230	0.650000	0.86243	TCC	.	.		0.353	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808	
ZNF18	7566	hgsc.bcm.edu	37	17	11896054	11896054	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:11896054T>C	ENST00000322748.3	-	4	697	c.93A>G	c.(91-93)caA>caG	p.Q31Q	ZNF18_ENST00000454073.3_Silent_p.Q31Q|ZNF18_ENST00000580306.2_Silent_p.Q31Q	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	31					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(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		AGAGTTCCTCTTGAAGGGCAG	0.592																																					p.Q31Q		Atlas-SNP	.											.	ZNF18	42	.	0			c.A93G						.						76.0	72.0	73.0					17																	11896054		2203	4300	6503	SO:0001819	synonymous_variant	7566	exon4			TTCCTCTTGAAGG	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12969	protein-coding gene	gene with protein product		194524	"""zinc finger protein 18 (KOX 11)"""			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.93A>G	chr17.hg19:g.11896054T>C		96.0	0.0		95.0	4.0	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Silent	SNP	ENST00000322748.3	hg19	CCDS32568.1																																																																																			.	.		0.592	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596	
TOM1L2	146691	hgsc.bcm.edu	37	17	17801962	17801962	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:17801962T>C	ENST00000379504.3	-	3	247	c.164A>G	c.(163-165)aAg>aGg	p.K55R	TOM1L2_ENST00000535933.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000581396.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000395739.4_Missense_Mutation_p.K55R|TOM1L2_ENST00000318094.10_Missense_Mutation_p.K55R|TOM1L2_ENST00000542206.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000540946.1_Missense_Mutation_p.K55R	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	55	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GAGCCGCTTCTTCAGGGCTCG	0.468																																					p.K55R	Melanoma(192;2505 2909 14455 25269)	Atlas-SNP	.											.	TOM1L2	54	.	0			c.A164G						.						144.0	115.0	125.0					17																	17801962		2203	4300	6503	SO:0001583	missense	146691	exon3			CGCTTCTTCAGGG	AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"""target of myb1 (chicken) homolog-like 1"""			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.164A>G	chr17.hg19:g.17801962T>C	ENSP00000368818:p.Lys55Arg	314.0	1.0		295.0	119.0	NM_001033551	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Missense_Mutation	SNP	ENST00000379504.3	hg19	CCDS42270.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367733	0.61513	.	.	ENSG00000175662	ENST00000379504;ENST00000318094;ENST00000395739;ENST00000535933;ENST00000540946;ENST00000542206;ENST00000537091	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	5.21	4.1	0.47936	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.089139	0.85682	D	0.000000	T	0.22936	0.0554	N	0.25647	0.755	0.24949	N	0.991804	B;B;B;B;P;B;P	0.36010	0.151;0.233;0.011;0.036;0.532;0.444;0.532	B;B;B;B;B;B;B	0.43680	0.17;0.389;0.01;0.033;0.427;0.262;0.281	T	0.12293	-1.0553	10	0.33141	T	0.24	-32.9027	11.3667	0.49677	0.0:0.0726:0.0:0.9274	.	55;55;55;55;55;55;55	B7Z8F0;B7Z2U2;F5H3S6;B7Z2L7;Q6ZVM7-3;Q6ZVM7;Q6ZVM7-2	.;.;.;.;.;TM1L2_HUMAN;.	R	55	ENSP00000368818:K55R;ENSP00000312860:K55R;ENSP00000379088:K55R;ENSP00000438621:K55R;ENSP00000437655:K55R;ENSP00000445188:K55R	ENSP00000312860:K55R	K	-	2	0	TOM1L2	17742687	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.315000	0.51951	2.198000	0.70561	0.533000	0.62120	AAG	.	.		0.468	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1		
ATPAF2	91647	hgsc.bcm.edu	37	17	17921898	17921898	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:17921898T>C	ENST00000474627.3	-	8	989	c.835A>G	c.(835-837)Agc>Ggc	p.S279G	ATPAF2_ENST00000585101.1_Intron|ATPAF2_ENST00000469327.1_5'Flank	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	279					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					ACTGTGGTGCTCTCGGAGCAG	0.637																																					p.S279G		Atlas-SNP	.											.	ATPAF2	15	.	0			c.A835G						.						96.0	99.0	98.0					17																	17921898		2203	4300	6503	SO:0001583	missense	91647	exon8			TGGTGCTCTCGGA	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.835A>G	chr17.hg19:g.17921898T>C	ENSP00000417190:p.Ser279Gly	120.0	0.0		86.0	4.0	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	hg19	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814834	0.70912	.	.	ENSG00000171953	ENST00000474627	T	0.78246	-1.16	5.16	5.16	0.70880	.	0.187046	0.64402	D	0.000002	T	0.77219	0.4098	M	0.70595	2.14	0.53005	D	0.99996	B	0.27853	0.191	B	0.26770	0.073	T	0.77370	-0.2613	10	0.62326	D	0.03	-30.7591	14.9951	0.71425	0.0:0.0:0.0:1.0	.	279	Q8N5M1	ATPF2_HUMAN	G	279	ENSP00000417190:S279G	ENSP00000417190:S279G	S	-	1	0	ATPAF2	17862623	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	7.945000	0.87732	1.947000	0.56498	0.459000	0.35465	AGC	.	.		0.637	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
RNF112	7732	hgsc.bcm.edu	37	17	19314770	19314770	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:19314770A>G	ENST00000461366.1	+	1	264	c.49A>G	c.(49-51)Aaa>Gaa	p.K17E	CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	17						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						TCGGCTTGGCAAACGGGCAAG	0.652																																					p.K17E		Atlas-SNP	.											.	RNF112	37	.	0			c.A49G						.						39.0	40.0	40.0					17																	19314770		1893	4097	5990	SO:0001583	missense	7732	exon1			CTTGGCAAACGGG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.49A>G	chr17.hg19:g.19314770A>G	ENSP00000454919:p.Lys17Glu	35.0	0.0		28.0	4.0	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	hg19	CCDS58529.1																																																																																			.	.		0.652	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
SLC47A1	55244	hgsc.bcm.edu	37	17	19476161	19476161	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:19476161T>C	ENST00000270570.4	+	16	1559	c.1473T>C	c.(1471-1473)gaT>gaC	p.D491D	SLC47A1_ENST00000395585.1_Silent_p.D491D|SLC47A1_ENST00000457293.1_Silent_p.D491D|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000575023.1_Silent_p.D189D|SLC47A1_ENST00000436810.2_Missense_Mutation_p.S437P|RP11-1113L8.1_ENST00000574267.1_RNA	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	491					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TCCCTCAGGATCCGCTTCACC	0.517																																					p.D491D		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T1473C						.						111.0	95.0	100.0					17																	19476161		2203	4300	6503	SO:0001819	synonymous_variant	55244	exon16			TCAGGATCCGCTT		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"""Solute carriers"""	25588	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 1"""	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1473T>C	chr17.hg19:g.19476161T>C		110.0	0.0		100.0	4.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Silent	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787349	0.31593	.	.	ENSG00000142494	ENST00000436810	T	0.33216	1.42	5.04	-8.56	0.00904	.	.	.	.	.	T	0.16428	0.0395	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	8	0.33940	T	0.23	-9.0137	8.7303	0.34494	0.0:0.4564:0.3006:0.243	.	437	E7EX57	.	P	437	ENSP00000407155:S437P	ENSP00000407155:S437P	S	+	1	0	SLC47A1	19416753	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.713000	0.00816	-2.054000	0.00900	-1.431000	0.01090	TCC	.	.		0.517	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242	
SPECC1	92521	hgsc.bcm.edu	37	17	20107661	20107661	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:20107661C>G	ENST00000261503.5	+	4	350	c.299C>G	c.(298-300)aCt>aGt	p.T100S	SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Missense_Mutation_p.T100S|SPECC1_ENST00000395525.3_Missense_Mutation_p.T19S|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395529.3_Missense_Mutation_p.T100S|SPECC1_ENST00000395522.2_Missense_Mutation_p.T19S|SPECC1_ENST00000395530.2_Missense_Mutation_p.T19S|SPECC1_ENST00000472876.1_Intron|AC004702.2_ENST00000580225.1_lincRNA	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	100					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		TTTACAACAACTAAACGGACA	0.433																																					p.T100S		Atlas-SNP	.											.	SPECC1	100	.	0			c.C299G						.						140.0	153.0	148.0					17																	20107661		2203	4300	6503	SO:0001583	missense	92521	exon4			CAACAACTAAACG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.299C>G	chr17.hg19:g.20107661C>G	ENSP00000261503:p.Thr100Ser	102.0	0.0		63.0	26.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829683	0.32329	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.62364	0.03;2.97;2.92;2.92	5.13	5.13	0.70059	.	0.379873	0.32244	N	0.006373	T	0.49423	0.1556	L	0.28115	0.83	0.80722	D	1	B;B;B;B	0.21381	0.035;0.035;0.035;0.055	B;B;B;B	0.20955	0.02;0.032;0.032;0.015	T	0.40831	-0.9542	10	0.19590	T	0.45	-6.8572	16.4284	0.83832	0.0:1.0:0.0:0.0	.	19;19;100;100	Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;CYTSB_HUMAN	S	100;100;100;19;19;19	ENSP00000261503:T100S;ENSP00000378900:T100S;ENSP00000378893:T19S;ENSP00000378896:T19S	ENSP00000261503:T100S	T	+	2	0	SPECC1	20048253	0.011000	0.17503	0.744000	0.31058	0.874000	0.50279	0.888000	0.28268	2.558000	0.86282	0.591000	0.81541	ACT	.	.		0.433	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
SPAG5	10615	hgsc.bcm.edu	37	17	26907029	26907029	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:26907029T>C	ENST00000321765.5	-	16	3127	c.2795A>G	c.(2794-2796)gAa>gGa	p.E932G	ALDOC_ENST00000226253.4_5'Flank	NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	932					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTTTAACCTTCATCTGCCAC	0.542																																					p.E932G		Atlas-SNP	.											.	SPAG5	92	.	0			c.A2795G						.						78.0	57.0	64.0					17																	26907029		2203	4300	6503	SO:0001583	missense	10615	exon16			TAACCTTCATCTG	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2795A>G	chr17.hg19:g.26907029T>C	ENSP00000323300:p.Glu932Gly	134.0	0.0		140.0	6.0	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	t	17.84	3.487710	0.64074	.	.	ENSG00000076382	ENST00000321765	T	0.35973	1.28	6.04	4.78	0.61160	.	0.100234	0.43919	D	0.000504	T	0.36276	0.0961	N	0.24115	0.695	0.41174	D	0.986189	D	0.59357	0.985	P	0.56612	0.802	T	0.18618	-1.0331	10	0.62326	D	0.03	-1.4794	8.6759	0.34179	0.0:0.0954:0.0:0.9046	.	932	Q96R06	SPAG5_HUMAN	G	932	ENSP00000323300:E932G	ENSP00000323300:E932G	E	-	2	0	SPAG5	23931156	0.990000	0.36364	0.999000	0.59377	0.894000	0.52154	2.412000	0.44609	2.319000	0.78375	0.524000	0.50904	GAA	.	.		0.542	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
SUPT6H	6830	hgsc.bcm.edu	37	17	27022398	27022398	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27022398T>C	ENST00000314616.6	+	29	4086	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.M1268T	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1268	Interaction with KDM6A. {ECO:0000250}.|S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TGCCGCATCATGAAGATTGAC	0.493																																					p.M1268T		Atlas-SNP	.											.	SUPT6H	165	.	0			c.T3803C						.						121.0	90.0	100.0					17																	27022398		2203	4300	6503	SO:0001583	missense	6830	exon29			GCATCATGAAGAT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3803T>C	chr17.hg19:g.27022398T>C	ENSP00000319104:p.Met1268Thr	113.0	0.0		158.0	7.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	T	11.72	1.723610	0.30593	.	.	ENSG00000109111	ENST00000314616	T	0.38401	1.14	5.59	5.59	0.84812	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.20292	0.0488	N	0.05050	-0.12	0.80722	D	1	B	0.20887	0.049	B	0.22880	0.042	T	0.10520	-1.0626	10	0.15499	T	0.54	-19.2578	15.7706	0.78164	0.0:0.0:0.0:1.0	.	1268	Q7KZ85	SPT6H_HUMAN	T	1268	ENSP00000319104:M1268T	ENSP00000319104:M1268T	M	+	2	0	SUPT6H	24046525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.603000	0.82811	2.123000	0.65237	0.533000	0.62120	ATG	.	.		0.493	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
SUPT6H	6830	hgsc.bcm.edu	37	17	27027431	27027431	+	Silent	SNP	G	G	T	rs373264371		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27027431G>T	ENST00000314616.6	+	35	4990	c.4707G>T	c.(4705-4707)gcG>gcT	p.A1569A	SUPT6H_ENST00000347486.4_Silent_p.A1569A	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1569					chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCATTGCTGCGGTGACAGGCC	0.597																																					p.A1569A		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G4707T						.						121.0	111.0	114.0					17																	27027431		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon35			TGCTGCGGTGACA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4707G>T	chr17.hg19:g.27027431G>T		86.0	0.0		94.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.597	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
MYO18A	399687	hgsc.bcm.edu	37	17	27438814	27438814	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27438814A>G	ENST00000527372.1	-	16	2846	c.2666T>C	c.(2665-2667)gTg>gCg	p.V889A	MYO18A_ENST00000533112.1_Missense_Mutation_p.V889A|MYO18A_ENST00000531253.1_Missense_Mutation_p.V889A|MYO18A_ENST00000354329.4_Missense_Mutation_p.V889A	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	889	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GGCCCCTGGCACCAGAGCCTC	0.592											OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V889A	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T2666C						.						40.0	45.0	44.0					17																	27438814		1880	4101	5981	SO:0001583	missense	399687	exon16			CCTGGCACCAGAG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2666T>C	chr17.hg19:g.27438814A>G	ENSP00000437073:p.Val889Ala	81.0	0.0	794	68.0	4.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.320411	0.60634	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.42	5.42	0.78866	Myosin head, motor domain (2);	0.113719	0.64402	D	0.000015	T	0.64681	0.2620	M	0.64404	1.975	0.39114	D	0.961534	B;P;B;P;P	0.36837	0.046;0.571;0.205;0.571;0.473	B;B;B;B;B	0.33846	0.015;0.085;0.078;0.085;0.171	T	0.69826	-0.5040	10	0.54805	T	0.06	.	9.1803	0.37138	0.7227:0.0:0.0:0.2773	.	558;501;889;889;889	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	A	889;889;889;889;889;501	ENSP00000346291:V889A;ENSP00000435932:V889A;ENSP00000434228:V889A;ENSP00000437073:V889A	ENSP00000346291:V889A	V	-	2	0	MYO18A	24462940	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.178000	0.65037	2.052000	0.61016	0.533000	0.62120	GTG	.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
CRYBA1	1411	hgsc.bcm.edu	37	17	27580737	27580737	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27580737C>T	ENST00000225387.3	+	5	438	c.437C>T	c.(436-438)cCc>cTc	p.P146L		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	146	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			GACGACTACCCCTCCTTGCAA	0.428																																					p.P146L		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C437T						.						84.0	83.0	84.0					17																	27580737		2203	4300	6503	SO:0001583	missense	1411	exon5			ACTACCCCTCCTT		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"""eye lens structural protein"""	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.437C>T	chr17.hg19:g.27580737C>T	ENSP00000225387:p.Pro146Leu	123.0	0.0		162.0	27.0	NM_005208	Q13633|Q14CM9	Missense_Mutation	SNP	ENST00000225387.3	hg19	CCDS11249.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815854	0.90790	.	.	ENSG00000108255	ENST00000225387	T	0.78126	-1.15	5.43	4.45	0.53987	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.88415	0.6430	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89672	0.3884	10	0.62326	D	0.03	.	14.2229	0.65839	0.0:0.9255:0.0:0.0745	.	146	P05813	CRBA1_HUMAN	L	146	ENSP00000225387:P146L	ENSP00000225387:P146L	P	+	2	0	CRYBA1	24604863	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.686000	0.68211	2.538000	0.85594	0.491000	0.48974	CCC	.	.		0.428	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208	
ANKRD13B	124930	hgsc.bcm.edu	37	17	27920706	27920706	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27920706T>C	ENST00000394859.3	+	1	221	c.67T>C	c.(67-69)Tgg>Cgg	p.W23R	RP11-68I3.7_ENST00000584986.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	23						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CTACCTCGTGTGGCACAACCG	0.766																																					p.W23R		Atlas-SNP	.											.	ANKRD13B	39	.	0			c.T67C						.						5.0	6.0	6.0					17																	27920706		1909	3777	5686	SO:0001583	missense	124930	exon1			CTCGTGTGGCACA	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"""Ankyrin repeat domain containing"""	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.67T>C	chr17.hg19:g.27920706T>C	ENSP00000378328:p.Trp23Arg	95.0	0.0		97.0	4.0	NM_152345	Q8N7S9	Missense_Mutation	SNP	ENST00000394859.3	hg19	CCDS11251.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.296019	0.60086	.	.	ENSG00000198720	ENST00000394859	T	0.68903	-0.36	3.77	3.77	0.43336	Ankyrin repeat-containing domain (4);	0.135392	0.53938	D	0.000052	T	0.57051	0.2027	N	0.20357	0.565	0.58432	D	0.999994	P	0.35348	0.496	B	0.43728	0.429	T	0.62402	-0.6862	10	0.87932	D	0	-11.1939	10.1105	0.42559	0.0:0.0:0.0:1.0	.	23	Q86YJ7	AN13B_HUMAN	R	23	ENSP00000378328:W23R	ENSP00000378328:W23R	W	+	1	0	ANKRD13B	24944832	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	4.740000	0.62087	1.570000	0.49709	0.147000	0.16070	TGG	.	.		0.766	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345	
ATAD5	79915	hgsc.bcm.edu	37	17	29192785	29192785	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:29192785T>C	ENST00000321990.4	+	11	3578	c.3200T>C	c.(3199-3201)aTa>aCa	p.I1067T	CTD-2349P21.11_ENST00000580873.1_RNA|RP13-753N3.1_ENST00000584157.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1067					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AGTGAACTTATAGGAAATGAG	0.303																																					p.I1067T		Atlas-SNP	.											.	ATAD5	150	.	0			c.T3200C						.						75.0	76.0	76.0					17																	29192785		2203	4292	6495	SO:0001583	missense	79915	exon11			AACTTATAGGAAA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3200T>C	chr17.hg19:g.29192785T>C	ENSP00000313171:p.Ile1067Thr	279.0	0.0		229.0	68.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.254797	0.39896	.	.	ENSG00000176208	ENST00000321990	T	0.20463	2.07	5.18	5.18	0.71444	.	0.292105	0.37348	N	0.002125	T	0.29588	0.0738	M	0.75615	2.305	0.40062	D	0.975905	B;B	0.30727	0.292;0.19	B;B	0.32022	0.139;0.035	T	0.17289	-1.0374	10	0.87932	D	0	.	15.1186	0.72423	0.0:0.0:0.0:1.0	.	1067;1067	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	T	1067	ENSP00000313171:I1067T	ENSP00000313171:I1067T	I	+	2	0	ATAD5	26216911	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.186000	0.77722	1.970000	0.57323	0.529000	0.55759	ATA	.	.		0.303	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
SPACA3	124912	hgsc.bcm.edu	37	17	31323887	31323887	+	Missense_Mutation	SNP	G	G	T	rs548141074		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:31323887G>T	ENST00000269053.3	+	3	440	c.370G>T	c.(370-372)Ggt>Tgt	p.G124C	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000394638.1_Missense_Mutation_p.G21C|SPACA3_ENST00000580599.1_Missense_Mutation_p.G55C	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	124					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			TTTCACAAGCGGTTTCAACGC	0.582																																					p.G124C		Atlas-SNP	.											.	SPACA3	35	.	0			c.G370T						.						105.0	94.0	98.0					17																	31323887		2203	4300	6503	SO:0001583	missense	124912	exon3			ACAAGCGGTTTCA	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"""cancer/testis antigen 54"", ""sperm lyzozyme-like acrosomal protein 1"""	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.370G>T	chr17.hg19:g.31323887G>T	ENSP00000269053:p.Gly124Cys	141.0	0.0		123.0	5.0	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	hg19	CCDS11275.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464729	0.43736	.	.	ENSG00000141316	ENST00000269053;ENST00000394638;ENST00000394637;ENST00000411740	T;T	0.78126	-1.15;-1.15	4.59	3.62	0.41486	Lysozyme-like domain (1);	0.112963	0.42821	D	0.000642	D	0.88876	0.6556	M	0.92970	3.365	0.35113	D	0.766342	D	0.89917	1.0	D	0.85130	0.997	D	0.91633	0.5320	10	0.87932	D	0	-6.5689	8.2126	0.31492	0.108:0.0:0.892:0.0	.	124	Q8IXA5	SACA3_HUMAN	C	124;21;125;32	ENSP00000269053:G124C;ENSP00000378134:G21C	ENSP00000269053:G124C	G	+	1	0	SPACA3	28348000	1.000000	0.71417	0.955000	0.39395	0.345000	0.29048	1.265000	0.33027	1.148000	0.42385	0.448000	0.29417	GGT	.	.		0.582	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847	
RAD51D	5892	hgsc.bcm.edu	37	17	33445530	33445530	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:33445530C>A	ENST00000345365.6	-	3	508	c.253G>T	c.(253-255)Ggc>Tgc	p.G85C	RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000590016.1_Intron|RAD51D_ENST00000394589.4_Missense_Mutation_p.G85C|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000360276.3_Missense_Mutation_p.G85C|RAD51D_ENST00000357906.3_Missense_Mutation_p.G85C|RAD51D_ENST00000460118.2_5'UTR|RAD51D_ENST00000590380.1_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	85					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTGCCAATGCCAGTGGACAGG	0.577								Direct reversal of damage																													p.G85C		Atlas-SNP	.											.	RAD51D	53	.	0			c.G253T						.						83.0	86.0	85.0					17																	33445530		2203	4300	6503	SO:0001583	missense	5892	exon3			CAATGCCAGTGGA	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.253G>T	chr17.hg19:g.33445530C>A	ENSP00000338790:p.Gly85Cys	62.0	0.0		79.0	4.0	NM_002878	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	hg19	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349456	0.82132	.	.	ENSG00000185379	ENST00000345365;ENST00000335858;ENST00000360276;ENST00000418935;ENST00000415064;ENST00000357906	T;T;T	0.76060	-0.11;-0.99;-0.92	4.79	4.79	0.61399	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.104572	0.64402	D	0.000004	D	0.89104	0.6620	M	0.94021	3.485	0.53005	D	0.999967	D	0.89917	1.0	D	0.77557	0.99	D	0.91691	0.5366	10	0.87932	D	0	.	14.6952	0.69115	0.0:1.0:0.0:0.0	.	85	O75771	RA51D_HUMAN	C	85;85;85;85;88;85	ENSP00000338790:G85C;ENSP00000353417:G85C;ENSP00000350581:G85C	ENSP00000338408:G85C	G	-	1	0	RAD51D	30469643	1.000000	0.71417	0.512000	0.27736	0.992000	0.81027	4.690000	0.61731	2.499000	0.84300	0.555000	0.69702	GGC	.	.		0.577	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
TAF15	8148	hgsc.bcm.edu	37	17	34171487	34171487	+	Missense_Mutation	SNP	G	G	T	rs71381481	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:34171487G>T	ENST00000588240.1	+	15	1299	c.1184G>T	c.(1183-1185)cGg>cTg	p.R395L	TAF15_ENST00000311979.3_Missense_Mutation_p.R392L|TAF15_ENST00000592237.1_Missense_Mutation_p.R304L	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	33					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GCAGATTTCCGGGGGAGAGGC	0.542			T	"""TEC, CHN1, ZNF384"""	"""extraskeletal myxoid chondrosarcomas, ALL"""																																p.R395L		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"""TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"""		"""L, M"""	.	TAF15	46	.	0			c.G1184T						.						108.0	120.0	116.0					17																	34171487		2202	4299	6501	SO:0001583	missense	8148	exon15			ATTTCCGGGGGAG	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"""RNA binding motif (RRM) containing"""	11547	protein-coding gene	gene with protein product		601574	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1184G>T	chr17.hg19:g.34171487G>T	ENSP00000466950:p.Arg395Leu	158.0	0.0		182.0	8.0	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532489	0.45073	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	.	.	.	4.84	3.86	0.44501	.	.	.	.	.	T	0.33059	0.0850	N	0.08118	0	0.40380	D	0.979438	P;P	0.38300	0.492;0.626	B;B	0.38712	0.145;0.28	T	0.33701	-0.9858	8	0.49607	T	0.09	-5.036	11.3543	0.49607	0.093:0.0:0.907:0.0	.	395;392	Q92804;Q92804-2	RBP56_HUMAN;.	L	395;198	.	ENSP00000309558:R395L	R	+	2	0	TAF15	31195600	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	3.369000	0.52365	2.249000	0.74217	0.591000	0.81541	CGG	.	G|0.999;A|0.001		0.542	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215	
ERBB2	2064	hgsc.bcm.edu	37	17	37872839	37872839	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:37872839C>A	ENST00000269571.5	+	14	1877	c.1718C>A	c.(1717-1719)tCa>tAa	p.S573*	ERBB2_ENST00000406381.2_Nonsense_Mutation_p.S543*|ERBB2_ENST00000540042.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000584601.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000445658.2_Nonsense_Mutation_p.S297*|ERBB2_ENST00000578199.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000541774.1_Nonsense_Mutation_p.S558*|ERBB2_ENST00000540147.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000584450.1_Nonsense_Mutation_p.S573*			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	573					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.S573L(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CAGAATGGCTCAGTGACCTGT	0.637		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																											p.S573X		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	ERBB2,bladder,carcinoma,0,1	ERBB2	429	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C1718A						.						68.0	58.0	61.0					17																	37872839		2203	4300	6503	SO:0001587	stop_gained	2064	exon14			ATGGCTCAGTGAC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1718C>A	chr17.hg19:g.37872839C>A	ENSP00000269571:p.Ser573*	132.0	0.0		73.0	4.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Nonsense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	41	8.694728	0.98918	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	18.9076	0.92469	0.0:1.0:0.0:0.0	.	.	.	.	X	543;558;297;573;543;543	.	ENSP00000269571:S573X	S	+	2	0	ERBB2	35126365	0.992000	0.36948	0.973000	0.42090	0.981000	0.71138	3.052000	0.49893	2.815000	0.96918	0.561000	0.74099	TCA	.	.		0.637	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
NR1D1	9572	hgsc.bcm.edu	37	17	38252091	38252091	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:38252091A>G	ENST00000246672.3	-	5	1484	c.854T>C	c.(853-855)gTg>gCg	p.V285A		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	285	Ligand-binding.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CACATCCTCCACTGTGGGCTC	0.627																																					p.V285A		Atlas-SNP	.											.	NR1D1	45	.	0			c.T854C						.						52.0	47.0	48.0					17																	38252091		2203	4300	6503	SO:0001583	missense	9572	exon5			TCCTCCACTGTGG	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"""Nuclear hormone receptors"""	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.854T>C	chr17.hg19:g.38252091A>G	ENSP00000246672:p.Val285Ala	115.0	0.0		97.0	4.0	NM_021724	Q0P5Z4|Q15304	Missense_Mutation	SNP	ENST00000246672.3	hg19	CCDS11361.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.420312	0.25552	.	.	ENSG00000126368	ENST00000246672	D	0.90004	-2.6	4.43	4.43	0.53597	.	0.187850	0.34879	N	0.003614	D	0.83653	0.5301	L	0.50333	1.59	0.32845	D	0.505831	B	0.18863	0.031	B	0.20184	0.028	T	0.78257	-0.2274	10	0.07813	T	0.8	.	13.1012	0.59219	1.0:0.0:0.0:0.0	.	285	P20393	NR1D1_HUMAN	A	285	ENSP00000246672:V285A	ENSP00000246672:V285A	V	-	2	0	NR1D1	35505617	0.551000	0.26497	1.000000	0.80357	0.996000	0.88848	0.996000	0.29719	1.990000	0.58119	0.533000	0.62120	GTG	.	.		0.627	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
KRT27	342574	hgsc.bcm.edu	37	17	38936687	38936687	+	Silent	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:38936687A>T	ENST00000301656.3	-	3	589	c.549T>A	c.(547-549)ctT>ctA	p.L183L	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CGCTCTGGTGAAGCGCTAGCT	0.458																																					p.L183L		Atlas-SNP	.											.	KRT27	41	.	0			c.T549A						.						62.0	56.0	58.0					17																	38936687		2203	4300	6503	SO:0001819	synonymous_variant	342574	exon3			CTGGTGAAGCGCT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.549T>A	chr17.hg19:g.38936687A>T		123.0	0.0		82.0	4.0	NM_181537		Silent	SNP	ENST00000301656.3	hg19	CCDS11375.1																																																																																			.	.		0.458	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411917	39411917	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39411917A>G	ENST00000394008.1	+	1	282	c.280A>G	c.(280-282)Acc>Gcc	p.T94A		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	79	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGTGGCCAAACCAGCTGTGG	0.627																																					p.T94A		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.A280G						.						60.0	63.0	62.0					17																	39411917		2203	4298	6501	SO:0001583	missense	81870	exon1			GGCCAAACCAGCT	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.280A>G	chr17.hg19:g.39411917A>G	ENSP00000377576:p.Thr94Ala	148.0	0.0		100.0	5.0	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	hg19	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	9.827	1.187478	0.21870	.	.	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.01406	4.93	3.56	-2.15	0.07102	.	.	.	.	.	T	0.01523	0.0049	L	0.51422	1.61	0.09310	N	1	P	0.35033	0.481	B	0.36335	0.222	T	0.45512	-0.9256	9	0.19147	T	0.46	.	5.4575	0.16598	0.3291:0.4684:0.2025:0.0	.	79	Q9BYP9	KRA99_HUMAN	A	100;94	ENSP00000377576:T94A	ENSP00000377576:T94A	T	+	1	0	KRTAP9-9	36665443	0.366000	0.25014	0.000000	0.03702	0.007000	0.05969	0.765000	0.26546	-0.589000	0.05874	-0.501000	0.04562	ACC	.	.		0.627	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
KRT16	3868	hgsc.bcm.edu	37	17	39766790	39766790	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39766790T>C	ENST00000301653.4	-	6	1137	c.1073A>G	c.(1072-1074)gAg>gGg	p.E358G		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	358	Coil 2.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				CAGGCTGTTCTCCAGGGATGC	0.557																																					p.E358G		Atlas-SNP	.											.	KRT16	45	.	0			c.A1073G						.						40.0	40.0	40.0					17																	39766790		2203	4300	6503	SO:0001583	missense	3868	exon6			CTGTTCTCCAGGG	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.1073A>G	chr17.hg19:g.39766790T>C	ENSP00000301653:p.Glu358Gly	98.0	0.0		83.0	4.0	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	hg19	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922437	0.73213	.	.	ENSG00000186832	ENST00000301653	D	0.91407	-2.84	4.28	4.28	0.50868	Filament (1);	0.000000	0.51477	D	0.000085	D	0.96658	0.8909	H	0.96111	3.77	0.49051	D	0.999749	D	0.89917	1.0	D	0.97110	1.0	D	0.97760	1.0220	10	0.87932	D	0	.	13.864	0.63576	0.0:0.0:0.0:1.0	.	358	P08779	K1C16_HUMAN	G	358	ENSP00000301653:E358G	ENSP00000301653:E358G	E	-	2	0	KRT16	37020316	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	7.549000	0.82163	1.929000	0.55896	0.379000	0.24179	GAG	.	.		0.557	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
KLHL10	317719	hgsc.bcm.edu	37	17	39998458	39998458	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39998458A>G	ENST00000293303.4	+	2	731	c.578A>G	c.(577-579)gAt>gGt	p.D193G		NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	193					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				ATTGAGAAAGATGAGCTCAAT	0.398																																					p.D193G		Atlas-SNP	.											.	KLHL10	67	.	0			c.A578G						.						92.0	82.0	85.0					17																	39998458		1877	4122	5999	SO:0001583	missense	317719	exon2			AGAAAGATGAGCT	AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"""Kelch-like"", ""BTB/POZ domain containing"""	18829	protein-coding gene	gene with protein product		608778	"""kelch-like 10 (Drosophila)"""				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.578A>G	chr17.hg19:g.39998458A>G	ENSP00000293303:p.Asp193Gly	121.0	0.0		87.0	4.0	NM_152467	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	hg19	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556300	0.86231	.	.	ENSG00000161594	ENST00000293303	T	0.75260	-0.92	5.73	5.73	0.89815	BTB/Kelch-associated (2);	0.085572	0.85682	D	0.000000	D	0.87819	0.6273	M	0.88105	2.93	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	D	0.89628	0.3853	9	.	.	.	.	14.8475	0.70270	1.0:0.0:0.0:0.0	.	187;193	B4DXV2;Q6JEL2	.;KLH10_HUMAN	G	193	ENSP00000293303:D193G	.	D	+	2	0	KLHL10	37251984	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	9.027000	0.93706	2.177000	0.69029	0.533000	0.62120	GAT	.	.		0.398	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467	
KCNH4	23415	hgsc.bcm.edu	37	17	40321671	40321671	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40321671C>T	ENST00000264661.3	-	9	1746	c.1414G>A	c.(1414-1416)Ggg>Agg	p.G472R	KCNH4_ENST00000607371.1_Missense_Mutation_p.G472R	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	472					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTCACGTTCCCGAACACCACA	0.662																																					p.G472R	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.G1414A						.						78.0	62.0	68.0					17																	40321671		2203	4300	6503	SO:0001583	missense	23415	exon9			CGTTCCCGAACAC	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.1414G>A	chr17.hg19:g.40321671C>T	ENSP00000264661:p.Gly472Arg	73.0	0.0		66.0	4.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186962	0.94923	.	.	ENSG00000089558	ENST00000264661	D	0.99060	-5.38	4.36	4.36	0.52297	Ion transport (1);	0.000000	0.37219	N	0.002199	D	0.99477	0.9814	H	0.96833	3.89	0.80722	D	1	D	0.55800	0.973	P	0.60789	0.879	D	0.98087	1.0407	10	0.87932	D	0	.	17.084	0.86605	0.0:1.0:0.0:0.0	.	472	Q9UQ05	KCNH4_HUMAN	R	472	ENSP00000264661:G472R	ENSP00000264661:G472R	G	-	1	0	KCNH4	37575197	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.616000	0.83018	2.255000	0.74692	0.462000	0.41574	GGG	.	.		0.662	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285	
VPS25	84313	hgsc.bcm.edu	37	17	40928289	40928289	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40928289C>A	ENST00000253794.2	+	5	409	c.369C>A	c.(367-369)tcC>tcA	p.S123S		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	123					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		AGAACAACTCCGTCTTTACCC	0.423																																					p.S123S		Atlas-SNP	.											.	VPS25	11	.	0			c.C369A						.						91.0	88.0	89.0					17																	40928289		2203	4300	6503	SO:0001819	synonymous_variant	84313	exon5			CAACTCCGTCTTT	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.369C>A	chr17.hg19:g.40928289C>A		174.0	0.0		121.0	5.0	NM_032353	B2R581	Silent	SNP	ENST00000253794.2	hg19	CCDS11438.1																																																																																			.	.		0.423	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353	
CNTD1	124817	hgsc.bcm.edu	37	17	40959859	40959859	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40959859C>A	ENST00000588408.1	+	6	1075	c.799C>A	c.(799-801)Caa>Aaa	p.Q267K	CNTD1_ENST00000315066.5_3'UTR|CNTD1_ENST00000588527.1_Missense_Mutation_p.Q184K	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	267										central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TGCTTTCATCCAAAACCATGA	0.408																																					p.Q267K		Atlas-SNP	.											.	CNTD1	22	.	0			c.C799A						.						127.0	111.0	116.0					17																	40959859		2203	4300	6503	SO:0001583	missense	124817	exon6			TTCATCCAAAACC	AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"""cyclin N-terminal domain containing"""	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.799C>A	chr17.hg19:g.40959859C>A	ENSP00000465204:p.Gln267Lys	110.0	0.0		86.0	5.0	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	hg19	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.552239	0.27739	.	.	ENSG00000176563	ENST00000315066	.	.	.	5.92	5.92	0.95590	.	0.174500	0.49305	D	0.000148	T	0.49575	0.1565	L	0.51422	1.61	0.35743	D	0.818857	B	0.31581	0.329	B	0.25987	0.065	T	0.56263	-0.8008	9	0.27785	T	0.31	-4.1829	13.5121	0.61519	0.0:0.929:0.0:0.0709	.	267	Q8N815	CNTD1_HUMAN	K	267	.	ENSP00000316647:Q267K	Q	+	1	0	CNTD1	38213385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.062000	0.49971	2.811000	0.96726	0.555000	0.69702	CAA	.	.		0.408	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478	
AARSD1	80755	hgsc.bcm.edu	37	17	41108253	41108253	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41108253C>T	ENST00000427569.2	-	6	666	c.631G>A	c.(631-633)Ggg>Agg	p.G211R	PTGES3L-AARSD1_ENST00000409399.1_Missense_Mutation_p.G385R|PTGES3L-AARSD1_ENST00000409103.1_Missense_Mutation_p.G294R|PTGES3L-AARSD1_ENST00000360221.4_Missense_Mutation_p.G324R|AARSD1_ENST00000416949.1_5'Flank|PTGES3L-AARSD1_ENST00000421990.2_Missense_Mutation_p.G385R	NM_001261434.1	NP_001248363.1	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	211					alanyl-tRNA aminoacylation (GO:0006419)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	alanine-tRNA ligase activity (GO:0004813)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|Ser-tRNA(Ala) hydrolase activity (GO:0002196)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|skin(1)	17		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		ACATGGGTCCCACAGCACATG	0.567																																					p.G385R		Atlas-SNP	.											AARSD1,NS,carcinoma,0,1	PTGES3L-AARSD1	15	.	0			c.G1153A						.						131.0	126.0	128.0					17																	41108253		2203	4300	6503	SO:0001583	missense	100885850	exon11			GGGTCCCACAGCA	BC004172	CCDS11447.1, CCDS45691.1, CCDS58552.1	17q21.31	2012-10-05			ENSG00000266967	ENSG00000266967			28417	protein-coding gene	gene with protein product		613212					Standard	NM_001261434		Approved	MGC2744		Q9BTE6	OTTHUMG00000153515	ENST00000427569.2:c.631G>A	chr17.hg19:g.41108253C>T	ENSP00000400870:p.Gly211Arg	86.0	0.0		47.0	2.0	NM_001136042	B4DI73	Missense_Mutation	SNP	ENST00000427569.2	hg19	CCDS58552.1	.	.	.	.	.	.	.	.	.	.	C	34	5.293630	0.95546	.	.	ENSG00000108825	ENST00000360221;ENST00000409399;ENST00000421990;ENST00000427569;ENST00000409103;ENST00000423601	D;D	0.90324	-2.65;-2.65	5.4	5.4	0.78164	Threonyl/alanyl tRNA synthetase, SAD (2);Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.119673	0.56097	D	0.000029	D	0.97729	0.9255	H	0.99312	4.51	0.52501	D	0.999957	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99501	1.0953	9	0.87932	D	0	-34.1661	19.1719	0.93581	0.0:1.0:0.0:0.0	.	324;385;294;342;211	Q9BTE6-2;B4DI73;C9J5N1;B3KSP9;Q9BTE6	.;.;.;.;AASD1_HUMAN	R	324;385;385;211;294;93	ENSP00000386621:G385R;ENSP00000409924:G385R	ENSP00000353355:G324R	G	-	1	0	AARSD1	38361779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.582000	0.82546	2.515000	0.84797	0.555000	0.69702	GGG	.	.		0.567	AARSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467729.1	NM_001261434	
MEOX1	4222	hgsc.bcm.edu	37	17	41720883	41720883	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41720883C>A	ENST00000318579.4	-	2	1034	c.615G>T	c.(613-615)gcG>gcT	p.A205A	MEOX1_ENST00000549132.1_Intron|MEOX1_ENST00000329168.3_Intron|MEOX1_ENST00000393661.2_Silent_p.A90A	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	205					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		CCAGGTTTACCGCAATCTCAT	0.607																																					p.A205A		Atlas-SNP	.											.	MEOX1	29	.	0			c.G615T						.						62.0	54.0	56.0					17																	41720883		2203	4300	6503	SO:0001819	synonymous_variant	4222	exon2			GTTTACCGCAATC		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	7013	protein-coding gene	gene with protein product		600147	"""mesenchyme homeo box 1"""			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.615G>T	chr17.hg19:g.41720883C>A		114.0	0.0		87.0	4.0	NM_004527	A8K524|A8MWF9|Q15069	Silent	SNP	ENST00000318579.4	hg19	CCDS11466.1																																																																																			.	.		0.607	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1		
CD300LG	146894	hgsc.bcm.edu	37	17	41924620	41924620	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41924620G>A	ENST00000317310.4	+	1	77	c.36G>A	c.(34-36)ctG>ctA	p.L12L	CD300LG_ENST00000586233.1_Silent_p.L12L|CD300LG_ENST00000588884.1_Silent_p.L12L|CD300LG_ENST00000293396.8_Silent_p.L12L|CD300LG_ENST00000539718.1_Silent_p.L12L|CD300LG_ENST00000377203.4_Silent_p.L12L	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	12					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GTTGCCTGCTGCTCCCAGGTG	0.622																																					p.L12L		Atlas-SNP	.											.	CD300LG	46	.	0			c.G36A						.						90.0	86.0	87.0					17																	41924620		2203	4300	6503	SO:0001819	synonymous_variant	146894	exon1			CCTGCTGCTCCCA	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.36G>A	chr17.hg19:g.41924620G>A		106.0	0.0		94.0	22.0	NM_001168323	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	hg19	CCDS11470.1																																																																																			.	.		0.622	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273	
TMUB2	79089	hgsc.bcm.edu	37	17	42266555	42266555	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:42266555G>A	ENST00000587989.1	+	3	354	c.201G>A	c.(199-201)ctG>ctA	p.L67L	ASB16-AS1_ENST00000588785.1_RNA|TMUB2_ENST00000357984.3_Silent_p.L47L|TMUB2_ENST00000589184.1_Intron|TMUB2_ENST00000587172.1_Silent_p.L47L|TMUB2_ENST00000538716.2_Silent_p.L67L|TMUB2_ENST00000589785.1_Silent_p.L47L|TMUB2_ENST00000446571.3_Silent_p.L47L|TMUB2_ENST00000589856.1_Silent_p.L47L|ASB16-AS1_ENST00000592897.1_RNA|TMUB2_ENST00000590235.1_Silent_p.L47L|ASB16-AS1_ENST00000591166.1_RNA|TMUB2_ENST00000319511.6_Silent_p.L47L|ASB16-AS1_ENST00000585457.1_RNA|TMUB2_ENST00000592825.1_Silent_p.L47L			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	67						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		ACCAGCTCCTGGGCGCTATTG	0.607																																					p.L67L		Atlas-SNP	.											.	TMUB2	29	.	0			c.G201A						.						117.0	105.0	109.0					17																	42266555		2203	4300	6503	SO:0001819	synonymous_variant	79089	exon3			GCTCCTGGGCGCT		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.201G>A	chr17.hg19:g.42266555G>A		114.0	0.0		94.0	4.0	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Silent	SNP	ENST00000587989.1	hg19	CCDS54134.1																																																																																			.	.		0.607	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441	
EFTUD2	9343	hgsc.bcm.edu	37	17	42937415	42937415	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:42937415T>C	ENST00000426333.2	-	18	2017		c.e18-2		EFTUD2_ENST00000592576.1_Splice_Site|EFTUD2_ENST00000402521.3_Splice_Site|EFTUD2_ENST00000591382.1_Splice_Site	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2						gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				AATCTGAGCCTGAGATCCAAA	0.493																																					.	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.1720-2A>G						.						94.0	88.0	90.0					17																	42937415		2203	4300	6503	SO:0001630	splice_region_variant	9343	exon19			TGAGCCTGAGATC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 116 kD"""	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1720-2A>G	chr17.hg19:g.42937415T>C		145.0	0.0		116.0	5.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Splice_Site	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450043	0.84101	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0055	0.71510	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EFTUD2	40292941	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.850000	0.86915	2.135000	0.66039	0.454000	0.30748	.	.	.		0.493	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	Intron
KIF18B	146909	hgsc.bcm.edu	37	17	43005599	43005599	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43005599G>T	ENST00000593135.1	-	13	2168	c.2071C>A	c.(2071-2073)Cca>Aca	p.P691T	KIF18B_ENST00000339151.4_Missense_Mutation_p.P694T|KIF18B_ENST00000438933.2_Missense_Mutation_p.P703T|KIF18B_ENST00000590129.1_Missense_Mutation_p.P712T|KIF18B_ENST00000587309.1_Missense_Mutation_p.P703T	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	703					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				ACTGTGGCTGGGCAAACGCGA	0.642																																					p.P703T		Atlas-SNP	.											.	KIF18B	63	.	0			c.C2107A						.						28.0	33.0	31.0					17																	43005599		2017	4157	6174	SO:0001583	missense	146909	exon13			TGGCTGGGCAAAC		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2071C>A	chr17.hg19:g.43005599G>T	ENSP00000465992:p.Pro691Thr	127.0	0.0		79.0	4.0	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414533	0.42817	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.75050	-0.88;-0.9	4.39	3.34	0.38264	.	.	.	.	.	T	0.81004	0.4733	M	0.70595	2.14	0.29974	N	0.818311	P;D;P	0.64830	0.91;0.994;0.946	P;P;P	0.60949	0.469;0.881;0.67	T	0.75297	-0.3367	9	0.66056	D	0.02	.	7.5899	0.28015	0.0991:0.0:0.7327:0.1682	.	703;700;712	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	T	703;694;703	ENSP00000412798:P703T;ENSP00000341466:P694T	ENSP00000341466:P694T	P	-	1	0	KIF18B	40361125	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	1.807000	0.38902	2.275000	0.75901	0.561000	0.74099	CCA	.	.		0.642	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
KIF18B	146909	hgsc.bcm.edu	37	17	43012257	43012257	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43012257A>G	ENST00000593135.1	-	4	615	c.518T>C	c.(517-519)cTt>cCt	p.L173P	KIF18B_ENST00000339151.4_Missense_Mutation_p.L173P|KIF18B_ENST00000438933.2_Missense_Mutation_p.L173P|KIF18B_ENST00000590129.1_Missense_Mutation_p.L182P|KIF18B_ENST00000587309.1_Missense_Mutation_p.L173P	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	182	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GCGGATGGCAAGGGGCCCCTT	0.592																																					p.L173P		Atlas-SNP	.											.	KIF18B	63	.	0			c.T518C						.						11.0	13.0	13.0					17																	43012257		1821	3991	5812	SO:0001583	missense	146909	exon4			ATGGCAAGGGGCC		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.518T>C	chr17.hg19:g.43012257A>G	ENSP00000465992:p.Leu173Pro	57.0	0.0		56.0	5.0	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615706	0.87359	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.80033	-1.33;-1.33	5.7	5.7	0.88788	Kinesin, motor domain (4);	0.000000	0.34200	N	0.004163	D	0.92502	0.7619	H	0.94222	3.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.94443	0.7660	10	0.87932	D	0	.	15.6259	0.76855	1.0:0.0:0.0:0.0	.	182;182;182	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	P	173	ENSP00000412798:L173P;ENSP00000341466:L173P	ENSP00000341466:L173P	L	-	2	0	KIF18B	40367783	1.000000	0.71417	0.953000	0.39169	0.995000	0.86356	9.182000	0.94881	2.175000	0.68902	0.454000	0.30748	CTT	.	.		0.592	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
FMNL1	752	hgsc.bcm.edu	37	17	43314685	43314685	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43314685T>C	ENST00000331495.3	+	8	1097	c.761T>C	c.(760-762)gTc>gCc	p.V254A	FMNL1_ENST00000328118.3_Missense_Mutation_p.V254A|CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000592006.1_3'UTR|CTD-2020K17.3_ENST00000393507.2_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	254	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)	p.V254A(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CCAGCCTGTGTCAATGAGATT	0.572																																					p.V254A	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											FMNL1,caecum,carcinoma,0,1	FMNL1	78	.	1	Substitution - Missense(1)	large_intestine(1)	c.T761C						.						119.0	107.0	111.0					17																	43314685		2203	4300	6503	SO:0001583	missense	752	exon8			CCTGTGTCAATGA	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.761T>C	chr17.hg19:g.43314685T>C	ENSP00000329219:p.Val254Ala	120.0	0.0		97.0	4.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	hg19	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	T	18.35	3.605830	0.66445	.	.	ENSG00000184922	ENST00000328118;ENST00000331495	D;D	0.90620	-2.7;-2.7	3.83	3.83	0.44106	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	D	0.95214	0.8448	M	0.87827	2.91	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.95396	0.8486	10	0.56958	D	0.05	.	12.8373	0.57780	0.0:0.0:0.0:1.0	.	254	O95466	FMNL_HUMAN	A	254	ENSP00000327442:V254A;ENSP00000329219:V254A	ENSP00000327442:V254A	V	+	2	0	FMNL1	40670468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	1.972000	0.57404	0.379000	0.24179	GTC	.	.		0.572	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	
CDC27	996	hgsc.bcm.edu	37	17	45249328	45249328	+	Missense_Mutation	SNP	G	G	A	rs142853734		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:45249328G>A	ENST00000066544.3	-	3	299	c.206C>T	c.(205-207)cCg>cTg	p.P69L	RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000446365.2_Intron|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Missense_Mutation_p.P69L|CDC27_ENST00000527547.1_Missense_Mutation_p.P69L	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	69					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTGCATTGCGGTGTAGTACA	0.358																																					p.P69L		Atlas-SNP	.											CDC27_ENST00000531206,NS,haematopoietic_neoplasm,0,2	CDC27	337	.	0			c.C206T						.						42.0	42.0	42.0					17																	45249328		2202	4300	6502	SO:0001583	missense	996	exon3			CATTGCGGTGTAG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.206C>T	chr17.hg19:g.45249328G>A	ENSP00000066544:p.Pro69Leu	76.0	0.0		55.0	3.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916798	0.92249	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000527547;ENST00000526866	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.69	4.7	0.59300	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.81389	0.4812	L	0.57536	1.79	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.992	P;P;P	0.57425	0.742;0.803;0.82	T	0.78183	-0.2303	10	0.19147	T	0.46	-28.2366	13.6664	0.62398	0.0:0.0:0.844:0.156	.	69;69;69	G5EA36;G3V1C4;P30260	.;.;CDC27_HUMAN	L	69	ENSP00000066544:P69L;ENSP00000434614:P69L;ENSP00000437339:P69L;ENSP00000432105:P69L	ENSP00000066544:P69L	P	-	2	0	CDC27	42604327	1.000000	0.71417	0.906000	0.35671	0.977000	0.68977	9.568000	0.98166	1.376000	0.46267	0.591000	0.81541	CCG	.	.		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
SPATA20	64847	hgsc.bcm.edu	37	17	48628203	48628203	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48628203C>A	ENST00000356488.4	+	10	1343	c.1260C>A	c.(1258-1260)acC>acA	p.T420T	SPATA20_ENST00000393244.3_Silent_p.T376T|SPATA20_ENST00000006658.6_Silent_p.T436T|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	420					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGGGTGCCACCGAGCCGCTGA	0.642											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T436T		Atlas-SNP	.											.	SPATA20	59	.	0			c.C1308A						.						68.0	78.0	74.0					17																	48628203		2203	4298	6501	SO:0001819	synonymous_variant	64847	exon11			TGCCACCGAGCCG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1260C>A	chr17.hg19:g.48628203C>A		169.0	0.0	119	125.0	5.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	hg19	CCDS58563.1																																																																																			.	.		0.642	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
ABCC3	8714	hgsc.bcm.edu	37	17	48750986	48750986	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48750986G>T	ENST00000285238.8	+	19	2646	c.2566G>T	c.(2566-2568)Gag>Tag	p.E856*		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	856					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGCCCCCGATGAGGACCAAGG	0.607																																					p.E856X		Atlas-SNP	.											.	ABCC3	138	.	0			c.G2566T						.						80.0	77.0	78.0					17																	48750986		2203	4300	6503	SO:0001587	stop_gained	8714	exon19			CCCGATGAGGACC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.2566G>T	chr17.hg19:g.48750986G>T	ENSP00000285238:p.Glu856*	138.0	0.0		87.0	4.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Nonsense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.0|29.0	4.964881|4.964881	0.92855|0.92855	.|.	.|.	ENSG00000108846|ENSG00000108846	ENST00000285238|ENST00000513745	.|.	.|.	.|.	5.05|5.05	4.08|4.08	0.47627|0.47627	.|.	0.273836|.	0.35936|.	N|.	0.002891|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.40728|.	T|.	0.16|.	-11.9696|-11.9696	14.4024|14.4024	0.67056|0.67056	0.0728:0.0:0.9272:0.0|0.0728:0.0:0.9272:0.0	.|.	.|.	.|.	.|.	X|L	856|4	.|.	ENSP00000285238:E856X|.	E|X	+|+	1|2	0|2	ABCC3|ABCC3	46105985|46105985	1.000000|1.000000	0.71417|0.71417	0.266000|0.266000	0.24541|0.24541	0.141000|0.141000	0.21300|0.21300	4.398000|4.398000	0.59697|0.59697	1.448000|1.448000	0.47680|0.47680	0.561000|0.561000	0.74099|0.74099	GAG|TGA	.	.		0.607	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48913333	48913333	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48913333G>A	ENST00000311378.4	+	1	563	c.35G>A	c.(34-36)cGc>cAc	p.R12H	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	12					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TTCTGGTCTCGCTGGGAGCAG	0.706																																					p.R12H		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G35A						.						14.0	15.0	15.0					17																	48913333		2199	4296	6495	SO:0001583	missense	124857	exon1			GGTCTCGCTGGGA	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.35G>A	chr17.hg19:g.48913333G>A	ENSP00000311184:p.Arg12His	127.0	0.0		110.0	41.0	NM_175575	Q6UXZ9	Missense_Mutation	SNP	ENST00000311378.4	hg19	CCDS11575.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361150	0.24684	.	.	ENSG00000173714	ENST00000311378	T	0.81415	-1.49	5.24	0.186	0.15105	.	1.186510	0.05938	N	0.636435	T	0.58652	0.2137	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.40001	-0.9586	10	0.13853	T	0.58	.	4.3165	0.10995	0.3569:0.1618:0.4813:0.0	.	12	Q8TEU8	WFKN2_HUMAN	H	12	ENSP00000311184:R12H	ENSP00000311184:R12H	R	+	2	0	WFIKKN2	46268332	0.000000	0.05858	0.613000	0.29037	0.950000	0.60333	-0.841000	0.04359	-0.239000	0.09710	0.655000	0.94253	CGC	.	.		0.706	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
STXBP4	252983	hgsc.bcm.edu	37	17	53150293	53150293	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:53150293C>A	ENST00000376352.2	+	13	1251	c.1044C>A	c.(1042-1044)gcC>gcA	p.A348A	STXBP4_ENST00000434978.2_Silent_p.A326A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	348					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						AAACAAGAGCCCTGCGTAGTC	0.378																																					p.A348A		Atlas-SNP	.											.	STXBP4	41	.	0			c.C1044A						.						79.0	75.0	76.0					17																	53150293		2203	4300	6503	SO:0001819	synonymous_variant	252983	exon13			AAGAGCCCTGCGT	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1044C>A	chr17.hg19:g.53150293C>A		102.0	0.0		74.0	5.0	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	hg19	CCDS11584.2																																																																																			.	.		0.378	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
LPO	4025	hgsc.bcm.edu	37	17	56344752	56344752	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:56344752A>G	ENST00000262290.4	+	12	2052	c.1736A>G	c.(1735-1737)cAg>cGg	p.Q579R	LPO_ENST00000582328.1_Missense_Mutation_p.Q496R|LPO_ENST00000543544.1_Missense_Mutation_p.Q520R|LPO_ENST00000421678.2_Missense_Mutation_p.Q496R	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	579					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TCACAGCCGCAGACACTAGAG	0.547																																					p.Q579R		Atlas-SNP	.											.	LPO	73	.	0			c.A1736G						.						70.0	64.0	66.0					17																	56344752		2203	4300	6503	SO:0001583	missense	4025	exon12			AGCCGCAGACACT	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1736A>G	chr17.hg19:g.56344752A>G	ENSP00000262290:p.Gln579Arg	88.0	0.0		62.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.809130	0.00606	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.68903	-0.36;-0.36;-0.36	5.11	4.01	0.46588	.	0.748721	0.13539	N	0.380388	T	0.44008	0.1273	N	0.20610	0.595	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.34576	-0.9823	10	0.02654	T	1	.	6.804	0.23766	0.8069:0.0:0.1931:0.0	.	496;579	E7EMJ3;P22079	.;PERL_HUMAN	R	579;496;520;324	ENSP00000262290:Q579R;ENSP00000400245:Q496R;ENSP00000445344:Q520R	ENSP00000262290:Q579R	Q	+	2	0	LPO	53699751	0.022000	0.18835	0.073000	0.20177	0.076000	0.17211	1.540000	0.36115	0.779000	0.33543	0.455000	0.32223	CAG	.	.		0.547	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
TEX14	56155	hgsc.bcm.edu	37	17	56690838	56690838	+	Missense_Mutation	SNP	G	G	T	rs150820263	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:56690838G>T	ENST00000240361.8	-	9	1052	c.967C>A	c.(967-969)Cgc>Agc	p.R323S	TEX14_ENST00000389934.3_Missense_Mutation_p.R317S|TEX14_ENST00000349033.5_Missense_Mutation_p.R317S			Q8IWB6	TEX14_HUMAN	testis expressed 14	323	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TACACAAGGCGGGTTTTCTCT	0.502																																					p.R323S		Atlas-SNP	.											TEX14_ENST00000240361,colon,carcinoma,0,2	TEX14	343	.	0			c.C967A						.						168.0	144.0	152.0					17																	56690838		2203	4300	6503	SO:0001583	missense	56155	exon9			CAAGGCGGGTTTT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.967C>A	chr17.hg19:g.56690838G>T	ENSP00000240361:p.Arg323Ser	198.0	1.0		144.0	7.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	8.134	0.783782	0.16189	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.40756	1.02;1.02;1.02	5.68	3.72	0.42706	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.538685	0.18620	N	0.135891	T	0.28400	0.0702	N	0.13235	0.315	0.09310	N	1	P;B;B	0.37781	0.608;0.232;0.227	B;B;B	0.41466	0.358;0.159;0.114	T	0.09509	-1.0671	10	0.40728	T	0.16	-3.5586	8.7353	0.34525	0.2317:0.0:0.7683:0.0	.	323;317;317	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	S	323;317;317	ENSP00000240361:R323S;ENSP00000374584:R317S;ENSP00000268910:R317S	ENSP00000240361:R323S	R	-	1	0	TEX14	54045837	0.988000	0.35896	0.005000	0.12908	0.004000	0.04260	3.332000	0.52083	0.770000	0.33336	-0.254000	0.11334	CGC	.	G|1.000;A|0.000		0.502	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
DDX42	11325	hgsc.bcm.edu	37	17	61889542	61889542	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:61889542C>A	ENST00000578681.1	+	15	2250	c.1649C>A	c.(1648-1650)cCa>cAa	p.P550Q	DDX42_ENST00000583590.1_Missense_Mutation_p.P550Q|DDX42_ENST00000359353.5_Missense_Mutation_p.P431Q|DDX42_ENST00000457800.2_Missense_Mutation_p.P550Q|DDX42_ENST00000389924.2_Missense_Mutation_p.P550Q	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	550	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						AAGGACATCCCAGTCCTGGTG	0.418																																					p.P550Q		Atlas-SNP	.											.	DDX42	86	.	0			c.C1649A						.						60.0	57.0	58.0					17																	61889542		2203	4300	6503	SO:0001583	missense	11325	exon14			ACATCCCAGTCCT	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1649C>A	chr17.hg19:g.61889542C>A	ENSP00000464050:p.Pro550Gln	170.0	0.0		100.0	4.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668879	0.88348	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.75260	-0.92;-0.92	5.74	5.74	0.90152	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.75184	0.3815	N	0.25031	0.7	0.80722	D	1	P;P	0.42620	0.785;0.594	P;B	0.52031	0.688;0.403	T	0.76597	-0.2901	10	0.62326	D	0.03	-8.01	19.2994	0.94138	0.0:1.0:0.0:0.0	.	96;550	B3KV84;Q86XP3	.;DDX42_HUMAN	Q	550;550;286	ENSP00000374574:P550Q;ENSP00000390121:P550Q	ENSP00000352308:P286Q	P	+	2	0	DDX42	59243274	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.082000	0.71318	2.890000	0.99128	0.650000	0.86243	CCA	.	.		0.418	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
SCN4A	6329	hgsc.bcm.edu	37	17	62022891	62022891	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:62022891G>T	ENST00000435607.1	-	19	3625	c.3549C>A	c.(3547-3549)gcC>gcA	p.A1183A	SCN4A_ENST00000578147.1_Silent_p.A1183A	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1183					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGAACTTGCCGGCAAACAGGT	0.542																																					p.A1183A		Atlas-SNP	.											.	SCN4A	205	.	0			c.C3549A						.						252.0	252.0	252.0					17																	62022891		2200	4300	6500	SO:0001819	synonymous_variant	6329	exon19			CTTGCCGGCAAAC	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3549C>A	chr17.hg19:g.62022891G>T		204.0	0.0		136.0	6.0	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.		0.542	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ABCA9	10350	hgsc.bcm.edu	37	17	67017907	67017907	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:67017907C>T	ENST00000340001.4	-	18	2588	c.2377G>A	c.(2377-2379)Gga>Aga	p.G793R	ABCA9_ENST00000370732.2_Missense_Mutation_p.G793R|ABCA9_ENST00000453985.2_Missense_Mutation_p.G793R	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	793					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GTTGATTTTCCTTCTAATTTC	0.338																																					p.G793R		Atlas-SNP	.											.	ABCA9	192	.	0			c.G2377A						.						89.0	88.0	89.0					17																	67017907		2202	4295	6497	SO:0001583	missense	10350	exon18			ATTTTCCTTCTAA	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2377G>A	chr17.hg19:g.67017907C>T	ENSP00000342216:p.Gly793Arg	62.0	0.0		57.0	4.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031549	0.75504	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	D;D	0.82619	-1.63;-1.63	5.12	4.15	0.48705	.	0.000000	0.47455	D	0.000223	D	0.89451	0.6719	M	0.70595	2.14	0.40094	D	0.97628	D;D	0.89917	1.0;0.982	D;D	0.87578	0.998;0.942	D	0.90222	0.4272	10	0.59425	D	0.04	.	12.4951	0.55923	0.0:0.9178:0.0:0.0822	.	793;793	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	R	793;776;793;788	ENSP00000342216:G793R;ENSP00000359767:G793R	ENSP00000342216:G793R	G	-	1	0	ABCA9	64529502	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.584000	0.60971	1.300000	0.44818	0.603000	0.83216	GGA	.	.		0.338	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
CPSF4L	642843	hgsc.bcm.edu	37	17	71257927	71257927	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:71257927A>G	ENST00000344935.4	-	1	92	c.31T>C	c.(31-33)Ttc>Ctc	p.F11L	CPSF4L_ENST00000397671.1_Intron	NM_001129885.1	NP_001123357.1	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor 4-like	11							metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|prostate(1)	2						GCAAAGGTGAACCGCTCTAGC	0.597																																					p.F11L		Atlas-SNP	.											.	CPSF4L	8	.	0			c.T31C						.						178.0	159.0	164.0					17																	71257927		692	1591	2283	SO:0001583	missense	642843	exon1			AGGTGAACCGCTC		CCDS45768.1	17q25.1	2010-07-06			ENSG00000187959	ENSG00000187959			33632	protein-coding gene	gene with protein product							Standard	NM_001129885		Approved		uc010dfk.1	A6NMK7	OTTHUMG00000132640	ENST00000344935.4:c.31T>C	chr17.hg19:g.71257927A>G	ENSP00000343900:p.Phe11Leu	95.0	0.0		62.0	4.0	NM_001129885	A8MU95|B2RXI9	Missense_Mutation	SNP	ENST00000344935.4	hg19	CCDS45768.1	.	.	.	.	.	.	.	.	.	.	A	3.867	-0.028595	0.07589	.	.	ENSG00000187959	ENST00000344935	T	0.20738	2.05	5.11	-0.029	0.13920	.	.	.	.	.	T	0.11196	0.0273	L	0.33485	1.01	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21895	-1.0232	9	0.13108	T	0.6	.	3.8229	0.08843	0.5:0.0:0.1782:0.3218	.	11	A6NMK7	CPS4L_HUMAN	L	11	ENSP00000343900:F11L	ENSP00000343900:F11L	F	-	1	0	CPSF4L	68769522	0.000000	0.05858	0.154000	0.22540	0.070000	0.16714	-0.555000	0.05999	0.006000	0.14734	0.459000	0.35465	TTC	.	.		0.597	CPSF4L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441896.1	NM_001129885	
KIF19	124602	hgsc.bcm.edu	37	17	72324604	72324604	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:72324604A>G	ENST00000389916.4	+	2	218	c.80A>G	c.(79-81)gAg>gGg	p.E27G		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	27	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCAGAGCTGGAGGAAGGAGCT	0.617																																					p.E27G		Atlas-SNP	.											.	KIF19	102	.	0			c.A80G						.						49.0	44.0	46.0					17																	72324604		2203	4299	6502	SO:0001583	missense	124602	exon2			AGCTGGAGGAAGG	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.80A>G	chr17.hg19:g.72324604A>G	ENSP00000374566:p.Glu27Gly	78.0	0.0		49.0	4.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265121	0.59431	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.76060	-0.67;-0.99	4.96	4.96	0.65561	Kinesin, motor domain (4);	0.707634	0.11041	U	0.606080	T	0.67002	0.2847	L	0.33189	0.99	0.41417	D	0.987773	B;B;B;B	0.22604	0.056;0.072;0.016;0.016	B;B;B;B	0.27608	0.081;0.066;0.019;0.019	T	0.60234	-0.7303	10	0.38643	T	0.18	.	12.2462	0.54572	1.0:0.0:0.0:0.0	.	27;27;27;27	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	G	27	ENSP00000449134:E27G;ENSP00000374566:E27G	ENSP00000374566:E27G	E	+	2	0	KIF19	69836199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.295000	0.72744	1.878000	0.54408	0.529000	0.55759	GAG	.	.		0.617	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
CD300C	10871	hgsc.bcm.edu	37	17	72537867	72537867	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:72537867A>G	ENST00000330793.1	-	4	896	c.536T>C	c.(535-537)tTc>tCc	p.F179S		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	179					cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						GACATTGCTGAACAGGGAGCT	0.627																																					p.F179S	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											.	CD300C	41	.	0			c.T536C						.						83.0	65.0	71.0					17																	72537867		2203	4300	6503	SO:0001583	missense	10871	exon4			TTGCTGAACAGGG	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19320	protein-coding gene	gene with protein product		606786	"""CD300c antigen"""			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.536T>C	chr17.hg19:g.72537867A>G	ENSP00000329507:p.Phe179Ser	76.0	0.0		55.0	4.0	NM_006678		Missense_Mutation	SNP	ENST00000330793.1	hg19	CCDS11701.1	.	.	.	.	.	.	.	.	.	.	A	6.368	0.436008	0.12104	.	.	ENSG00000167850	ENST00000330793	T	0.03242	4.0	4.74	3.66	0.41972	.	0.567919	0.14416	N	0.320989	T	0.02083	0.0065	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.15484	0.013	T	0.48592	-0.9022	10	0.19590	T	0.45	.	7.4927	0.27471	0.8983:0.0:0.1017:0.0	.	179	Q08708	CLM6_HUMAN	S	179	ENSP00000329507:F179S	ENSP00000329507:F179S	F	-	2	0	CD300C	70049462	0.003000	0.15002	0.072000	0.20136	0.001000	0.01503	1.620000	0.36976	0.930000	0.37217	0.477000	0.44152	TTC	.	.		0.627	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678	
SLC16A5	9121	hgsc.bcm.edu	37	17	73100204	73100204	+	Silent	SNP	G	G	C	rs141647560	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73100204G>C	ENST00000450736.2	+	5	1708	c.1293G>C	c.(1291-1293)gcG>gcC	p.A431A	SLC16A5_ENST00000538213.2_Silent_p.A471A|SLC16A5_ENST00000580123.1_Silent_p.A431A|SLC16A5_ENST00000329783.4_Silent_p.A431A			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	431					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CTGTCGCGGCGGATGCCCTGG	0.567																																					p.A431A		Atlas-SNP	.											SLC16A5_ENST00000450736,colon,carcinoma,+1,2	SLC16A5	80	.	0			c.G1293C						.						71.0	66.0	68.0					17																	73100204		2203	4300	6503	SO:0001819	synonymous_variant	9121	exon6			CGCGGCGGATGCC	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.1293G>C	chr17.hg19:g.73100204G>C		176.0	0.0		133.0	39.0	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	hg19	CCDS11713.1																																																																																			.	G|0.999;A|0.001		0.567	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
CASKIN2	57513	hgsc.bcm.edu	37	17	73501024	73501024	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73501024G>T	ENST00000321617.3	-	11	1647	c.1061C>A	c.(1060-1062)gCc>gAc	p.A354D	CASKIN2_ENST00000433559.2_Missense_Mutation_p.A272D	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	354						cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGGAGGCGGGCTGCAGGGAT	0.682																																					p.A354D		Atlas-SNP	.											CASKIN2,NS,carcinoma,0,1	CASKIN2	66	.	0			c.C1061A						.						22.0	23.0	23.0					17																	73501024		2201	4294	6495	SO:0001583	missense	57513	exon11			AGGCGGGCTGCAG	AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.1061C>A	chr17.hg19:g.73501024G>T	ENSP00000325355:p.Ala354Asp	97.0	2.0		71.0	3.0	NM_020753	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	hg19	CCDS11723.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760757	0.31137	.	.	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.70516	-0.49;-0.3	5.07	5.07	0.68467	Src homology-3 domain (1);	0.978162	0.08318	N	0.964242	T	0.54631	0.1870	N	0.14661	0.345	0.80722	D	1	B	0.23058	0.079	B	0.20384	0.029	T	0.44019	-0.9355	10	0.33940	T	0.23	.	9.3643	0.38215	0.0943:0.0:0.9057:0.0	.	354	Q8WXE0	CSKI2_HUMAN	D	354;272	ENSP00000325355:A354D;ENSP00000406963:A272D	ENSP00000325355:A354D	A	-	2	0	CASKIN2	71012619	0.960000	0.32886	0.956000	0.39512	0.024000	0.10985	1.900000	0.39828	2.644000	0.89710	0.561000	0.74099	GCC	.	.		0.682	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753	
LLGL2	3993	hgsc.bcm.edu	37	17	73570325	73570325	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73570325T>C	ENST00000392550.3	+	23	3054	c.2937T>C	c.(2935-2937)gcT>gcC	p.A979A	LLGL2_ENST00000577200.1_Silent_p.A979A|LLGL2_ENST00000167462.5_Silent_p.A979A	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	979					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGGAGCGCGCTCTGCTCAGTG	0.692																																					p.A979A		Atlas-SNP	.											.	LLGL2	155	.	0			c.T2937C						.						3.0	4.0	4.0					17																	73570325		1643	3154	4797	SO:0001819	synonymous_variant	3993	exon23			GCGCGCTCTGCTC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2937T>C	chr17.hg19:g.73570325T>C		113.0	0.0		96.0	4.0	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	.		0.692	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
RECQL5	9400	hgsc.bcm.edu	37	17	73657713	73657713	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73657713C>A	ENST00000317905.5	-	5	1006	c.847G>T	c.(847-849)Ggt>Tgt	p.G283C	RECQL5_ENST00000420326.2_Missense_Mutation_p.G283C|RECQL5_ENST00000340830.5_Missense_Mutation_p.G283C|RECQL5_ENST00000584999.1_Missense_Mutation_p.G283C|RECQL5_ENST00000423245.2_Missense_Mutation_p.G256C	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	283	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GCGTTCACACCCCTGCAGCTG	0.532								Other identified genes with known or suspected DNA repair function																													p.G283C		Atlas-SNP	.											.	RECQL5	77	.	0			c.G847T						.						96.0	89.0	91.0					17																	73657713		2203	4300	6503	SO:0001583	missense	9400	exon5			TCACACCCCTGCA	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.847G>T	chr17.hg19:g.73657713C>A	ENSP00000317636:p.Gly283Cys	73.0	0.0		56.0	4.0	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	hg19	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.287710	0.59976	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	T;T;T	0.09163	3.01;3.01;3.01	5.95	5.95	0.96441	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.53530	0.1802	H	0.98048	4.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.70887	-0.4750	10	0.87932	D	0	-7.074	20.3932	0.98965	0.0:1.0:0.0:0.0	.	283;256;283	O94762;Q6P4G0;O94762-3	RECQ5_HUMAN;.;.	C	283	ENSP00000317636:G283C;ENSP00000414933:G283C;ENSP00000341983:G283C	ENSP00000317636:G283C	G	-	1	0	RECQL5	71169308	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.677000	0.84024	2.824000	0.97209	0.655000	0.94253	GGT	.	.		0.532	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
EXOC7	23265	hgsc.bcm.edu	37	17	74081819	74081819	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:74081819G>T	ENST00000335146.7	-	15	1761	c.1708C>A	c.(1708-1710)Cca>Aca	p.P570T	EXOC7_ENST00000591724.1_5'Flank|EXOC7_ENST00000467929.2_Missense_Mutation_p.P491T|EXOC7_ENST00000405575.4_Missense_Mutation_p.P542T|EXOC7_ENST00000607838.1_Missense_Mutation_p.P542T|EXOC7_ENST00000589210.1_Missense_Mutation_p.P519T|EXOC7_ENST00000332065.5_Missense_Mutation_p.P488T|EXOC7_ENST00000411744.2_Missense_Mutation_p.P511T			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	570					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCAGAGCTGGGTCCTCGTAC	0.547																																					p.P570T		Atlas-SNP	.											.	EXOC7	47	.	0			c.C1708A						.						119.0	111.0	114.0					17																	74081819		2203	4300	6503	SO:0001583	missense	23265	exon15			GAGCTGGGTCCTC	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1708C>A	chr17.hg19:g.74081819G>T	ENSP00000334100:p.Pro570Thr	127.0	0.0		91.0	4.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	G	5.532	0.283140	0.10458	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.06	4.06	0.47325	Cullin repeat-like-containing domain (1);	0.126283	0.53938	D	0.000051	T	0.60534	0.2276	L	0.43152	1.355	0.80722	D	1	B;B;P;B;B;B;B	0.42692	0.039;0.024;0.787;0.022;0.049;0.027;0.022	B;B;P;B;B;B;B	0.51516	0.014;0.036;0.672;0.022;0.054;0.012;0.054	T	0.56025	-0.8047	9	0.21540	T	0.41	-16.0913	16.449	0.83973	0.0:0.0:1.0:0.0	.	511;542;491;456;570;488;519	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	T	488;408;542;570;519;456;511	.	ENSP00000333806:P488T	P	-	1	0	EXOC7	71593414	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	5.981000	0.70524	2.110000	0.64415	0.585000	0.79938	CCA	.	.		0.547	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
TNRC6C	57690	hgsc.bcm.edu	37	17	76045435	76045435	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:76045435C>A	ENST00000588061.1	+	5	1019	c.292C>A	c.(292-294)Ctt>Att	p.L98I	TNRC6C_ENST00000588847.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000541771.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000301624.4_Missense_Mutation_p.L98I|TNRC6C_ENST00000544502.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000335749.4_Missense_Mutation_p.L98I			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	98	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TGGCATTAATCTTAACCTTAA	0.502																																					p.L98I		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C292A						.						48.0	52.0	50.0					17																	76045435		2034	4184	6218	SO:0001583	missense	57690	exon4			ATTAATCTTAACC	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.292C>A	chr17.hg19:g.76045435C>A	ENSP00000468647:p.Leu98Ile	188.0	0.0		114.0	5.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307755	0.40795	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.17054	2.3;2.32;2.32;2.3	4.82	4.82	0.62117	.	0.125823	0.56097	D	0.000040	T	0.37073	0.0990	L	0.47716	1.5	0.58432	D	0.999996	D;D;D	0.89917	0.998;1.0;0.997	D;D;D	0.83275	0.996;0.996;0.991	T	0.04811	-1.0925	10	0.54805	T	0.06	-10.7183	18.4841	0.90823	0.0:1.0:0.0:0.0	.	98;98;98	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	I	98	ENSP00000336783:L98I;ENSP00000301624:L98I;ENSP00000440310:L98I;ENSP00000442421:L98I	ENSP00000301624:L98I	L	+	1	0	TNRC6C	73557030	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.361000	0.59461	2.673000	0.90976	0.655000	0.94253	CTT	.	.		0.502	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
TNRC6C	57690	hgsc.bcm.edu	37	17	76046560	76046560	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:76046560G>A	ENST00000588061.1	+	5	2144	c.1417G>A	c.(1417-1419)Gac>Aac	p.D473N	TNRC6C_ENST00000588847.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000541771.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000301624.4_Missense_Mutation_p.D473N|TNRC6C_ENST00000544502.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000335749.4_Missense_Mutation_p.D473N			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	473	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGGAAAAATGACAATGGGAC	0.478																																					p.D473N		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G1417A						.						75.0	76.0	76.0					17																	76046560		1883	4117	6000	SO:0001583	missense	57690	exon4			AAAAATGACAATG	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.1417G>A	chr17.hg19:g.76046560G>A	ENSP00000468647:p.Asp473Asn	99.0	0.0		76.0	4.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582408	0.65992	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.23348	1.91;2.1;2.1;1.91	5.07	5.07	0.68467	.	0.268851	0.41396	D	0.000885	T	0.51143	0.1657	M	0.71036	2.16	0.46222	D	0.998935	D;D;B	0.89917	0.999;1.0;0.397	D;D;B	0.91635	0.995;0.999;0.085	T	0.40040	-0.9584	10	0.31617	T	0.26	-26.0189	18.6486	0.91421	0.0:0.0:1.0:0.0	.	473;473;473	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	N	473	ENSP00000336783:D473N;ENSP00000301624:D473N;ENSP00000440310:D473N;ENSP00000442421:D473N	ENSP00000301624:D473N	D	+	1	0	TNRC6C	73558155	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	5.249000	0.65427	2.644000	0.89710	0.563000	0.77884	GAC	.	.		0.478	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
EIF4A3	9775	hgsc.bcm.edu	37	17	78109863	78109863	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:78109863G>T	ENST00000269349.3	-	11	1380	c.1159C>A	c.(1159-1161)Cgc>Agc	p.R387S		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	387	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			CTGAGGATGCGGATGTCGTCA	0.428																																					p.R387S		Atlas-SNP	.											.	EIF4A3	35	.	0			c.C1159A						.						128.0	120.0	123.0					17																	78109863		2203	4300	6503	SO:0001583	missense	9775	exon11			GGATGCGGATGTC	BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"""DEAD-boxes"""	18683	protein-coding gene	gene with protein product		608546	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 48"", ""eukaryotic translation initiation factor 4A, isoform 3"""	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.1159C>A	chr17.hg19:g.78109863G>T	ENSP00000269349:p.Arg387Ser	81.0	0.0		58.0	4.0	NM_014740	Q15033|Q6IBQ2|Q96A18	Missense_Mutation	SNP	ENST00000269349.3	hg19	CCDS11767.1	.	.	.	.	.	.	.	.	.	.	G	9.791	1.178053	0.21787	.	.	ENSG00000141543	ENST00000269349	T	0.04551	3.6	4.18	2.12	0.27331	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.03348	0.0097	N	0.20845	0.615	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.44605	-0.9317	10	0.72032	D	0.01	-18.3621	6.2572	0.20879	0.1016:0.0:0.7137:0.1847	.	387	P38919	IF4A3_HUMAN	S	387	ENSP00000269349:R387S	ENSP00000269349:R387S	R	-	1	0	EIF4A3	75724458	1.000000	0.71417	0.809000	0.32408	0.155000	0.21991	5.903000	0.69877	0.397000	0.25310	0.555000	0.69702	CGC	.	.		0.428	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740	
RNF213	57674	hgsc.bcm.edu	37	17	78341922	78341922	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:78341922C>A	ENST00000582970.1	+	44	12277	c.12134C>A	c.(12133-12135)cCa>cAa	p.P4045Q	RNF213_ENST00000508628.2_Missense_Mutation_p.P4094Q|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.P2118Q|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4045					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GAATTCTCTCCAGCTGTTTCC	0.468																																					p.P4045Q		Atlas-SNP	.											.	RNF213	766	.	0			c.C12134A						.						152.0	146.0	148.0					17																	78341922		2203	4300	6503	SO:0001583	missense	57674	exon44			TCTCTCCAGCTGT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.12134C>A	chr17.hg19:g.78341922C>A	ENSP00000464087:p.Pro4045Gln	138.0	0.0		110.0	5.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438437	0.43326	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.24723	2.06;1.84	4.67	-5.25	0.02781	Zinc finger, RING/FYVE/PHD-type (1);	1.235290	0.05537	N	0.565002	T	0.47728	0.1461	M	0.80183	2.485	0.09310	N	1	D;P	0.61080	0.989;0.944	P;P	0.61201	0.885;0.642	T	0.58222	-0.7674	10	0.48119	T	0.1	.	13.5295	0.61613	0.0:0.278:0.0:0.722	.	4094;2118	C9JCP4;Q63HN8	.;RN213_HUMAN	Q	4045;4094;2118	ENSP00000425956:P4045Q;ENSP00000338218:P2118Q	ENSP00000338218:P2118Q	P	+	2	0	RNF213	75956517	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.289000	0.08365	-1.017000	0.03367	-0.768000	0.03414	CCA	.	.		0.468	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
C17orf70	80233	hgsc.bcm.edu	37	17	79514378	79514378	+	Missense_Mutation	SNP	C	C	A	rs72854496	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:79514378C>A	ENST00000327787.8	-	5	1776	c.1730G>T	c.(1729-1731)cGg>cTg	p.R577L	C17orf70_ENST00000425898.2_Missense_Mutation_p.R226L|C17orf70_ENST00000537152.1_Missense_Mutation_p.R426L			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	577					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CACCTCCCGCCGAGCACCGGG	0.677																																					p.R577L		Atlas-SNP	.											.	C17orf70	79	.	0			c.G1730T						.						38.0	38.0	38.0					17																	79514378		2202	4292	6494	SO:0001583	missense	80233	exon5			TCCCGCCGAGCAC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.1730G>T	chr17.hg19:g.79514378C>A	ENSP00000333283:p.Arg577Leu	42.0	0.0		45.0	4.0	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	hg19	CCDS32765.2	.	.	.	.	.	.	.	.	.	.	C	9.341	1.063042	0.19987	.	.	ENSG00000185504	ENST00000327787;ENST00000425898;ENST00000537152	T;T;T	0.34472	1.36;1.36;1.36	4.49	-4.3	0.03710	.	0.906018	0.09076	N	0.852135	T	0.31136	0.0787	L	0.54323	1.7	0.09310	N	1	B;P	0.35226	0.275;0.491	B;B	0.32724	0.061;0.151	T	0.34650	-0.9820	10	0.66056	D	0.02	.	12.654	0.56778	0.0:0.2074:0.0:0.7926	.	577;226	Q0VG06;E7EVV8	FP100_HUMAN;.	L	577;226;426	ENSP00000333283:R577L;ENSP00000399674:R226L;ENSP00000440151:R426L	ENSP00000333283:R577L	R	-	2	0	C17orf70	77124831	0.000000	0.05858	0.028000	0.17463	0.054000	0.15201	0.098000	0.15189	-0.676000	0.05238	-1.069000	0.02264	CGG	.	C|1.000;T|0.000		0.677	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161	
P4HB	5034	hgsc.bcm.edu	37	17	79817083	79817083	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:79817083T>C	ENST00000331483.4	-	2	548	c.326A>G	c.(325-327)gAc>gGc	p.D109G	P4HB_ENST00000472244.1_5'Flank|P4HB_ENST00000439918.2_Missense_Mutation_p.D109G|P4HB_ENST00000576390.1_Intron	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	109	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			GGAAGCCGTGTCTCCATTCCT	0.602																																					p.D109G	Colon(49;444 983 1296 7887 42561)	Atlas-SNP	.											.	P4HB	43	.	0			c.A326G						.						152.0	143.0	146.0					17																	79817083		2203	4298	6501	SO:0001583	missense	5034	exon2			GCCGTGTCTCCAT	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"""Protein disulfide isomerases"""	8548	protein-coding gene	gene with protein product	"""protein disulfide isomerase-associated 1"", ""protein disulfide isomerase family A, member 1"", ""collagen prolyl 4-hydroxylase beta"""	176790	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"""	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.326A>G	chr17.hg19:g.79817083T>C	ENSP00000327801:p.Asp109Gly	116.0	0.0		82.0	6.0	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Missense_Mutation	SNP	ENST00000331483.4	hg19	CCDS11787.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.639882	0.47153	.	.	ENSG00000185624	ENST00000331483;ENST00000537205;ENST00000436463	T	0.03242	4.0	4.59	3.49	0.39957	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.173592	0.49305	D	0.000154	T	0.02455	0.0075	N	0.02120	-0.675	0.38770	D	0.954535	P	0.39964	0.697	P	0.44732	0.459	T	0.61623	-0.7025	10	0.59425	D	0.04	.	10.9514	0.47332	0.0:0.0:0.1576:0.8424	.	109	P07237	PDIA1_HUMAN	G	109;109;93	ENSP00000327801:D109G	ENSP00000327801:D109G	D	-	2	0	P4HB	77410372	1.000000	0.71417	0.864000	0.33941	0.022000	0.10575	7.768000	0.85345	0.605000	0.29947	-0.460000	0.05396	GAC	.	.		0.602	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918	
FASN	2194	hgsc.bcm.edu	37	17	80046286	80046286	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:80046286G>A	ENST00000306749.2	-	16	2791	c.2573C>T	c.(2572-2574)tCa>tTa	p.S858L		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	858					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GATGGCGGCTGAGGGGGAACC	0.682																																					p.S858L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C2573T						.						28.0	36.0	33.0					17																	80046286		2196	4292	6488	SO:0001583	missense	2194	exon16			GCGGCTGAGGGGG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.2573C>T	chr17.hg19:g.80046286G>A	ENSP00000304592:p.Ser858Leu	54.0	0.0		40.0	4.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192936	0.38707	.	.	ENSG00000169710	ENST00000306749	D	0.84800	-1.9	4.24	3.25	0.37280	.	0.145982	0.47455	D	0.000239	D	0.88771	0.6527	M	0.80616	2.505	0.20196	N	0.999921	P	0.41131	0.739	P	0.48795	0.59	T	0.82112	-0.0618	10	0.48119	T	0.1	-5.9456	14.0528	0.64749	0.0:0.1524:0.8476:0.0	.	858	P49327	FAS_HUMAN	L	858	ENSP00000304592:S858L	ENSP00000304592:S858L	S	-	2	0	FASN	77639575	0.999000	0.42202	0.002000	0.10522	0.005000	0.04900	6.083000	0.71326	0.977000	0.38444	0.462000	0.41574	TCA	.	.		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
EMILIN2	84034	hgsc.bcm.edu	37	18	2891118	2891118	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:2891118G>T	ENST00000254528.3	+	4	1152	c.993G>T	c.(991-993)gaG>gaT	p.E331D		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	331					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AGCTCATGGAGGGCATGGACA	0.552																																					p.E331D		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G993T						.						113.0	116.0	115.0					18																	2891118		2203	4300	6503	SO:0001583	missense	84034	exon4			CATGGAGGGCATG	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.993G>T	chr18.hg19:g.2891118G>T	ENSP00000254528:p.Glu331Asp	88.0	0.0		78.0	5.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.915026	0.33815	.	.	ENSG00000132205	ENST00000254528	T	0.32753	1.44	5.09	0.0109	0.14085	.	0.078107	0.52532	D	0.000066	T	0.24275	0.0588	M	0.61703	1.905	0.29809	N	0.831758	B	0.27882	0.192	B	0.29176	0.099	T	0.16453	-1.0402	10	0.21540	T	0.41	-40.7192	5.6585	0.17656	0.4833:0.0:0.3862:0.1306	.	331	Q9BXX0	EMIL2_HUMAN	D	331	ENSP00000254528:E331D	ENSP00000254528:E331D	E	+	3	2	EMILIN2	2881118	0.734000	0.28142	0.987000	0.45799	0.989000	0.77384	-0.068000	0.11561	0.002000	0.14630	0.557000	0.71058	GAG	.	.		0.552	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
PTPRM	5797	hgsc.bcm.edu	37	18	8378411	8378411	+	Splice_Site	SNP	G	G	T	rs202020478		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:8378411G>T	ENST00000332175.8	+	25	4609	c.3572G>T	c.(3571-3573)cGg>cTg	p.R1191L	PTPRM_ENST00000580170.1_Splice_Site_p.R1204L|PTPRM_ENST00000400053.4_Splice_Site_p.R1129L|PTPRM_ENST00000444013.1_Splice_Site_p.R978L|PTPRM_ENST00000400060.4_Splice_Site_p.R1205L	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1191	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GAGGAATTCCGGGTAAGTGAT	0.498																																					p.R1204L		Atlas-SNP	.											.	PTPRM	185	.	0			c.G3611T						.						116.0	97.0	103.0					18																	8378411		2203	4300	6503	SO:0001630	splice_region_variant	5797	exon27			AATTCCGGGTAAG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3573+1G>T	chr18.hg19:g.8378411G>T		156.0	0.0		87.0	4.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.455861	0.84209	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.7	4.82	0.62117	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.058926	0.64402	D	0.000004	T	0.21186	0.0510	N	0.11673	0.155	0.80722	D	1	B;B;B	0.19817	0.006;0.039;0.039	B;B;B	0.22880	0.016;0.042;0.042	T	0.04203	-1.0969	10	0.72032	D	0.01	.	16.6777	0.85283	0.0:0.1298:0.8702:0.0	.	978;1204;1191	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	L	1191;1205;1129;978	ENSP00000331418:R1191L;ENSP00000382933:R1205L;ENSP00000382927:R1129L;ENSP00000387608:R978L	ENSP00000331418:R1191L	R	+	2	0	PTPRM	8368411	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.812000	0.75226	1.380000	0.46344	0.591000	0.81541	CGG	.	G|0.999;A|0.001		0.498	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Missense_Mutation
PPP4R1	9989	hgsc.bcm.edu	37	18	9557375	9557375	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:9557375T>C	ENST00000400556.3	-	15	2107	c.2034A>G	c.(2032-2034)aaA>aaG	p.K678K	PPP4R1_ENST00000400555.3_Silent_p.K661K	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	678					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						TTCGTCGAACTTTCCACTGCA	0.358																																					p.K678K	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.A2034G						.						109.0	103.0	105.0					18																	9557375		1860	4103	5963	SO:0001819	synonymous_variant	9989	exon15			TCGAACTTTCCAC	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2034A>G	chr18.hg19:g.9557375T>C		94.0	0.0		78.0	4.0	NM_001042388	Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.		0.358	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
MC2R	4158	hgsc.bcm.edu	37	18	13884772	13884772	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:13884772G>T	ENST00000327606.3	-	2	926	c.746C>A	c.(745-747)cCc>cAc	p.P249H		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	249					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	GGCGCAGTAGGGGTTACTTGG	0.537																																					p.P249H	Colon(141;1584 1782 35999 48227 48692)	Atlas-SNP	.											.	MC2R	78	.	0			c.C746A						.						88.0	80.0	82.0					18																	13884772		2203	4300	6503	SO:0001583	missense	4158	exon2			CAGTAGGGGTTAC		CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"""GPCR / Class A : Melanocortin receptors"""	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.746C>A	chr18.hg19:g.13884772G>T	ENSP00000333821:p.Pro249His	171.0	0.0		94.0	4.0	NM_000529	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	hg19	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.071346	0.76301	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T	0.71579	-0.58	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86686	0.5992	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88941	0.3380	10	0.72032	D	0.01	.	18.6835	0.91556	0.0:0.0:1.0:0.0	.	249	Q01718	ACTHR_HUMAN	H	249	ENSP00000333821:P249H	ENSP00000333821:P249H	P	-	2	0	MC2R	13874772	1.000000	0.71417	0.560000	0.28344	0.652000	0.38707	7.252000	0.78309	2.411000	0.81874	0.655000	0.94253	CCC	.	.		0.537	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2		
ZNF519	162655	hgsc.bcm.edu	37	18	14105088	14105088	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:14105088C>A	ENST00000590202.1	-	3	1603	c.1451G>T	c.(1450-1452)gGa>gTa	p.G484V	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	484					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G484V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						GAATTTCTCTCCAGTATGGAC	0.398																																					p.G484V		Atlas-SNP	.											ZNF519,NS,carcinoma,0,1	ZNF519	53	.	1	Substitution - Missense(1)	lung(1)	c.G1451T						.						59.0	61.0	61.0					18																	14105088		2203	4298	6501	SO:0001583	missense	162655	exon3			TTCTCTCCAGTAT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1451G>T	chr18.hg19:g.14105088C>A	ENSP00000464872:p.Gly484Val	78.0	0.0		75.0	3.0	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	hg19	CCDS32797.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223679	0.39300	.	.	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67126	0.2860	M	0.66439	2.03	0.58432	D	0.999994	D	0.76494	0.999	D	0.67548	0.952	T	0.66795	-0.5833	8	0.66056	D	0.02	.	7.2226	0.25997	0.0:0.9999:0.0:1.0E-4	.	484	Q8TB69	ZN519_HUMAN	V	484	.	ENSP00000307908:G484V	G	-	2	0	ZNF519	14095088	0.370000	0.25047	0.075000	0.20258	0.293000	0.27360	2.033000	0.41136	0.661000	0.30985	0.089000	0.15464	GGA	.	.		0.398	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
GREB1L	80000	hgsc.bcm.edu	37	18	19079688	19079688	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:19079688A>G	ENST00000580732.2	+	22	3772		c.e22-1		GREB1L_ENST00000269218.6_Splice_Site|GREB1L_ENST00000400483.4_Splice_Site|GREB1L_ENST00000424526.1_Splice_Site			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like							integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						GTTCTCTCACAGGTTCCATCA	0.567																																					.		Atlas-SNP	.											.	GREB1L	69	.	0			c.3392-2A>G						.						50.0	46.0	47.0					18																	19079688		692	1591	2283	SO:0001630	splice_region_variant	80000	exon22			TCTCACAGGTTCC	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.3392-1A>G	chr18.hg19:g.19079688A>G		77.0	0.0		67.0	4.0	NM_001142966	A4QN17|Q9H8F1	Splice_Site	SNP	ENST00000580732.2	hg19	CCDS45836.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.540024	0.65085	.	.	ENSG00000141449	ENST00000424526;ENST00000269218	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1663	0.65477	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GREB1L	17333686	1.000000	0.71417	0.998000	0.56505	0.785000	0.44390	8.285000	0.89914	1.937000	0.56155	0.459000	0.35465	.	.	.		0.567	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	Intron
NPC1	4864	hgsc.bcm.edu	37	18	21120466	21120466	+	Silent	SNP	G	G	T	rs542171272		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:21120466G>T	ENST00000269228.5	-	17	3104	c.2550C>A	c.(2548-2550)atC>atA	p.I850I	NPC1_ENST00000412552.2_Silent_p.I532I|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	850					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCAGGACTGCGATGCTGAATG	0.348																																					p.I850I		Atlas-SNP	.											.	NPC1	114	.	0			c.C2550A						.						96.0	88.0	90.0					18																	21120466		2203	4300	6503	SO:0001819	synonymous_variant	4864	exon17			GACTGCGATGCTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2550C>A	chr18.hg19:g.21120466G>T		114.0	0.0		69.0	4.0	NM_000271	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	hg19	CCDS11878.1																																																																																			.	.		0.348	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
ZNF521	25925	hgsc.bcm.edu	37	18	22804712	22804712	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:22804712C>A	ENST00000361524.3	-	4	3318	c.3170G>T	c.(3169-3171)cGg>cTg	p.R1057L	ZNF521_ENST00000538137.2_Missense_Mutation_p.R1057L|ZNF521_ENST00000584787.1_Missense_Mutation_p.R837L|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1057					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GTGCTGGCCCCGCCCTGTGGT	0.498			T	PAX5	ALL																																p.R1057L		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,NS,carcinoma,0,1	ZNF521	269	.	0			c.G3170T						.						72.0	58.0	63.0					18																	22804712		2203	4300	6503	SO:0001583	missense	25925	exon4			TGGCCCCGCCCTG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3170G>T	chr18.hg19:g.22804712C>A	ENSP00000354794:p.Arg1057Leu	61.0	0.0		41.0	3.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847957	0.32699	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.08720	3.06;3.07	5.98	5.98	0.97165	.	0.115877	0.64402	D	0.000008	T	0.06645	0.0170	N	0.08118	0	0.40933	D	0.984402	P	0.43094	0.799	B	0.43331	0.416	T	0.37641	-0.9697	10	0.56958	D	0.05	-26.7352	13.6254	0.62161	0.0:0.9297:0.0:0.0702	.	1057	Q96K83	ZN521_HUMAN	L	1057;1091;1057	ENSP00000354794:R1057L;ENSP00000382352:R1057L	ENSP00000354794:R1057L	R	-	2	0	ZNF521	21058710	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.785000	0.68998	2.835000	0.97688	0.650000	0.86243	CGG	.	.		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ZNF521	25925	hgsc.bcm.edu	37	18	22806400	22806400	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:22806400T>C	ENST00000361524.3	-	4	1630	c.1482A>G	c.(1480-1482)gaA>gaG	p.E494E	ZNF521_ENST00000538137.2_Silent_p.E494E|ZNF521_ENST00000584787.1_Silent_p.E274E|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	494					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ATCGGATGTGTTCCTGAAGAG	0.463			T	PAX5	ALL																																p.E494E		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,caecum,carcinoma,-1,1	ZNF521	269	.	0			c.A1482G						.						101.0	100.0	101.0					18																	22806400		2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			GATGTGTTCCTGA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.1482A>G	chr18.hg19:g.22806400T>C		183.0	0.0		135.0	6.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	hg19	CCDS32806.1																																																																																			.	.		0.463	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
CDH2	1000	hgsc.bcm.edu	37	18	25589802	25589802	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:25589802C>A	ENST00000269141.3	-	5	1004	c.581G>T	c.(580-582)cGg>cTg	p.R194L	CDH2_ENST00000399380.3_Missense_Mutation_p.R163L	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	194	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TACACTGTACCGCAGTGAAAG	0.478																																					p.R194L		Atlas-SNP	.											.	CDH2	194	.	0			c.G581T						.						93.0	85.0	88.0					18																	25589802		2203	4300	6503	SO:0001583	missense	1000	exon5			CTGTACCGCAGTG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.581G>T	chr18.hg19:g.25589802C>A	ENSP00000269141:p.Arg194Leu	85.0	0.0		61.0	4.0	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	hg19	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	34	5.308741	0.95629	.	.	ENSG00000170558	ENST00000269141;ENST00000399380;ENST00000418492;ENST00000430882	T;T;T;T	0.61040	0.59;0.59;0.59;0.14	5.77	5.77	0.91146	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.75539	0.3863	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.949;0.999	T	0.69993	-0.4994	10	0.32370	T	0.25	.	20.3559	0.98840	0.0:1.0:0.0:0.0	.	163;194	A8MWK3;P19022	.;CADH2_HUMAN	L	194;163;143;109	ENSP00000269141:R194L;ENSP00000382312:R163L;ENSP00000411360:R143L;ENSP00000412120:R109L	ENSP00000269141:R194L	R	-	2	0	CDH2	23843800	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.438000	0.80431	2.890000	0.99128	0.585000	0.79938	CGG	.	.		0.478	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
ASXL3	80816	hgsc.bcm.edu	37	18	31326158	31326158	+	Missense_Mutation	SNP	G	G	T	rs117661115	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:31326158G>T	ENST00000269197.5	+	12	6346	c.6346G>T	c.(6346-6348)Gcg>Tcg	p.A2116S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2116					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAAAGCATTCGCGCTAAAAAG	0.413																																					p.A2116S		Atlas-SNP	.											.	ASXL3	405	.	0			c.G6346T						.						76.0	78.0	77.0					18																	31326158		1860	4109	5969	SO:0001583	missense	80816	exon12			GCATTCGCGCTAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6346G>T	chr18.hg19:g.31326158G>T	ENSP00000269197:p.Ala2116Ser	114.0	0.0		96.0	4.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712149	0.48517	.	.	ENSG00000141431	ENST00000269197	T	0.18502	2.21	6.04	6.04	0.98038	.	.	.	.	.	T	0.16214	0.0390	N	0.19112	0.55	0.37404	D	0.91298	P	0.51653	0.947	B	0.42916	0.402	T	0.01940	-1.1243	9	0.49607	T	0.09	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	2116	Q9C0F0	ASXL3_HUMAN	S	2116	ENSP00000269197:A2116S	ENSP00000269197:A2116S	A	+	1	0	ASXL3	29580156	1.000000	0.71417	0.993000	0.49108	0.933000	0.57130	3.659000	0.54489	2.873000	0.98535	0.563000	0.77884	GCG	.	G|0.998;A|0.002		0.413	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
NOL4	8715	hgsc.bcm.edu	37	18	31523052	31523052	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:31523052T>C	ENST00000261592.5	-	9	1816	c.1519A>G	c.(1519-1521)Agg>Ggg	p.R507G	NOL4_ENST00000589544.1_Intron|NOL4_ENST00000535384.1_Missense_Mutation_p.R222G|NOL4_ENST00000538587.1_Missense_Mutation_p.R433G|NOL4_ENST00000269185.4_Intron|NOL4_ENST00000535475.1_Missense_Mutation_p.R288G	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	507						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						AGACGCATCCTCTTGGCGGCA	0.433																																					p.R507G		Atlas-SNP	.											NOL4,NS,carcinoma,0,1	NOL4	139	.	0			c.A1519G						.						105.0	95.0	98.0					18																	31523052		2203	4299	6502	SO:0001583	missense	8715	exon9			GCATCCTCTTGGC	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"""cancer/testis antigen 125"""	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1519A>G	chr18.hg19:g.31523052T>C	ENSP00000261592:p.Arg507Gly	89.0	0.0		65.0	4.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	T	18.13	3.554596	0.65425	.	.	ENSG00000101746	ENST00000261592;ENST00000399171;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.87	3.36	0.38483	.	0.000000	0.85682	D	0.000000	T	0.76471	0.3992	M	0.71206	2.165	0.42947	D	0.994361	D;D;D;D;D;P	0.89917	0.989;1.0;1.0;0.997;1.0;0.51	D;D;D;D;D;B	0.87578	0.985;0.998;0.998;0.971;0.998;0.419	T	0.79070	-0.1954	9	0.62326	D	0.03	-18.6544	13.3487	0.60589	0.0:0.0:0.3698:0.6302	.	192;222;433;507;222;288	F8W825;B7Z3Z7;B4DSQ0;O94818;F5H1E3;B3KRF4	.;.;.;NOL4_HUMAN;.;.	G	507;192;222;288;433	.	ENSP00000261592:R507G	R	-	1	2	NOL4	29777050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.415000	0.52700	1.025000	0.39708	0.528000	0.53228	AGG	.	.		0.433	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787	
MOCOS	55034	hgsc.bcm.edu	37	18	33775243	33775243	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:33775243G>T	ENST00000261326.5	+	2	187	c.166G>T	c.(166-168)Ggt>Tgt	p.G56C		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TGACCATGCAGGTGCCACCTT	0.388																																					p.G56C		Atlas-SNP	.											.	MOCOS	84	.	0			c.G166T						.						149.0	152.0	151.0					18																	33775243		2203	4300	6503	SO:0001583	missense	55034	exon2			CATGCAGGTGCCA	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.166G>T	chr18.hg19:g.33775243G>T	ENSP00000261326:p.Gly56Cys	92.0	0.0		99.0	4.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457306	0.84317	.	.	ENSG00000075643	ENST00000261326	D	0.88818	-2.43	5.41	5.41	0.78517	Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.068985	0.64402	D	0.000014	D	0.96071	0.8720	H	0.95079	3.62	0.52501	D	0.999959	D	0.89917	1.0	D	0.97110	1.0	D	0.97014	0.9738	10	0.87932	D	0	-12.8987	14.718	0.69284	0.0:0.0:1.0:0.0	.	56	Q96EN8	MOCOS_HUMAN	C	56	ENSP00000261326:G56C	ENSP00000261326:G56C	G	+	1	0	MOCOS	32029241	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.116000	0.77119	2.538000	0.85594	0.563000	0.77884	GGT	.	.		0.388	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44190747	44190747	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:44190747G>A	ENST00000441551.2	-	6	750	c.751C>T	c.(751-753)Ctg>Ttg	p.L251L	LOXHD1_ENST00000536736.1_Silent_p.L251L			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	826	PLAT 2. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						ACCTGGGACAGGAACCAACCT	0.552																																					p.L251L		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C751T						.						108.0	125.0	120.0					18																	44190747		692	1591	2283	SO:0001819	synonymous_variant	125336	exon6			GGGACAGGAACCA	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000441551.2:c.751C>T	chr18.hg19:g.44190747G>A		83.0	0.0		79.0	4.0	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000441551.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.586	0.476472	0.12521	.	.	ENSG00000167210	ENST00000441551	.	.	.	5.7	4.82	0.62117	.	.	.	.	.	T	0.70343	0.3213	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69698	-0.5075	4	.	.	.	.	14.5374	0.67971	0.0705:0.0:0.9295:0.0	.	.	.	.	L	231	.	.	P	-	2	0	LOXHD1	42444745	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	6.318000	0.72866	1.403000	0.46800	0.467000	0.42956	CCT	.	.		0.552	LOXHD1-013	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000446054.1	NM_144612	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566520	45566520	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:45566520C>A	ENST00000588982.1	-	3	1460	c.959G>T	c.(958-960)gGg>gTg	p.G320V	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.G320V|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.G320V|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.G320V|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.G320V			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	320	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TCCCAGAGGCCCCCCCGGCAG	0.627																																					p.G320V		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.G959T						.																																			SO:0001583	missense	201501	exon2			AGAGGCCCCCCCG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.959G>T	chr18.hg19:g.45566520C>A	ENSP00000468782:p.Gly320Val	58.0	0.0		57.0	4.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	C	7.703	0.693455	0.15039	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.11604	2.76;2.76	5.34	5.34	0.76211	.	0.286197	0.37261	N	0.002164	T	0.07908	0.0198	N	0.14661	0.345	0.47374	D	0.999406	B;B	0.30068	0.267;0.267	B;B	0.27380	0.079;0.079	T	0.32161	-0.9917	10	0.44086	T	0.13	.	15.6117	0.76727	0.0:0.8525:0.1475:0.0	.	320;320	B2RG49;A1YPR0	.;ZBT7C_HUMAN	V	320	ENSP00000439781:G320V;ENSP00000328732:G320V	ENSP00000328732:G320V	G	-	2	0	ZBTB7C	43820518	0.997000	0.39634	0.998000	0.56505	0.278000	0.26855	3.569000	0.53827	2.491000	0.84063	0.561000	0.74099	GGG	.	.		0.627	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
TCF4	6925	hgsc.bcm.edu	37	18	52895541	52895541	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:52895541T>C	ENST00000356073.4	-	19	2530	c.1919A>G	c.(1918-1920)aAg>aGg	p.K640R	TCF4_ENST00000566279.1_Missense_Mutation_p.K584R|TCF4_ENST00000564228.1_Missense_Mutation_p.K569R|TCF4_ENST00000543082.1_Missense_Mutation_p.K598R|TCF4_ENST00000561831.3_Missense_Mutation_p.K480R|TCF4_ENST00000544241.2_Missense_Mutation_p.K573R|TCF4_ENST00000540999.1_Missense_Mutation_p.K616R|TCF4_ENST00000537856.3_Missense_Mutation_p.K510R|TCF4_ENST00000567880.1_Missense_Mutation_p.K580R|TCF4_ENST00000568740.1_Missense_Mutation_p.K615R|TCF4_ENST00000537578.1_Missense_Mutation_p.K620R|TCF4_ENST00000568673.1_Missense_Mutation_p.K620R|TCF4_ENST00000570177.2_Missense_Mutation_p.K510R|TCF4_ENST00000566286.1_Missense_Mutation_p.K637R|TCF4_ENST00000564403.2_Missense_Mutation_p.K650R|TCF4_ENST00000457482.3_Missense_Mutation_p.K484R|TCF4_ENST00000354452.3_Missense_Mutation_p.K644R|TCF4_ENST00000561992.1_Missense_Mutation_p.K510R|TCF4_ENST00000564999.1_Missense_Mutation_p.K640R|TCF4_ENST00000570287.2_Missense_Mutation_p.K480R|TCF4_ENST00000565018.2_Missense_Mutation_p.K644R|TCF4_ENST00000398339.1_Missense_Mutation_p.K746R	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	640	Class A specific domain.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|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)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TGAGGACACCTTCTCTTCCTC	0.507																																					p.K746R		Atlas-SNP	.											.	TCF4	178	.	0			c.A2237G						.						130.0	122.0	125.0					18																	52895541		2203	4300	6503	SO:0001583	missense	6925	exon20			GACACCTTCTCTT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1919A>G	chr18.hg19:g.52895541T>C	ENSP00000348374:p.Lys640Arg	62.0	0.0		44.0	4.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	T	33	5.257190	0.95368	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.27557	1.84;1.66;1.86;1.86;1.88;1.86;1.88;1.67;1.81	5.72	5.72	0.89469	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.57636	0.2067	M	0.79011	2.435	0.58432	D	0.999991	D;D;D;D;P;D;D;D;D	0.89917	1.0;1.0;1.0;0.996;0.956;0.999;0.999;0.974;0.997	D;D;D;D;P;D;D;D;D	0.91635	0.999;0.995;0.997;0.979;0.899;0.989;0.997;0.953;0.988	T	0.62671	-0.6805	10	0.87932	D	0	-16.954	14.991	0.71387	0.0:0.0:0.0:1.0	.	620;644;480;746;640;598;573;484;637	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	R	644;484;640;598;616;620;573;510;746	ENSP00000346440:K644R;ENSP00000409447:K484R;ENSP00000348374:K640R;ENSP00000439656:K598R;ENSP00000445202:K616R;ENSP00000440731:K620R;ENSP00000441562:K573R;ENSP00000439827:K510R;ENSP00000381382:K746R	ENSP00000346440:K644R	K	-	2	0	TCF4	51046539	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.997000	0.88414	2.172000	0.68678	0.528000	0.53228	AAG	.	.		0.507	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
NEDD4L	23327	hgsc.bcm.edu	37	18	56002763	56002763	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:56002763A>G	ENST00000400345.3	+	13	1402	c.1119A>G	c.(1117-1119)gaA>gaG	p.E373E	NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000431212.2_Silent_p.E252E|NEDD4L_ENST00000256832.7_Intron|NEDD4L_ENST00000357895.5_Silent_p.E365E|NEDD4L_ENST00000456986.1_Silent_p.E252E|NEDD4L_ENST00000456173.2_Intron|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000586263.1_Intron|NEDD4L_ENST00000435432.2_Intron|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000382850.4_Intron	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	373					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						GTGGTGAGGAACCAACGGTAA	0.448																																					p.E373E		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A1119G						.						121.0	110.0	113.0					18																	56002763		1568	3582	5150	SO:0001819	synonymous_variant	23327	exon13			TGAGGAACCAACG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1119A>G	chr18.hg19:g.56002763A>G		110.0	0.0		115.0	5.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.448	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1		
PMAIP1	5366	hgsc.bcm.edu	37	18	57569926	57569926	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:57569926C>T	ENST00000316660.6	+	2	336	c.106C>T	c.(106-108)Ctg>Ttg	p.L36L	PMAIP1_ENST00000269518.9_Missense_Mutation_p.T86I	NM_021127.2	NP_066950.1	Q13794	APR_HUMAN	phorbol-12-myristate-13-acetate-induced protein 1	36					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|defense response to virus (GO:0051607)|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)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neuron apoptotic process (GO:0043525)|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 release of cytochrome c from mitochondria (GO:0090200)|proteasomal protein catabolic process (GO:0010498)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to dsRNA (GO:0043331)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)	1		Colorectal(73;0.0946)				TGGAGACAAACTGAACTTCCG	0.428																																					p.L36L		Atlas-SNP	.											.	PMAIP1	1	.	0			c.C106T						.						102.0	103.0	103.0					18																	57569926		2203	4300	6503	SO:0001819	synonymous_variant	5366	exon2			GACAAACTGAACT	D90070	CCDS11975.1	18q21.32	2014-03-07			ENSG00000141682	ENSG00000141682			9108	protein-coding gene	gene with protein product		604959				2398525, 12879012	Standard	NM_021127		Approved	APR, NOXA	uc002lic.2	Q13794	OTTHUMG00000132765	ENST00000316660.6:c.106C>T	chr18.hg19:g.57569926C>T		82.0	0.0		79.0	4.0	NM_021127	B2R4T7|Q8N589	Silent	SNP	ENST00000316660.6	hg19	CCDS11975.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.235159	0.22626	.	.	ENSG00000141682	ENST00000269518	.	.	.	5.0	-0.0021	0.14031	.	0.495687	0.15116	N	0.279646	T	0.20901	0.0503	.	.	.	0.21984	N	0.999437	P	0.37955	0.612	B	0.35470	0.203	T	0.19679	-1.0298	8	0.87932	D	0	.	0.7495	0.00988	0.166:0.3741:0.1738:0.286	.	86	Q8N589	.	I	86	.	ENSP00000269518:T86I	T	+	2	0	PMAIP1	55720906	0.920000	0.31207	0.971000	0.41717	0.659000	0.38960	0.010000	0.13242	0.059000	0.16252	0.655000	0.94253	ACT	.	.		0.428	PMAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256137.1	NM_021127	
KDSR	2531	hgsc.bcm.edu	37	18	61034244	61034244	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:61034244C>T	ENST00000406396.3	-	1	499	c.108G>A	c.(106-108)gtG>gtA	p.V36V	RP11-635N19.1_ENST00000589905.1_RNA|KDSR_ENST00000326575.5_Splice_Site_p.V36V	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	36					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)			endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						GGCCACTCACCACCACATGCG	0.701																																					p.V36V		Atlas-SNP	.											.	KDSR	17	.	0			c.G108A						.						17.0	21.0	20.0					18																	61034244		2191	4287	6478	SO:0001630	splice_region_variant	2531	exon1			ACTCACCACCACA		CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	4021	protein-coding gene	gene with protein product	"""3-dehydrosphinganine reductase"", ""short chain dehydrogenase/reductase family 35C, member 1"""	136440	"""follicular lymphoma variant translocation 1"""	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.108+1G>A	chr18.hg19:g.61034244C>T		226.0	0.0		134.0	6.0	NM_002035	B2R5Y1|B4DMX0	Silent	SNP	ENST00000406396.3	hg19	CCDS11982.1																																																																																			.	.		0.701	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2		Silent
TSHZ1	10194	hgsc.bcm.edu	37	18	72999514	72999514	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:72999514C>A	ENST00000580243.1	+	2	2500	c.2152C>A	c.(2152-2154)Cct>Act	p.P718T	TSHZ1_ENST00000322038.5_Missense_Mutation_p.P673T			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	718					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		TGGCACAGAGCCTCTCAAAGC	0.577																																					p.P673T		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C2017A						.						123.0	103.0	109.0					18																	72999514		2203	4300	6503	SO:0001583	missense	10194	exon2			ACAGAGCCTCTCA	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2152C>A	chr18.hg19:g.72999514C>A	ENSP00000464391:p.Pro718Thr	85.0	0.0		64.0	4.0	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	hg19		.	.	.	.	.	.	.	.	.	.	C	3.444	-0.113403	0.06881	.	.	ENSG00000179981	ENST00000322038	T	0.38560	1.13	5.12	4.21	0.49690	.	0.183175	0.48286	N	0.000185	T	0.33933	0.0880	L	0.54323	1.7	0.36873	D	0.88902	B	0.22346	0.068	B	0.13407	0.009	T	0.30416	-0.9979	10	0.30078	T	0.28	-11.3758	8.1816	0.31313	0.158:0.7633:0.0:0.0786	.	718	Q6ZSZ6	TSH1_HUMAN	T	673	ENSP00000323584:P673T	ENSP00000323584:P673T	P	+	1	0	TSHZ1	71128502	1.000000	0.71417	0.832000	0.32986	0.592000	0.36648	1.284000	0.33249	2.385000	0.81259	0.561000	0.74099	CCT	.	.		0.577	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
MEX3D	399664	hgsc.bcm.edu	37	19	1556545	1556545	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1556545C>T	ENST00000402693.4	-	2	972	c.973G>A	c.(973-975)Gag>Aag	p.E325K	MEX3D_ENST00000388824.6_Missense_Mutation_p.E325K|AC027307.1_ENST00000410788.1_RNA|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D	325	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCACGTTCTCGGGCATCCCA	0.697																																					p.E325K		Atlas-SNP	.											.	MEX3D	11	.	0			c.G973A						.						22.0	23.0	22.0					19																	1556545		2197	4296	6493	SO:0001583	missense	399664	exon2			CGTTCTCGGGCAT	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	16734	protein-coding gene	gene with protein product	"""bcl-2 ARE RNA binding protein"""	611009	"""ring finger and KH domain containing 1"", ""mex-3 homolog D (C. elegans)"""	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.973G>A	chr19.hg19:g.1556545C>T	ENSP00000384398:p.Glu325Lys	75.0	0.0		89.0	4.0	NM_203304	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448362	0.84101	.	.	ENSG00000181588	ENST00000402693;ENST00000388824	T;T	0.35973	1.28;1.28	4.61	4.61	0.57282	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.75264	2.295	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	T	0.60954	-0.7160	10	0.41790	T	0.15	-28.4273	16.4135	0.83727	0.0:1.0:0.0:0.0	.	325	Q86XN8	MEX3D_HUMAN	K	325	ENSP00000384398:E325K;ENSP00000373476:E325K	ENSP00000373476:E325K	E	-	1	0	MEX3D	1507545	1.000000	0.71417	0.999000	0.59377	0.349000	0.29174	7.445000	0.80570	2.120000	0.65058	0.313000	0.20887	GAG	.	.		0.697	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304	
TCF3	6929	hgsc.bcm.edu	37	19	1611812	1611812	+	Missense_Mutation	SNP	C	C	A	rs538013937		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1611812C>A	ENST00000262965.5	-	19	2203	c.1859G>T	c.(1858-1860)cGg>cTg	p.R620L	TCF3_ENST00000453954.2_Missense_Mutation_p.R532L|TCF3_ENST00000395423.3_Missense_Mutation_p.R624L|TCF3_ENST00000344749.5_Missense_Mutation_p.R617L|TCF3_ENST00000588136.1_Missense_Mutation_p.R617L	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCTTCTCGCCGTTTCAAACA	0.617			T	"""PBX1, HLF, TFPT"""	pre B-ALL																																p.R620L		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G1859T						.						77.0	61.0	66.0					19																	1611812		2203	4300	6503	SO:0001583	missense	6929	exon19			TCTCGCCGTTTCA	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.1859G>T	chr19.hg19:g.1611812C>A	ENSP00000262965:p.Arg620Leu	168.0	0.0		122.0	5.0	NM_003200	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	hg19	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307236	0.81247	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.58652	1.76;1.63;0.32	4.69	4.69	0.59074	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.77538	0.4145	M	0.79693	2.465	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;1.0	D;D;D;D	0.91635	0.999;0.987;0.999;0.998	T	0.81658	-0.0833	10	0.87932	D	0	-13.7286	16.981	0.86327	0.0:1.0:0.0:0.0	.	617;620;624;557	P15923-2;P15923;Q2TB39;Q6PJU3	.;TFE2_HUMAN;.;.	L	620;617;617;624	ENSP00000262965:R620L;ENSP00000344375:R617L;ENSP00000378813:R624L	ENSP00000262965:R620L	R	-	2	0	TCF3	1562812	1.000000	0.71417	0.863000	0.33907	0.418000	0.31294	7.631000	0.83237	2.309000	0.77851	0.561000	0.74099	CGG	.	.		0.617	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
ADAT3	113179	hgsc.bcm.edu	37	19	1912939	1912939	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1912939A>G	ENST00000602400.1	+	2	1073	c.845A>G	c.(844-846)tAc>tGc	p.Y282C	SCAMP4_ENST00000414057.2_Intron|ADAT3_ENST00000329478.2_Missense_Mutation_p.Y298C|SCAMP4_ENST00000316097.8_Intron|SCAMP4_ENST00000409472.1_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	282					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCACTGGCTACGACCTGTAC	0.721																																					p.Y298C		Atlas-SNP	.											.	ADAT3	15	.	0			c.A893G						.						56.0	52.0	53.0					19																	1912939		2200	4294	6494	SO:0001583	missense	113179	exon2			CTGGCTACGACCT	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"""tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"""	615302	"""adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"""			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.845A>G	chr19.hg19:g.1912939A>G	ENSP00000473571:p.Tyr282Cys	53.0	0.0		87.0	4.0	NM_138422		Missense_Mutation	SNP	ENST00000602400.1	hg19		.	.	.	.	.	.	.	.	.	.	a	12.67	2.006145	0.35415	.	.	ENSG00000213638	ENST00000329478	.	.	.	5.04	5.04	0.67666	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.138667	0.49916	D	0.000125	T	0.46502	0.1396	N	0.02368	-0.58	0.50813	D	0.999892	D	0.89917	1.0	D	0.77004	0.989	T	0.58691	-0.7592	9	0.40728	T	0.16	-22.3745	12.7244	0.57162	1.0:0.0:0.0:0.0	.	282	Q96EY9	ADAT3_HUMAN	C	282	.	ENSP00000332448:Y282C	Y	+	2	0	ADAT3	1863939	0.997000	0.39634	0.995000	0.50966	0.452000	0.32318	3.100000	0.50275	1.897000	0.54924	0.448000	0.29417	TAC	.	.		0.721	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422	
MOB3A	126308	hgsc.bcm.edu	37	19	2076903	2076903	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:2076903C>T	ENST00000357066.3	-	4	910	c.531G>A	c.(529-531)atG>atA	p.M177I	MOB3A_ENST00000592280.1_Missense_Mutation_p.M177I|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	177						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCTCGGAGCCCATCTGCGCGA	0.587																																					p.M177I		Atlas-SNP	.											.	.	.	.	0			c.G531A						.						89.0	74.0	79.0					19																	2076903		2203	4300	6503	SO:0001583	missense	126308	exon4			GGAGCCCATCTGC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.531G>A	chr19.hg19:g.2076903C>T	ENSP00000349575:p.Met177Ile	99.0	0.0		147.0	6.0	NM_130807	B3KTF1|O75249|Q8TF69	Missense_Mutation	SNP	ENST00000357066.3	hg19	CCDS12081.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.918636	0.52546	.	.	ENSG00000172081	ENST00000357066	.	.	.	3.74	3.74	0.42951	.	0.131387	0.64402	D	0.000002	T	0.24851	0.0603	N	0.01277	-0.915	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08006	-1.0743	9	0.33940	T	0.23	-37.9465	14.2648	0.66110	0.0:1.0:0.0:0.0	.	177	Q96BX8	MOB3A_HUMAN	I	177	.	ENSP00000349575:M177I	M	-	3	0	MOBKL2A	2027903	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.608000	0.67654	1.937000	0.56155	0.491000	0.48974	ATG	.	.		0.587	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2413833	2413833	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:2413833T>C	ENST00000332578.3	+	9	1288	c.1288T>C	c.(1288-1290)Tgg>Cgg	p.W430R		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	430	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTACGTGACTGGATCCTGGA	0.672																																					p.W430R		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.T1288C						.						40.0	42.0	41.0					19																	2413833		2203	4300	6503	SO:0001583	missense	360200	exon9			CGTGACTGGATCC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1288T>C	chr19.hg19:g.2413833T>C	ENSP00000330264:p.Trp430Arg	116.0	0.0		96.0	4.0	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	hg19	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564621	0.45694	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	T	0.78707	-1.2	4.04	4.04	0.47022	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.313142	0.23424	N	0.048337	D	0.92077	0.7489	H	0.98559	4.265	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93880	0.7170	10	0.87932	D	0	.	11.8763	0.52550	0.0:0.0:0.0:1.0	.	430;464	Q7Z410;E7EMP4	TMPS9_HUMAN;.	R	464;430	ENSP00000330264:W430R	ENSP00000330264:W430R	W	+	1	0	TMPRSS9	2364833	1.000000	0.71417	0.950000	0.38849	0.070000	0.16714	7.930000	0.87610	1.493000	0.48517	0.454000	0.30748	TGG	.	.		0.672	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
UBXN6	80700	hgsc.bcm.edu	37	19	4448329	4448329	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4448329C>A	ENST00000301281.6	-	5	649	c.525G>T	c.(523-525)gtG>gtT	p.V175V	MIR4746_ENST00000579802.1_RNA|CTB-50L17.7_ENST00000588798.1_RNA|UBXN6_ENST00000394765.3_Silent_p.V122V	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	175	PUB.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						CAATGGTGTCCACACCCAGCT	0.637																																					p.V175V		Atlas-SNP	.											.	UBXN6	27	.	0			c.G525T						.						117.0	87.0	97.0					19																	4448329		2202	4299	6501	SO:0001819	synonymous_variant	80700	exon5			GGTGTCCACACCC	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.525G>T	chr19.hg19:g.4448329C>A		71.0	0.0		65.0	4.0	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	hg19	CCDS12129.1																																																																																			.	.		0.637	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
DPP9	91039	hgsc.bcm.edu	37	19	4700261	4700261	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4700261T>C	ENST00000598800.1	-	11	1459	c.954A>G	c.(952-954)aaA>aaG	p.K318K	DPP9_ENST00000597849.1_Silent_p.K347K|DPP9_ENST00000594671.1_Silent_p.K318K|DPP9_ENST00000262960.9_Silent_p.K347K			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	318						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		ACTCAGCCAGTTTCAAGGCAA	0.592																																					p.K347K		Atlas-SNP	.											.	DPP9	59	.	0			c.A1041G						.						41.0	44.0	43.0					19																	4700261		1929	4138	6067	SO:0001819	synonymous_variant	91039	exon10			AGCCAGTTTCAAG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"""dipeptidylpeptidase 9"""				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.954A>G	chr19.hg19:g.4700261T>C		87.0	0.0		94.0	5.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Silent	SNP	ENST00000598800.1	hg19																																																																																				.	.		0.592	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		
FEM1A	55527	hgsc.bcm.edu	37	19	4792961	4792961	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4792961C>A	ENST00000269856.3	+	1	1234	c.1095C>A	c.(1093-1095)acC>acA	p.T365T	AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	365					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		CGCTGATCACCGACCCGGATG	0.637																																					p.T365T		Atlas-SNP	.											.	FEM1A	41	.	0			c.C1095A						.						48.0	50.0	50.0					19																	4792961		2203	4300	6503	SO:0001819	synonymous_variant	55527	exon1			GATCACCGACCCG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"""Ankyrin repeat domain containing"""	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1095C>A	chr19.hg19:g.4792961C>A		37.0	0.0		53.0	5.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.		0.637	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1		
PTPRS	5802	hgsc.bcm.edu	37	19	5208037	5208037	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:5208037T>C	ENST00000587303.1	-	36	5773	c.5674A>G	c.(5674-5676)Acg>Gcg	p.T1892A	PTPRS_ENST00000588012.1_Missense_Mutation_p.T1854A|PTPRS_ENST00000357368.4_Missense_Mutation_p.T1892A|PTPRS_ENST00000348075.2_Missense_Mutation_p.T1854A|PTPRS_ENST00000592099.1_Missense_Mutation_p.T1445A|PTPRS_ENST00000353284.2_Missense_Mutation_p.T1445A|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.T1872A|PTPRS_ENST00000372412.4_Missense_Mutation_p.T1893A			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1892	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ATGCTAAGCGTGATGAAGACG	0.617																																					p.T1892A		Atlas-SNP	.											.	PTPRS	169	.	0			c.A5674G						.						78.0	59.0	66.0					19																	5208037		2203	4300	6503	SO:0001583	missense	5802	exon37			TAAGCGTGATGAA	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.5674A>G	chr19.hg19:g.5208037T>C	ENSP00000467537:p.Thr1892Ala	63.0	0.0		52.0	4.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.685739	0.47991	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96	2.78	2.78	0.32641	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	U	0.000002	T	0.08223	0.0205	N	0.00563	-1.375	0.80722	D	1	D;B;P;B;D;D	0.76494	0.999;0.05;0.882;0.384;0.995;0.995	D;B;P;B;D;D	0.87578	0.998;0.042;0.693;0.302;0.997;0.997	T	0.54609	-0.8268	10	0.66056	D	0.02	.	10.8984	0.47036	0.0:0.0:0.0:1.0	.	1474;1445;1449;1854;1892;1487	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	A	1487;1893;1892;1892;1883;1872;1854;1474;1449;1445	ENSP00000361489:T1893A;ENSP00000349932:T1892A;ENSP00000262963:T1872A;ENSP00000269907:T1854A;ENSP00000327313:T1445A	ENSP00000262963:T1872A	T	-	1	0	PTPRS	5159037	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	4.918000	0.63376	1.147000	0.42369	0.386000	0.25728	ACG	.	.		0.617	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
PTPRS	5802	hgsc.bcm.edu	37	19	5216748	5216748	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:5216748G>A	ENST00000587303.1	-	25	4178	c.4079C>T	c.(4078-4080)cCg>cTg	p.P1360L	PTPRS_ENST00000588012.1_Intron|PTPRS_ENST00000357368.4_Missense_Mutation_p.P1360L|PTPRS_ENST00000348075.2_Intron|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000353284.2_Intron|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Intron|PTPRS_ENST00000372412.4_Missense_Mutation_p.P1361L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1360					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTGAAACCCCGGCTCCCTGAG	0.532																																					p.P1360L		Atlas-SNP	.											.	PTPRS	169	.	0			c.C4079T						.						36.0	44.0	41.0					19																	5216748		1851	4080	5931	SO:0001583	missense	5802	exon26			AACCCCGGCTCCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4079C>T	chr19.hg19:g.5216748G>A	ENSP00000467537:p.Pro1360Leu	460.0	0.0		369.0	69.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056332	0.36277	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000355322	T;T	0.52526	0.68;0.66	3.42	3.42	0.39159	.	0.947250	0.08463	U	0.942100	T	0.25419	0.0618	N	0.14661	0.345	0.80722	D	1	P;P	0.49253	0.524;0.921	B;B	0.26517	0.029;0.07	T	0.15065	-1.0450	10	0.72032	D	0.01	.	10.6094	0.45412	0.0:0.0:0.8074:0.1926	.	1360;955	Q13332;Q59FX6	PTPRS_HUMAN;.	L	955;1361;1360;1360;1351;942	ENSP00000361489:P1361L;ENSP00000349932:P1360L	ENSP00000347106:P1360L	P	-	2	0	PTPRS	5167748	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.412000	0.66392	1.614000	0.50241	0.462000	0.41574	CCG	.	.		0.532	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
MLLT1	4298	hgsc.bcm.edu	37	19	6222582	6222582	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:6222582A>G	ENST00000252674.7	-	6	823	c.660T>C	c.(658-660)cgT>cgC	p.R220R		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	220					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						TGGCCTGCTCACGCTCCAGCT	0.647			T	MLL	AL																																p.R220R		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	.	MLLT1	47	.	0			c.T660C						.						42.0	39.0	40.0					19																	6222582		2203	4300	6503	SO:0001819	synonymous_variant	4298	exon6			CTGCTCACGCTCC		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.660T>C	chr19.hg19:g.6222582A>G		58.0	0.0		71.0	5.0	NM_005934	Q14768	Silent	SNP	ENST00000252674.7	hg19	CCDS12160.1																																																																																			.	.		0.647	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934	
SLC25A23	79085	hgsc.bcm.edu	37	19	6456473	6456473	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:6456473C>T	ENST00000301454.4	-	4	547	c.441G>A	c.(439-441)ctG>ctA	p.L147L	SLC25A23_ENST00000334510.5_Silent_p.L147L|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	147	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CCACATTTTCCAGCGAATGCA	0.592																																					p.L147L		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G441A						.						167.0	125.0	139.0					19																	6456473		2203	4300	6503	SO:0001819	synonymous_variant	79085	exon4			ATTTTCCAGCGAA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.441G>A	chr19.hg19:g.6456473C>T		103.0	0.0		64.0	4.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	hg19	CCDS32882.1																																																																																			.	.		0.592	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
ZNF557	79230	hgsc.bcm.edu	37	19	7083073	7083073	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7083073G>T	ENST00000439035.2	+	8	830	c.590G>T	c.(589-591)gGg>gTg	p.G197V	ZNF557_ENST00000414706.1_Missense_Mutation_p.G204V|ZNF557_ENST00000252840.6_Missense_Mutation_p.G204V			Q8N988	ZN557_HUMAN	zinc finger protein 557	197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		ATCCACAATGGGGAGAAACCC	0.438																																					p.G204V		Atlas-SNP	.											.	ZNF557	40	.	0			c.G611T						.						62.0	70.0	67.0					19																	7083073		2192	4298	6490	SO:0001583	missense	79230	exon8			ACAATGGGGAGAA	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"""Zinc fingers, C2H2-type"", ""-"""	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.590G>T	chr19.hg19:g.7083073G>T	ENSP00000398965:p.Gly197Val	158.0	0.0		99.0	4.0	NM_001044387	Q6PEJ3|Q9BTZ1	Missense_Mutation	SNP	ENST00000439035.2	hg19	CCDS45945.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.186093	0.57909	.	.	ENSG00000130544	ENST00000252840;ENST00000414706;ENST00000439035	T;T;T	0.23552	1.9;1.9;1.9	0.786	0.786	0.18590	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48857	0.1523	M	0.85299	2.745	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.51576	-0.8688	9	0.72032	D	0.01	.	7.5376	0.27719	1.0E-4:0.0:0.9999:0.0	.	197;204	Q8N988;Q8N988-2	ZN557_HUMAN;.	V	204;204;197	ENSP00000252840:G204V;ENSP00000404065:G204V;ENSP00000398965:G197V	ENSP00000252840:G204V	G	+	2	0	ZNF557	7034073	1.000000	0.71417	0.576000	0.28549	0.361000	0.29550	5.252000	0.65445	0.757000	0.33036	0.134000	0.15878	GGG	.	.		0.438	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341	
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747234	7747234	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7747234T>C	ENST00000317378.5	+	2	282	c.95T>C	c.(94-96)cTg>cCg	p.L32P	TRAPPC5_ENST00000426877.2_Missense_Mutation_p.L32P|CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.C91R|TRAPPC5_ENST00000596148.1_Missense_Mutation_p.L32P|TRAPPC5_ENST00000595985.1_Intron	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	32					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)				NS(1)|lung(2)	3						TTCGCACTGCTGTTCTCCGAG	0.751																																					p.L32P		Atlas-SNP	.											.	TRAPPC5	11	.	0			c.T95C						.						11.0	13.0	13.0					19																	7747234		1741	3675	5416	SO:0001583	missense	126003	exon2			CACTGCTGTTCTC	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"""Trafficking protein particle complex"""	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.95T>C	chr19.hg19:g.7747234T>C	ENSP00000316990:p.Leu32Pro	83.0	0.0		45.0	4.0	NM_001042461	A8K7I6	Missense_Mutation	SNP	ENST00000317378.5	hg19	CCDS42490.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.697840	0.68386	.	.	ENSG00000181029	ENST00000317378;ENST00000426877	T;T	0.63913	-0.07;-0.07	4.09	4.09	0.47781	NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.64402	U	0.000007	D	0.83931	0.5361	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87606	0.2500	10	0.87932	D	0	-10.4913	11.0504	0.47884	0.0:0.0:0.0:1.0	.	32	Q8IUR0	TPPC5_HUMAN	P	32	ENSP00000316990:L32P;ENSP00000399025:L32P	ENSP00000316990:L32P	L	+	2	0	TRAPPC5	7653234	1.000000	0.71417	0.996000	0.52242	0.433000	0.31745	7.354000	0.79424	1.497000	0.48584	0.454000	0.30748	CTG	.	.		0.751	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961	
CLEC4M	10332	hgsc.bcm.edu	37	19	7830731	7830731	+	Missense_Mutation	SNP	G	G	A	rs76899402		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7830731G>A	ENST00000327325.5	+	4	540	c.422G>A	c.(421-423)cGg>cAg	p.R141Q	CLEC4M_ENST00000597522.1_Missense_Mutation_p.R141Q|CLEC4M_ENST00000596363.1_Missense_Mutation_p.R113Q|CLEC4M_ENST00000334806.5_Intron|CLEC4M_ENST00000248228.4_Intron|CLEC4M_ENST00000357361.2_Missense_Mutation_p.R141Q|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000595496.1_Missense_Mutation_p.R120Q|CLEC4M_ENST00000596707.1_Missense_Mutation_p.R120Q|CLEC4M_ENST00000394122.2_Missense_Mutation_p.R129Q	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	141	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.R141Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						GAGCTGACCCGGCTGAAGGCT	0.582																																					p.R141Q		Atlas-SNP	.											CLEC4M,colon,carcinoma,0,1	CLEC4M	58	.	1	Substitution - Missense(1)	large_intestine(1)	c.G422A						.						13.0	13.0	13.0					19																	7830731		1642	3266	4908	SO:0001583	missense	10332	exon4			TGACCCGGCTGAA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.422G>A	chr19.hg19:g.7830731G>A	ENSP00000316228:p.Arg141Gln	19.0	0.0		31.0	3.0	NM_001144908	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	hg19	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.920834	0.00498	.	.	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000357361;ENST00000358690	T;T;T	0.22336	1.97;1.96;1.97	0.905	-1.81	0.07882	.	.	.	.	.	T	0.07188	0.0182	N	0.04636	-0.2	0.09310	N	1	B;B;B;B;B;B;B	0.17268	0.004;0.001;0.001;0.0;0.007;0.021;0.001	B;B;B;B;B;B;B	0.10450	0.003;0.005;0.001;0.0;0.002;0.003;0.005	T	0.33059	-0.9883	9	0.07482	T	0.82	.	6.6496	0.22955	0.409:0.0:0.591:0.0	.	120;113;141;113;120;141;85	Q9H2X3-5;B4DNV9;Q9H2X3;Q9H2X3-9;Q9H2X3-7;Q9H2X3-4;Q9H2X3-10	.;.;CLC4M_HUMAN;.;.;.;.	Q	141;129;141;85	ENSP00000316228:R141Q;ENSP00000377680:R129Q;ENSP00000349924:R141Q	ENSP00000316228:R141Q	R	+	2	0	CLEC4M	7736731	0.001000	0.12720	0.004000	0.12327	0.024000	0.10985	-1.792000	0.01756	-2.527000	0.00494	-2.768000	0.00120	CGG	.	G|0.250;A|0.750		0.582	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
MAP2K7	5609	hgsc.bcm.edu	37	19	7975215	7975215	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7975215G>T	ENST00000397979.3	+	4	458	c.404G>T	c.(403-405)tGg>tTg	p.W135L	MAP2K7_ENST00000397983.3_Missense_Mutation_p.W151L|MAP2K7_ENST00000397981.3_Missense_Mutation_p.W135L|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000545011.1_Missense_Mutation_p.W177L	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	135	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						GGCCAGGTGTGGAAGATGCGC	0.667																																					p.W135L		Atlas-SNP	.											.	MAP2K7	66	.	0			c.G404T						.						32.0	39.0	37.0					19																	7975215		2038	4183	6221	SO:0001583	missense	5609	exon4			AGGTGTGGAAGAT	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.404G>T	chr19.hg19:g.7975215G>T	ENSP00000381066:p.Trp135Leu	135.0	0.0		96.0	4.0	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Missense_Mutation	SNP	ENST00000397979.3	hg19	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811931	0.32053	.	.	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	5.31	5.31	0.75309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.122835	0.64402	D	0.000020	T	0.46776	0.1410	N	0.20574	0.59	0.48762	D	0.999704	B;B	0.13145	0.003;0.007	B;B	0.17979	0.002;0.02	T	0.39165	-0.9627	10	0.11485	T	0.65	-6.9431	16.4609	0.84044	0.0:0.0:1.0:0.0	.	135;135	O14733-4;O14733	.;MP2K7_HUMAN	L	135;151;177;151;135	ENSP00000381068:W135L;ENSP00000381070:W151L;ENSP00000443946:W177L;ENSP00000381066:W135L	ENSP00000381066:W135L	W	+	2	0	MAP2K7	7881215	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.632000	0.74281	2.502000	0.84385	0.561000	0.74099	TGG	.	.		0.667	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1		
TIMM44	10469	hgsc.bcm.edu	37	19	7999080	7999080	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7999080T>C	ENST00000270538.3	-	5	705	c.437A>G	c.(436-438)aAg>aGg	p.K146R	TIMM44_ENST00000598968.1_5'Flank	NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	146					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						CACGCCCTCCTTGATTTTCCG	0.642																																					p.K146R		Atlas-SNP	.											.	TIMM44	47	.	0			c.A437G						.						82.0	88.0	86.0					19																	7999080		2203	4300	6503	SO:0001583	missense	10469	exon5			CCCTCCTTGATTT	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.437A>G	chr19.hg19:g.7999080T>C	ENSP00000270538:p.Lys146Arg	119.0	0.0		93.0	4.0	NM_006351	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	hg19	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	T	9.884	1.202439	0.22121	.	.	ENSG00000104980	ENST00000270538	T	0.76578	-1.03	5.52	3.33	0.38152	.	0.128073	0.64402	D	0.000001	T	0.56031	0.1958	L	0.34521	1.04	0.44685	D	0.997673	B	0.06786	0.001	B	0.08055	0.003	T	0.49370	-0.8947	10	0.02654	T	1	-42.1433	2.7702	0.05332	0.1443:0.085:0.1493:0.6214	.	146	O43615	TIM44_HUMAN	R	146	ENSP00000270538:K146R	ENSP00000270538:K146R	K	-	2	0	TIMM44	7905080	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	2.939000	0.48995	2.106000	0.64143	0.459000	0.35465	AAG	.	.		0.642	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3		
ELAVL1	1994	hgsc.bcm.edu	37	19	8056658	8056658	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:8056658C>A	ENST00000407627.2	-	2	171	c.42G>T	c.(40-42)agG>agT	p.R14S	ELAVL1_ENST00000596459.1_Missense_Mutation_p.R14S|ELAVL1_ENST00000593807.1_Missense_Mutation_p.R14S|ELAVL1_ENST00000351593.5_Missense_Mutation_p.R41S	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	14					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CGATGTCACCCCTGCAGTCTT	0.413																																					p.R14S		Atlas-SNP	.											.	ELAVL1	44	.	0			c.G42T						.						159.0	138.0	145.0					19																	8056658		2203	4300	6503	SO:0001583	missense	1994	exon2			GTCACCCCTGCAG	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.42G>T	chr19.hg19:g.8056658C>A	ENSP00000385269:p.Arg14Ser	150.0	0.0		111.0	5.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.919459	0.33908	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.14766	2.48;2.5	5.67	4.62	0.57501	.	0.105878	0.64402	D	0.000004	T	0.05960	0.0155	N	0.03154	-0.405	0.42422	D	0.992643	B	0.06786	0.001	B	0.04013	0.001	T	0.23440	-1.0188	10	0.08837	T	0.75	.	13.6273	0.62173	0.156:0.844:0.0:0.0	.	14	Q15717	ELAV1_HUMAN	S	14;41	ENSP00000385269:R14S;ENSP00000264073:R41S	ENSP00000264073:R41S	R	-	3	2	ELAVL1	7962658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.526000	0.35964	1.362000	0.46000	0.655000	0.94253	AGG	.	.		0.413	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
CD320	51293	hgsc.bcm.edu	37	19	8370014	8370014	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:8370014T>A	ENST00000301458.5	-	2	233	c.169A>T	c.(169-171)Acc>Tcc	p.T57S	CD320_ENST00000596246.1_5'Flank|CD320_ENST00000537716.2_Intron	NM_016579.3	NP_057663.1	Q9NPF0	CD320_HUMAN	CD320 molecule	57	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cobalamin metabolic process (GO:0009235)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)	6						TGGAACTTGGTGGGTGGGCAC	0.622																																					p.T57S		Atlas-SNP	.											.	CD320	20	.	0			c.A169T						.						59.0	51.0	53.0					19																	8370014		2203	4300	6503	SO:0001583	missense	51293	exon2			ACTTGGTGGGTGG	AF161254	CCDS12198.1, CCDS54210.1	19p13.3-p13.2	2008-02-05	2006-03-28			ENSG00000167775		"""CD molecules"""	16692	protein-coding gene	gene with protein product	"""8D6 antigen"""	606475	"""CD320 antigen"""			10727470	Standard	NM_016579		Approved	8D6, 8D6A	uc002mjj.2	Q9NPF0		ENST00000301458.5:c.169A>T	chr19.hg19:g.8370014T>A	ENSP00000301458:p.Thr57Ser	67.0	0.0		75.0	4.0	NM_016579	B2RDS5|D6W668|F5H6D3|Q53HF7	Missense_Mutation	SNP	ENST00000301458.5	hg19	CCDS12198.1	.	.	.	.	.	.	.	.	.	.	T	7.989	0.752775	0.15778	.	.	ENSG00000167775	ENST00000301458	D	0.95238	-3.65	4.87	-6.35	0.01975	.	1.638950	0.03345	N	0.195314	D	0.83294	0.5223	N	0.16266	0.395	0.09310	N	1	B	0.22346	0.068	B	0.22386	0.039	T	0.79560	-0.1753	10	0.05959	T	0.93	-3.2044	0.9076	0.01288	0.3864:0.2712:0.1187:0.2238	.	57	Q9NPF0	CD320_HUMAN	S	57	ENSP00000301458:T57S	ENSP00000301458:T57S	T	-	1	0	CD320	8276014	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.729000	0.01856	-1.522000	0.01769	-0.408000	0.06270	ACC	.	.		0.622	CD320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461366.1	NM_016579	
FBXL12	54850	hgsc.bcm.edu	37	19	9922014	9922014	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:9922014G>T	ENST00000247977.4	-	3	780	c.539C>A	c.(538-540)tCg>tAg	p.S180*	FBXL12_ENST00000589626.1_3'UTR|FBXL12_ENST00000588922.1_3'UTR|FBXL12_ENST00000591009.1_Nonsense_Mutation_p.S127*|FBXL12_ENST00000592067.1_3'UTR|FBXL12_ENST00000585379.1_Nonsense_Mutation_p.S127*|FBXL12_ENST00000586651.1_3'UTR	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12	180					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)				endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						CAGCACCAGCGAGCGCAAGGC	0.672																																					p.S180X		Atlas-SNP	.											FBXL12,NS,carcinoma,0,1	FBXL12	17	.	0			c.C539A						.						42.0	42.0	42.0					19																	9922014		2202	4298	6500	SO:0001587	stop_gained	54850	exon3			ACCAGCGAGCGCA	AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"""F-boxes / Leucine-rich repeats"""	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8		ENST00000247977.4:c.539C>A	chr19.hg19:g.9922014G>T	ENSP00000247977:p.Ser180*	44.0	0.0		42.0	2.0	NM_017703	B3KSJ8|Q9H5K4	Nonsense_Mutation	SNP	ENST00000247977.4	hg19	CCDS12218.1	.	.	.	.	.	.	.	.	.	.	G	37	6.064635	0.97251	.	.	ENSG00000127452	ENST00000247977	.	.	.	4.76	4.76	0.60689	.	0.412737	0.24516	N	0.037847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1447	0.59454	0.0:0.0:1.0:0.0	.	.	.	.	X	180	.	.	S	-	2	0	FBXL12	9783014	0.980000	0.34600	0.984000	0.44739	0.817000	0.46193	1.977000	0.40589	2.474000	0.83562	0.655000	0.94253	TCG	.	.		0.672	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450265.1	NM_017703	
ECSIT	51295	hgsc.bcm.edu	37	19	11625035	11625035	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:11625035A>G	ENST00000270517.7	-	3	233	c.98T>C	c.(97-99)gTc>gCc	p.V33A	RN7SL833P_ENST00000498758.2_RNA|ECSIT_ENST00000417981.2_Intron|ECSIT_ENST00000252440.7_Splice_Site_p.V33A|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000592312.1_5'UTR|ECSIT_ENST00000588998.1_Intron|ECSIT_ENST00000591104.1_Splice_Site_p.V33A	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	33					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CCGGCGAGGGACCTGGGGAGG	0.677																																					p.V33A		Atlas-SNP	.											.	ECSIT	32	.	0			c.T98C						.						10.0	13.0	12.0					19																	11625035		2123	4217	6340	SO:0001630	splice_region_variant	51295	exon3			CGAGGGACCTGGG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"""Mitochondrial respiratory chain complex assembly factors"""	29548	protein-coding gene	gene with protein product	"""signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"""	608388	"""ECSIT homolog (Drosophila)"""			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.97-1T>C	chr19.hg19:g.11625035A>G		82.0	0.0		65.0	4.0	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	hg19	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	a	11.39	1.624248	0.28889	.	.	ENSG00000130159	ENST00000270517;ENST00000252440	T	0.34667	1.35	5.71	-2.04	0.07343	.	0.825234	0.10603	N	0.655468	T	0.16854	0.0405	N	0.19112	0.55	0.26408	N	0.976312	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.21827	-1.0234	10	0.26408	T	0.33	-12.2393	1.797	0.03063	0.4283:0.2381:0.226:0.1076	.	33;33	Q9BQ95-2;Q9BQ95	.;ECSIT_HUMAN	A	33	ENSP00000270517:V33A	ENSP00000252440:V33A	V	-	2	0	ECSIT	11486035	0.017000	0.18338	0.048000	0.18961	0.025000	0.11179	0.375000	0.20518	-0.161000	0.10983	0.444000	0.29173	GTC	.	.		0.677	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	Missense_Mutation
MAN2B1	4125	hgsc.bcm.edu	37	19	12775761	12775761	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:12775761C>T	ENST00000456935.2	-	4	515	c.475G>A	c.(475-477)Gat>Aat	p.D159N	CTD-2192J16.24_ENST00000597961.1_Missense_Mutation_p.D156N|WDR83_ENST00000418543.3_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.D159N	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	159			D -> N (in MANSA; results in less than 20% of wild-type enzyme activity). {ECO:0000269|PubMed:22161967}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GCTGCCTCATCGTTCATCACC	0.622																																					p.D159N		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	.	0			c.G475A						.						82.0	58.0	66.0					19																	12775761		2203	4300	6503	SO:0001583	missense	4125	exon4			CCTCATCGTTCAT		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.475G>A	chr19.hg19:g.12775761C>T	ENSP00000395473:p.Asp159Asn	53.0	0.0		29.0	2.0	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	hg19	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	C	36	5.789382	0.96945	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.85773	-2.03;-2.03	5.69	5.69	0.88448	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.000000	0.48767	D	0.000172	D	0.95582	0.8564	H	0.98005	4.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97005	0.9732	10	0.87932	D	0	-50.6729	17.3077	0.87199	0.0:1.0:0.0:0.0	.	159;159	G5E928;O00754	.;MA2B1_HUMAN	N	159;98;159	ENSP00000395473:D159N;ENSP00000221363:D159N	ENSP00000221363:D159N	D	-	1	0	MAN2B1	12636761	1.000000	0.71417	0.974000	0.42286	0.898000	0.52572	7.417000	0.80156	2.688000	0.91661	0.491000	0.48974	GAT	.	.		0.622	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
GIPC1	10755	hgsc.bcm.edu	37	19	14589371	14589371	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:14589371T>C	ENST00000393033.4	-	9	1128	c.859A>G	c.(859-861)Atg>Gtg	p.M287V	GIPC1_ENST00000393029.3_Missense_Mutation_p.M190V|GIPC1_ENST00000591349.1_Missense_Mutation_p.M190V|GIPC1_ENST00000586027.1_Missense_Mutation_p.M287V|GIPC1_ENST00000393028.1_Missense_Mutation_p.M190V|GIPC1_ENST00000345425.2_Missense_Mutation_p.M287V	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	287					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						AGCTCCACCATGGTGGCCGCT	0.617																																					p.M287V	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.A859G						.						43.0	47.0	46.0					19																	14589371		2203	4300	6503	SO:0001583	missense	10755	exon8			CCACCATGGTGGC	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.859A>G	chr19.hg19:g.14589371T>C	ENSP00000376753:p.Met287Val	149.0	0.0		107.0	6.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	t	15.53	2.861072	0.51482	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;D;D	0.84944	-1.41;-1.41;-1.92;-1.92	4.28	4.28	0.50868	.	0.089037	0.85682	D	0.000000	D	0.83303	0.5225	M	0.72576	2.205	0.53005	D	0.999964	B	0.09022	0.002	B	0.14578	0.011	T	0.81254	-0.1016	10	0.54805	T	0.06	-19.0869	11.3771	0.49735	0.0:0.0:0.0:1.0	.	287	O14908	GIPC1_HUMAN	V	287;287;190;190;287	ENSP00000376753:M287V;ENSP00000340698:M287V;ENSP00000376749:M190V;ENSP00000376748:M190V	ENSP00000340698:M287V	M	-	1	0	GIPC1	14450371	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.690000	0.68241	1.586000	0.49944	0.454000	0.30748	ATG	.	.		0.617	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
NOTCH3	4854	hgsc.bcm.edu	37	19	15281634	15281634	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:15281634G>T	ENST00000263388.2	-	26	4814	c.4739C>A	c.(4738-4740)tCg>tAg	p.S1580*		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1580					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CATTACTACCGAGCTGCAGGG	0.617																																					p.S1580X		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C4739A						.						28.0	25.0	26.0					19																	15281634		2203	4299	6502	SO:0001587	stop_gained	4854	exon26			ACTACCGAGCTGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.4739C>A	chr19.hg19:g.15281634G>T	ENSP00000263388:p.Ser1580*	108.0	0.0		58.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Nonsense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	43	10.050665	0.99325	.	.	ENSG00000074181	ENST00000263388	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8921	0.70617	0.0:0.0:1.0:0.0	.	.	.	.	X	1580	.	ENSP00000263388:S1580X	S	-	2	0	NOTCH3	15142634	1.000000	0.71417	0.996000	0.52242	0.197000	0.23852	8.926000	0.92839	2.053000	0.61076	0.485000	0.47835	TCG	.	.		0.617	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
WIZ	58525	hgsc.bcm.edu	37	19	15533977	15533977	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:15533977G>A	ENST00000389282.4	-	10	5079	c.4866C>T	c.(4864-4866)caC>caT	p.H1622H	WIZ_ENST00000599910.2_Silent_p.H939H|WIZ_ENST00000599686.3_Silent_p.H806H|WIZ_ENST00000545156.1_Silent_p.H936H|WIZ_ENST00000263381.7_Silent_p.H765H			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	1622					positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						TCTCCAGGATGTGCCGCTGTA	0.622																																					p.H765H		Atlas-SNP	.											.	WIZ	152	.	0			c.C2295T						.						40.0	45.0	43.0					19																	15533977		1946	4144	6090	SO:0001819	synonymous_variant	58525	exon8			CAGGATGTGCCGC	AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"""Zinc fingers, C2H2-type"""	30917	protein-coding gene	gene with protein product			"""WIZ zinc finger"""			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.4866C>T	chr19.hg19:g.15533977G>A		72.0	0.0		55.0	4.0	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Silent	SNP	ENST00000389282.4	hg19																																																																																				.	.		0.622	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241	
EPS15L1	58513	hgsc.bcm.edu	37	19	16488025	16488025	+	Missense_Mutation	SNP	G	G	A	rs369284918		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:16488025G>A	ENST00000248070.6	-	22	2427	c.2288C>T	c.(2287-2289)gCa>gTa	p.A763V	EPS15L1_ENST00000455140.2_Missense_Mutation_p.A763V|EPS15L1_ENST00000535753.2_Intron|EPS15L1_ENST00000594975.1_Intron	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	763	15 X 3 AA repeats of D-P-F.|Pro-rich.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TGAGAATCCTGCCCCTCCCAA	0.517											OREG0025332	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A763V		Atlas-SNP	.											.	EPS15L1	81	.	0			c.C2288T						.						101.0	108.0	106.0					19																	16488025		2203	4300	6503	SO:0001583	missense	58513	exon22			AATCCTGCCCCTC	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"""EF-hand domain containing"""	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2288C>T	chr19.hg19:g.16488025G>A	ENSP00000248070:p.Ala763Val	97.0	0.0	710	89.0	4.0	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.998919	0.35226	.	.	ENSG00000127527	ENST00000455140;ENST00000248070	T;T	0.22945	1.93;1.94	4.58	3.29	0.37713	.	0.607232	0.17007	N	0.190673	T	0.12347	0.0300	N	0.08118	0	0.32606	N	0.525299	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11717	-1.0576	10	0.17369	T	0.5	.	11.6044	0.51024	0.1572:0.0:0.8428:0.0	.	763;763	Q9UBC2;G3V0H2	EP15R_HUMAN;.	V	763	ENSP00000393313:A763V;ENSP00000248070:A763V	ENSP00000248070:A763V	A	-	2	0	EPS15L1	16349025	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.799000	0.38824	2.093000	0.63338	0.555000	0.69702	GCA	.	.		0.517	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235	
UNC13A	23025	hgsc.bcm.edu	37	19	17785490	17785490	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:17785490G>T	ENST00000519716.2	-	3	127	c.128C>A	c.(127-129)cCc>cAc	p.P43H	UNC13A_ENST00000252773.7_Missense_Mutation_p.P43H|UNC13A_ENST00000428389.2_Missense_Mutation_p.P131H|UNC13A_ENST00000551649.1_Missense_Mutation_p.P43H|UNC13A_ENST00000550896.1_Missense_Mutation_p.P43H|UNC13A_ENST00000552293.1_Missense_Mutation_p.P43H	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	43	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CTCCCAGCTGGGCTGGCTGCC	0.597																																					p.P43H		Atlas-SNP	.											.	UNC13A	299	.	0			c.C128A						.						94.0	96.0	95.0					19																	17785490		2110	4241	6351	SO:0001583	missense	23025	exon3			CAGCTGGGCTGGC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.128C>A	chr19.hg19:g.17785490G>T	ENSP00000429562:p.Pro43His	90.0	0.0		75.0	4.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523432	0.85600	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17;-3.17;-3.17	4.93	4.93	0.64822	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.96577	0.8883	M	0.80183	2.485	0.51012	D	0.999904	D	0.89917	1.0	D	0.97110	1.0	D	0.97190	0.9857	10	0.87932	D	0	-18.2853	15.6143	0.76753	0.0:0.0:1.0:0.0	.	43	Q9UPW8	UN13A_HUMAN	H	43;131;43;43;43;43	ENSP00000429562:P43H;ENSP00000400409:P131H;ENSP00000252773:P43H;ENSP00000447236:P43H;ENSP00000447572:P43H;ENSP00000446831:P43H	ENSP00000252773:P43H	P	-	2	0	UNC13A	17646490	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.674000	0.98633	2.288000	0.76882	0.313000	0.20887	CCC	.	.		0.597	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
UNC13A	23025	hgsc.bcm.edu	37	19	17785532	17785532	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:17785532T>C	ENST00000519716.2	-	3	85	c.86A>G	c.(85-87)cAg>cGg	p.Q29R	UNC13A_ENST00000252773.7_Missense_Mutation_p.Q29R|UNC13A_ENST00000428389.2_Missense_Mutation_p.Q117R|UNC13A_ENST00000551649.1_Missense_Mutation_p.Q29R|UNC13A_ENST00000550896.1_Missense_Mutation_p.Q29R|UNC13A_ENST00000552293.1_Missense_Mutation_p.Q29R	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	29	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CTTGACATTCTGCACTTTCAG	0.587																																					p.Q29R		Atlas-SNP	.											.	UNC13A	299	.	0			c.A86G						.						133.0	130.0	131.0					19																	17785532		2109	4251	6360	SO:0001583	missense	23025	exon3			ACATTCTGCACTT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.86A>G	chr19.hg19:g.17785532T>C	ENSP00000429562:p.Gln29Arg	131.0	0.0		87.0	4.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841232	0.71488	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	4.93	4.93	0.64822	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000001	T	0.80894	0.4711	M	0.65975	2.015	0.42449	D	0.992748	D	0.57257	0.979	D	0.68192	0.956	T	0.81924	-0.0710	10	0.49607	T	0.09	-18.4567	12.5081	0.55991	0.0:0.0:0.0:1.0	.	29	Q9UPW8	UN13A_HUMAN	R	29;117;29;29;29;29	ENSP00000429562:Q29R;ENSP00000400409:Q117R;ENSP00000252773:Q29R;ENSP00000447236:Q29R;ENSP00000447572:Q29R;ENSP00000446831:Q29R	ENSP00000252773:Q29R	Q	-	2	0	UNC13A	17646532	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	7.888000	0.87302	1.854000	0.53819	0.260000	0.18958	CAG	.	.		0.587	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
IL12RB1	3594	hgsc.bcm.edu	37	19	18183013	18183013	+	Silent	SNP	C	C	A	rs144647048		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:18183013C>A	ENST00000600835.2	-	10	1228	c.930G>T	c.(928-930)tcG>tcT	p.S310S	IL12RB1_ENST00000322153.7_Silent_p.S310S|IL12RB1_ENST00000593993.2_Silent_p.S310S			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	310	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						AGGCAGCACCCGAGAGATAGG	0.602																																					p.S310S		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G930T						.						106.0	76.0	86.0					19																	18183013		2203	4300	6503	SO:0001819	synonymous_variant	3594	exon9			AGCACCCGAGAGA	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.930G>T	chr19.hg19:g.18183013C>A		118.0	0.0		95.0	4.0	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	hg19	CCDS54232.1																																																																																			.	C|1.000;T|0.000		0.602	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
ZNF90	7643	hgsc.bcm.edu	37	19	20228952	20228952	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:20228952G>T	ENST00000418063.2	+	4	701	c.589G>T	c.(589-591)Gga>Tga	p.G197*	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	197					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						AATTCATACTGGAGAGATAAC	0.383																																					p.G197X		Atlas-SNP	.											.	ZNF90	93	.	0			c.G589T						.						30.0	29.0	29.0					19																	20228952		692	1591	2283	SO:0001587	stop_gained	7643	exon4			CATACTGGAGAGA	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"""Zinc fingers, C2H2-type"", ""-"""	13165	protein-coding gene	gene with protein product		603973	"""zinc finger protein 90 (HTF9)"""			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.589G>T	chr19.hg19:g.20228952G>T	ENSP00000410466:p.Gly197*	86.0	0.0		58.0	4.0	NM_007138	B9EH87	Nonsense_Mutation	SNP	ENST00000418063.2	hg19	CCDS46028.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559742	0.27827	.	.	ENSG00000213988	ENST00000418063	.	.	.	1.18	-2.35	0.06684	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8526	0.13543	0.2058:0.2191:0.5751:0.0	.	.	.	.	X	197	.	.	G	+	1	0	ZNF90	20089952	0.994000	0.37717	0.003000	0.11579	0.003000	0.03518	2.780000	0.47742	-0.850000	0.04152	-0.856000	0.03024	GGA	.	.		0.383	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138	
ZNF85	7639	hgsc.bcm.edu	37	19	21132473	21132473	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21132473C>A	ENST00000328178.8	+	4	1266	c.1153C>A	c.(1153-1155)Ctt>Att	p.L385I	ZNF85_ENST00000345030.6_Missense_Mutation_p.L352I|ZNF85_ENST00000601023.1_Missense_Mutation_p.L326I	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	385					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						TTTCTCACACCTTACTACACA	0.348																																					p.L415I		Atlas-SNP	.											.	ZNF85	72	.	0			c.C1243A						.						35.0	38.0	37.0					19																	21132473		2195	4295	6490	SO:0001583	missense	7639	exon5			TCACACCTTACTA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1153C>A	chr19.hg19:g.21132473C>A	ENSP00000329793:p.Leu385Ile	82.0	0.0		72.0	4.0	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551047	0.27739	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.53857	0.6;0.6	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69691	0.3139	M	0.85542	2.76	0.09310	N	0.999997	D;P;D	0.89917	0.957;0.95;1.0	D;D;D	0.91635	0.937;0.991;0.999	T	0.55029	-0.8204	9	0.72032	D	0.01	.	4.9635	0.14078	0.0:0.79:0.0:0.2099	.	352;326;385	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	I	385;352;260	ENSP00000329793:L385I;ENSP00000342340:L352I	ENSP00000329793:L385I	L	+	1	0	ZNF85	20924313	0.068000	0.21057	0.002000	0.10522	0.002000	0.02628	0.707000	0.25704	0.681000	0.31386	0.462000	0.41574	CTT	.	.		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
ZNF431	170959	hgsc.bcm.edu	37	19	21366793	21366793	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21366793T>C	ENST00000311048.7	+	5	1831	c.1687T>C	c.(1687-1689)Tgg>Cgg	p.W563R	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000600692.1_3'UTR	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	563					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						TAATTCATACTGGAGAGAAAC	0.373																																					p.W563R		Atlas-SNP	.											.	ZNF431	71	.	0			c.T1687C						.						37.0	43.0	41.0					19																	21366793		2201	4298	6499	SO:0001583	missense	170959	exon5			TCATACTGGAGAG	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"""Zinc fingers, C2H2-type"", ""-"""	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.1687T>C	chr19.hg19:g.21366793T>C	ENSP00000308578:p.Trp563Arg	157.0	0.0		99.0	4.0	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	hg19	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.899406	0.00517	.	.	ENSG00000196705	ENST00000311048	T	0.05786	3.39	1.05	1.05	0.20165	.	.	.	.	.	T	0.01940	0.0061	N	0.01048	-1.04	0.25746	N	0.985104	B	0.02656	0.0	B	0.04013	0.001	T	0.42548	-0.9445	9	0.87932	D	0	.	2.0647	0.03600	0.2853:0.0:0.2868:0.4278	.	563	Q8TF32	ZN431_HUMAN	R	563	ENSP00000308578:W563R	ENSP00000308578:W563R	W	+	1	0	ZNF431	21158633	0.008000	0.16893	0.151000	0.22473	0.141000	0.21300	-0.941000	0.03925	0.389000	0.25086	0.379000	0.24179	TGG	.	.		0.373	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098	
ZNF708	7562	hgsc.bcm.edu	37	19	21476562	21476562	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21476562G>T	ENST00000356929.3	-	4	1403	c.1206C>A	c.(1204-1206)acC>acA	p.T402T		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	338					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K403fs*10(1)		breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TTGAGGACTTGGTAAAGGCTT	0.368																																					p.T402T		Atlas-SNP	.											.,1	ZNF708	66	.	1	Deletion - Frameshift(1)	ovary(1)	c.C1206A						.						61.0	66.0	64.0					19																	21476562		2201	4296	6497	SO:0001819	synonymous_variant	7562	exon4			GGACTTGGTAAAG	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.1206C>A	chr19.hg19:g.21476562G>T		77.0	0.0		59.0	3.0	NM_021269	Q6ZMR0	Silent	SNP	ENST00000356929.3	hg19	CCDS32980.1																																																																																			.	.		0.368	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
ZNF429	353088	hgsc.bcm.edu	37	19	21712459	21712459	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21712459G>T	ENST00000358491.4	+	2	211		c.e2-1		ZNF429_ENST00000594022.1_Splice_Site|ZNF429_ENST00000597078.1_Splice_Site	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GTGTGTTTCAGGGACCATTGA	0.403																																					.		Atlas-SNP	.											.	ZNF429	338	.	0			c.4-1G>T						.						72.0	79.0	76.0					19																	21712459		2200	4299	6499	SO:0001630	splice_region_variant	353088	exon2			GTTTCAGGGACCA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.4-1G>T	chr19.hg19:g.21712459G>T		109.0	0.0		59.0	4.0	NM_001001415	A6NLV7|Q9BZE6	Splice_Site	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	G	3.591	-0.083509	0.07141	.	.	ENSG00000197013	ENST00000358491	.	.	.	0.926	0.926	0.19430	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6024	0.33754	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF429	21504299	0.994000	0.37717	0.179000	0.23059	0.257000	0.26127	3.033000	0.49743	0.308000	0.22923	0.313000	0.20887	.	.	.		0.403	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	Intron
ZNF429	353088	hgsc.bcm.edu	37	19	21720450	21720450	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21720450C>G	ENST00000358491.4	+	4	1803	c.1595C>G	c.(1594-1596)aCt>aGt	p.T532S	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						AAAATTCATACTGGAGAGAAA	0.363																																					p.T532S		Atlas-SNP	.											ZNF429,colon,carcinoma,0,2	ZNF429	338	.	0			c.C1595G						.						39.0	43.0	42.0					19																	21720450		2113	4256	6369	SO:0001583	missense	353088	exon4			TTCATACTGGAGA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1595C>G	chr19.hg19:g.21720450C>G	ENSP00000351280:p.Thr532Ser	49.0	2.0		29.0	2.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	12.73	2.026350	0.35701	.	.	ENSG00000197013	ENST00000358491	T	0.24151	1.87	0.81	0.81	0.18732	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23289	0.0563	N	0.05280	-0.08	0.29292	N	0.869277	D	0.65815	0.995	D	0.63703	0.917	T	0.19192	-1.0313	9	0.46703	T	0.11	.	8.393	0.32540	0.0:1.0:0.0:0.0	.	532	Q86V71	ZN429_HUMAN	S	532	ENSP00000351280:T532S	ENSP00000351280:T532S	T	+	2	0	ZNF429	21512290	0.204000	0.23447	0.477000	0.27303	0.478000	0.33099	0.600000	0.24104	0.181000	0.19994	0.184000	0.17185	ACT	.	.		0.363	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
ZNF429	353088	hgsc.bcm.edu	37	19	21720666	21720666	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21720666G>T	ENST00000358491.4	+	4	2019	c.1811G>T	c.(1810-1812)cGg>cTg	p.R604L	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	604					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.R604Q(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GCTTTTAATCGGTCCTCAAGA	0.373																																					p.R604L		Atlas-SNP	.											ZNF429,caecum,carcinoma,+1,1	ZNF429	338	.	1	Substitution - Missense(1)	soft_tissue(1)	c.G1811T						.						57.0	62.0	60.0					19																	21720666		2085	4256	6341	SO:0001583	missense	353088	exon4			TTAATCGGTCCTC	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1811G>T	chr19.hg19:g.21720666G>T	ENSP00000351280:p.Arg604Leu	82.0	0.0		74.0	3.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	1.503	-0.551530	0.03996	.	.	ENSG00000197013	ENST00000358491	T	0.06142	3.34	1.09	-1.05	0.10036	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03827	0.0108	L	0.49513	1.565	0.09310	N	1	P	0.40032	0.699	B	0.27715	0.082	T	0.42515	-0.9447	9	0.10377	T	0.69	.	4.965	0.14085	0.7681:0.0:0.2319:0.0	.	604	Q86V71	ZN429_HUMAN	L	604	ENSP00000351280:R604L	ENSP00000351280:R604L	R	+	2	0	ZNF429	21512506	0.001000	0.12720	0.001000	0.08648	0.054000	0.15201	0.519000	0.22862	-0.272000	0.09259	0.298000	0.19748	CGG	.	.		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
ZNF208	7757	hgsc.bcm.edu	37	19	22155050	22155050	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:22155050A>G	ENST00000397126.4	-	4	2934	c.2786T>C	c.(2785-2787)tTg>tCg	p.L929S	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	929					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)				AAAGACTGACAACCAGCTGAA	0.378																																					p.L929S		Atlas-SNP	.											.	ZNF208	817	.	0			c.T2786C						.						51.0	54.0	53.0					19																	22155050		2057	4205	6262	SO:0001583	missense	7757	exon4			ACTGACAACCAGC	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.2786T>C	chr19.hg19:g.22155050A>G	ENSP00000380315:p.Leu929Ser	179.0	0.0		127.0	6.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.700444	0.00725	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.07216	3.21	3.07	-5.09	0.02920	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02047	0.0064	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.41305	-0.9516	8	0.02654	T	1	.	1.7227	0.02915	0.1479:0.3719:0.2861:0.1941	.	829	O43345	ZN208_HUMAN	S	929;829	ENSP00000380315:L929S	ENSP00000380315:L929S	L	-	2	0	ZNF208	21946890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.339000	0.01102	-1.085000	0.03088	-1.661000	0.00750	TTG	.	.		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF91	7644	hgsc.bcm.edu	37	19	23544210	23544210	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:23544210C>T	ENST00000300619.7	-	4	1776	c.1571G>A	c.(1570-1572)gGc>gAc	p.G524D	ZNF91_ENST00000397082.2_Missense_Mutation_p.G492D|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	524					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				AAAAGCTTTGCCACATTCTTC	0.333																																					p.G524D		Atlas-SNP	.											.	ZNF91	349	.	0			c.G1571A						.						40.0	43.0	42.0					19																	23544210		2064	4235	6299	SO:0001583	missense	7644	exon4			GCTTTGCCACATT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1571G>A	chr19.hg19:g.23544210C>T	ENSP00000300619:p.Gly524Asp	77.0	0.0		89.0	4.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.098493	0.37048	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.20881	2.04;2.1	1.71	0.452	0.16634	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36853	0.0982	M	0.63169	1.94	0.26875	N	0.967662	P;D	0.89917	0.861;1.0	P;D	0.67900	0.498;0.954	T	0.14643	-1.0465	9	0.49607	T	0.09	.	8.4203	0.32696	0.0:0.7544:0.2455:0.0	.	492;524	Q05481-2;Q05481	.;ZNF91_HUMAN	D	524;492	ENSP00000300619:G524D;ENSP00000380272:G492D	ENSP00000300619:G524D	G	-	2	0	ZNF91	23336050	0.510000	0.26171	0.031000	0.17742	0.024000	0.10985	1.300000	0.33436	0.003000	0.14656	0.205000	0.17691	GGC	.	.		0.333	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
ZNF675	171392	hgsc.bcm.edu	37	19	23836432	23836432	+	Silent	SNP	G	G	T	rs199957959		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:23836432G>T	ENST00000359788.4	-	4	1471	c.1303C>A	c.(1303-1305)Cga>Aga	p.R435R	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	435					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGAGGATCGGTTAAAAGCT	0.378																																					p.R435R		Atlas-SNP	.											.	ZNF675	88	.	0			c.C1303A						.						52.0	55.0	54.0					19																	23836432		2202	4300	6502	SO:0001819	synonymous_variant	171392	exon4			AGGATCGGTTAAA		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.1303C>A	chr19.hg19:g.23836432G>T		54.0	0.0		33.0	4.0	NM_138330	Q8N211	Silent	SNP	ENST00000359788.4	hg19	CCDS32981.1																																																																																			.	G|0.999;A|0.001		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
DPY19L3	147991	hgsc.bcm.edu	37	19	32968497	32968497	+	Silent	SNP	G	G	T	rs571491381		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:32968497G>T	ENST00000342179.5	+	17	1982	c.1767G>T	c.(1765-1767)acG>acT	p.T589T	DPY19L3_ENST00000586987.1_Silent_p.T589T|DPY19L3_ENST00000392250.2_Silent_p.T589T	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	589						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					AGCTGTGCACGGGAAGGACCC	0.562																																					p.T589T		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G1767T						.						131.0	112.0	119.0					19																	32968497		2203	4300	6503	SO:0001819	synonymous_variant	147991	exon17			GTGCACGGGAAGG		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1767G>T	chr19.hg19:g.32968497G>T		120.0	0.0		80.0	5.0	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	hg19	CCDS12422.1																																																																																			.	.		0.562	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
WDR88	126248	hgsc.bcm.edu	37	19	33647426	33647426	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:33647426T>C	ENST00000355868.3	+	7	1051	c.975T>C	c.(973-975)agT>agC	p.S325S	WDR88_ENST00000361680.2_Silent_p.S325S	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	325										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					GTTCTGTCAGTTCCTGTCACT	0.488																																					p.S325S		Atlas-SNP	.											.	WDR88	50	.	0			c.T975C						.						88.0	84.0	85.0					19																	33647426		2203	4300	6503	SO:0001819	synonymous_variant	126248	exon7			TGTCAGTTCCTGT	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.975T>C	chr19.hg19:g.33647426T>C		93.0	0.0		100.0	4.0	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	hg19	CCDS12429.1																																																																																			.	.		0.488	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
CD22	933	hgsc.bcm.edu	37	19	35832318	35832318	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:35832318T>C	ENST00000085219.5	+	8	1646	c.1580T>C	c.(1579-1581)cTc>cCc	p.L527P	CD22_ENST00000594250.1_Missense_Mutation_p.L350P|CD22_ENST00000341773.6_Missense_Mutation_p.L350P|CD22_ENST00000270311.6_Missense_Mutation_p.L407P|CD22_ENST00000544992.2_Missense_Mutation_p.L527P|CD22_ENST00000536635.2_Missense_Mutation_p.L439P|CD22_ENST00000419549.2_Missense_Mutation_p.L355P	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	527	Ig-like C2-type 5.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TCGGTCAGCCTCCAATGTGAC	0.542																																					p.L527P	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T1580C						.						48.0	48.0	48.0					19																	35832318		2203	4300	6503	SO:0001583	missense	933	exon8			TCAGCCTCCAATG	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1580T>C	chr19.hg19:g.35832318T>C	ENSP00000085219:p.Leu527Pro	33.0	0.0		64.0	4.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146397	0.57044	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	D;D;D;D;D;D	0.93076	-3.16;-3.16;-3.16;-3.16;-3.16;-3.16	4.84	4.84	0.62591	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000167	D	0.97676	0.9238	H	0.97340	3.985	0.51482	D	0.999927	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.98150	1.0441	10	0.87932	D	0	.	10.7356	0.46122	0.0:0.0:0.0:1.0	.	355;527;439;527;350	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	P	527;439;350;527;407;355	ENSP00000085219:L527P;ENSP00000442279:L439P;ENSP00000339349:L350P;ENSP00000441237:L527P;ENSP00000270311:L407P;ENSP00000403822:L355P	ENSP00000085219:L527P	L	+	2	0	CD22	40524158	0.818000	0.29161	0.160000	0.22671	0.040000	0.13550	3.703000	0.54808	2.031000	0.59945	0.459000	0.35465	CTC	.	.		0.542	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
ATP4A	495	hgsc.bcm.edu	37	19	36051450	36051450	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36051450A>G	ENST00000262623.3	-	6	630	c.602T>C	c.(601-603)cTg>cCg	p.L201P		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	201					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CATCTCCACCAGGTCGCCCAC	0.622																																					p.L201P		Atlas-SNP	.											.	ATP4A	123	.	0			c.T602C						.						52.0	49.0	50.0					19																	36051450		2203	4300	6503	SO:0001583	missense	495	exon6			TCCACCAGGTCGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.602T>C	chr19.hg19:g.36051450A>G	ENSP00000262623:p.Leu201Pro	65.0	0.0		48.0	4.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	a	19.64	3.865896	0.71949	.	.	ENSG00000105675	ENST00000262623	D	0.92397	-3.03	4.16	4.16	0.48862	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.122063	0.34802	N	0.003670	D	0.96300	0.8793	M	0.92649	3.33	0.80722	D	1	D	0.57571	0.98	D	0.65443	0.935	D	0.96764	0.9563	10	0.87932	D	0	.	11.454	0.50169	1.0:0.0:0.0:0.0	.	201	P20648	ATP4A_HUMAN	P	201	ENSP00000262623:L201P	ENSP00000262623:L201P	L	-	2	0	ATP4A	40743290	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	7.279000	0.78599	1.875000	0.54330	0.398000	0.26397	CTG	.	.		0.622	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	
KMT2B	9757	hgsc.bcm.edu	37	19	36229093	36229093	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36229093G>T	ENST00000222270.7	+	36	7872		c.e36+1		KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Splice_Site|IGFLR1_ENST00000587101.1_5'Flank	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGATGGGAAGGTGGGCTCCCA	0.607																																					.		Atlas-SNP	.											.	MLL4	229	.	0			c.7872+1G>T						.						55.0	61.0	59.0					19																	36229093		2090	4240	6330	SO:0001630	splice_region_variant	8085	exon36			GGGAAGGTGGGCT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7872+1G>T	chr19.hg19:g.36229093G>T		123.0	0.0		46.0	16.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812288	0.70912	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6212	0.84931	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40920933	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.210000	0.65214	2.467000	0.83353	0.462000	0.41574	.	.	.		0.607	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron
POLR2I	5438	hgsc.bcm.edu	37	19	36605106	36605106	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36605106G>T	ENST00000221859.4	-	4	725	c.236C>A	c.(235-237)cCg>cAg	p.P79Q	TBCB_ENST00000586868.1_5'Flank|TBCB_ENST00000589996.1_5'Flank|TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000221855.3_5'Flank	NM_006233.4	NP_006224.1	P36954	RPB9_HUMAN	polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa	79					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO:0001193)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTCGGTCCGCGGCAACGTGGG	0.627											OREG0025437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P79Q		Atlas-SNP	.											.	POLR2I	10	.	0			c.C236A						.						58.0	57.0	57.0					19																	36605106		2203	4300	6503	SO:0001583	missense	5438	exon4			GTCCGCGGCAACG		CCDS12487.1	19q13.12	2013-10-17	2002-08-29		ENSG00000105258	ENSG00000105258	2.7.7.6	"""RNA polymerase subunits"""	9196	protein-coding gene	gene with protein product		180662	"""polymerase (RNA) II (DNA directed) polypeptide I (14.5kD)"""			8034326	Standard	NM_006233		Approved	RPB9, hRPB14.5	uc002ode.3	P36954	OTTHUMG00000181749	ENST00000221859.4:c.236C>A	chr19.hg19:g.36605106G>T	ENSP00000221859:p.Pro79Gln	129.0	0.0	864	123.0	7.0	NM_006233	B2R5J2|Q6NW05	Missense_Mutation	SNP	ENST00000221859.4	hg19	CCDS12487.1	.	.	.	.	.	.	.	.	.	.	G	31	5.066869	0.93898	.	.	ENSG00000105258	ENST00000221859	T	0.46063	0.88	5.55	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.80847	2.515	0.80722	D	1	D	0.67145	0.996	P	0.61132	0.884	T	0.63928	-0.6526	10	0.59425	D	0.04	-33.6734	12.6656	0.56840	0.0816:0.0:0.9184:0.0	.	79	P36954	RPB9_HUMAN	Q	79	ENSP00000221859:P79Q	ENSP00000221859:P79Q	P	-	2	0	POLR2I	41296946	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	8.708000	0.91372	2.894000	0.99253	0.655000	0.94253	CCG	.	.		0.627	POLR2I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457442.1	NM_006233	
ZNF565	147929	hgsc.bcm.edu	37	19	36685225	36685225	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36685225A>G	ENST00000355114.5	-	4	988	c.262T>C	c.(262-264)Tcc>Ccc	p.S88P	ZNF565_ENST00000304116.5_Missense_Mutation_p.S48P|ZNF565_ENST00000392173.2_Missense_Mutation_p.S48P			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			TTAGAAATGGAGAGTCCTGTT	0.488																																					p.S48P		Atlas-SNP	.											.	ZNF565	46	.	0			c.T142C						.						63.0	53.0	56.0					19																	36685225		2203	4300	6503	SO:0001583	missense	147929	exon4			AAATGGAGAGTCC	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"""Zinc fingers, C2H2-type"", ""-"""	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.262T>C	chr19.hg19:g.36685225A>G	ENSP00000347234:p.Ser88Pro	104.0	0.0		73.0	4.0	NM_001042474	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	hg19		.	.	.	.	.	.	.	.	.	.	a	7.724	0.697802	0.15106	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.00776	5.71;5.71;5.71	5.08	-0.579	0.11720	Krueppel-associated box (3);	0.208186	0.24386	N	0.038968	T	0.00468	0.0015	N	0.24115	0.695	0.09310	N	1	P	0.37864	0.61	B	0.29524	0.103	T	0.52961	-0.8505	10	0.17369	T	0.5	.	5.7466	0.18124	0.3113:0.5581:0.1306:0.0	.	48	Q8N9K5	ZN565_HUMAN	P	48;48;88	ENSP00000376013:S48P;ENSP00000306869:S48P;ENSP00000347234:S88P	ENSP00000306869:S48P	S	-	1	0	ZNF565	41377065	0.989000	0.36119	0.992000	0.48379	0.912000	0.54170	0.291000	0.18994	0.222000	0.20900	0.459000	0.35465	TCC	.	.		0.488	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477	
ZNF345	25850	hgsc.bcm.edu	37	19	37368101	37368101	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:37368101T>C	ENST00000529555.1	+	2	1157	c.369T>C	c.(367-369)tgT>tgC	p.C123C	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000589046.1_Silent_p.C123C|ZNF345_ENST00000420450.1_Silent_p.C123C			Q14585	ZN345_HUMAN	zinc finger protein 345	123					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTAAAGAATGTGGGAAGGCCT	0.423																																					p.C123C		Atlas-SNP	.											.	ZNF345	68	.	0			c.T369C						.						64.0	65.0	65.0					19																	37368101		2203	4300	6503	SO:0001819	synonymous_variant	25850	exon4			AGAATGTGGGAAG	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.369T>C	chr19.hg19:g.37368101T>C		98.0	0.0		99.0	4.0	NM_001242476		Silent	SNP	ENST00000529555.1	hg19	CCDS12497.1																																																																																			.	.		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
ZNF585B	92285	hgsc.bcm.edu	37	19	37677107	37677107	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:37677107C>T	ENST00000532828.2	-	5	1583	c.1332G>A	c.(1330-1332)ggG>ggA	p.G444G	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000312908.5_Silent_p.G32G|ZNF585B_ENST00000531805.1_Silent_p.G389G	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAAACAATTTCCCACAGTGAC	0.403																																					p.G444G	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.G1332A						.						111.0	111.0	111.0					19																	37677107		2203	4300	6503	SO:0001819	synonymous_variant	92285	exon5			CAATTTCCCACAG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1332G>A	chr19.hg19:g.37677107C>T		243.0	0.0		198.0	61.0	NM_152279	Q8IZD3|Q96JW6	Silent	SNP	ENST00000532828.2	hg19	CCDS12500.1																																																																																			.	.		0.403	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
RASGRP4	115727	hgsc.bcm.edu	37	19	38903605	38903605	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38903605C>T	ENST00000587738.1	-	12	1571	c.1501G>A	c.(1501-1503)Gcc>Acc	p.A501T	RASGRP4_ENST00000293062.9_Missense_Mutation_p.A404T|RASGRP4_ENST00000587753.1_Missense_Mutation_p.A432T|RASGRP4_ENST00000426920.2_Missense_Mutation_p.A312T|RASGRP4_ENST00000433821.2_Missense_Mutation_p.A409T|RASGRP4_ENST00000586305.1_Missense_Mutation_p.A487T|RASGRP4_ENST00000454404.2_Missense_Mutation_p.A467T			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	501	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCATGGCAGGCGAAGGGAAAA	0.567																																					p.A501T		Atlas-SNP	.											.	RASGRP4	54	.	0			c.G1501A						.						54.0	59.0	58.0					19																	38903605		1928	4138	6066	SO:0001583	missense	115727	exon12			GGCAGGCGAAGGG	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"""EF-hand domain containing"""	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1501G>A	chr19.hg19:g.38903605C>T	ENSP00000465772:p.Ala501Thr	81.0	0.0		42.0	4.0	NM_170604	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	hg19	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885836	0.72410	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T	0.76709	-1.04;-0.79;-0.9	5.42	5.42	0.78866	.	0.049276	0.85682	D	0.000000	T	0.80265	0.4591	L	0.34521	1.04	0.37264	D	0.90709	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.996;0.998;0.996;0.971;0.998	D;D;P;P;P;P;P	0.77557	0.943;0.99;0.557;0.67;0.557;0.742;0.67	T	0.79227	-0.1890	10	0.27082	T	0.32	-23.7961	11.764	0.51920	0.1758:0.8242:0.0:0.0	.	312;404;409;467;432;487;501	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	T	409;404;312;501;501	ENSP00000411878:A409T;ENSP00000293062:A404T;ENSP00000445966:A312T	ENSP00000293062:A404T	A	-	1	0	RASGRP4	43595445	0.994000	0.37717	0.273000	0.24645	0.580000	0.36256	3.070000	0.50033	2.560000	0.86352	0.650000	0.86243	GCC	.	.		0.567	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604	
RYR1	6261	hgsc.bcm.edu	37	19	38959769	38959769	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38959769A>G	ENST00000359596.3	+	26	3545	c.3545A>G	c.(3544-3546)gAg>gGg	p.E1182G	RYR1_ENST00000360985.3_Missense_Mutation_p.E1182G|RYR1_ENST00000355481.4_Missense_Mutation_p.E1182G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1182	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGGAGATTGAGATTGGGGAC	0.547																																					p.E1182G		Atlas-SNP	.											.	RYR1	708	.	0			c.A3545G						.						99.0	85.0	90.0					19																	38959769		2203	4300	6503	SO:0001583	missense	6261	exon26			AGATTGAGATTGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3545A>G	chr19.hg19:g.38959769A>G	ENSP00000352608:p.Glu1182Gly	96.0	0.0		86.0	4.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	a	13.91	2.378899	0.42207	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.70399	-0.48;-0.48;-0.48	3.84	3.84	0.44239	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.168293	0.34386	U	0.004017	T	0.63768	0.2539	L	0.45228	1.405	0.44562	D	0.997521	B;B	0.24483	0.05;0.104	B;B	0.35470	0.041;0.203	T	0.60840	-0.7183	10	0.36615	T	0.2	.	8.4991	0.33148	0.9025:0.0:0.0975:0.0	.	1182;1182	P21817-2;P21817	.;RYR1_HUMAN	G	1182	ENSP00000352608:E1182G;ENSP00000347667:E1182G;ENSP00000354254:E1182G	ENSP00000347667:E1182G	E	+	2	0	RYR1	43651609	1.000000	0.71417	0.981000	0.43875	0.899000	0.52679	6.976000	0.76135	1.632000	0.50472	0.310000	0.20435	GAG	.	.		0.547	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
RYR1	6261	hgsc.bcm.edu	37	19	38976759	38976759	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38976759G>T	ENST00000359596.3	+	34	5464	c.5464G>T	c.(5464-5466)Ggt>Tgt	p.G1822C	RYR1_ENST00000360985.3_Missense_Mutation_p.G1822C|RYR1_ENST00000355481.4_Missense_Mutation_p.G1822C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1822	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.G1822C(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGTGCGCGACGGTGGGCAGCA	0.701																																					p.G1822C		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	.	1	Substitution - Missense(1)	lung(1)	c.G5464T						.						67.0	66.0	66.0					19																	38976759		2202	4293	6495	SO:0001583	missense	6261	exon34			CGCGACGGTGGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5464G>T	chr19.hg19:g.38976759G>T	ENSP00000352608:p.Gly1822Cys	57.0	0.0		34.0	2.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.319976	0.41096	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74106	-0.81;-0.81;-0.81	3.7	3.7	0.42460	.	0.000000	0.64402	U	0.000003	D	0.83147	0.5191	M	0.71036	2.16	0.49389	D	0.99978	D;P	0.89917	1.0;0.912	D;P	0.97110	1.0;0.706	D	0.84188	0.0443	10	0.62326	D	0.03	.	10.4488	0.44509	0.1008:0.0:0.8992:0.0	.	1822;1822	P21817-2;P21817	.;RYR1_HUMAN	C	1822	ENSP00000352608:G1822C;ENSP00000347667:G1822C;ENSP00000354254:G1822C	ENSP00000347667:G1822C	G	+	1	0	RYR1	43668599	1.000000	0.71417	0.084000	0.20598	0.774000	0.43823	5.449000	0.66619	1.886000	0.54624	0.585000	0.79938	GGT	.	.		0.701	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
ACTN4	81	hgsc.bcm.edu	37	19	39214663	39214663	+	Missense_Mutation	SNP	C	C	A	rs527527101		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39214663C>A	ENST00000252699.2	+	14	1714	c.1638C>A	c.(1636-1638)agC>agA	p.S546R	ACTN4_ENST00000390009.3_Missense_Mutation_p.S327R|ACTN4_ENST00000424234.2_Missense_Mutation_p.S156R	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	546					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGATGGAGAGCGCCATGGAGG	0.607																																					p.S546R	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1638A						.						56.0	58.0	57.0					19																	39214663		2203	4300	6503	SO:0001583	missense	81	exon14			GGAGAGCGCCATG	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1638C>A	chr19.hg19:g.39214663C>A	ENSP00000252699:p.Ser546Arg	145.0	0.0		94.0	4.0	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	hg19	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087913	0.36855	.	.	ENSG00000130402	ENST00000252699;ENST00000424234;ENST00000390009	T;T;T	0.49432	0.78;0.78;0.78	3.75	-4.54	0.03452	.	0.209202	0.40302	N	0.001127	T	0.33731	0.0873	N	0.19112	0.55	0.45634	D	0.998568	P	0.41232	0.743	P	0.49502	0.613	T	0.23476	-1.0187	10	0.54805	T	0.06	.	6.7228	0.23340	0.1153:0.3807:0.0:0.504	.	546	O43707	ACTN4_HUMAN	R	546;156;327	ENSP00000252699:S546R;ENSP00000411187:S156R;ENSP00000439497:S327R	ENSP00000252699:S546R	S	+	3	2	ACTN4	43906503	0.000000	0.05858	0.985000	0.45067	0.978000	0.69477	-2.382000	0.01064	-0.711000	0.04995	-1.036000	0.02392	AGC	.	.		0.607	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
HNRNPL	3191	hgsc.bcm.edu	37	19	39336338	39336338	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39336338A>G	ENST00000221419.5	-	4	1028	c.662T>C	c.(661-663)gTc>gCc	p.V221A	HNRNPL_ENST00000600873.1_Missense_Mutation_p.V88A|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	221	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			AATTCTCTGGACAGGGCCACA	0.498																																					p.V221A		Atlas-SNP	.											.	HNRNPL	67	.	0			c.T662C						.						85.0	80.0	82.0					19																	39336338		2203	4300	6503	SO:0001583	missense	3191	exon4			CTCTGGACAGGGC	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.662T>C	chr19.hg19:g.39336338A>G	ENSP00000221419:p.Val221Ala	79.0	0.0		66.0	4.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	A	31	5.072243	0.93950	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750;ENST00000423415;ENST00000536292	.	.	.	5.51	5.51	0.81932	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.86045	0.5839	H	0.95780	3.72	0.80722	D	1	P	0.42993	0.797	P	0.59487	0.858	D	0.89543	0.3794	9	0.87932	D	0	.	14.6052	0.68472	1.0:0.0:0.0:0.0	.	221	P14866	HNRPL_HUMAN	A	221;88;88;88;149	.	ENSP00000221419:V221A	V	-	2	0	HNRNPL	44028178	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	9.161000	0.94739	2.105000	0.64084	0.455000	0.32223	GTC	.	.		0.498	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39913584	39913584	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39913584C>T	ENST00000409794.3	+	18	2740	c.1890C>T	c.(1888-1890)ccC>ccT	p.P630P	PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000458508.2_Silent_p.P571P|PLEKHG2_ENST00000425673.1_Silent_p.P601P|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	630					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCAGCATTCCCTGCCTTACCA	0.547																																					p.P630P		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1890T						.						80.0	77.0	78.0					19																	39913584		2203	4300	6503	SO:0001819	synonymous_variant	64857	exon18			CATTCCCTGCCTT	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1890C>T	chr19.hg19:g.39913584C>T		141.0	0.0		94.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	4.617	0.114662	0.08831	.	.	ENSG00000090924	ENST00000205135	T	0.73789	-0.78	4.96	-0.411	0.12370	.	0.170426	0.28488	N	0.015179	T	0.70815	0.3267	.	.	.	0.48288	D	0.999626	.	.	.	.	.	.	T	0.65919	-0.6051	7	0.66056	D	0.02	.	2.7681	0.05327	0.1408:0.5307:0.1378:0.1907	.	.	.	.	L	498	ENSP00000205135:P498L	ENSP00000205135:P498L	P	+	2	0	PLEKHG2	44605424	0.107000	0.21998	0.101000	0.21167	0.643000	0.38383	0.099000	0.15210	0.134000	0.18681	0.467000	0.42956	CCT	.	.		0.547	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
AKT2	208	hgsc.bcm.edu	37	19	40743931	40743931	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:40743931A>G	ENST00000392038.2	-	9	1074	c.776T>C	c.(775-777)aTt>aCt	p.I259T	AKT2_ENST00000579047.1_Missense_Mutation_p.I197T|AKT2_ENST00000424901.1_Missense_Mutation_p.I259T|AKT2_ENST00000311278.6_Missense_Mutation_p.I259T	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			AGCCGAGACAATCTCTGCACC	0.607			A		"""ovarian, pancreatic """																																p.I259T		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.T776C						.						132.0	97.0	109.0					19																	40743931		2203	4300	6503	SO:0001583	missense	208	exon9			GAGACAATCTCTG	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.776T>C	chr19.hg19:g.40743931A>G	ENSP00000375892:p.Ile259Thr	128.0	0.0		82.0	4.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.511015	0.85389	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.31769	1.48;1.48;1.48	4.79	4.79	0.61399	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097802	0.64402	D	0.000002	T	0.54078	0.1836	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.58769	-0.7578	10	0.87932	D	0	.	13.7243	0.62748	1.0:0.0:0.0:0.0	.	197;259;259	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	T	259;160;259;259;79	ENSP00000375892:I259T;ENSP00000399532:I259T;ENSP00000309428:I259T	ENSP00000309428:I259T	I	-	2	0	AKT2	45435771	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.057000	0.93889	2.140000	0.66376	0.533000	0.62120	ATT	.	.		0.607	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626	
SPTBN4	57731	hgsc.bcm.edu	37	19	41038617	41038617	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41038617G>A	ENST00000352632.3	+	19	4120	c.4034G>A	c.(4033-4035)cGg>cAg	p.R1345Q	SPTBN4_ENST00000392025.1_Missense_Mutation_p.R88Q|SPTBN4_ENST00000595535.1_Missense_Mutation_p.R1345Q|SPTBN4_ENST00000598249.1_Missense_Mutation_p.R1345Q|SPTBN4_ENST00000392023.1_Missense_Mutation_p.R21Q|SPTBN4_ENST00000338932.3_Missense_Mutation_p.R1345Q			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1345					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R1345Q(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGATGGCTCCGGCACCAGGCA	0.602																																					p.R1345Q		Atlas-SNP	.											SPTBN4,NS,carcinoma,0,1	SPTBN4	213	.	1	Substitution - Missense(1)	ovary(1)	c.G4034A						.						64.0	53.0	57.0					19																	41038617		2203	4300	6503	SO:0001583	missense	57731	exon19			GGCTCCGGCACCA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.4034G>A	chr19.hg19:g.41038617G>A	ENSP00000263373:p.Arg1345Gln	118.0	0.0		69.0	3.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	31	5.076301	0.94000	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.67523	0.79;0.79;-0.27;0.79	4.86	4.86	0.63082	.	0.204266	0.32175	N	0.006477	T	0.72061	0.3414	L	0.41492	1.28	0.37052	D	0.897641	D;D;D;D;D;D	0.76494	0.979;0.981;0.996;0.998;0.992;0.999	P;P;P;P;P;D	0.68943	0.788;0.535;0.709;0.905;0.709;0.961	T	0.76884	-0.2794	10	0.66056	D	0.02	.	10.4908	0.44750	0.0898:0.0:0.9102:0.0	.	1345;88;88;21;1345;1345	E9PDB1;Q9H254-3;C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;.;.;SPTN4_HUMAN;.	Q	1345;1345;1345;88;21	ENSP00000263373:R1345Q;ENSP00000340345:R1345Q;ENSP00000375879:R88Q;ENSP00000375877:R21Q	ENSP00000340345:R1345Q	R	+	2	0	SPTBN4	45730457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.304000	0.59104	2.499000	0.84300	0.561000	0.74099	CGG	.	.		0.602	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
ADCK4	79934	hgsc.bcm.edu	37	19	41206291	41206291	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41206291C>A	ENST00000324464.3	-	11	1260	c.959G>T	c.(958-960)cGg>cTg	p.R320L	ADCK4_ENST00000450541.1_Missense_Mutation_p.R279L|ADCK4_ENST00000243583.6_Missense_Mutation_p.R279L	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	320	Protein kinase.		R -> W (in NPHS9). {ECO:0000269|PubMed:24270420}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			GCCCAGCACCCGTGTCGTGCA	0.642																																					p.R320L		Atlas-SNP	.											.	ADCK4	92	.	0			c.G959T						.						39.0	39.0	39.0					19																	41206291		2203	4300	6503	SO:0001583	missense	79934	exon11			AGCACCCGTGTCG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.959G>T	chr19.hg19:g.41206291C>A	ENSP00000315118:p.Arg320Leu	109.0	0.0		77.0	29.0	NM_024876	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664953	0.88251	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.52295	0.67;0.67;0.67	5.75	5.75	0.90469	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.69869	0.3159	M	0.87547	2.89	0.58432	D	0.999997	D;D	0.63046	0.978;0.992	P;D	0.66196	0.81;0.942	T	0.74312	-0.3706	10	0.66056	D	0.02	-31.0909	12.1003	0.53780	0.0:0.9204:0.0:0.0796	.	320;279	Q96D53;Q96D53-2	ADCK4_HUMAN;.	L	320;279;279	ENSP00000315118:R320L;ENSP00000412839:R279L;ENSP00000243583:R279L	ENSP00000243583:R279L	R	-	2	0	ADCK4	45898131	0.186000	0.23225	0.994000	0.49952	0.747000	0.42532	2.066000	0.41452	2.720000	0.93068	0.563000	0.77884	CGG	.	.		0.642	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
EGLN2	112398	hgsc.bcm.edu	37	19	41306565	41306565	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41306565G>A	ENST00000593726.1	+	1	1116	c.88G>A	c.(88-90)Ggc>Agc	p.G30S	EGLN2_ENST00000406058.2_Missense_Mutation_p.G30S|RAB4B-EGLN2_ENST00000594136.1_3'UTR|EGLN2_ENST00000303961.4_Missense_Mutation_p.G30S|EGLN2_ENST00000594140.1_5'Flank|CTC-490E21.12_ENST00000601627.1_5'Flank			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	30					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GCCTGAGCCTGGCCGGGCCAG	0.652																																					p.G30S		Atlas-SNP	.											.	EGLN2	31	.	0			c.G88A						.						45.0	39.0	41.0					19																	41306565		2203	4300	6503	SO:0001583	missense	112398	exon2			GAGCCTGGCCGGG	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.88G>A	chr19.hg19:g.41306565G>A	ENSP00000469686:p.Gly30Ser	108.0	0.0		96.0	4.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536840	0.27475	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.30448	1.53;1.53	4.04	0.449	0.16619	.	0.434068	0.21393	N	0.075276	T	0.08980	0.0222	N	0.02539	-0.55	0.28523	N	0.912943	B	0.02656	0.0	B	0.04013	0.001	T	0.34850	-0.9812	10	0.08837	T	0.75	-6.1654	6.3273	0.21251	0.6573:0.0:0.3427:0.0	.	30	Q96KS0	EGLN2_HUMAN	S	30	ENSP00000307080:G30S;ENSP00000385253:G30S	ENSP00000307080:G30S	G	+	1	0	EGLN2	45998405	0.123000	0.22298	1.000000	0.80357	0.994000	0.84299	0.411000	0.21115	0.301000	0.22738	0.491000	0.48974	GGC	.	.		0.652	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
BCKDHA	593	hgsc.bcm.edu	37	19	41916689	41916689	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41916689G>A	ENST00000269980.2	+	2	624	c.256G>A	c.(256-258)Ggc>Agc	p.G86S	CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.G120S|BCKDHA_ENST00000595085.1_Missense_Mutation_p.G120S|CTC-435M10.3_ENST00000604424.1_3'UTR|BCKDHA_ENST00000457836.2_Missense_Mutation_p.G64S	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	86					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)	p.G86C(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GGACCGGCAAGGCCAGATCAT	0.627																																					p.G86S		Atlas-SNP	.											BCKDHA,colon,carcinoma,0,1	BCKDHA	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.G256A						.						62.0	64.0	64.0					19																	41916689		2203	4300	6503	SO:0001583	missense	593	exon2			CGGCAAGGCCAGA	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.256G>A	chr19.hg19:g.41916689G>A	ENSP00000269980:p.Gly86Ser	117.0	0.0		95.0	4.0	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	hg19	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	G	35	5.554705	0.96501	.	.	ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	D;D;D;D	0.99167	-5.51;-5.51;-5.51;-5.51	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.99001	0.9659	L	0.54908	1.71	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;0.978	D;D;D;D	0.76575	0.988;0.975;0.985;0.932	D	0.99909	1.1192	10	0.87932	D	0	-41.0027	17.9433	0.89031	0.0:0.0:1.0:0.0	.	64;86;86;120	B4DP47;Q59EI3;P12694;F5H5P2	.;.;ODBA_HUMAN;.	S	120;86;86;64;86	ENSP00000443246:G120S;ENSP00000269980:G86S;ENSP00000440345:G86S;ENSP00000416000:G64S	ENSP00000269980:G86S	G	+	1	0	BCKDHA;CTC-435M10.3	46608529	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.316000	0.96319	2.550000	0.86006	0.643000	0.83706	GGC	.	.		0.627	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
PSG9	5678	hgsc.bcm.edu	37	19	43766182	43766182	+	Missense_Mutation	SNP	C	C	A	rs149244305		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:43766182C>A	ENST00000270077.3	-	3	635	c.539G>T	c.(538-540)tGg>tTg	p.W180L	PSG9_ENST00000418820.2_Intron|PSG9_ENST00000443718.3_Intron|PSG9_ENST00000244293.7_Missense_Mutation_p.W180L|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000593948.1_Missense_Mutation_p.W180L|PSG9_ENST00000596730.1_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	180	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.W180*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				ATTCATCCACCATAGGTAGCT	0.517																																					p.W180L		Atlas-SNP	.											PSG9,arm,malignant_melanoma,0,1	PSG9	77	.	1	Substitution - Nonsense(1)	skin(1)	c.G539T						.						252.0	247.0	249.0					19																	43766182		2203	4300	6503	SO:0001583	missense	5678	exon3			ATCCACCATAGGT	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.539G>T	chr19.hg19:g.43766182C>A	ENSP00000270077:p.Trp180Leu	242.0	0.0		122.0	5.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	13.06	2.125030	0.37533	.	.	ENSG00000183668	ENST00000270077;ENST00000435220;ENST00000244293	T;T	0.14022	2.54;2.54	2.12	2.12	0.27331	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41488	0.1161	M	0.90977	3.165	0.26934	N	0.966398	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.999	T	0.15464	-1.0436	9	0.87932	D	0	.	7.8962	0.29708	0.0:1.0:0.0:0.0	.	180;180;180	Q15227;Q6LEU7;Q00887	.;.;PSG9_HUMAN	L	180;141;180	ENSP00000270077:W180L;ENSP00000244293:W180L	ENSP00000244293:W180L	W	-	2	0	PSG9	48458022	0.024000	0.19004	0.047000	0.18901	0.005000	0.04900	0.295000	0.19065	0.860000	0.35481	0.194000	0.17425	TGG	.	.		0.517	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
PHLDB3	653583	hgsc.bcm.edu	37	19	43998856	43998856	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:43998856G>A	ENST00000292140.5	-	9	1507	c.1147C>T	c.(1147-1149)Cag>Tag	p.Q383*		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	383							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGAGGCACCTGCAGGGAGCTG	0.602																																					p.Q383X		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1147T						.						27.0	32.0	30.0					19																	43998856		1968	4160	6128	SO:0001587	stop_gained	653583	exon9			GCACCTGCAGGGA		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1147C>T	chr19.hg19:g.43998856G>A	ENSP00000292140:p.Gln383*	157.0	0.0		96.0	4.0	NM_198850	Q8N7Z4	Nonsense_Mutation	SNP	ENST00000292140.5	hg19	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	40	8.240158	0.98722	.	.	ENSG00000176531	ENST00000292140	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	13.3415	0.60547	0.0:0.0:1.0:0.0	.	.	.	.	X	383	.	ENSP00000292140:Q383X	Q	-	1	0	PHLDB3	48690696	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	3.119000	0.50422	2.266000	0.75297	0.460000	0.39030	CAG	.	.		0.602	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
ZNF229	7772	hgsc.bcm.edu	37	19	44934658	44934658	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:44934658G>T	ENST00000588931.1	-	6	731	c.298C>A	c.(298-300)Cac>Aac	p.H100N	ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.H94N	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	100	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AGCTCTTTGTGTGAAAAGAAC	0.398																																					p.H100N		Atlas-SNP	.											.	ZNF229	123	.	0			c.C298A						.						57.0	55.0	56.0					19																	44934658		1841	4091	5932	SO:0001583	missense	7772	exon6			CTTTGTGTGAAAA	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.298C>A	chr19.hg19:g.44934658G>T	ENSP00000466519:p.His100Asn	118.0	0.0		95.0	4.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	G	2.312	-0.357768	0.05138	.	.	ENSG00000167383	ENST00000291187	.	.	.	2.99	0.432	0.16529	Krueppel-associated box (1);	.	.	.	.	T	0.19565	0.0470	N	0.24115	0.695	0.09310	N	1	B	0.30068	0.267	B	0.27500	0.08	T	0.20472	-1.0274	8	0.25106	T	0.35	.	5.1714	0.15112	0.1491:0.2006:0.6504:0.0	.	100	Q9UJW7	ZN229_HUMAN	N	100	.	ENSP00000291187:H100N	H	-	1	0	ZNF229	49626498	0.001000	0.12720	0.002000	0.10522	0.295000	0.27426	0.233000	0.17911	0.145000	0.18977	0.609000	0.83330	CAC	.	.		0.398	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
CLPTM1	1209	hgsc.bcm.edu	37	19	45489769	45489769	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45489769C>A	ENST00000337392.5	+	7	879	c.729C>A	c.(727-729)acC>acA	p.T243T	CLPTM1_ENST00000541297.2_Silent_p.T229T|CLPTM1_ENST00000546079.1_Silent_p.T141T|CLPTM1_ENST00000589158.1_3'UTR	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	243					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CCAACATCACCATCAACATCG	0.622																																					p.T243T		Atlas-SNP	.											.	CLPTM1	109	.	0			c.C729A						.						164.0	125.0	138.0					19																	45489769		2203	4300	6503	SO:0001819	synonymous_variant	1209	exon7			CATCACCATCAAC	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.729C>A	chr19.hg19:g.45489769C>A		93.0	0.0		72.0	4.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	hg19	CCDS12651.1																																																																																			.	.		0.622	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
KLC3	147700	hgsc.bcm.edu	37	19	45850019	45850019	+	Missense_Mutation	SNP	C	C	A	rs76874841	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45850019C>A	ENST00000391946.2	+	3	578	c.476C>A	c.(475-477)cCg>cAg	p.P159Q	KLC3_ENST00000470402.1_Missense_Mutation_p.P173Q|KLC3_ENST00000585434.1_Missense_Mutation_p.P159Q	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	159					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TACGACCCACCGGCGGAGAGC	0.701																																					p.P159Q		Atlas-SNP	.											.	KLC3	37	.	0			c.C476A						.						5.0	6.0	5.0					19																	45850019		1973	4041	6014	SO:0001583	missense	147700	exon3			ACCCACCGGCGGA	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.476C>A	chr19.hg19:g.45850019C>A	ENSP00000375810:p.Pro159Gln	102.0	0.0		65.0	4.0	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	hg19	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	C	11.10	1.538685	0.27475	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	T;T	0.40756	1.02;1.02	4.26	3.22	0.36961	Rabaptin, GTPase-Rab5 binding (1);	0.285619	0.29537	N	0.011862	T	0.26629	0.0651	N	0.04508	-0.205	0.09310	N	1	P;P;P	0.47762	0.878;0.878;0.9	P;P;P	0.50352	0.505;0.505;0.638	T	0.04255	-1.0965	10	0.46703	T	0.11	-8.1633	7.3624	0.26754	0.0:0.8817:0.0:0.1183	.	159;173;159	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	Q	159;173	ENSP00000375810:P159Q;ENSP00000436019:P173Q	ENSP00000375810:P159Q	P	+	2	0	KLC3	50541859	0.269000	0.24143	0.141000	0.22245	0.022000	0.10575	2.700000	0.47085	2.390000	0.81377	0.455000	0.32223	CCG	.	C|0.998;G|0.002		0.701	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
ERCC2	2068	hgsc.bcm.edu	37	19	45871940	45871940	+	Missense_Mutation	SNP	G	G	T	rs142462393		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45871940G>T	ENST00000391945.4	-	5	385	c.308C>A	c.(307-309)cCg>cAg	p.P103Q	ERCC2_ENST00000221481.6_Missense_Mutation_p.P103Q|ERCC2_ENST00000391944.3_Missense_Mutation_p.P103Q|ERCC2_ENST00000485403.2_Missense_Mutation_p.P79Q|ERCC2_ENST00000391940.4_Missense_Mutation_p.P79Q	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	103	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TCCCAGAAACGGCAGCTTCTC	0.527			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.P103Q		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.C308A						.						44.0	44.0	44.0					19																	45871940		2203	4300	6503	SO:0001583	missense	2068	exon5	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGAAACGGCAGCT		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.308C>A	chr19.hg19:g.45871940G>T	ENSP00000375809:p.Pro103Gln	125.0	0.0		86.0	4.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	G	8.502	0.864534	0.17250	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940;ENST00000221481	T;D;T;T	0.82526	-0.45;-1.62;1.0;-0.45	5.09	0.408	0.16377	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.608859	0.17906	N	0.158018	T	0.74176	0.3682	L	0.27053	0.805	0.09310	N	1	B;P;B	0.39920	0.097;0.695;0.011	B;B;B	0.43478	0.076;0.421;0.048	T	0.63233	-0.6683	10	0.18276	T	0.48	-9.7991	13.6809	0.62484	0.0:0.0:0.3149:0.6851	.	103;79;103	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	Q	53;79;103;103;79;103	ENSP00000375809:P103Q;ENSP00000375808:P103Q;ENSP00000375804:P79Q;ENSP00000221481:P103Q	ENSP00000221481:P103Q	P	-	2	0	ERCC2	50563780	0.191000	0.23288	0.034000	0.17996	0.553000	0.35397	0.322000	0.19576	0.033000	0.15463	-0.226000	0.12346	CCG	.	G|1.000;A|0.000		0.527	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
ERCC1	2067	hgsc.bcm.edu	37	19	45920105	45920105	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45920105G>T	ENST00000300853.3	-	6	1167	c.576C>A	c.(574-576)gcC>gcA	p.A192A	ERCC1_ENST00000340192.7_Silent_p.A192A|ERCC1_ENST00000591636.1_Silent_p.A192A|ERCC1_ENST00000423698.2_Silent_p.A120A|ERCC1_ENST00000588738.1_5'Flank|ERCC1_ENST00000013807.5_Silent_p.A192A|ERCC1_ENST00000589165.1_Silent_p.A192A	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	192					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		ATGTGCAGTCGGCCAGGATAC	0.547								Nucleotide excision repair (NER)																													p.A192A		Atlas-SNP	.											.	ERCC1	46	.	0			c.C576A						.						77.0	63.0	68.0					19																	45920105		2203	4300	6503	SO:0001819	synonymous_variant	2067	exon6			GCAGTCGGCCAGG		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.576C>A	chr19.hg19:g.45920105G>T		111.0	0.0		77.0	4.0	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Silent	SNP	ENST00000300853.3	hg19	CCDS12662.1																																																																																			.	.		0.547	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
PPM1N	147699	hgsc.bcm.edu	37	19	46003767	46003767	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:46003767C>A	ENST00000451287.2	+	3	1111	c.1111C>A	c.(1111-1113)Ctg>Atg	p.L371M	PPM1N_ENST00000396736.2_Missense_Mutation_p.L53M|PPM1N_ENST00000456399.2_Missense_Mutation_p.L53M|PPM1N_ENST00000396737.2_Missense_Mutation_p.L53M|PPM1N_ENST00000396735.2_Missense_Mutation_p.L53M|PPM1N_ENST00000401593.1_Missense_Mutation_p.L53M|PPM1N_ENST00000401705.1_Missense_Mutation_p.L53M|PPM1N_ENST00000324688.4_3'UTR	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	371							magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						TTTCAGGACTCTGGCCTCAGA	0.587																																					p.L371M		Atlas-SNP	.											.	PPM1N	25	.	0			c.C1111A						.						27.0	27.0	27.0					19																	46003767		1909	4119	6028	SO:0001583	missense	147699	exon3			AGGACTCTGGCCT	AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.1111C>A	chr19.hg19:g.46003767C>A	ENSP00000397050:p.Leu371Met	108.0	0.0		91.0	4.0	NM_001080401	Q6P662	Missense_Mutation	SNP	ENST00000451287.2	hg19	CCDS46115.1	.	.	.	.	.	.	.	.	.	.	c	14.15	2.449375	0.43531	.	.	ENSG00000213889	ENST00000401705;ENST00000456399;ENST00000396737;ENST00000451287;ENST00000396734;ENST00000396735;ENST00000401593;ENST00000402807;ENST00000396736	T	0.38240	1.15	3.55	2.5	0.30297	Protein serine/threonine phosphatase 2C, C-terminal (3);	.	.	.	.	T	0.51839	0.1698	M	0.74258	2.255	0.80722	D	1	D	0.56287	0.975	D	0.67382	0.951	T	0.49409	-0.8943	9	0.45353	T	0.12	.	6.08	0.19936	0.0:0.7676:0.0:0.2324	.	371	Q8N819	PPM1N_HUMAN	M	53;53;53;371;371;53;53;53;53	ENSP00000397050:L371M	ENSP00000379960:L371M	L	+	1	2	PPM1N	50695607	0.332000	0.24722	1.000000	0.80357	0.807000	0.45602	0.735000	0.26115	1.077000	0.40990	0.651000	0.88453	CTG	.	.		0.587	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401	
MEIS3	56917	hgsc.bcm.edu	37	19	47920594	47920594	+	Missense_Mutation	SNP	G	G	T	rs200901098		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:47920594G>T	ENST00000558555.1	-	2	213	c.26C>A	c.(25-27)cCg>cAg	p.P9Q	MEIS3_ENST00000559524.1_Missense_Mutation_p.P9Q|MEIS3_ENST00000561096.1_Missense_Mutation_p.P97Q|MEIS3_ENST00000441740.2_Missense_Mutation_p.P9Q|MEIS3_ENST00000331559.5_Missense_Mutation_p.P9Q|MEIS3_ENST00000561293.1_Missense_Mutation_p.P9Q			Q99687	MEIS3_HUMAN	Meis homeobox 3	9					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		TGGGTAGTGCGGCAGCTCATC	0.662																																					p.P9Q		Atlas-SNP	.											.	MEIS3	40	.	0			c.C26A						.						30.0	36.0	34.0					19																	47920594		2202	4299	6501	SO:0001583	missense	56917	exon2			TAGTGCGGCAGCT	BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"""Homeoboxes / TALE class"""	29537	protein-coding gene	gene with protein product			"""Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"""			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.26C>A	chr19.hg19:g.47920594G>T	ENSP00000454073:p.Pro9Gln	121.0	0.0		99.0	4.0	NM_001009813	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.19	2.460721	0.43736	.	.	ENSG00000105419	ENST00000331559;ENST00000441740	T;T	0.34859	1.34;1.34	3.49	2.41	0.29592	.	0.442693	0.20577	N	0.089613	T	0.35364	0.0929	L	0.52573	1.65	0.24190	N	0.995559	B;B;D	0.55385	0.286;0.144;0.971	B;B;P	0.49597	0.155;0.091;0.616	T	0.15954	-1.0419	10	0.62326	D	0.03	-12.1835	4.7832	0.13213	0.1237:0.2398:0.6365:0.0	.	9;9;9	Q99687;Q99687-3;Q99687-2	MEIS3_HUMAN;.;.	Q	9	ENSP00000333552:P9Q;ENSP00000388667:P9Q	ENSP00000333552:P9Q	P	-	2	0	MEIS3	52612406	0.994000	0.37717	0.989000	0.46669	0.890000	0.51754	1.642000	0.37207	1.008000	0.39264	0.555000	0.69702	CCG	.	G|1.000;A|0.000		0.662	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48259071	48259071	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:48259071A>G	ENST00000246802.5	+	10	1326	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	SNORD23_ENST00000408876.1_RNA|GLTSCR2_ENST00000598681.1_Intron|CTD-2571L23.6_ENST00000602048.1_RNA	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	430						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CTCGCTCAGGACCCTGAAGGT	0.642																																					p.T430A	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.A1288G						.						62.0	44.0	50.0					19																	48259071		2202	4299	6501	SO:0001583	missense	29997	exon10			CTCAGGACCCTGA	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1288A>G	chr19.hg19:g.48259071A>G	ENSP00000246802:p.Thr430Ala	134.0	0.0		94.0	4.0	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	hg19	CCDS12705.1	.	.	.	.	.	.	.	.	.	.	A	7.565	0.665510	0.14710	.	.	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.45668	0.89	5.09	4.08	0.47627	.	0.420791	0.25291	N	0.031725	T	0.40297	0.1111	M	0.76328	2.33	0.29348	N	0.865573	B	0.13145	0.007	B	0.12156	0.007	T	0.37596	-0.9699	10	0.36615	T	0.2	-16.0127	7.2814	0.26314	0.9014:0.0:0.0986:0.0	.	430	Q9NZM5	GSCR2_HUMAN	A	430;424;215	ENSP00000246802:T430A	ENSP00000246802:T430A	T	+	1	0	GLTSCR2	52950883	0.808000	0.29022	0.998000	0.56505	0.675000	0.39556	1.383000	0.34385	0.960000	0.38005	0.533000	0.62120	ACC	.	.		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
TPRX1	284355	hgsc.bcm.edu	37	19	48305658	48305658	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:48305658G>A	ENST00000322175.3	-	2	765	c.610C>T	c.(610-612)Cca>Tca	p.P204S	TPRX1_ENST00000535759.1_Missense_Mutation_p.P301S|TPRX1_ENST00000543508.1_Missense_Mutation_p.P194S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	204	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		atcgggcctgggatcgggact	0.662																																					p.P204S	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,caecum,carcinoma,0,1	TPRX1	46	.	0			c.C610T						.																																			SO:0001583	missense	284355	exon2			GGCCTGGGATCGG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.610C>T	chr19.hg19:g.48305658G>A	ENSP00000323455:p.Pro204Ser	97.0	1.0		86.0	5.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	4.478	0.088566	0.08583	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.65549	-0.16;-0.16;-0.16	0.361	-0.722	0.11184	.	.	.	.	.	T	0.44414	0.1292	N	0.08118	0	0.09310	N	1	D	0.55172	0.97	P	0.50791	0.65	T	0.34700	-0.9818	8	0.46703	T	0.11	.	.	.	.	.	204	Q8N7U7	TPRX1_HUMAN	S	204;301;194	ENSP00000323455:P204S;ENSP00000438832:P301S;ENSP00000438712:P194S	ENSP00000323455:P204S	P	-	1	0	TPRX1	52997470	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-2.095000	0.01350	-0.452000	0.07087	-0.459000	0.05422	CCA	.	.		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48609797	48609797	+	5'UTR	SNP	G	G	T	rs570635333		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:48609797G>T	ENST00000599921.1	-	0	347				PLA2G4C_ENST00000599111.1_Silent_p.T17T|PLA2G4C_ENST00000354276.3_5'UTR|PLA2G4C_ENST00000413144.2_5'Flank			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)						arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GGTGCACTGCGGTCAGAAAAT	0.517													g|||	1	0.000199681	0.0008	0.0	5008	,	,		18239	0.0		0.0	False		,,,				2504	0.0				p.T17T		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C51A						.						157.0	130.0	140.0					19																	48609797		2203	4300	6503	SO:0001623	5_prime_UTR_variant	8605	exon2			CACTGCGGTCAGA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.-11C>A	chr19.hg19:g.48609797G>T		200.0	0.0		121.0	5.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	hg19	CCDS12710.1																																																																																			.	.		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
PPFIA3	8541	hgsc.bcm.edu	37	19	49632641	49632641	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:49632641G>T	ENST00000334186.4	+	5	861	c.512G>T	c.(511-513)cGg>cTg	p.R171L	PPFIA3_ENST00000602351.1_Missense_Mutation_p.R171L	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	171					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		CCCCAGGTCCGGGAGCGGCTG	0.622																																					p.R171L		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G512T						.						8.0	10.0	9.0					19																	49632641		2110	4138	6248	SO:0001583	missense	8541	exon5			AGGTCCGGGAGCG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"""Sterile alpha motif (SAM) domain containing"""	9247	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3"", ""liprin-alpha 3"", ""liprin"""	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.512G>T	chr19.hg19:g.49632641G>T	ENSP00000335614:p.Arg171Leu	133.0	0.0		113.0	5.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	36	5.735724	0.96865	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.55588	0.51	4.56	4.56	0.56223	.	0.000000	0.43579	D	0.000551	T	0.74045	0.3665	M	0.83312	2.635	0.80722	D	1	D;P;D	0.76494	0.982;0.865;0.999	P;P;D	0.71656	0.869;0.673;0.974	T	0.79009	-0.1978	10	0.87932	D	0	-21.0017	16.6387	0.85066	0.0:0.0:1.0:0.0	.	95;171;171	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	L	171;95	ENSP00000335614:R171L	ENSP00000335614:R171L	R	+	2	0	PPFIA3	54324453	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.670000	0.74467	2.563000	0.86464	0.561000	0.74099	CGG	.	.		0.622	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660	
RPL13A	23521	hgsc.bcm.edu	37	19	49994320	49994320	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:49994320T>C	ENST00000391857.4	+	6	442	c.366T>C	c.(364-366)gcT>gcC	p.A122A	SNORD32A_ENST00000364805.1_RNA|RPL13A_ENST00000477613.2_3'UTR|SNORD34_ENST00000365633.1_RNA|SNORD35A_ENST00000363389.1_RNA|SNORD33_ENST00000362761.1_RNA	NM_001270491.1|NM_012423.3	NP_001257420.1|NP_036555.1	P40429	RL13A_HUMAN	ribosomal protein L13a	122					cellular protein metabolic process (GO:0044267)|cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of formation of translation preinitiation complex (GO:1901194)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|GAIT complex (GO:0097452)|large ribosomal subunit (GO:0015934)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)	2		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		TGGTTCCTGCTGCCCTCAAGG	0.582																																					p.A122A		Atlas-SNP	.											.	RPL13A	13	.	0			c.T366C						.						55.0	52.0	53.0					19																	49994320		2203	4300	6503	SO:0001819	synonymous_variant	23521	exon6			TCCTGCTGCCCTC	X56932	CCDS12768.1, CCDS74421.1	19q13.3	2011-04-06			ENSG00000142541	ENSG00000142541		"""L ribosomal proteins"""	10304	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 1"""	TSTA1			Standard	NM_012423		Approved	L13A	uc031rlt.1	P40429	OTTHUMG00000134289	ENST00000391857.4:c.366T>C	chr19.hg19:g.49994320T>C		100.0	0.0		85.0	4.0	NM_012423	A8K505	Silent	SNP	ENST00000391857.4	hg19	CCDS12768.1																																																																																			.	.		0.582	RPL13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258989.1		
MYH14	79784	hgsc.bcm.edu	37	19	50792838	50792838	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:50792838A>G	ENST00000596571.1	+	32	4775	c.4775A>G	c.(4774-4776)cAg>cGg	p.Q1592R	MYH14_ENST00000425460.1_Missense_Mutation_p.Q1600R|MYH14_ENST00000376970.2_Missense_Mutation_p.Q1625R|MYH14_ENST00000601313.1_Missense_Mutation_p.Q1633R|MYH14_ENST00000440075.2_Missense_Mutation_p.Q1633R|MYH14_ENST00000262269.8_Missense_Mutation_p.Q1633R|MYH14_ENST00000598205.1_Missense_Mutation_p.Q1600R			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1592					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CTCAAGACTCAGCATGAGCGT	0.597																																					p.Q1633R		Atlas-SNP	.											.	MYH14	261	.	0			c.A4898G						.						49.0	60.0	56.0					19																	50792838		2194	4294	6488	SO:0001583	missense	79784	exon35			AGACTCAGCATGA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4775A>G	chr19.hg19:g.50792838A>G	ENSP00000472819:p.Gln1592Arg	82.0	0.0		70.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.070818	0.76301	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	3.95	3.95	0.45737	Myosin tail (1);	.	.	.	.	D	0.85217	0.5646	M	0.67625	2.065	0.47374	D	0.999401	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.86385	0.1732	9	0.87932	D	0	.	11.0935	0.48130	1.0:0.0:0.0:0.0	.	1633;1592;1600	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	R	1633;1625;1600;1376;1633	ENSP00000406273:Q1633R;ENSP00000366169:Q1625R;ENSP00000407879:Q1600R;ENSP00000262269:Q1633R	ENSP00000262269:Q1633R	Q	+	2	0	MYH14	55484650	1.000000	0.71417	0.763000	0.31416	0.971000	0.66376	8.881000	0.92415	1.800000	0.52685	0.402000	0.26972	CAG	.	.		0.597	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
MYH14	79784	hgsc.bcm.edu	37	19	50794172	50794172	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:50794172A>G	ENST00000596571.1	+	33	4871	c.4871A>G	c.(4870-4872)gAg>gGg	p.E1624G	MYH14_ENST00000425460.1_Missense_Mutation_p.E1632G|MYH14_ENST00000376970.2_Missense_Mutation_p.E1657G|MYH14_ENST00000601313.1_Missense_Mutation_p.E1665G|MYH14_ENST00000440075.2_Missense_Mutation_p.E1665G|MYH14_ENST00000262269.8_Missense_Mutation_p.E1665G|MYH14_ENST00000598205.1_Missense_Mutation_p.E1632G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1624					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GAGCGGGATGAGGAGCGGAAG	0.652																																					p.E1665G		Atlas-SNP	.											.	MYH14	261	.	0			c.A4994G						.						17.0	22.0	21.0					19																	50794172		2064	4191	6255	SO:0001583	missense	79784	exon36			GGGATGAGGAGCG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4871A>G	chr19.hg19:g.50794172A>G	ENSP00000472819:p.Glu1624Gly	151.0	0.0		99.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.127735	0.77549	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15	4.42	4.42	0.53409	Myosin tail (1);	.	.	.	.	D	0.89962	0.6867	M	0.65975	2.015	0.47994	D	0.999561	D;P;P	0.54964	0.969;0.763;0.721	P;P;B	0.56960	0.81;0.507;0.373	D	0.89650	0.3869	9	0.45353	T	0.12	.	11.9119	0.52743	1.0:0.0:0.0:0.0	.	1665;1624;1632	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	G	1665;1657;1632;1408;1665	ENSP00000406273:E1665G;ENSP00000366169:E1657G;ENSP00000407879:E1632G;ENSP00000262269:E1665G	ENSP00000262269:E1665G	E	+	2	0	MYH14	55485984	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	5.644000	0.67902	1.979000	0.57680	0.402000	0.26972	GAG	.	.		0.652	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
KLK7	5650	hgsc.bcm.edu	37	19	51485084	51485084	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:51485084G>A	ENST00000391807.1	-	3	261	c.160C>T	c.(160-162)Cac>Tac	p.H54Y	KLK7_ENST00000595820.1_Missense_Mutation_p.H54Y|KLK7_ENST00000597707.1_5'UTR|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_Intron|KLK7_ENST00000595638.1_5'Flank	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	54	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		CCTCCGCAGTGGAGCTGATTG	0.617																																					p.H54Y		Atlas-SNP	.											.	KLK7	40	.	0			c.C160T						.						43.0	38.0	39.0					19																	51485084		2203	4300	6503	SO:0001583	missense	5650	exon3			CGCAGTGGAGCTG	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6368	protein-coding gene	gene with protein product		604438	"""kallikrein 7 (chymotryptic, stratum corneum)"""	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.160C>T	chr19.hg19:g.51485084G>A	ENSP00000375683:p.His54Tyr	136.0	0.0		54.0	4.0	NM_139277	A8K0U5|Q8N5N9|Q8NFV7	Missense_Mutation	SNP	ENST00000391807.1	hg19	CCDS12812.1	.	.	.	.	.	.	.	.	.	.	g	4.683	0.127019	0.08931	.	.	ENSG00000169035	ENST00000304045;ENST00000391807	D	0.88354	-2.37	4.39	2.22	0.28083	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.225297	0.22369	U	0.060966	T	0.79185	0.4403	N	0.13235	0.315	0.53688	D	0.999978	B	0.27656	0.184	B	0.32393	0.145	T	0.71477	-0.4581	10	0.54805	T	0.06	.	8.5579	0.33492	0.1963:0.0:0.8037:0.0	.	54	P49862	KLK7_HUMAN	Y	54	ENSP00000375683:H54Y	ENSP00000304791:H54Y	H	-	1	0	KLK7	56176896	0.916000	0.31088	0.007000	0.13788	0.037000	0.13140	1.203000	0.32284	0.324000	0.23333	0.552000	0.68991	CAC	.	.		0.617	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046	
KLK9	284366	hgsc.bcm.edu	37	19	51506518	51506518	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:51506518T>C	ENST00000594211.1	-	5	604		c.e5-2		KLK8_ENST00000391806.2_5'Flank|KLK8_ENST00000320838.5_5'Flank|KLK8_ENST00000347619.4_5'Flank|KLK8_ENST00000593490.1_5'Flank|KLK9_ENST00000376832.4_Splice_Site|KLK9_ENST00000250366.6_Splice_Site|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000291726.7_5'Flank|KLK8_ENST00000600767.1_5'Flank			Q9UKQ9	KLK9_HUMAN	kallikrein-related peptidase 9							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7		all_neural(266;0.0652)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		AGAGTCACCCTGTACGCGAGA	0.632																																					.		Atlas-SNP	.											KLK9,colon,carcinoma,0,1	KLK9	27	.	0			c.604-2A>G						.						36.0	39.0	38.0					19																	51506518		2203	4300	6503	SO:0001630	splice_region_variant	284366	exon6			TCACCCTGTACGC	AF135026	CCDS12816.1	19q13.33	2008-02-05	2006-10-27					"""Kallikreins"""	6370	protein-coding gene	gene with protein product		605504	"""kallikrein 9"""			16800724, 16800723	Standard	NM_012315		Approved	KLK-L3	uc002pux.1	Q9UKQ9		ENST00000594211.1:c.604-2A>G	chr19.hg19:g.51506518T>C		55.0	0.0		35.0	2.0	NM_012315	Q6QA55	Splice_Site	SNP	ENST00000594211.1	hg19	CCDS12816.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.408344	0.62399	.	.	ENSG00000213022	ENST00000376832;ENST00000250366	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4408	0.55623	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLK9	56198330	1.000000	0.71417	0.995000	0.50966	0.781000	0.44180	6.068000	0.71201	2.099000	0.63709	0.459000	0.35465	.	.	.		0.632	KLK9-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465226.1	NM_012315	Intron
ZNF841	284371	hgsc.bcm.edu	37	19	52569527	52569527	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:52569527G>T	ENST00000426391.2	-	5	1811	c.1260C>A	c.(1258-1260)acC>acA	p.T420T	ZNF841_ENST00000594295.1_Silent_p.T536T|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000389534.4_Silent_p.T536T|ZNF841_ENST00000359973.2_Intron|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	420					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)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GTTTCTCTCCGGTATGAATTC	0.398																																					p.T536T		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1608A						.						87.0	81.0	83.0					19																	52569527		692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			CTCTCCGGTATGA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1260C>A	chr19.hg19:g.52569527G>T		74.0	0.0		79.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	hg19																																																																																				.	.		0.398	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ZNF841	284371	hgsc.bcm.edu	37	19	52570470	52570470	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:52570470G>T	ENST00000426391.2	-	5	868	c.317C>A	c.(316-318)cCa>cAa	p.P106Q	ZNF841_ENST00000594295.1_Missense_Mutation_p.P222Q|ZNF841_ENST00000389534.4_Missense_Mutation_p.P222Q|ZNF841_ENST00000359973.2_Missense_Mutation_p.P106Q|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	106					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)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TCTTTGAAGTGGTGAAGCTAA	0.353																																					p.P222Q		Atlas-SNP	.											.	ZNF841	183	.	0			c.C665A						.						81.0	63.0	69.0					19																	52570470		692	1591	2283	SO:0001583	missense	284371	exon7			TGAAGTGGTGAAG	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.317C>A	chr19.hg19:g.52570470G>T	ENSP00000415453:p.Pro106Gln	103.0	0.0		76.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459228	0.04508	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.08370	3.51;3.33;3.1	1.74	0.511	0.16989	.	.	.	.	.	T	0.04679	0.0127	N	0.00869	-1.13	0.09310	N	1	D;P;D	0.76494	0.999;0.946;0.998	D;P;D	0.83275	0.996;0.654;0.987	T	0.29701	-1.0003	9	0.10636	T	0.68	.	1.9647	0.03393	0.2407:0.0:0.4599:0.2994	.	222;106;106	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	Q	222;106;106	ENSP00000374185:P222Q;ENSP00000415453:P106Q;ENSP00000353060:P106Q	ENSP00000353060:P106Q	P	-	2	0	ZNF841	57262282	0.001000	0.12720	0.016000	0.15963	0.322000	0.28314	-0.184000	0.09698	0.195000	0.20347	0.313000	0.20887	CCA	.	.		0.353	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ZNF460	10794	hgsc.bcm.edu	37	19	57802158	57802158	+	Silent	SNP	A	A	G	rs368592252		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:57802158A>G	ENST00000360338.3	+	3	571	c.249A>G	c.(247-249)ggA>ggG	p.G83G	ZNF460_ENST00000537645.1_Silent_p.G42G	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	83	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGGCACAGGGAGTCCCAAGAT	0.527																																					p.G83G		Atlas-SNP	.											.	ZNF460	59	.	0			c.A249G						.	A		0,4406		0,0,2203	73.0	69.0	70.0		249	-0.4	0.0	19		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		83/563	57802158	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			ACAGGGAGTCCCA	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.249A>G	chr19.hg19:g.57802158A>G		111.0	0.0		80.0	4.0	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	hg19	CCDS12949.1																																																																																			.	.		0.527	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
ZNF587B	100293516	hgsc.bcm.edu	37	19	58352852	58352852	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58352852T>C	ENST00000442832.4	+	3	1044	c.810T>C	c.(808-810)taT>taC	p.Y270Y	ZNF587B_ENST00000594901.1_Silent_p.Y270Y|CTD-2583A14.10_ENST00000598031.1_Intron|ZNF587B_ENST00000316462.4_Intron	NM_001204818.1	NP_001191747.1	E7ETH6	Z587B_HUMAN	zinc finger protein 587B	270					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAAGACCTTATGAATGTGGAG	0.388																																					p.Y270Y		Atlas-SNP	.											.	.	.	.	0			c.T810C						.																																			SO:0001819	synonymous_variant	100293516	exon3			ACCTTATGAATGT	AK299091	CCDS56109.1	19q13.43	2013-01-08				ENSG00000269343		"""Zinc fingers, C2H2-type"", ""-"""	37142	protein-coding gene	gene with protein product							Standard	NM_001204818		Approved		uc021vcp.1	E7ETH6		ENST00000442832.4:c.810T>C	chr19.hg19:g.58352852T>C		125.0	0.0		97.0	4.0	NM_001204818	B4DR41	Silent	SNP	ENST00000442832.4	hg19	CCDS56109.1																																																																																			.	.		0.388	ZNF587B-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466834.2	NM_001204818	
ZNF418	147686	hgsc.bcm.edu	37	19	58438656	58438656	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58438656T>C	ENST00000396147.1	-	4	1184	c.893A>G	c.(892-894)aAg>aGg	p.K298R	ZNF418_ENST00000599852.1_Missense_Mutation_p.K213R|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000425570.3_Missense_Mutation_p.K319R|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Missense_Mutation_p.K298R	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		AAGGCTGCCCTTATGACTAAA	0.408																																					p.K298R		Atlas-SNP	.											.	ZNF418	76	.	0			c.A893G						.						87.0	92.0	90.0					19																	58438656		2195	4300	6495	SO:0001583	missense	147686	exon4			CTGCCCTTATGAC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.893A>G	chr19.hg19:g.58438656T>C	ENSP00000379451:p.Lys298Arg	117.0	0.0		100.0	4.0	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	hg19	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	7.945	0.743538	0.15642	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.12879	2.64;2.64	2.47	-3.22	0.05125	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15262	0.0368	L	0.31371	0.925	0.09310	N	1	P	0.48911	0.917	P	0.61132	0.884	T	0.13469	-1.0508	9	0.08599	T	0.76	.	8.7265	0.34471	0.0:0.485:0.0:0.515	.	298	Q8TF45	ZN418_HUMAN	R	298;319;264	ENSP00000379451:K298R;ENSP00000407039:K319R	ENSP00000379451:K298R	K	-	2	0	ZNF418	63130468	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.711000	0.04995	0.254000	0.18369	AAG	.	.		0.408	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58565111	58565111	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58565111T>C	ENST00000282326.1	+	6	1166	c.919T>C	c.(919-921)Ttc>Ctc	p.F307L		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	307					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GGTCACCCACTTCATCGAGCA	0.632																																					p.F307L		Atlas-SNP	.											ZSCAN1,right_upper_lobe,carcinoma,0,1	ZSCAN1	102	.	0			c.T919C						.						75.0	66.0	69.0					19																	58565111		2203	4300	6503	SO:0001583	missense	284312	exon6			ACCCACTTCATCG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.919T>C	chr19.hg19:g.58565111T>C	ENSP00000282326:p.Phe307Leu	88.0	0.0		73.0	3.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	T	1.923	-0.447795	0.04572	.	.	ENSG00000152467	ENST00000282326	T	0.17854	2.25	1.38	-0.848	0.10727	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.00121	-2.07	0.45318	D	0.998317	B	0.33883	0.43	B	0.33454	0.164	T	0.41106	-0.9527	9	0.02654	T	1	.	5.9707	0.19351	0.0:0.611:0.0:0.389	.	307	Q8NBB4	ZSCA1_HUMAN	L	307	ENSP00000282326:F307L	ENSP00000282326:F307L	F	+	1	0	ZSCAN1	63256923	0.007000	0.16637	0.004000	0.12327	0.030000	0.12068	-0.226000	0.09139	-0.363000	0.08101	-0.415000	0.06103	TTC	.	.		0.632	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
ZNF132	7691	hgsc.bcm.edu	37	19	58945140	58945140	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58945140A>G	ENST00000254166.3	-	3	2071	c.1671T>C	c.(1669-1671)acT>acC	p.T557T	CTD-2619J13.17_ENST00000594816.1_lincRNA	NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	557					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)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		GTTCAATGAGAGTGGAGCTGT	0.458																																					p.T557T		Atlas-SNP	.											.	ZNF132	56	.	0			c.T1671C						.						90.0	90.0	90.0					19																	58945140		2203	4300	6503	SO:0001819	synonymous_variant	7691	exon3			AATGAGAGTGGAG	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"""Zinc fingers, C2H2-type"", ""-"""	12916	protein-coding gene	gene with protein product		604074	"""zinc finger protein 132 (clone pHZ-12)"""			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1671T>C	chr19.hg19:g.58945140A>G		166.0	0.0		91.0	4.0	NM_003433	Q32MI9	Silent	SNP	ENST00000254166.3	hg19	CCDS12980.1																																																																																			.	.		0.458	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433	
ZNF446	55663	hgsc.bcm.edu	37	19	58988926	58988926	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58988926G>T	ENST00000594369.1	+	2	722	c.341G>T	c.(340-342)tGg>tTg	p.W114L	ZNF446_ENST00000596341.1_Splice_Site_p.W114L|ZNF446_ENST00000335841.4_Splice_Site_p.W114L|CTD-2619J13.23_ENST00000598051.1_RNA	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	114					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CTGTTGGGCTGGGTGAGTGTG	0.612																																					p.W114L		Atlas-SNP	.											.	ZNF446	22	.	0			c.G341T						.						54.0	53.0	53.0					19																	58988926		2203	4300	6503	SO:0001630	splice_region_variant	55663	exon2			TGGGCTGGGTGAG		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.342+1G>T	chr19.hg19:g.58988926G>T		105.0	0.0		90.0	4.0	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	hg19	CCDS12982.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500718	0.64298	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000539679	T	0.05081	3.5	4.35	4.35	0.52113	Transcription regulator SCAN (1);	0.000000	0.33591	N	0.004752	T	0.13500	0.0327	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.995	D;D;P	0.91635	0.999;0.961;0.791	T	0.05099	-1.0906	10	0.42905	T	0.14	-25.7239	13.0913	0.59167	0.0:0.0:1.0:0.0	.	114;114;114	F5H201;Q96AF5;Q9NWS9	.;.;ZN446_HUMAN	L	114	ENSP00000336565:W114L	ENSP00000336565:W114L	W	+	2	0	ZNF446	63680738	0.999000	0.42202	1.000000	0.80357	0.677000	0.39632	2.328000	0.43867	2.360000	0.80028	0.491000	0.48974	TGG	.	.		0.612	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	Missense_Mutation
RBCK1	10616	hgsc.bcm.edu	37	20	400215	400215	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:400215G>A	ENST00000356286.5	+	6	1301	c.596G>A	c.(595-597)tGc>tAc	p.C199Y	RBCK1_ENST00000353660.3_Missense_Mutation_p.C157Y|RBCK1_ENST00000382181.2_Missense_Mutation_p.A83T	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	199	Interaction with IRF3.|Interaction with TAB2.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				GGCTGGCAGTGCCCCGGGTGC	0.677																																					p.C199Y		Atlas-SNP	.											.	RBCK1	38	.	0			c.G596A						.						23.0	22.0	22.0					20																	400215		2197	4299	6496	SO:0001583	missense	10616	exon6			GGCAGTGCCCCGG	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, RAN-binding domain containing"""	15864	protein-coding gene	gene with protein product	"""heme-oxidized IRP2 ubiquitin ligase 1"""	610924	"""chromosome 20 open reading frame 18"""	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.596G>A	chr20.hg19:g.400215G>A	ENSP00000348632:p.Cys199Tyr	95.0	0.0		61.0	4.0	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	hg19	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.46|18.46	3.629185|3.629185	0.67015|0.67015	.|.	.|.	ENSG00000125826|ENSG00000125826	ENST00000382181;ENST00000414880|ENST00000356286;ENST00000353660;ENST00000400244;ENST00000400243	T|T;T	0.53423|0.73681	0.62|-0.77;-0.77	4.94|4.94	4.94|4.94	0.65067|0.65067	.|Zinc finger, RanBP2-type (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85682|0.85682	0.5753|0.5753	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|1	D|D;D;D	0.76494|0.89917	0.999|1.0;1.0;1.0	P|D;D;D	0.58520|0.97110	0.84|0.999;1.0;0.999	D|D	0.87476|0.87476	0.2417|0.2417	9|10	0.62326|0.87932	D|D	0.03|0	-0.394|-0.394	16.0103|16.0103	0.80399|0.80399	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	83|189;157;199	A6PVK0|B4E0F5;Q9BYM8-3;Q9BYM8	.|.;.;HOIL1_HUMAN	T|Y	83;232|199;157;199;240	ENSP00000371616:A83T|ENSP00000348632:C199Y;ENSP00000254960:C157Y	ENSP00000371616:A83T|ENSP00000254960:C157Y	A|C	+|+	1|2	0|0	RBCK1|RBCK1	348215|348215	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.410000|9.410000	0.97335|0.97335	2.445000|2.445000	0.82738|0.82738	0.462000|0.462000	0.41574|0.41574	GCC|TGC	.	.		0.677	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229	
C20orf141	128653	hgsc.bcm.edu	37	20	2796266	2796266	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:2796266G>T	ENST00000380589.4	+	2	517	c.343G>T	c.(343-345)Gag>Tag	p.E115*	TMEM239_ENST00000554164.1_Intron|TMEM239_ENST00000361033.1_5'Flank|TMEM239_ENST00000380593.4_Intron|C20orf141_ENST00000603872.1_Nonsense_Mutation_p.E115*|TMEM239_ENST00000380585.1_5'Flank	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	115	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						TGGACAGCAGGAGGCTCTACT	0.632																																					p.E115X		Atlas-SNP	.											.	C20orf141	21	.	0			c.G343T						.						51.0	49.0	50.0					20																	2796266		2203	4300	6503	SO:0001587	stop_gained	128653	exon2			CAGCAGGAGGCTC		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	ENST00000380589.4:c.343G>T	chr20.hg19:g.2796266G>T	ENSP00000369963:p.Glu115*	120.0	0.0		90.0	4.0	NM_080739		Nonsense_Mutation	SNP	ENST00000380589.4	hg19	CCDS13034.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.925051	0.73213	.	.	ENSG00000258713	ENST00000380589	.	.	.	4.43	3.43	0.39272	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.99999	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	18.7417	9.8357	0.40968	0.0:0.2093:0.7907:0.0	.	.	.	.	X	115	.	ENSP00000369963:E115X	E	+	1	0	AL035460.3	2744266	0.009000	0.17119	0.035000	0.18076	0.170000	0.22686	1.817000	0.39002	1.025000	0.39708	0.655000	0.94253	GAG	.	.		0.632	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739	
TASP1	55617	hgsc.bcm.edu	37	20	13371068	13371068	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:13371068A>G	ENST00000337743.4	-	14	1322	c.1202T>C	c.(1201-1203)gTg>gCg	p.V401A	TASP1_ENST00000539805.1_3'UTR|TASP1_ENST00000480436.1_5'UTR	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	401					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CTGTCCTGCCACCGCACCAGG	0.587																																					p.V401A		Atlas-SNP	.											.	TASP1	52	.	0			c.T1202C						.						73.0	56.0	61.0					20																	13371068		2203	4300	6503	SO:0001583	missense	55617	exon14			CCTGCCACCGCAC	AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"""chromosome 20 open reading frame 13"""	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.1202T>C	chr20.hg19:g.13371068A>G	ENSP00000338624:p.Val401Ala	77.0	0.0		65.0	4.0	NM_017714	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	hg19	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.409482	0.42715	.	.	ENSG00000089123	ENST00000337743	D	0.92647	-3.08	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.90068	0.6898	L	0.47716	1.5	0.80722	D	1	P	0.45569	0.861	B	0.42555	0.391	D	0.90767	0.4669	10	0.59425	D	0.04	-11.4904	14.9446	0.71020	1.0:0.0:0.0:0.0	.	401	Q9H6P5	TASP1_HUMAN	A	401	ENSP00000338624:V401A	ENSP00000338624:V401A	V	-	2	0	TASP1	13319068	1.000000	0.71417	0.996000	0.52242	0.782000	0.44232	7.079000	0.76829	2.273000	0.75805	0.482000	0.46254	GTG	.	.		0.587	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714	
PCSK2	5126	hgsc.bcm.edu	37	20	17462588	17462588	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:17462588C>T	ENST00000262545.2	+	12	2105	c.1790C>T	c.(1789-1791)gCc>gTc	p.A597V	PCSK2_ENST00000459871.1_3'UTR|PCSK2_ENST00000377899.1_Missense_Mutation_p.A578V|PCSK2_ENST00000536609.1_Missense_Mutation_p.A562V	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	597					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	ACTCAGAGTGCCCCGTACATC	0.622																																					p.A597V		Atlas-SNP	.											.	PCSK2	112	.	0			c.C1790T						.						33.0	30.0	31.0					20																	17462588		2203	4300	6503	SO:0001583	missense	5126	exon12			AGAGTGCCCCGTA	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1790C>T	chr20.hg19:g.17462588C>T	ENSP00000262545:p.Ala597Val	126.0	0.0		75.0	4.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.196933	0.79015	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.64260	-0.09;-0.09;-0.09	5.47	5.47	0.80525	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	L	0.52573	1.65	0.80722	D	1	P;P;P	0.48230	0.907;0.82;0.515	P;P;B	0.51229	0.663;0.652;0.265	T	0.67043	-0.5770	10	0.44086	T	0.13	-35.8095	18.2492	0.89997	0.0:1.0:0.0:0.0	.	562;578;597	B4DFQ3;B1ANH9;P16519	.;.;NEC2_HUMAN	V	578;597;562	ENSP00000367131:A578V;ENSP00000262545:A597V;ENSP00000437458:A562V	ENSP00000262545:A597V	A	+	2	0	PCSK2	17410588	1.000000	0.71417	0.995000	0.50966	0.666000	0.39218	7.745000	0.85046	2.718000	0.92993	0.460000	0.39030	GCC	.	.		0.622	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	
CFAP61	26074	hgsc.bcm.edu	37	20	20055874	20055874	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:20055874T>C	ENST00000245957.5	+	5	489	c.413T>C	c.(412-414)cTc>cCc	p.L138P	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_Missense_Mutation_p.L138P|C20orf26_ENST00000451767.2_Missense_Mutation_p.L138P	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		138										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TTCATATTTCTCATCGTGCCA	0.522																																					p.L138P		Atlas-SNP	.											.	C20orf26	188	.	0			c.T413C						.						175.0	149.0	158.0					20																	20055874		2203	4300	6503	SO:0001583	missense	26074	exon5			TATTTCTCATCGT																												ENST00000245957.5:c.413T>C	chr20.hg19:g.20055874T>C	ENSP00000245957:p.Leu138Pro	218.0	0.0		140.0	42.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.265822	0.80358	.	.	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000377303;ENST00000451767;ENST00000472660	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	T	0.66528	-0.5901	10	0.87932	D	0	.	12.3497	0.55141	0.0:0.0:0.0:1.0	.	138;138;92;138	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	P	92;138;138;138;138;138;138;34	ENSP00000345553:L92P;ENSP00000245957:L138P;ENSP00000366521:L138P;ENSP00000366518:L138P;ENSP00000414537:L138P;ENSP00000420498:L34P	ENSP00000245957:L138P	L	+	2	0	C20orf26	20003874	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	4.704000	0.61831	2.178000	0.69098	0.533000	0.62120	CTC	.	.		0.522	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
GZF1	64412	hgsc.bcm.edu	37	20	23345335	23345335	+	Silent	SNP	G	G	T	rs376361468		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:23345335G>T	ENST00000338121.5	+	2	392	c.315G>T	c.(313-315)cgG>cgT	p.R105R	GZF1_ENST00000377051.2_Silent_p.R105R|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000544236.1_Intron			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	105					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					AAGAAGATCGGGTGCAGCGAA	0.393																																					p.R105R		Atlas-SNP	.											.	GZF1	61	.	0			c.G315T						.						83.0	86.0	85.0					20																	23345335		2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			AGATCGGGTGCAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.315G>T	chr20.hg19:g.23345335G>T		123.0	0.0		93.0	4.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	.		0.393	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
NINL	22981	hgsc.bcm.edu	37	20	25498459	25498459	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:25498459A>G	ENST00000278886.6	-	3	280	c.207T>C	c.(205-207)ggT>ggC	p.G69G	NINL_ENST00000422516.1_Silent_p.G69G	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	69	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CAGCCACAAAACCTTCCTTAA	0.408																																					p.G69G		Atlas-SNP	.											.	NINL	148	.	0			c.T207C						.						132.0	114.0	120.0					20																	25498459		2203	4300	6503	SO:0001819	synonymous_variant	22981	exon3			CACAAAACCTTCC		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.207T>C	chr20.hg19:g.25498459A>G		147.0	0.0		99.0	4.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Silent	SNP	ENST00000278886.6	hg19	CCDS33452.1																																																																																			.	.		0.408	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
ZNF337	26152	hgsc.bcm.edu	37	20	25656557	25656557	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:25656557T>C	ENST00000376436.1	-	4	1906	c.1367A>G	c.(1366-1368)gAg>gGg	p.E456G	RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000538750.1_Missense_Mutation_p.E424G|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.E456G|RP4-694B14.5_ENST00000414393.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	456					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(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGGCTTCTCCTCTGAGTGTGT	0.453																																					p.E456G		Atlas-SNP	.											.	ZNF337	65	.	0			c.A1367G						.						154.0	132.0	139.0					20																	25656557		2203	4300	6503	SO:0001583	missense	26152	exon5			TTCTCCTCTGAGT		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1367A>G	chr20.hg19:g.25656557T>C	ENSP00000365619:p.Glu456Gly	136.0	0.0		96.0	4.0	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	hg19	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	7.778	0.708927	0.15239	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.11821	2.74;2.74;2.74	1.1	0.0346	0.14184	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03263	0.0095	N	0.01505	-0.83	0.26061	N	0.981343	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43702	-0.9375	9	0.02654	T	1	.	4.9952	0.14235	0.0:0.7431:0.0:0.2568	.	424;456	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	G	456;456;456;424	ENSP00000365619:E456G;ENSP00000252979:E456G;ENSP00000442181:E424G	ENSP00000252979:E456G	E	-	2	0	ZNF337	25604557	0.093000	0.21703	0.024000	0.17045	0.481000	0.33189	1.428000	0.34892	0.004000	0.14682	0.248000	0.18094	GAG	.	.		0.453	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
TTLL9	164395	hgsc.bcm.edu	37	20	30521650	30521650	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:30521650C>A	ENST00000375938.4	+	11	1049	c.796C>A	c.(796-798)Cac>Aac	p.H266N	TTLL9_ENST00000375922.4_Missense_Mutation_p.H208N|TTLL9_ENST00000375934.4_Silent_p.T233T|TTLL9_ENST00000310998.4_Missense_Mutation_p.H231N|TTLL9_ENST00000375921.2_Missense_Mutation_p.H208N|TTLL9_ENST00000535842.1_Missense_Mutation_p.H266N			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	266	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TCCCGACTACCACCCAAAGAA	0.607																																					p.H266N		Atlas-SNP	.											.	TTLL9	95	.	0			c.C796A						.						73.0	71.0	72.0					20																	30521650		1979	4173	6152	SO:0001583	missense	164395	exon11			GACTACCACCCAA	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.796C>A	chr20.hg19:g.30521650C>A	ENSP00000365105:p.His266Asn	123.0	0.0		98.0	4.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	hg19	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.740961	0.49151	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375921;ENST00000375935;ENST00000375922	T;T;T;T;T	0.07114	3.67;3.67;3.67;3.22;3.67	5.64	4.68	0.58851	.	0.156566	0.56097	D	0.000037	T	0.03136	0.0092	N	0.02266	-0.62	0.40990	D	0.984843	B;B	0.11235	0.003;0.004	B;B	0.15052	0.012;0.007	T	0.43130	-0.9410	10	0.08179	T	0.78	.	11.5189	0.50539	0.0:0.7283:0.2717:0.0	.	266;168	Q3SXZ7;B1ANK8	TTLL9_HUMAN;.	N	266;266;231;208;226;208	ENSP00000365105:H266N;ENSP00000442515:H266N;ENSP00000308980:H231N;ENSP00000365086:H208N;ENSP00000365088:H208N	ENSP00000308980:H231N	H	+	1	0	TTLL9	29985311	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.954000	0.63631	2.656000	0.90262	0.561000	0.74099	CAC	.	.		0.607	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
TM9SF4	9777	hgsc.bcm.edu	37	20	30734649	30734649	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:30734649G>T	ENST00000398022.2	+	9	1180	c.945G>T	c.(943-945)gaG>gaT	p.E315D	TM9SF4_ENST00000217315.5_Missense_Mutation_p.E298D	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	315						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACAACAAGGAGGATGACATTG	0.493																																					p.E315D		Atlas-SNP	.											.	TM9SF4	65	.	0			c.G945T						.						115.0	90.0	99.0					20																	30734649		2203	4300	6503	SO:0001583	missense	9777	exon9			CAAGGAGGATGAC	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.945G>T	chr20.hg19:g.30734649G>T	ENSP00000381104:p.Glu315Asp	108.0	0.0		95.0	5.0	NM_014742	B0QYT7|Q9NUA3	Missense_Mutation	SNP	ENST00000398022.2	hg19	CCDS13196.2	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669176	0.47677	.	.	ENSG00000101337	ENST00000398022;ENST00000421148;ENST00000217315	T;T	0.42513	0.97;0.97	5.61	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.22360	0.0539	N	0.11698	0.16	0.80722	D	1	B;B;B	0.19935	0.04;0.015;0.013	B;B;B	0.21917	0.037;0.021;0.023	T	0.06899	-1.0801	10	0.11182	T	0.66	-20.6441	9.548	0.39293	0.201:0.0:0.799:0.0	.	241;222;315	F5H3B5;B4DH88;Q92544	.;.;TM9S4_HUMAN	D	315;241;298	ENSP00000381104:E315D;ENSP00000217315:E298D	ENSP00000217315:E298D	E	+	3	2	TM9SF4	30198310	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.776000	0.38594	1.505000	0.48720	0.655000	0.94253	GAG	.	.		0.493	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742	
DNMT3B	1789	hgsc.bcm.edu	37	20	31367950	31367950	+	Intron	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:31367950T>C	ENST00000328111.2	+	2	315				DNMT3B_ENST00000375623.4_Intron|DNMT3B_ENST00000353855.2_Intron|DNMT3B_ENST00000443239.3_Intron|DNMT3B_ENST00000348286.2_Intron|DNMT3B_ENST00000344505.4_Intron|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000201963.3_Splice_Site_p.L10S	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTCCAAGCTTGGTGAGGGGG	0.632																																					p.L10S		Atlas-SNP	.											.	DNMT3B	196	.	0			c.T29C						.						19.0	20.0	20.0					20																	31367950		2201	4299	6500	SO:0001627	intron_variant	1789	exon1			CAAGCTTGGTGAG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.-6-174T>C	chr20.hg19:g.31367950T>C		84.0	0.0		66.0	4.0	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040099	0.35989	.	.	ENSG00000088305	ENST00000201963	D	0.97378	-4.36	4.54	3.35	0.38373	.	.	.	.	.	D	0.97402	0.9150	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.66351	0.943	D	0.96051	0.9031	8	0.37606	T	0.19	.	9.3283	0.38005	0.0:0.0:0.1794:0.8206	.	10	Q9UBC3-6	.	S	10	ENSP00000201963:L10S	ENSP00000201963:L10S	L	+	2	0	DNMT3B	30831611	0.881000	0.30235	0.986000	0.45419	0.653000	0.38743	0.728000	0.26013	2.043000	0.60533	0.459000	0.35465	TTG	.	.		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
BPIFB1	92747	hgsc.bcm.edu	37	20	31889200	31889200	+	Missense_Mutation	SNP	G	G	A	rs267605886		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:31889200G>A	ENST00000253354.1	+	9	1070	c.909G>A	c.(907-909)atG>atA	p.M303I	BPIFB1_ENST00000464032.1_3'UTR	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	303					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AAGAATTCATGGTCCTGTTGG	0.547																																					p.M303I		Atlas-SNP	.											.	.	.	.	0			c.G909A						.						97.0	83.0	87.0					20																	31889200		2203	4300	6503	SO:0001583	missense	92747	exon9			ATTCATGGTCCTG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.909G>A	chr20.hg19:g.31889200G>A	ENSP00000253354:p.Met303Ile	75.0	0.0		58.0	4.0	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	G	2.964	-0.214051	0.06101	.	.	ENSG00000125999	ENST00000253354;ENST00000375378	T	0.06371	3.31	4.81	-4.5	0.03493	.	2.143790	0.01639	N	0.023931	T	0.04497	0.0123	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35051	-0.9804	10	0.32370	T	0.25	-0.3569	2.8073	0.05431	0.4107:0.1109:0.366:0.1125	.	303	Q8TDL5	BPIB1_HUMAN	I	303;134	ENSP00000253354:M303I	ENSP00000253354:M303I	M	+	3	0	BPIFB1	31352861	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.736000	0.01845	-1.282000	0.02396	-1.644000	0.00765	ATG	.	.		0.547	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
ZNF341	84905	hgsc.bcm.edu	37	20	32328755	32328755	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:32328755C>A	ENST00000375200.1	+	2	444	c.79C>A	c.(79-81)Caa>Aaa	p.Q27K	ZNF341_ENST00000342427.2_Missense_Mutation_p.Q27K	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	27					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						ATTGGATGGCCAAGGAGCAGT	0.537																																					p.Q27K		Atlas-SNP	.											.	ZNF341	73	.	0			c.C79A						.						110.0	93.0	99.0					20																	32328755		2203	4300	6503	SO:0001583	missense	84905	exon2			GATGGCCAAGGAG	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.79C>A	chr20.hg19:g.32328755C>A	ENSP00000364346:p.Gln27Lys	105.0	0.0		55.0	4.0	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.50	3.637217	0.67130	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.11169	3.05;2.8	5.27	4.32	0.51571	.	0.062422	0.64402	N	0.000004	T	0.10680	0.0261	L	0.34521	1.04	0.54753	D	0.999984	B;B	0.17268	0.012;0.021	B;B	0.20184	0.012;0.028	T	0.06445	-1.0826	10	0.54805	T	0.06	-11.631	14.361	0.66771	0.1497:0.8503:0.0:0.0	.	27;27	Q9BYN7;Q9BYN7-2	ZN341_HUMAN;.	K	27	ENSP00000344308:Q27K;ENSP00000364346:Q27K	ENSP00000344308:Q27K	Q	+	1	0	ZNF341	31792416	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.378000	0.79679	1.344000	0.45657	-0.293000	0.09583	CAA	.	.		0.537	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
UQCC1	55245	hgsc.bcm.edu	37	20	33981955	33981955	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:33981955T>C	ENST00000374385.5	-	2	246	c.69A>G	c.(67-69)cgA>cgG	p.R23R	UQCC1_ENST00000359226.2_Silent_p.R23R|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_5'UTR|UQCC1_ENST00000374384.2_Silent_p.R23R|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000397554.1_Silent_p.R23R|UQCC1_ENST00000374377.5_Missense_Mutation_p.I4V|UQCC1_ENST00000407996.2_Silent_p.R23R|UQCC1_ENST00000374380.2_Silent_p.R23R|UQCC1_ENST00000542501.1_Silent_p.R23R|UQCC1_ENST00000349714.5_Silent_p.R23R	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	23						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											CAGGTATCAATCGGCTGCATA	0.433																																					p.R23R		Atlas-SNP	.											.	UQCC	41	.	0			c.A69G						.						126.0	118.0	120.0					20																	33981955		2203	4300	6503	SO:0001819	synonymous_variant	55245	exon2			TATCAATCGGCTG	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.69A>G	chr20.hg19:g.33981955T>C		132.0	0.0		98.0	4.0	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Silent	SNP	ENST00000374385.5	hg19	CCDS13252.1	.	.	.	.	.	.	.	.	.	.	T	8.859	0.946417	0.18356	.	.	ENSG00000101019	ENST00000374377	.	.	.	5.04	1.46	0.22682	.	.	.	.	.	T	0.12944	0.0314	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	T	0.31833	-0.9929	5	0.02654	T	1	-0.1852	6.839	0.23953	0.0:0.2836:0.0:0.7164	.	.	.	.	V	4	.	ENSP00000363497:I4V	I	-	1	0	UQCC	33445369	0.239000	0.23836	0.446000	0.26920	0.870000	0.49936	0.302000	0.19192	0.404000	0.25506	0.528000	0.53228	ATT	.	.		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
TGM2	7052	hgsc.bcm.edu	37	20	36766769	36766769	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:36766769T>C	ENST00000361475.2	-	10	1534	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	TGM2_ENST00000536701.1_Missense_Mutation_p.E373G|TGM2_ENST00000536724.1_Missense_Mutation_p.E394G	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	454					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TGTGAAGGCCTCCCTCTCCTC	0.587																																					p.E454G		Atlas-SNP	.											.	TGM2	88	.	0			c.A1361G						.						88.0	82.0	84.0					20																	36766769		2203	4300	6503	SO:0001583	missense	7052	exon10			AAGGCCTCCCTCT	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1361A>G	chr20.hg19:g.36766769T>C	ENSP00000355330:p.Glu454Gly	127.0	0.0		94.0	4.0	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Missense_Mutation	SNP	ENST00000361475.2	hg19	CCDS13302.1	.	.	.	.	.	.	.	.	.	.	T	7.361	0.624909	0.14193	.	.	ENSG00000198959	ENST00000361475;ENST00000536701;ENST00000536724	T;T;T	0.26810	1.71;1.71;1.71	4.88	2.51	0.30379	.	0.817852	0.11755	N	0.532706	T	0.28300	0.0699	M	0.75447	2.3	0.21652	N	0.99961	B;P;B;B;P	0.41188	0.404;0.602;0.404;0.282;0.741	B;B;B;B;B	0.41466	0.238;0.229;0.096;0.12;0.358	T	0.15407	-1.0438	10	0.30854	T	0.27	-9.3226	4.9211	0.13871	0.0:0.1618:0.2999:0.5383	.	394;373;454;394;454	F5H6P0;B4DIT7;P21980-2;B4DTN7;P21980	.;.;.;.;TGM2_HUMAN	G	454;373;394	ENSP00000355330:E454G;ENSP00000444701:E373G;ENSP00000437479:E394G	ENSP00000355330:E454G	E	-	2	0	TGM2	36200183	0.002000	0.14202	0.140000	0.22221	0.010000	0.07245	1.104000	0.31074	0.188000	0.20168	-0.290000	0.09829	GAG	.	.		0.587	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
LPIN3	64900	hgsc.bcm.edu	37	20	39986061	39986061	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:39986061C>A	ENST00000373257.3	+	16	2104	c.2013C>A	c.(2011-2013)atC>atA	p.I671I		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	671	C-LIP.				fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				ACCAGGGCATCACCAGTCTCT	0.592																																					p.I671I		Atlas-SNP	.											.	LPIN3	69	.	0			c.C2013A						.						78.0	68.0	71.0					20																	39986061		2203	4300	6503	SO:0001819	synonymous_variant	64900	exon16			GGGCATCACCAGT	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2013C>A	chr20.hg19:g.39986061C>A		66.0	0.0		65.0	5.0	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Silent	SNP	ENST00000373257.3	hg19	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	C	9.152	1.016607	0.19355	.	.	ENSG00000132793	ENST00000445975	.	.	.	5.2	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.5033	5.3388	0.15973	0.1626:0.6535:0.0:0.1839	.	.	.	.	X	161	.	.	S	+	2	0	LPIN3	39419475	0.996000	0.38824	1.000000	0.80357	0.893000	0.52053	0.453000	0.21811	1.155000	0.42497	0.563000	0.77884	TCA	.	.		0.592	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
SNX21	90203	hgsc.bcm.edu	37	20	44469556	44469556	+	Silent	SNP	G	G	T	rs533001979	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:44469556G>T	ENST00000491381.1	+	4	794	c.726G>T	c.(724-726)ccG>ccT	p.P242P	SNX21_ENST00000372542.1_Silent_p.P233P|SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000462307.1_3'UTR|SNX21_ENST00000342644.5_Intron			Q969T3	SNX21_HUMAN	sorting nexin family member 21	242	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				TCGTGCTGCCGGAGCTGCGGC	0.662																																					p.P242P		Atlas-SNP	.											SNX21,colon,carcinoma,0,1	SNX21	23	.	0			c.G726T						.						23.0	26.0	25.0					20																	44469556		2202	4284	6486	SO:0001819	synonymous_variant	90203	exon4			GCTGCCGGAGCTG	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.726G>T	chr20.hg19:g.44469556G>T		99.0	2.0		90.0	5.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Silent	SNP	ENST00000491381.1	hg19	CCDS13377.1																																																																																			.	.		0.662	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
SLC12A5	57468	hgsc.bcm.edu	37	20	44676618	44676618	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:44676618A>G	ENST00000454036.2	+	16	2025		c.e16-1		SLC12A5_ENST00000243964.3_Splice_Site	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5						cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCCGGCTCCCAGGGCAGAGAA	0.612																																					.		Atlas-SNP	.											.	SLC12A5	181	.	0			c.1977-2A>G						.						46.0	41.0	43.0					20																	44676618		2203	4300	6503	SO:0001630	splice_region_variant	57468	exon16			GCTCCCAGGGCAG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1977-1A>G	chr20.hg19:g.44676618A>G		60.0	0.0		42.0	4.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Splice_Site	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.237439	0.39498	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7426	0.51801	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A5	44110025	1.000000	0.71417	0.995000	0.50966	0.308000	0.27856	9.067000	0.93955	1.621000	0.50320	0.374000	0.22700	.	.	.		0.612	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		Intron
OCSTAMP	128506	hgsc.bcm.edu	37	20	45174433	45174433	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:45174433A>G	ENST00000279028.2	-	2	593	c.580T>C	c.(580-582)Tct>Cct	p.S194P		NM_080721.1	NP_542452.1	Q9BR26	OCSTP_HUMAN	osteoclast stimulatory transmembrane protein	194					cellular response to estrogen stimulus (GO:0071391)|cellular response to tumor necrosis factor (GO:0071356)|multinuclear osteoclast differentiation (GO:0072674)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of osteoclast proliferation (GO:0090290)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						TAGAAGGCAGAGCCATTGTCC	0.642																																					p.S194P		Atlas-SNP	.											.	OCSTAMP	34	.	0			c.T580C						.						24.0	27.0	26.0					20																	45174433		692	1591	2283	SO:0001583	missense	128506	exon2			AGGCAGAGCCATT	AL034424	CCDS54468.1	20q13.12	2012-03-27	2012-03-27	2012-03-27	ENSG00000149635	ENSG00000149635			16116	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 123"""	C20orf123		18064667	Standard	NM_080721		Approved	dJ257E24.3	uc010zxu.2	Q9BR26	OTTHUMG00000032652	ENST00000279028.2:c.580T>C	chr20.hg19:g.45174433A>G	ENSP00000279028:p.Ser194Pro	108.0	0.0		92.0	5.0	NM_080721		Missense_Mutation	SNP	ENST00000279028.2	hg19	CCDS54468.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500714	0.64298	.	.	ENSG00000149635	ENST00000279028	T	0.53423	0.62	5.11	4.0	0.46444	.	0.337220	0.21961	U	0.066591	T	0.58293	0.2112	M	0.67953	2.075	0.33113	D	0.540763	D	0.57899	0.981	P	0.55161	0.77	T	0.69423	-0.5149	10	0.48119	T	0.1	-11.0258	12.0802	0.53667	0.8559:0.1441:0.0:0.0	.	194	Q9BR26	CT123_HUMAN	P	194	ENSP00000279028:S194P	ENSP00000279028:S194P	S	-	1	0	C20orf123	44607840	0.985000	0.35326	0.992000	0.48379	0.969000	0.65631	1.313000	0.33585	0.762000	0.33152	0.528000	0.53228	TCT	.	.		0.642	OCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079573.2	XM_496476	
PTPN1	5770	hgsc.bcm.edu	37	20	49197898	49197898	+	Silent	SNP	C	C	A	rs150584289		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:49197898C>A	ENST00000371621.3	+	9	1359	c.1185C>A	c.(1183-1185)ccC>ccA	p.P395P	PTPN1_ENST00000541713.1_Silent_p.P322P	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	395					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	CGTCACTGCCCGAGAAGGACG	0.607																																					p.P395P		Atlas-SNP	.											PTPN1,NS,carcinoma,0,1	PTPN1	36	.	0			c.C1185A						.						98.0	69.0	79.0					20																	49197898		2203	4300	6503	SO:0001819	synonymous_variant	5770	exon9			ACTGCCCGAGAAG		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.1185C>A	chr20.hg19:g.49197898C>A		142.0	0.0		68.0	3.0	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	hg19	CCDS13430.1																																																																																			.	C|1.000;T|0.000		0.607	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		
SYCP2	10388	hgsc.bcm.edu	37	20	58468228	58468228	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:58468228A>G	ENST00000357552.3	-	22	1987	c.1762T>C	c.(1762-1764)Tca>Cca	p.S588P	SYCP2_ENST00000371001.2_Missense_Mutation_p.S588P			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	588					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)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GCTGCCTGTGAATCTGGTATA	0.328																																					p.S588P		Atlas-SNP	.											.	SYCP2	204	.	0			c.T1762C						.						111.0	102.0	105.0					20																	58468228		2202	4299	6501	SO:0001583	missense	10388	exon21			CCTGTGAATCTGG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1762T>C	chr20.hg19:g.58468228A>G	ENSP00000350162:p.Ser588Pro	87.0	0.0		84.0	4.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128301	0.56721	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.26518	1.94;1.94;1.73	5.77	0.724	0.18236	.	0.362966	0.23926	N	0.043198	T	0.21062	0.0507	M	0.61703	1.905	0.09310	N	1	B	0.17038	0.02	B	0.21546	0.035	T	0.29822	-0.9999	10	0.72032	D	0.01	-0.0018	1.6469	0.02764	0.4837:0.1554:0.0809:0.28	.	588	Q9BX26	SYCP2_HUMAN	P	588	ENSP00000360040:S588P;ENSP00000350162:S588P;ENSP00000402456:S588P	ENSP00000350162:S588P	S	-	1	0	SYCP2	57901623	0.998000	0.40836	0.001000	0.08648	0.844000	0.47949	1.252000	0.32874	-0.077000	0.12752	0.477000	0.44152	TCA	.	.		0.328	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
GRIK1	2897	hgsc.bcm.edu	37	21	30971254	30971254	+	Silent	SNP	G	G	T	rs113829116		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:30971254G>T	ENST00000399907.1	-	8	1513	c.1102C>A	c.(1102-1104)Cgg>Agg	p.R368R	GRIK1_ENST00000399914.1_Silent_p.R368R|GRIK1_ENST00000327783.4_Silent_p.R368R|GRIK1_ENST00000389125.3_Silent_p.R368R|GRIK1_ENST00000399913.1_Silent_p.R368R|BACH1_ENST00000462262.1_Intron|GRIK1_ENST00000389124.2_Silent_p.R368R|GRIK1_ENST00000472429.1_5'UTR|GRIK1-AS2_ENST00000333765.4_Intron|GRIK1_ENST00000399909.1_Silent_p.R368R|GRIK1_ENST00000535441.1_Silent_p.R370R|GRIK1_ENST00000309434.7_Silent_p.R370R	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	368					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	CCATCCCACCGGGCCTGTGGA	0.383																																					p.R368R		Atlas-SNP	.											.	GRIK1	293	.	0			c.C1102A						.						78.0	77.0	77.0					21																	30971254		2203	4300	6503	SO:0001819	synonymous_variant	2897	exon8			CCCACCGGGCCTG		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.1102C>A	chr21.hg19:g.30971254G>T		48.0	0.0		45.0	4.0	NM_175611	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	hg19	CCDS42913.1																																																																																			.	G|1.000;A|0.000		0.383	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		
TIAM1	7074	hgsc.bcm.edu	37	21	32639202	32639202	+	Silent	SNP	G	G	T	rs139712298		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:32639202G>T	ENST00000286827.3	-	5	558	c.87C>A	c.(85-87)tcC>tcA	p.S29S	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Silent_p.S29S	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	29					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AGAGGCGCAGGGAGCGGGAAG	0.582																																					p.S29S		Atlas-SNP	.											.	TIAM1	522	.	0			c.C87A						.						45.0	47.0	46.0					21																	32639202		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon5			GCGCAGGGAGCGG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.87C>A	chr21.hg19:g.32639202G>T		87.0	0.0		41.0	4.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	G|0.999;A|0.001		0.582	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
SCAF4	57466	hgsc.bcm.edu	37	21	33068944	33068944	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:33068944G>T	ENST00000286835.7	-	8	1279	c.897C>A	c.(895-897)acC>acA	p.T299T	SCAF4_ENST00000434667.3_Silent_p.T284T|SCAF4_ENST00000399804.1_Silent_p.T299T	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	299				T -> A (in Ref. 1; AAD09327). {ECO:0000305}.		nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCACGGTGGCGGTGGGTGCAG	0.532																																					p.T299T		Atlas-SNP	.											.	SCAF4	142	.	0			c.C897A						.						75.0	77.0	76.0					21																	33068944		2203	4300	6503	SO:0001819	synonymous_variant	57466	exon8			GGTGGCGGTGGGT	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.897C>A	chr21.hg19:g.33068944G>T		147.0	0.0		114.0	5.0	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	hg19	CCDS33537.1																																																																																			.	.		0.532	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
SLC5A3	6526	hgsc.bcm.edu	37	21	35469094	35469094	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:35469094A>T	ENST00000381151.3	+	2	2109	c.1597A>T	c.(1597-1599)Aca>Tca	p.T533S	MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.T533S			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	533					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GAGCCTTCTCACACCACCTCC	0.468																																					p.T533S		Atlas-SNP	.											SLC5A3,rectum,NS,0,1	SLC5A3	52	.	0			c.A1597T						.						80.0	69.0	73.0					21																	35469094		2203	4300	6503	SO:0001583	missense	6526	exon2			CTTCTCACACCAC		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"""Solute carriers"""	11038	protein-coding gene	gene with protein product		600444	"""solute carrier family 5 (inositol transporter), member 3"""			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1597A>T	chr21.hg19:g.35469094A>T	ENSP00000370543:p.Thr533Ser	146.0	0.0		100.0	5.0	NM_006933	O43489	Missense_Mutation	SNP	ENST00000381151.3	hg19	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646766	0.67358	.	.	ENSG00000198743	ENST00000381151	T	0.66460	-0.21	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.77219	0.4098	L	0.53729	1.69	0.46499	D	0.999071	D	0.63880	0.993	D	0.65010	0.931	T	0.79032	-0.1969	10	0.66056	D	0.02	.	15.1328	0.72539	1.0:0.0:0.0:0.0	.	533	P53794	SC5A3_HUMAN	S	533	ENSP00000370543:T533S	ENSP00000370543:T533S	T	+	1	0	SLC5A3	34390964	1.000000	0.71417	0.993000	0.49108	0.958000	0.62258	8.930000	0.92872	2.224000	0.72417	0.533000	0.62120	ACA	.	.		0.468	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1		
PSMG1	8624	hgsc.bcm.edu	37	21	40553799	40553799	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:40553799A>G	ENST00000331573.3	-	2	605	c.140T>C	c.(139-141)gTg>gCg	p.V47A	PSMG1_ENST00000380900.2_Missense_Mutation_p.V47A|AF129408.17_ENST00000608767.1_RNA	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	47					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				AAGGAGCCGCACTTCCCTAAC	0.328																																					p.V47A		Atlas-SNP	.											.	PSMG1	11	.	0			c.T140C						.						46.0	46.0	46.0					21																	40553799		2202	4299	6501	SO:0001583	missense	8624	exon2			AGCCGCACTTCCC	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"""Down syndrome critical region gene 2"""	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.140T>C	chr21.hg19:g.40553799A>G	ENSP00000329915:p.Val47Ala	94.0	0.0		89.0	6.0	NM_203433	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Missense_Mutation	SNP	ENST00000331573.3	hg19	CCDS13660.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.526782	0.64860	.	.	ENSG00000183527	ENST00000331573;ENST00000380900	T;T	0.57436	0.4;0.4	5.46	5.46	0.80206	.	0.191307	0.44285	D	0.000475	T	0.54951	0.1890	M	0.75264	2.295	0.42482	D	0.992866	B;B	0.33940	0.433;0.433	B;B	0.34452	0.183;0.183	T	0.61317	-0.7087	10	0.66056	D	0.02	-23.2354	13.4991	0.61442	1.0:0.0:0.0:0.0	.	47;47	O95456-2;O95456	.;PSMG1_HUMAN	A	47	ENSP00000329915:V47A;ENSP00000370286:V47A	ENSP00000329915:V47A	V	-	2	0	PSMG1	39475669	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.707000	0.68370	2.069000	0.61940	0.459000	0.35465	GTG	.	.		0.328	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720	
HMGN1	3150	hgsc.bcm.edu	37	21	40717157	40717157	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:40717157C>A	ENST00000380749.5	-	5	452	c.170G>T	c.(169-171)gGa>gTa	p.G57V	Y_RNA_ENST00000517106.1_RNA|snoU13_ENST00000459446.1_RNA|HMGN1_ENST00000380747.1_Missense_Mutation_p.G73V|HMGN1_ENST00000380748.1_Missense_Mutation_p.G47V|HMGN1_ENST00000361263.4_Nonsense_Mutation_p.E21*|HMGN1_ENST00000489072.1_5'UTR	NM_004965.6	NP_004956.5	P05114	HMGN1_HUMAN	high mobility group nucleosome binding domain 1	57					chromatin organization (GO:0006325)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|post-embryonic camera-type eye morphogenesis (GO:0048597)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of development, heterochronic (GO:0040034)|regulation of epithelial cell proliferation (GO:0050678)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to UV-B (GO:0010224)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(2)|lung(1)	3		Prostate(19;8.69e-07)				TCCCTTTGCTCCCCTTTTCCC	0.383																																					p.G57V		Atlas-SNP	.											.	HMGN1	8	.	0			c.G170T						.						77.0	66.0	70.0					21																	40717157		2203	4297	6500	SO:0001583	missense	3150	exon5			TTTGCTCCCCTTT		CCDS33559.1	21q22.3	2011-07-01	2011-04-05	2002-08-16	ENSG00000205581	ENSG00000205581		"""High-mobility group / Canonical"""	4984	protein-coding gene	gene with protein product	"""high-mobility group nucleosome binding 1"", ""nonhistone chromosomal protein HMG-14"""	163920	"""high-mobility group (nonhistone chromosomal) protein 14"", ""high-mobility group nucleosome binding domain 1"""	HMG14		3782107, 2563381	Standard	NM_004965		Approved	FLJ27265, FLJ31471, MGC104230, MGC117425	uc002yxo.3	P05114	OTTHUMG00000066178	ENST00000380749.5:c.170G>T	chr21.hg19:g.40717157C>A	ENSP00000370125:p.Gly57Val	151.0	0.0		118.0	5.0	NM_004965	Q3KQR8	Missense_Mutation	SNP	ENST00000380749.5	hg19	CCDS33559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.260701|9.260701	0.99117|0.99117	.|.	.|.	ENSG00000205581|ENSG00000205581	ENST00000361263|ENST00000380749;ENST00000380748;ENST00000380747	.|.	.|.	.|.	4.57|4.57	3.68|3.68	0.42216|0.42216	.|.	0.000000|.	0.34628|.	N|.	0.003812|.	.|T	.|0.59932	.|0.2230	L|L	0.49640|0.49640	1.575|1.575	0.80722|0.80722	A|A	1|1	.|P	.|0.48016	.|0.904	.|P	.|0.54629	.|0.757	.|T	.|0.71663	.|-0.4525	.|7	0.87932|0.87932	D|D	0|0	.|.	12.3827|12.3827	0.55315|0.55315	0.0:0.9177:0.0:0.0823|0.0:0.9177:0.0:0.0823	.|.	.|57	.|P05114	.|HMGN1_HUMAN	X|V	21|57;47;73	.|.	ENSP00000355293:E21X|ENSP00000370123:G73V	E|G	-|-	1|2	0|0	HMGN1|HMGN1	39639027|39639027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.451000|2.451000	0.44952|0.44952	0.925000|0.925000	0.37094|0.37094	0.591000|0.591000	0.81541|0.81541	GAG|GGA	.	.		0.383	HMGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141645.2	NM_004965	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020985	46020985	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:46020985C>A	ENST00000380102.2	+	1	489	c.464C>A	c.(463-465)cCc>cAc	p.P155H	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	155	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						ACCTCCTCCCCCTGCCAGCAG	0.592																																					p.P150H		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C449A						.						62.0	66.0	65.0					21																	46020985		2196	4293	6489	SO:0001583	missense	386675	exon2			CCTCCCCCTGCCA	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.464C>A	chr21.hg19:g.46020985C>A	ENSP00000369445:p.Pro155His	630.0	0.0		437.0	120.0	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	hg19		.	.	.	.	.	.	.	.	.	.	N	0.395	-0.921520	0.02396	.	.	ENSG00000205441	ENST00000380102	T	0.01397	4.94	3.06	-0.735	0.11137	.	.	.	.	.	T	0.04272	0.0118	M	0.90759	3.145	0.09310	N	1	D	0.55605	0.972	P	0.45449	0.481	T	0.28554	-1.0040	9	0.34782	T	0.22	.	11.7141	0.51641	0.0:0.5698:0.4302:0.0	.	150	P60409-2	.	H	155	ENSP00000369445:P155H	ENSP00000369445:P155H	P	+	2	0	KRTAP10-7	44845413	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.543000	0.06084	-0.048000	0.13401	0.460000	0.39030	CCC	.	.		0.592	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
LSS	4047	hgsc.bcm.edu	37	21	47616149	47616149	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47616149C>A	ENST00000397728.3	-	18	1781	c.1703G>T	c.(1702-1704)cGg>cTg	p.R568L	LSS_ENST00000457828.2_Missense_Mutation_p.R488L|LSS_ENST00000356396.4_Missense_Mutation_p.R568L|AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000522411.1_Missense_Mutation_p.R557L	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	568					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CTGCTGCCGCCGACAGAACTC	0.557																																					p.R568L	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G1703T						.						70.0	67.0	68.0					21																	47616149		2203	4300	6503	SO:0001583	missense	4047	exon18			TGCCGCCGACAGA	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1703G>T	chr21.hg19:g.47616149C>A	ENSP00000380837:p.Arg568Leu	72.0	0.0		41.0	4.0	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.422737	0.43020	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.4	3.52	0.40303	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.246093	0.39407	N	0.001376	T	0.12008	0.0292	N	0.26092	0.79	0.53688	D	0.999974	B;B	0.14438	0.008;0.01	B;B	0.14578	0.004;0.011	T	0.07328	-1.0778	10	0.44086	T	0.13	.	10.0437	0.42173	0.1371:0.7901:0.0:0.0728	.	557;568	E9PEI9;P48449	.;ERG7_HUMAN	L	568;488;568;557	ENSP00000348762:R568L;ENSP00000409191:R488L;ENSP00000380837:R568L;ENSP00000429133:R557L	ENSP00000348762:R568L	R	-	2	0	LSS	46440577	0.662000	0.27439	0.705000	0.30386	0.276000	0.26787	1.324000	0.33712	1.284000	0.44531	0.462000	0.41574	CGG	.	.		0.557	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
LSS	4047	hgsc.bcm.edu	37	21	47647541	47647541	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47647541T>C	ENST00000397728.3	-	3	322	c.244A>G	c.(244-246)Aca>Gca	p.T82A	MCM3AP-AS1_ENST00000588753.1_RNA|LSS_ENST00000457828.2_Missense_Mutation_p.T2A|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|LSS_ENST00000356396.4_Missense_Mutation_p.T82A|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000522411.1_Missense_Mutation_p.T82A|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	82					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					ACGTAAAATGTCATCCCGTTC	0.517																																					p.T82A	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.A244G						.						134.0	123.0	127.0					21																	47647541		2203	4300	6503	SO:0001583	missense	4047	exon3			AAAATGTCATCCC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.244A>G	chr21.hg19:g.47647541T>C	ENSP00000380837:p.Thr82Ala	148.0	0.0		89.0	4.0	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656718	0.29425	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.34	1.33	0.21861	.	1.211620	0.05461	N	0.551125	T	0.11836	0.0288	L	0.28556	0.865	0.09310	N	0.999993	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.001	T	0.34153	-0.9840	10	0.11794	T	0.64	.	6.8694	0.24113	0.0:0.0924:0.2739:0.6336	.	82;82	E9PEI9;P48449	.;ERG7_HUMAN	A	82;2;82;82;83	ENSP00000348762:T82A;ENSP00000409191:T2A;ENSP00000380837:T82A;ENSP00000429133:T82A;ENSP00000391368:T83A	ENSP00000348762:T82A	T	-	1	0	LSS	46471969	0.013000	0.17824	0.406000	0.26421	0.965000	0.64279	0.093000	0.15086	0.872000	0.35775	0.459000	0.35465	ACA	.	.		0.517	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
MCM3AP	8888	hgsc.bcm.edu	37	21	47680812	47680812	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47680812T>C	ENST00000397708.1	-	16	3730	c.3476A>G	c.(3475-3477)cAa>cGa	p.Q1159R	MCM3AP_ENST00000291688.1_Missense_Mutation_p.Q1159R|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000467026.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1159					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CTCTCTCTCTTGTTTCAACCT	0.483																																					p.Q1159R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A3476G						.						94.0	88.0	90.0					21																	47680812		2203	4300	6503	SO:0001583	missense	8888	exon15			CTCTCTTGTTTCA	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3476A>G	chr21.hg19:g.47680812T>C	ENSP00000380820:p.Gln1159Arg	122.0	0.0		54.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	6.224	0.409415	0.11812	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	D;D	0.84660	-1.88;-1.88	5.35	1.36	0.22044	.	0.058491	0.64402	D	0.000001	T	0.71341	0.3328	L	0.29908	0.895	0.33099	D	0.538958	B	0.06786	0.001	B	0.04013	0.001	T	0.64415	-0.6413	10	0.26408	T	0.33	-12.0821	5.4631	0.16627	0.1285:0.1491:0.0:0.7224	.	1159	O60318	MCM3A_HUMAN	R	1159	ENSP00000380820:Q1159R;ENSP00000291688:Q1159R	ENSP00000291688:Q1159R	Q	-	2	0	MCM3AP	46505240	0.659000	0.27411	0.998000	0.56505	0.212000	0.24457	0.104000	0.15313	0.869000	0.35703	-0.376000	0.06991	CAA	.	.		0.483	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
DGCR14	8220	hgsc.bcm.edu	37	22	19126802	19126802	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:19126802A>G	ENST00000252137.6	-	6	735	c.692T>C	c.(691-693)gTc>gCc	p.V231A		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	231					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					CTCGTCAGGGACACCTGGCAG	0.587																																					p.V231A		Atlas-SNP	.											.	DGCR14	43	.	0			c.T692C						.						33.0	33.0	33.0					22																	19126802		2203	4300	6503	SO:0001583	missense	8220	exon6			TCAGGGACACCTG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.692T>C	chr22.hg19:g.19126802A>G	ENSP00000252137:p.Val231Ala	61.0	0.0		78.0	4.0	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	hg19	CCDS13756.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518884	0.64634	.	.	ENSG00000100056	ENST00000252137	T	0.46819	0.86	5.03	5.03	0.67393	.	0.062809	0.64402	D	0.000006	T	0.54159	0.1841	L	0.52206	1.635	0.58432	D	0.999998	D	0.55605	0.972	P	0.56563	0.801	T	0.48410	-0.9038	10	0.15066	T	0.55	-33.843	14.4069	0.67088	1.0:0.0:0.0:0.0	.	231	Q96DF8	DGC14_HUMAN	A	231	ENSP00000252137:V231A	ENSP00000252137:V231A	V	-	2	0	DGCR14	17506802	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	6.453000	0.73488	1.887000	0.54652	0.460000	0.39030	GTC	.	.		0.587	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2		
CCDC116	164592	hgsc.bcm.edu	37	22	21989356	21989356	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:21989356T>C	ENST00000292779.3	+	4	1165	c.1004T>C	c.(1003-1005)cTg>cCg	p.L335P	CCDC116_ENST00000607942.1_Missense_Mutation_p.L335P	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	335										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCCGTCCTCTGTTCCCCACC	0.667																																					p.L335P		Atlas-SNP	.											.	CCDC116	56	.	0			c.T1004C						.						37.0	39.0	38.0					22																	21989356		2203	4300	6503	SO:0001583	missense	164592	exon4			GTCCTCTGTTCCC	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.1004T>C	chr22.hg19:g.21989356T>C	ENSP00000292779:p.Leu335Pro	103.0	0.0		60.0	6.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925438	0.34002	.	.	ENSG00000161180	ENST00000292779	T	0.28069	1.63	4.39	3.36	0.38483	.	0.000000	0.45606	D	0.000348	T	0.42381	0.1200	L	0.47190	1.495	0.54753	D	0.999985	D;D	0.89917	1.0;0.964	D;P	0.91635	0.999;0.684	T	0.34453	-0.9828	10	0.87932	D	0	-64.7756	6.0141	0.19592	0.0:0.1146:0.0:0.8854	.	335;335	B7Z7H5;Q8IYX3-2	.;.	P	335	ENSP00000292779:L335P	ENSP00000292779:L335P	L	+	2	0	CCDC116	20319356	0.980000	0.34600	0.996000	0.52242	0.027000	0.11550	1.841000	0.39240	1.986000	0.57962	0.459000	0.35465	CTG	.	.		0.667	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
SDF2L1	23753	hgsc.bcm.edu	37	22	21998435	21998435	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:21998435G>T	ENST00000248958.4	+	3	713	c.637G>T	c.(637-639)Gag>Tag	p.E213*	KB-1440D3.14_ENST00000609038.1_lincRNA	NM_022044.2	NP_071327.2	Q9HCN8	SDF2L_HUMAN	stromal cell-derived factor 2-like 1	213						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				prostate(1)	1	Colorectal(54;0.105)					GCCTAGTGTGGAGCCCTCTGC	0.592											OREG0026342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E213X		Atlas-SNP	.											.	SDF2L1	5	.	0			c.G637T						.						104.0	85.0	92.0					22																	21998435		2203	4300	6503	SO:0001587	stop_gained	23753	exon3			AGTGTGGAGCCCT		CCDS13792.1	22q11.21	2008-07-01			ENSG00000128228	ENSG00000128228			10676	protein-coding gene	gene with protein product	"""dihydropyrimidinase-like 2"", ""PWP1-interacting protein 8"""	607551				10591208, 11162531	Standard	NM_022044		Approved	AP000553.C22.4, OTTHUMT00000075032	uc002zvf.3	Q9HCN8	OTTHUMG00000150820	ENST00000248958.4:c.637G>T	chr22.hg19:g.21998435G>T	ENSP00000248958:p.Glu213*	110.0	0.0	752	87.0	4.0	NM_022044	A2RUD3|Q9BRI5	Nonsense_Mutation	SNP	ENST00000248958.4	hg19	CCDS13792.1	.	.	.	.	.	.	.	.	.	.	G	35	5.505302	0.96371	.	.	ENSG00000128228	ENST00000248958	.	.	.	4.62	4.62	0.57501	.	1.157710	0.07026	U	0.827620	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.494	12.8923	0.58078	0.0:0.0:1.0:0.0	.	.	.	.	X	213	.	ENSP00000248958:E213X	E	+	1	0	SDF2L1	20328435	1.000000	0.71417	0.469000	0.27204	0.991000	0.79684	4.782000	0.62396	2.404000	0.81709	0.479000	0.44913	GAG	.	.		0.592	SDF2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320197.1	NM_022044	
PIWIL3	440822	hgsc.bcm.edu	37	22	25153957	25153957	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:25153957C>A	ENST00000332271.5	-	4	689	c.273G>T	c.(271-273)caG>caT	p.Q91H	PIWIL3_ENST00000527701.1_De_novo_Start_OutOfFrame|PIWIL3_ENST00000533313.1_De_novo_Start_OutOfFrame|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	91					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TCCTTCTCTCCTGCAAGGGCG	0.443																																					p.Q91H		Atlas-SNP	.											.	PIWIL3	115	.	0			c.G273T						.						205.0	212.0	210.0					22																	25153957		2203	4300	6503	SO:0001583	missense	440822	exon4			TCTCTCCTGCAAG	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.273G>T	chr22.hg19:g.25153957C>A	ENSP00000330031:p.Gln91His	156.0	0.0		122.0	5.0	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	C	3.457	-0.110792	0.06924	.	.	ENSG00000184571	ENST00000332271	T	0.04406	3.63	2.32	1.29	0.21616	.	11.182200	0.01436	U	0.014939	T	0.04318	0.0119	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38585	-0.9654	10	0.45353	T	0.12	0.251	2.9136	0.05745	0.2713:0.5712:0.0:0.1575	.	91;91	B4DYF7;Q7Z3Z3	.;PIWL3_HUMAN	H	91	ENSP00000330031:Q91H	ENSP00000330031:Q91H	Q	-	3	2	PIWIL3	23483957	.	.	0.000000	0.03702	0.007000	0.05969	.	.	0.552000	0.29026	0.455000	0.32223	CAG	.	.		0.443	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
SGSM1	129049	hgsc.bcm.edu	37	22	25280066	25280066	+	Silent	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:25280066A>G	ENST00000400359.4	+	16	1714	c.1707A>G	c.(1705-1707)tcA>tcG	p.S569S	SGSM1_ENST00000400358.4_Silent_p.S514S	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	569						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CCCACCTATCAGCCCTGGTCA	0.582																																					p.S569S		Atlas-SNP	.											.	SGSM1	150	.	0			c.A1707G						.						66.0	66.0	66.0					22																	25280066		2048	4192	6240	SO:0001819	synonymous_variant	129049	exon16			CCTATCAGCCCTG	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1707A>G	chr22.hg19:g.25280066A>G		72.0	0.0		68.0	4.0	NM_133454	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	hg19	CCDS46674.1																																																																																			.	.		0.582	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
TTC28	23331	hgsc.bcm.edu	37	22	28389367	28389367	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:28389367G>A	ENST00000397906.2	-	18	5525	c.5384C>T	c.(5383-5385)cCa>cTa	p.P1795L	TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000433317.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000428584.1_RNA|TTC28-AS1_ENST00000435348.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1795					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						GCCACTGGTTGGGGGGTCCAG	0.657																																					p.P1795L		Atlas-SNP	.											.,1	TTC28	84	.	0			c.C5384T						.						32.0	37.0	36.0					22																	28389367		692	1591	2283	SO:0001583	missense	23331	exon18			CTGGTTGGGGGGT	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.5384C>T	chr22.hg19:g.28389367G>A	ENSP00000381003:p.Pro1795Leu	62.0	0.0		59.0	3.0	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	ENST00000397906.2	hg19	CCDS46678.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233197	0.58777	.	.	ENSG00000100154	ENST00000397906;ENST00000431039	D	0.87729	-2.29	4.99	4.99	0.66335	.	0.223031	0.39834	N	0.001258	T	0.77315	0.4112	N	0.08118	0	0.58432	D	0.999996	B	0.18863	0.031	B	0.15484	0.013	T	0.73892	-0.3839	10	0.59425	D	0.04	-21.5159	17.6499	0.88161	0.0:0.0:1.0:0.0	.	1795	Q96AY4	TTC28_HUMAN	L	1795;82	ENSP00000381003:P1795L	ENSP00000381003:P1795L	P	-	2	0	TTC28	26719367	1.000000	0.71417	0.995000	0.50966	0.656000	0.38851	5.260000	0.65490	2.491000	0.84063	0.563000	0.77884	CCA	.	.		0.657	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
ZNRF3	84133	hgsc.bcm.edu	37	22	29445350	29445350	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:29445350T>C	ENST00000544604.2	+	8	1356	c.1181T>C	c.(1180-1182)gTc>gCc	p.V394A	ZNRF3_ENST00000406323.3_Missense_Mutation_p.V294A|ZNRF3_ENST00000402174.1_Missense_Mutation_p.V294A|ZNRF3_ENST00000332811.4_Missense_Mutation_p.V294A	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	394					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GGCAACCCCGTCACCTTGCTG	0.667																																					p.V394A		Atlas-SNP	.											.	ZNRF3	75	.	0			c.T1181C						.						56.0	64.0	61.0					22																	29445350		2180	4280	6460	SO:0001583	missense	84133	exon8			ACCCCGTCACCTT	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1181T>C	chr22.hg19:g.29445350T>C	ENSP00000443824:p.Val394Ala	80.0	0.0		101.0	5.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345420	0.24426	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.53	4.5	0.54988	.	0.316033	0.36665	N	0.002471	T	0.67702	0.2921	L	0.44542	1.39	0.34781	D	0.734712	P	0.45531	0.86	B	0.37692	0.256	T	0.70029	-0.4984	10	0.07325	T	0.83	-5.454	10.3398	0.43870	0.0:0.0764:0.0:0.9236	.	394	Q9ULT6	ZNRF3_HUMAN	A	394;294;101;294;294	ENSP00000443824:V394A;ENSP00000328614:V294A;ENSP00000384456:V294A;ENSP00000384553:V294A	ENSP00000328614:V294A	V	+	2	0	ZNRF3	27775350	1.000000	0.71417	0.291000	0.24904	0.272000	0.26649	7.390000	0.79816	0.945000	0.37605	0.533000	0.62120	GTC	.	.		0.667	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972	
RASL10A	10633	hgsc.bcm.edu	37	22	29706428	29706428	+	IGR	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:29706428G>T	ENST00000216101.6	-	0	1490				GAS2L1_ENST00000403764.1_Splice_Site|GAS2L1_ENST00000471961.1_Splice_Site|GAS2L1_ENST00000407854.1_Splice_Site|GAS2L1_ENST00000341313.6_Splice_Site|GAS2L1_ENST00000407647.2_Splice_Site|GAS2L1_ENST00000406549.3_Splice_Site|GAS2L1_ENST00000360113.2_Splice_Site	NM_006477.4	NP_006468.1	Q92737	RSLAA_HUMAN	RAS-like, family 10, member A						small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)	1						TCTGGCCTCAGGTGAGGGAGA	0.592																																					.		Atlas-SNP	.											.	GAS2L1	54	.	0			c.634-1G>T						.						68.0	68.0	68.0					22																	29706428		2203	4300	6503	SO:0001628	intergenic_variant	10634	exon3			GCCTCAGGTGAGG	Y07847	CCDS13854.1	22q12.2	2014-05-09			ENSG00000100276	ENSG00000100276			16954	protein-coding gene	gene with protein product		602220				8975699, 15731001	Standard	NM_006477		Approved	RRP22	uc031rxl.1	Q92737	OTTHUMG00000151106		chr22.hg19:g.29706428G>T		129.0	0.0		173.0	72.0	NM_152237	Q49AU5|Q6PI03	Splice_Site	SNP	ENST00000216101.6	hg19	CCDS13854.1	.	.	.	.	.	.	.	.	.	.	g	17.35	3.366389	0.61513	.	.	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.031	0.86461	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAS2L1	28036428	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	9.633000	0.98432	2.104000	0.64026	0.486000	0.48141	.	.	.		0.592	RASL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321342.1		
PRR14L	253143	hgsc.bcm.edu	37	22	32084215	32084215	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:32084215T>C	ENST00000327423.6	-	8	6297		c.e8-2		PRR14L_ENST00000434485.1_Splice_Site|PRR14L_ENST00000397493.2_Splice_Site	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like											endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						TTCTTTAACCTGAAAAGAAAT	0.363																																					.		Atlas-SNP	.											.	PRR14L	198	.	0			c.6108-2A>G						.						45.0	44.0	44.0					22																	32084215		2200	4297	6497	SO:0001630	splice_region_variant	253143	exon9			TTAACCTGAAAAG	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.6108-2A>G	chr22.hg19:g.32084215T>C		100.0	0.0		80.0	4.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Splice_Site	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977291	0.74360	.	.	ENSG00000183530	ENST00000330495;ENST00000397493;ENST00000327423;ENST00000434485	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4468	0.67356	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRR14L	30414215	1.000000	0.71417	0.992000	0.48379	0.942000	0.58702	6.308000	0.72820	2.005000	0.58758	0.482000	0.46254	.	.	.		0.363	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	Intron
DEPDC5	9681	hgsc.bcm.edu	37	22	32275652	32275652	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:32275652T>C	ENST00000382112.3	+	37	3990	c.3920T>C	c.(3919-3921)cTg>cCg	p.L1307P	DEPDC5_ENST00000539165.1_Missense_Mutation_p.L133P|DEPDC5_ENST00000382105.2_Missense_Mutation_p.C1202R|DEPDC5_ENST00000266091.3_Missense_Mutation_p.L1294P|DEPDC5_ENST00000400249.2_Missense_Mutation_p.L1285P|DEPDC5_ENST00000400248.2_Missense_Mutation_p.L1285P|DEPDC5_ENST00000535622.1_Missense_Mutation_p.L1216P|DEPDC5_ENST00000382111.2_Missense_Mutation_p.L1316P|DEPDC5_ENST00000400246.1_Missense_Mutation_p.L1316P	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1316					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.L1285P(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CTGCCCTGGCTGCCTAGCCGG	0.582																																					p.L1316P		Atlas-SNP	.											DEPDC5,NS,carcinoma,0,1	DEPDC5	266	.	1	Substitution - Missense(1)	prostate(1)	c.T3947C						.						57.0	59.0	58.0					22																	32275652		2025	4196	6221	SO:0001583	missense	9681	exon38			CCTGGCTGCCTAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3920T>C	chr22.hg19:g.32275652T>C	ENSP00000371546:p.Leu1307Pro	66.0	1.0		46.0	4.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	16.75|16.75	3.210212|3.210212	0.58343|0.58343	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000382105|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248;ENST00000539165	T|T;T;T;T;T;T;T	0.31769|0.33865	1.48|1.39;1.81;1.81;1.76;1.82;1.76;1.81	5.72|5.72	5.72|5.72	0.89469|0.89469	.|Winged helix-turn-helix transcription repressor DNA-binding (1);	.|0.000000	.|0.64402	.|D	.|0.000003	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|0.999;1.0;1.0;1.0;0.999;0.999	.|D;D;D;D;D;D	.|0.97110	.|0.998;0.999;1.0;0.999;0.997;0.997	T|T	0.54957|0.54957	-0.8215|-0.8215	7|10	0.87932|0.62326	D|D	0|0.03	.|.	15.1862|15.1862	0.73002|0.73002	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1316;1216;702;1294;1307;1285	.|B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.|.;.;.;.;.;DEPD5_HUMAN	R|P	1202|1216;1294;1285;1216;1316;1307;1316;1285;133	ENSP00000371539:C1202R|ENSP00000440210:L1216P;ENSP00000266091:L1294P;ENSP00000383108:L1285P;ENSP00000383105:L1316P;ENSP00000371546:L1307P;ENSP00000371545:L1316P;ENSP00000383107:L1285P	ENSP00000371539:C1202R|ENSP00000266091:L1294P	C|L	+|+	1|2	0|0	DEPDC5|DEPDC5	30605652|30605652	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	7.654000|7.654000	0.83653|0.83653	2.183000|2.183000	0.69458|0.69458	0.529000|0.529000	0.55759|0.55759	TGC|CTG	.	.		0.582	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
PICK1	9463	hgsc.bcm.edu	37	22	38465060	38465060	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38465060C>A	ENST00000404072.3	+	6	717	c.370C>A	c.(370-372)Cgg>Agg	p.R124R	RP5-1039K5.13_ENST00000445483.1_RNA|PICK1_ENST00000356976.3_Silent_p.R124R|PICK1_ENST00000468288.1_3'UTR	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	124					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					AGTCAAGCACCGGCTGGTGGA	0.632																																					p.R124R		Atlas-SNP	.											.	PICK1	30	.	0			c.C370A						.						53.0	45.0	47.0					22																	38465060		2203	4300	6503	SO:0001819	synonymous_variant	9463	exon6			AAGCACCGGCTGG	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"""protein kinase C, alpha binding protein"", ""protein interacting with PRKCA"""	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.370C>A	chr22.hg19:g.38465060C>A		111.0	0.0		92.0	4.0	NM_012407	B3KS52|O95906	Silent	SNP	ENST00000404072.3	hg19	CCDS13965.1																																																																																			.	.		0.632	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407	
PLA2G6	8398	hgsc.bcm.edu	37	22	38536052	38536052	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38536052C>A	ENST00000332509.3	-	5	917	c.734G>T	c.(733-735)cGg>cTg	p.R245L	PLA2G6_ENST00000335539.3_Missense_Mutation_p.R245L|PLA2G6_ENST00000402064.1_Missense_Mutation_p.R245L	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	245					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	GATGTTGCACCGAGCATTGCA	0.627																																					p.R245L		Atlas-SNP	.											.	PLA2G6	54	.	0			c.G734T						.						57.0	54.0	55.0					22																	38536052		2203	4300	6503	SO:0001583	missense	8398	exon5			TTGCACCGAGCAT	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"""Patatin-like phospholipase domain containing"", ""Parkinson disease"", ""Ankyrin repeat domain containing"""	9039	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 2"""	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.734G>T	chr22.hg19:g.38536052C>A	ENSP00000333142:p.Arg245Leu	73.0	0.0		73.0	4.0	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	hg19	CCDS13967.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.96|16.96	3.266667|3.266667	0.59540|0.59540	.|.	.|.	ENSG00000184381|ENSG00000184381	ENST00000452542|ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860	.|T;T;T	.|0.53640	.|0.61;0.61;0.61	5.69|5.69	5.69|5.69	0.88448|0.88448	.|Ankyrin repeat-containing domain (3);	.|0.104492	.|0.64402	.|D	.|0.000006	T|T	0.51261|0.51261	0.1664|0.1664	N|N	0.21324|0.21324	0.655|0.655	0.80722|0.80722	D|D	1|1	.|D;D	.|0.57257	.|0.979;0.958	.|P;P	.|0.59948	.|0.668;0.866	T|T	0.53187|0.53187	-0.8474|-0.8474	5|10	.|0.62326	.|D	.|0.03	-33.0839|-33.0839	14.0201|14.0201	0.64547|0.64547	0.0:0.928:0.0:0.072|0.0:0.928:0.0:0.072	.|.	.|245;245	.|O60733-2;O60733	.|.;PA2G6_HUMAN	C|L	76|245;106;245;245;173;245	.|ENSP00000333142:R245L;ENSP00000335149:R245L;ENSP00000386100:R245L	.|ENSP00000333142:R245L	G|R	-|-	1|2	0|0	PLA2G6|PLA2G6	36865998|36865998	0.996000|0.996000	0.38824|0.38824	0.857000|0.857000	0.33713|0.33713	0.296000|0.296000	0.27459|0.27459	3.294000|3.294000	0.51787|0.51787	2.676000|2.676000	0.91093|0.91093	0.561000|0.561000	0.74099|0.74099	GGT|CGG	.	.		0.627	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	
DDX17	10521	hgsc.bcm.edu	37	22	38897259	38897259	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38897259A>G	ENST00000396821.3	-	2	413	c.314T>C	c.(313-315)cTt>cCt	p.L105P	DDX17_ENST00000381633.3_Missense_Mutation_p.L26P|DDX17_ENST00000432525.1_5'UTR	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	105					ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					CTTCGGGGGAAGGCCACCACC	0.388																																					p.L105P	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.T314C						.						72.0	73.0	72.0					22																	38897259		2203	4300	6503	SO:0001583	missense	10521	exon2			GGGGGAAGGCCAC	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"""DEAD-boxes"""	2740	protein-coding gene	gene with protein product		608469	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"""			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.314T>C	chr22.hg19:g.38897259A>G	ENSP00000380033:p.Leu105Pro	63.0	0.0		73.0	4.0	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453211	0.43531	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.30182	1.54;1.54;1.54	5.58	5.58	0.84498	.	9.185410	0.00166	N	0.000000	T	0.23451	0.0567	N	0.04508	-0.205	0.80722	D	1	B;B;B	0.20988	0.001;0.05;0.008	B;B;B	0.20184	0.001;0.028;0.023	T	0.02533	-1.1145	10	0.33141	T	0.24	-14.9317	15.756	0.78025	1.0:0.0:0.0:0.0	.	26;107;105	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	P	105;26;105;107	ENSP00000380033:L105P;ENSP00000371046:L26P;ENSP00000385536:L105P	ENSP00000371046:L26P	L	-	2	0	DDX17	37227205	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.645000	0.74343	2.122000	0.65172	0.482000	0.46254	CTT	.	.		0.388	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881	
CBX7	23492	hgsc.bcm.edu	37	22	39530449	39530449	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:39530449C>T	ENST00000216133.5	-	5	760	c.555G>A	c.(553-555)gcG>gcA	p.A185A	CBX7_ENST00000475962.1_Intron|CBX7_ENST00000401405.3_Silent_p.A92A	NM_175709.3	NP_783640.1	O95931	CBX7_HUMAN	chromobox homolog 7	185					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sebaceous gland development (GO:0048733)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7	Melanoma(58;0.04)					ACTCGCCAGCCGCCTGCAGGA	0.687																																					p.A185A	GBM(46;845 904 3560 9866 23971)	Atlas-SNP	.											CBX7,caecum,carcinoma,0,1	CBX7	18	.	0			c.G555A						.						13.0	17.0	16.0					22																	39530449		2151	4240	6391	SO:0001819	synonymous_variant	23492	exon5			GCCAGCCGCCTGC		CCDS13986.1	22q13.1	2010-07-06			ENSG00000100307	ENSG00000100307			1557	protein-coding gene	gene with protein product		608457					Standard	NM_175709		Approved		uc003axb.3	O95931	OTTHUMG00000150418	ENST00000216133.5:c.555G>A	chr22.hg19:g.39530449C>T		88.0	0.0		56.0	20.0	NM_175709	Q86T17	Silent	SNP	ENST00000216133.5	hg19	CCDS13986.1																																																																																			.	.		0.687	CBX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318020.1	NM_175709	
RPL3	6122	hgsc.bcm.edu	37	22	39711541	39711541	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:39711541C>T	ENST00000216146.4	-	5	694	c.521G>A	c.(520-522)cGc>cAc	p.R174H	SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000401609.1_Missense_Mutation_p.R122H|RPL3_ENST00000465618.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	174					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	CTTCTTCTGGCGCAGAGGAAG	0.627																																					p.R174H		Atlas-SNP	.											RPL3,NS,carcinoma,0,1	RPL3	29	.	0			c.G521A						.						43.0	40.0	41.0					22																	39711541		2203	4300	6503	SO:0001583	missense	6122	exon5			TTCTGGCGCAGAG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.521G>A	chr22.hg19:g.39711541C>T	ENSP00000346001:p.Arg174His	74.0	0.0		45.0	2.0	NM_000967	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554982	0.65425	.	.	ENSG00000100316	ENST00000401609;ENST00000216146;ENST00000402527;ENST00000453303	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.47	5.47	0.80525	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.050057	0.85682	D	0.000000	T	0.31544	0.0800	L	0.58302	1.8	0.80722	D	1	B;B;B	0.17667	0.023;0.002;0.005	B;B;B	0.19391	0.025;0.004;0.008	T	0.04737	-1.0930	10	0.44086	T	0.13	.	19.3177	0.94223	0.0:1.0:0.0:0.0	.	145;122;174	Q8TBW1;G5E9G0;P39023	.;.;RL3_HUMAN	H	122;174;122;201	ENSP00000386101:R122H;ENSP00000346001:R174H;ENSP00000385762:R122H;ENSP00000415198:R201H	ENSP00000346001:R174H	R	-	2	0	RPL3	38041487	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.864000	0.62990	2.584000	0.87258	0.462000	0.41574	CGC	.	.		0.627	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	
FAM83F	113828	hgsc.bcm.edu	37	22	40415332	40415332	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40415332G>A	ENST00000333407.6	+	2	744	c.650G>A	c.(649-651)cGg>cAg	p.R217Q	FAM83F_ENST00000473717.1_Missense_Mutation_p.R49Q	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	217								p.R217Q(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						ACTGACTTCCGGATTCGGGTA	0.582																																					p.R217Q		Atlas-SNP	.											FAM83F,NS,carcinoma,0,2	FAM83F	29	.	1	Substitution - Missense(1)	endometrium(1)	c.G650A						.						113.0	88.0	96.0					22																	40415332		2203	4300	6503	SO:0001583	missense	113828	exon2			ACTTCCGGATTCG		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.650G>A	chr22.hg19:g.40415332G>A	ENSP00000330432:p.Arg217Gln	110.0	0.0		74.0	3.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	G	9.725	1.160672	0.21538	.	.	ENSG00000133477	ENST00000333407	T	0.11169	2.8	4.94	3.93	0.45458	.	0.180528	0.49916	D	0.000135	T	0.03390	0.0098	N	0.10809	0.05	0.34242	D	0.677758	P	0.39404	0.672	B	0.25140	0.058	T	0.39901	-0.9591	10	0.23891	T	0.37	-6.1022	3.4047	0.07336	0.2311:0.0:0.5696:0.1993	.	217	Q8NEG4	FA83F_HUMAN	Q	217	ENSP00000330432:R217Q	ENSP00000330432:R217Q	R	+	2	0	FAM83F	38745278	1.000000	0.71417	0.998000	0.56505	0.590000	0.36582	4.686000	0.61700	1.310000	0.45006	0.561000	0.74099	CGG	.	.		0.582	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
SGSM3	27352	hgsc.bcm.edu	37	22	40803030	40803030	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40803030C>A	ENST00000248929.9	+	11	1384	c.1195C>A	c.(1195-1197)Cgc>Agc	p.R399S	SGSM3_ENST00000454798.2_Missense_Mutation_p.R332S	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						GGTTGTTCGCCGCAGGACCCA	0.612																																					p.R399S		Atlas-SNP	.											.	SGSM3	48	.	0			c.C1195A						.						45.0	35.0	39.0					22																	40803030		2197	4298	6495	SO:0001583	missense	27352	exon11			GTTCGCCGCAGGA	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"""Small G protein signaling modulators"""	25228	protein-coding gene	gene with protein product	"""RUN and SH3 containing 3"""	610440	"""RUN and TBC1 domain containing 3"""	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.1195C>A	chr22.hg19:g.40803030C>A	ENSP00000248929:p.Arg399Ser	108.0	0.0		70.0	4.0	NM_015705		Missense_Mutation	SNP	ENST00000248929.9	hg19	CCDS14002.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513408	0.85389	.	.	ENSG00000100359	ENST00000248929;ENST00000454798	T;T	0.18657	2.28;2.2	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.71674	0.994;0.994;0.977;0.998	P;P;P;P	0.61658	0.892;0.854;0.851;0.885	T	0.35773	-0.9775	10	0.72032	D	0.01	.	13.3361	0.60518	0.1577:0.8423:0.0:0.0	.	336;332;399;399	B4DVE3;B4DMS2;Q96HU1-2;Q96HU1	.;.;.;SGSM3_HUMAN	S	399;332	ENSP00000248929:R399S;ENSP00000390998:R332S	ENSP00000248929:R399S	R	+	1	0	SGSM3	39132976	0.993000	0.37304	0.971000	0.41717	0.949000	0.60115	3.125000	0.50469	2.578000	0.87016	0.563000	0.77884	CGC	.	.		0.612	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705	
SGSM3	27352	hgsc.bcm.edu	37	22	40803251	40803251	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40803251G>T	ENST00000248929.9	+	12	1476	c.1287G>T	c.(1285-1287)acG>acT	p.T429T	SGSM3_ENST00000454798.2_Silent_p.T362T	NM_015705.4	NP_056520.2			small G protein signaling modulator 3									p.T429T(1)		cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						TCAAGCAGACGGAACTGGTGG	0.632																																					p.T429T		Atlas-SNP	.											SGSM3,NS,carcinoma,0,1	SGSM3	48	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1287T						.						59.0	58.0	58.0					22																	40803251		2203	4300	6503	SO:0001819	synonymous_variant	27352	exon12			GCAGACGGAACTG	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"""Small G protein signaling modulators"""	25228	protein-coding gene	gene with protein product	"""RUN and SH3 containing 3"""	610440	"""RUN and TBC1 domain containing 3"""	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.1287G>T	chr22.hg19:g.40803251G>T		113.0	0.0		94.0	6.0	NM_015705		Silent	SNP	ENST00000248929.9	hg19	CCDS14002.1																																																																																			.	.		0.632	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705	
EP300	2033	hgsc.bcm.edu	37	22	41573037	41573037	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:41573037A>T	ENST00000263253.7	+	31	6541	c.5322A>T	c.(5320-5322)aaA>aaT	p.K1774N	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1774	Binding region for E1A adenovirus.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GCAAACGGAAAACCAATGGCG	0.562			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.K1774N		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A5322T						.						76.0	67.0	70.0					22																	41573037		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	ACGGAAAACCAAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.5322A>T	chr22.hg19:g.41573037A>T	ENSP00000263253:p.Lys1774Asn	78.0	0.0		85.0	6.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.586477	0.46110	.	.	ENSG00000100393	ENST00000263253	D	0.83250	-1.7	5.76	0.909	0.19332	Zinc finger, TAZ-type (5);	0.000000	0.51477	D	0.000098	D	0.90748	0.7096	M	0.88570	2.965	0.38829	D	0.955817	D	0.89917	1.0	D	0.87578	0.998	D	0.90571	0.4522	10	0.72032	D	0.01	-8.7941	10.9976	0.47585	0.6018:0.0:0.3982:0.0	.	1774	Q09472	EP300_HUMAN	N	1774	ENSP00000263253:K1774N	ENSP00000263253:K1774N	K	+	3	2	EP300	39902983	0.991000	0.36638	1.000000	0.80357	0.992000	0.81027	0.310000	0.19356	0.124000	0.18369	0.533000	0.62120	AAA	.	.		0.562	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
PARVB	29780	hgsc.bcm.edu	37	22	44564512	44564512	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:44564512T>C	ENST00000338758.7	+	13	1112	c.1049T>C	c.(1048-1050)cTg>cCg	p.L350P	PARVB_ENST00000406477.3_Missense_Mutation_p.L383P|PARVB_ENST00000404989.1_Missense_Mutation_p.L313P	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	350	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				AAATCCACCCTGAGGGTTCTT	0.532																																					p.L383P		Atlas-SNP	.											.	PARVB	44	.	0			c.T1148C						.						109.0	99.0	103.0					22																	44564512		2203	4300	6503	SO:0001583	missense	29780	exon14			CCACCCTGAGGGT	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.1049T>C	chr22.hg19:g.44564512T>C	ENSP00000342492:p.Leu350Pro	177.0	0.0		94.0	4.0	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	hg19	CCDS14056.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187719	0.78789	.	.	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000404989	D;D;D	0.96913	-4.17;-4.17;-4.17	5.11	5.11	0.69529	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.98251	0.9421	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99066	1.0832	10	0.87932	D	0	-1.6952	11.3021	0.49311	0.0:0.0:0.0:1.0	.	350;313;350;383	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	P	383;350;313	ENSP00000384515:L383P;ENSP00000342492:L350P;ENSP00000384353:L313P	ENSP00000342492:L350P	L	+	2	0	PARVB	42895845	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	6.125000	0.71627	1.929000	0.55896	0.533000	0.62120	CTG	.	.		0.532	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
WNT7B	7477	hgsc.bcm.edu	37	22	46319021	46319021	+	Silent	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:46319021T>C	ENST00000339464.4	-	4	1139	c.765A>G	c.(763-765)aaA>aaG	p.K255K	WNT7B_ENST00000410089.1_Silent_p.K239K|WNT7B_ENST00000409496.3_Silent_p.K259K	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	255					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		TGCGCAGCTGTTTGATGCGCA	0.642																																					p.K255K		Atlas-SNP	.											.	WNT7B	45	.	0			c.A765G						.						58.0	55.0	56.0					22																	46319021		2203	4300	6503	SO:0001819	synonymous_variant	7477	exon4			CAGCTGTTTGATG	AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.765A>G	chr22.hg19:g.46319021T>C		149.0	0.0		86.0	4.0	NM_058238	B8A596|Q96Q12	Silent	SNP	ENST00000339464.4	hg19	CCDS33667.1																																																																																			.	.		0.642	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238	
GTSE1	51512	hgsc.bcm.edu	37	22	46704834	46704834	+	Silent	SNP	G	G	T	rs200502529		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:46704834G>T	ENST00000454366.1	+	4	968	c.756G>T	c.(754-756)gcG>gcT	p.A252A		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	233					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CTGGGGCTGCGGAGAAGGTAA	0.622																																					p.A252A	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.G756T						.						33.0	38.0	36.0					22																	46704834		2195	4286	6481	SO:0001819	synonymous_variant	51512	exon4			GGCTGCGGAGAAG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.756G>T	chr22.hg19:g.46704834G>T		112.0	0.0		64.0	4.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	hg19	CCDS14074.2																																																																																			.	G|0.999;A|0.001		0.622	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
IL17REL	400935	hgsc.bcm.edu	37	22	50438927	50438927	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:50438927T>C	ENST00000389983.2	-	6	578	c.314A>G	c.(313-315)gAc>gGc	p.D105G	IL17REL_ENST00000341280.5_Missense_Mutation_p.D105G	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	105										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GTGCCTCTGGTCCAGCTGGAC	0.647																																					p.D105G		Atlas-SNP	.											.	IL17REL	21	.	0			c.A314G						.						71.0	70.0	70.0					22																	50438927		2203	4300	6503	SO:0001583	missense	400935	exon6			CTCTGGTCCAGCT	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.314A>G	chr22.hg19:g.50438927T>C	ENSP00000374633:p.Asp105Gly	91.0	0.0		85.0	4.0	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	hg19	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	t	3.800	-0.041800	0.07452	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.13657	2.57;2.57	3.99	0.135	0.14775	.	0.584334	0.15723	N	0.247831	T	0.09818	0.0241	L	0.51422	1.61	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.27123	-1.0083	10	0.27785	T	0.31	.	2.875	0.05628	0.0:0.2942:0.249:0.4568	.	105	Q6ZVW7	I17EL_HUMAN	G	105	ENSP00000374633:D105G;ENSP00000342520:D105G	ENSP00000342520:D105G	D	-	2	0	IL17REL	48781054	0.000000	0.05858	0.024000	0.17045	0.028000	0.11728	-0.252000	0.08806	0.431000	0.26258	0.529000	0.55759	GAC	.	.		0.647	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
PLXNB2	23654	hgsc.bcm.edu	37	22	50720691	50720691	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:50720691C>T	ENST00000449103.1	-	19	3179	c.3039G>A	c.(3037-3039)agG>agA	p.R1013R	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.R1013R			O15031	PLXB2_HUMAN	plexin B2	1013	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCATGGCAAACCTCTGGATCA	0.682																																					p.R1013R		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G3039A						.						46.0	50.0	49.0					22																	50720691		2087	4191	6278	SO:0001819	synonymous_variant	23654	exon19			GGCAAACCTCTGG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3039G>A	chr22.hg19:g.50720691C>T		122.0	0.0		90.0	20.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
SHANK3	85358	hgsc.bcm.edu	37	22	51143419	51143419	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:51143419G>T	ENST00000414786.2	+	16	2109	c.1882G>T	c.(1882-1884)Gga>Tga	p.G628*	SHANK3_ENST00000262795.3_Nonsense_Mutation_p.G658*|SHANK3_ENST00000445220.2_Nonsense_Mutation_p.G643*			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	642	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		GGTGAAGGTCGGACACAAGCA	0.637																																					p.G628X		Atlas-SNP	.											.	SHANK3	96	.	0			c.G1882T						.						126.0	142.0	137.0					22																	51143419		2186	4284	6470	SO:0001587	stop_gained	85358	exon16			AAGGTCGGACACA	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.1882G>T	chr22.hg19:g.51143419G>T	ENSP00000464552:p.Gly628*	117.0	0.0		72.0	5.0	NM_033517	D7UT47|Q8TET3	Nonsense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	40	7.936391	0.98571	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.7953	0.69873	0.0:0.0:1.0:0.0	.	.	.	.	X	658;643	.	ENSP00000442518:G658X	G	+	1	0	SHANK3	49490285	1.000000	0.71417	0.881000	0.34555	0.970000	0.65996	7.481000	0.81124	2.364000	0.80123	0.591000	0.81541	GGA	.	.		0.637	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
KAL1	3730	hgsc.bcm.edu	37	X	8565289	8565289	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:8565289G>T	ENST00000262648.3	-	4	476	c.327C>A	c.(325-327)ttC>ttA	p.F109L		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	109					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						TCTTCTTGGGGAAGAGAGGCT	0.428																																					p.F109L		Atlas-SNP	.											.	KAL1	78	.	0			c.C327A						.						39.0	33.0	35.0					X																	8565289		2203	4300	6503	SO:0001583	missense	3730	exon4			CTTGGGGAAGAGA		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.327C>A	chrX.hg19:g.8565289G>T	ENSP00000262648:p.Phe109Leu	156.0	0.0		94.0	4.0	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.739146	0.30774	.	.	ENSG00000011201	ENST00000262648	T	0.74947	-0.89	4.36	3.48	0.39840	.	0.000000	0.85682	D	0.000000	T	0.79417	0.4442	M	0.68952	2.095	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.77635	-0.2514	10	0.02654	T	1	.	10.1895	0.43017	0.1:0.0:0.9:0.0	.	109	P23352	KALM_HUMAN	L	109	ENSP00000262648:F109L	ENSP00000262648:F109L	F	-	3	2	KAL1	8525289	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	1.714000	0.37961	1.793000	0.52555	0.600000	0.82982	TTC	.	.		0.428	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
MID1	4281	hgsc.bcm.edu	37	X	10450648	10450648	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:10450648C>A	ENST00000317552.4	-	5	1285	c.885G>T	c.(883-885)ctG>ctT	p.L295L	MID1_ENST00000380780.1_Silent_p.L295L|MID1_ENST00000380782.2_Silent_p.L295L|MID1_ENST00000453318.2_Silent_p.L295L|MID1_ENST00000380787.1_Silent_p.L295L|MID1_ENST00000380785.1_Silent_p.L295L|MID1_ENST00000380779.1_Silent_p.L295L	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	295			L -> P (in OGS1). {ECO:0000269|PubMed:15558842}.		microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGCTGAGCCAGTTTGCGAA	0.488																																					p.L346L		Atlas-SNP	.											.	MID1	72	.	0			c.G1038T						.						131.0	102.0	112.0					X																	10450648		2203	4300	6503	SO:0001819	synonymous_variant	4281	exon5			CTGAGCCAGTTTG	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7095	protein-coding gene	gene with protein product	"""Opitz/BBB syndrome"""	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.885G>T	chrX.hg19:g.10450648C>A		43.0	0.0		21.0	4.0	NM_001193278	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	hg19	CCDS14138.1																																																																																			.	.		0.488	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1		
BMX	660	hgsc.bcm.edu	37	X	15534284	15534284	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:15534284C>T	ENST00000357607.2	+	5	563	c.375C>T	c.(373-375)ttC>ttT	p.F125F	BMX_ENST00000463891.1_3'UTR|BMX_ENST00000342014.6_Silent_p.F125F|BMX_ENST00000348343.6_Silent_p.F125F			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	125					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					GTGGGTTCTTCGTGGACGGGA	0.512																																					p.F125F		Atlas-SNP	.											.	BMX	73	.	0			c.C375T						.						169.0	152.0	158.0					X																	15534284		2203	4300	6503	SO:0001819	synonymous_variant	660	exon5			GTTCTTCGTGGAC	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1079	protein-coding gene	gene with protein product	"""BTK-like on X chromosome"""	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.375C>T	chrX.hg19:g.15534284C>T		177.0	0.0		89.0	4.0	NM_001721	A6NIH9|O60564|Q12871	Silent	SNP	ENST00000357607.2	hg19	CCDS14168.1																																																																																			.	.		0.512	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721	
CA5B	11238	hgsc.bcm.edu	37	X	15768181	15768181	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:15768181A>G	ENST00000318636.3	+	2	171	c.35A>G	c.(34-36)cAa>cGa	p.Q12R	CA5B_ENST00000380313.1_3'UTR|CA5B_ENST00000454127.2_Missense_Mutation_p.Q12R	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					GTCATTCTTCAAGCCTCTCCA	0.463																																					p.Q12R		Atlas-SNP	.											.	CA5B	23	.	0			c.A35G						.						117.0	114.0	115.0					X																	15768181		2203	4300	6503	SO:0001583	missense	11238	exon2			TTCTTCAAGCCTC	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"""Carbonic anhydrases"""	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.35A>G	chrX.hg19:g.15768181A>G	ENSP00000314099:p.Gln12Arg	169.0	0.0		87.0	4.0	NM_007220	A6NEZ4	Missense_Mutation	SNP	ENST00000318636.3	hg19	CCDS14171.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.433661	0.25813	.	.	ENSG00000169239	ENST00000498004;ENST00000318636;ENST00000479740;ENST00000454127	T;T;T	0.68479	-0.33;0.16;-0.33	5.37	4.13	0.48395	.	3.866790	0.00357	N	0.000025	T	0.56077	0.1961	L	0.27053	0.805	0.09310	N	1	B	0.16603	0.018	B	0.15484	0.013	T	0.40194	-0.9576	10	0.30078	T	0.28	-6.5656	7.0154	0.24885	0.795:0.0:0.0:0.205	.	12	Q9Y2D0	CAH5B_HUMAN	R	12	ENSP00000314099:Q12R;ENSP00000417553:Q12R;ENSP00000417021:Q12R	ENSP00000314099:Q12R	Q	+	2	0	CA5B	15678102	0.894000	0.30519	0.207000	0.23584	0.621000	0.37620	1.706000	0.37878	1.800000	0.52685	0.417000	0.27973	CAA	.	.		0.463	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220	
DMD	1756	hgsc.bcm.edu	37	X	32490308	32490308	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:32490308G>T	ENST00000357033.4	-	22	3128	c.2922C>A	c.(2920-2922)atC>atA	p.I974I	DMD_ENST00000378677.2_Silent_p.I970I	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	974					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCTGCTCCATGATTTCATAGT	0.423																																					p.I974I		Atlas-SNP	.											.	DMD	2127	.	0			c.C2922A						.						171.0	148.0	156.0					X																	32490308		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon22			CTCCATGATTTCA	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2922C>A	chrX.hg19:g.32490308G>T		216.0	0.0		156.0	45.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.423	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CXorf22	170063	hgsc.bcm.edu	37	X	35989740	35989740	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:35989740T>G	ENST00000297866.5	+	12	2074	c.2008T>G	c.(2008-2010)Tta>Gta	p.L670V		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	670										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AGACATAGGCTTAGAGCCAGG	0.373																																					p.L670V		Atlas-SNP	.											.	CXorf22	272	.	0			c.T2008G						.						23.0	19.0	20.0					X																	35989740		2202	4295	6497	SO:0001583	missense	170063	exon12			ATAGGCTTAGAGC	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2008T>G	chrX.hg19:g.35989740T>G	ENSP00000297866:p.Leu670Val	131.0	0.0		78.0	25.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	15.97	2.990875	0.54041	.	.	ENSG00000165164	ENST00000297866	T	0.16597	2.33	5.72	-5.22	0.02806	.	0.529703	0.17944	N	0.156732	T	0.12518	0.0304	M	0.65975	2.015	0.09310	N	1	P	0.43287	0.802	B	0.40677	0.337	T	0.25467	-1.0131	10	0.17369	T	0.5	-3.1402	4.9309	0.13917	0.5443:0.1892:0.0:0.2665	.	670	Q6ZTR5	CX022_HUMAN	V	670	ENSP00000297866:L670V	ENSP00000297866:L670V	L	+	1	2	CXorf22	35899661	0.009000	0.17119	0.000000	0.03702	0.118000	0.20060	-0.271000	0.08572	-0.719000	0.04942	0.486000	0.48141	TTA	.	.		0.373	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
CYBB	1536	hgsc.bcm.edu	37	X	37665717	37665717	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:37665717G>T	ENST00000378588.4	+	11	1459	c.1392G>T	c.(1390-1392)caG>caT	p.Q464H	CYBB_ENST00000545017.1_Missense_Mutation_p.Q432H|CYBB_ENST00000536160.1_Missense_Mutation_p.Q197H|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	464					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	TGGAGAGCCAGATGCAGGAAA	0.517																																					p.Q464H		Atlas-SNP	.											.	CYBB	62	.	0			c.G1392T						.						130.0	103.0	112.0					X																	37665717		2202	4300	6502	SO:0001583	missense	1536	exon11			GAGCCAGATGCAG	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1392G>T	chrX.hg19:g.37665717G>T	ENSP00000367851:p.Gln464His	103.0	0.0		72.0	4.0	NM_000397	A8K138|Q2PP16	Missense_Mutation	SNP	ENST00000378588.4	hg19	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284215	0.40394	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	D;D;D	0.94497	-3.44;-3.44;-3.44	5.61	4.63	0.57726	Ferric reductase, NAD binding (1);	0.102912	0.64402	D	0.000002	D	0.94653	0.8276	L	0.60455	1.87	0.54753	D	0.99998	D;D	0.56968	0.973;0.978	P;D	0.63703	0.847;0.917	D	0.93376	0.6739	10	0.52906	T	0.07	.	3.4369	0.07449	0.3362:0.0:0.6638:0.0	.	432;464	F5GWD2;P04839	.;CY24B_HUMAN	H	464;432;197	ENSP00000367851:Q464H;ENSP00000441896:Q432H;ENSP00000441958:Q197H	ENSP00000367851:Q464H	Q	+	3	2	CYBB	37550661	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	2.465000	0.45075	2.332000	0.79248	0.544000	0.68410	CAG	.	.		0.517	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1		
SRPX	8406	hgsc.bcm.edu	37	X	38013812	38013812	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:38013812G>T	ENST00000378533.3	-	9	1220	c.1114C>A	c.(1114-1116)Cga>Aga	p.R372R	SRPX_ENST00000544439.1_Silent_p.R352R|SRPX_ENST00000343800.6_Silent_p.R359R|SRPX_ENST00000538295.1_Intron|SRPX_ENST00000479015.1_Intron|SRPX_ENST00000432886.2_Silent_p.R313R|TM4SF2_ENST00000465127.1_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	372					autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GTGATGTGTCGAAGATCAAGG	0.502																																					p.R372R		Atlas-SNP	.											.	SRPX	53	.	0			c.C1114A						.						92.0	63.0	73.0					X																	38013812		2202	4300	6502	SO:0001819	synonymous_variant	8406	exon9			TGTGTCGAAGATC	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.1114C>A	chrX.hg19:g.38013812G>T		79.0	0.0		81.0	4.0	NM_006307	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Silent	SNP	ENST00000378533.3	hg19	CCDS14245.1																																																																																			.	.		0.502	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
BCOR	54880	hgsc.bcm.edu	37	X	39934379	39934379	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:39934379G>T	ENST00000378444.4	-	4	448	c.220C>A	c.(220-222)Cgc>Agc	p.R74S	BCOR_ENST00000397354.3_Missense_Mutation_p.R74S|BCOR_ENST00000378455.4_Missense_Mutation_p.R74S|BCOR_ENST00000342274.4_Missense_Mutation_p.R74S	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	74					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R74S(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						AGGCCAGTGCGGTCCATGCTC	0.582			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.R74S		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	1	Substitution - Missense(1)	lung(1)	c.C220A						.						29.0	22.0	24.0					X																	39934379		2202	4300	6502	SO:0001583	missense	54880	exon4			CAGTGCGGTCCAT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.220C>A	chrX.hg19:g.39934379G>T	ENSP00000367705:p.Arg74Ser	98.0	0.0		91.0	6.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	g	16.19	3.054336	0.55218	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42	5.08	4.13	0.48395	.	.	.	.	.	T	0.72439	0.3460	L	0.32530	0.975	0.44214	D	0.997042	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.997;0.997;0.994;0.997	T	0.74225	-0.3734	9	0.52906	T	0.07	-19.8797	13.5537	0.61747	0.0:0.0:0.7808:0.2192	.	74;74;74;74	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	S	74	ENSP00000367716:R74S;ENSP00000380512:R74S;ENSP00000367705:R74S;ENSP00000345923:R74S;ENSP00000384485:R74S	ENSP00000345923:R74S	R	-	1	0	BCOR	39819323	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.913000	0.56394	2.107000	0.64212	0.525000	0.51046	CGC	.	.		0.582	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
CHST7	56548	hgsc.bcm.edu	37	X	46433646	46433646	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:46433646G>T	ENST00000276055.3	+	1	428	c.280G>T	c.(280-282)Ggg>Tgg	p.G94W		NM_019886.2	NP_063939.2	Q9NS84	CHST7_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7	94					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|N-acetylglucosamine metabolic process (GO:0006044)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			breast(3)|endometrium(2)|kidney(1)|lung(2)	8						CGGCGCTGTCGGGGAGGCAGT	0.692																																					p.G94W		Atlas-SNP	.											.	CHST7	23	.	0			c.G280T						.						26.0	21.0	23.0					X																	46433646		2203	4300	6503	SO:0001583	missense	56548	exon1			GCTGTCGGGGAGG	AB040711	CCDS14268.1	Xp11.3	2008-02-05			ENSG00000147119	ENSG00000147119		"""Sulfotransferases, membrane-bound"""	13817	protein-coding gene	gene with protein product		300375				10781596	Standard	NM_019886		Approved	C6ST-2, C6ST2	uc004dgt.3	Q9NS84	OTTHUMG00000021423	ENST00000276055.3:c.280G>T	chrX.hg19:g.46433646G>T	ENSP00000276055:p.Gly94Trp	100.0	0.0		62.0	5.0	NM_019886	O75667	Missense_Mutation	SNP	ENST00000276055.3	hg19	CCDS14268.1	.	.	.	.	.	.	.	.	.	.	g	10.92	1.485710	0.26686	.	.	ENSG00000147119	ENST00000276055	D	0.97688	-4.49	4.3	1.14	0.20703	.	0.483859	0.15100	N	0.280593	D	0.96719	0.8929	N	0.19112	0.55	0.30814	N	0.738525	D	0.71674	0.998	D	0.70487	0.969	D	0.94084	0.7347	10	0.66056	D	0.02	.	12.3937	0.55373	0.0:0.4722:0.5278:0.0	.	94	Q9NS84	CHST7_HUMAN	W	94	ENSP00000276055:G94W	ENSP00000276055:G94W	G	+	1	0	CHST7	46318590	1.000000	0.71417	0.770000	0.31555	0.501000	0.33797	1.088000	0.30877	0.350000	0.24002	0.509000	0.49947	GGG	.	.		0.692	CHST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056362.1	NM_019886	
GRIPAP1	56850	hgsc.bcm.edu	37	X	48855662	48855662	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:48855662G>A	ENST00000376441.1	-	3	193	c.159C>T	c.(157-159)agC>agT	p.S53S	GRIPAP1_ENST00000376444.3_Silent_p.S53S|GRIPAP1_ENST00000376423.4_Silent_p.S53S|GRIPAP1_ENST00000376425.3_Silent_p.S53S	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	53						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TCTGAGCTTTGCTGAACTCCT	0.537																																					p.S53S		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.C159T						.						135.0	94.0	108.0					X																	48855662		2203	4300	6503	SO:0001819	synonymous_variant	56850	exon3			AGCTTTGCTGAAC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.159C>T	chrX.hg19:g.48855662G>A		175.0	0.0		137.0	6.0	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	hg19	CCDS35248.1																																																																																			.	.		0.537	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
CCDC22	28952	hgsc.bcm.edu	37	X	49105132	49105132	+	Silent	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:49105132G>T	ENST00000376227.3	+	12	1538	c.1368G>T	c.(1366-1368)ctG>ctT	p.L456L		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	456										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						TCCAAGAACTGCACCAGAGTG	0.602																																					p.L456L		Atlas-SNP	.											.	CCDC22	69	.	0			c.G1368T						.						32.0	33.0	33.0					X																	49105132		2197	4296	6493	SO:0001819	synonymous_variant	28952	exon12			AGAACTGCACCAG	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.1368G>T	chrX.hg19:g.49105132G>T		260.0	0.0		174.0	35.0	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	hg19	CCDS14322.1																																																																																			.	.		0.602	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
FOXR2	139628	hgsc.bcm.edu	37	X	55650629	55650629	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:55650629C>A	ENST00000339140.3	+	1	797	c.485C>A	c.(484-486)cCa>cAa	p.P162Q		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	162					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						GCTGAGGAACCAGACGACAAC	0.517																																					p.P162Q		Atlas-SNP	.											.	FOXR2	42	.	0			c.C485A						.						69.0	59.0	62.0					X																	55650629		2203	4300	6503	SO:0001583	missense	139628	exon1			AGGAACCAGACGA	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"""Forkhead boxes"""	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.485C>A	chrX.hg19:g.55650629C>A	ENSP00000427329:p.Pro162Gln	154.0	0.0		86.0	5.0	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	hg19	CCDS35308.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.940364	0.00479	.	.	ENSG00000189299	ENST00000339140	D	0.93763	-3.28	3.19	0.654	0.17833	.	1.825580	0.03342	N	0.194900	T	0.68897	0.3051	N	0.00170	-1.935	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.72676	-0.4221	10	0.02654	T	1	.	0.4452	0.00492	0.4251:0.2217:0.1345:0.2187	.	162	Q6PJQ5	FOXR2_HUMAN	Q	162	ENSP00000427329:P162Q	ENSP00000427329:P162Q	P	+	2	0	FOXR2	55667354	0.017000	0.18338	0.000000	0.03702	0.007000	0.05969	0.063000	0.14410	-0.255000	0.09486	-0.314000	0.08810	CCA	.	.		0.517	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451	
FAM155B	27112	hgsc.bcm.edu	37	X	68725240	68725240	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:68725240C>A	ENST00000252338.4	+	1	157	c.115C>A	c.(115-117)Cgg>Agg	p.R39R	AL158069.1_ENST00000579664.1_RNA	NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	39						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						CGACTCCGAGCGGGCGCAGCG	0.701																																					p.R39R		Atlas-SNP	.											.	FAM155B	44	.	0			c.C115A						.						11.0	6.0	8.0					X																	68725240		1882	3579	5461	SO:0001819	synonymous_variant	27112	exon1			TCCGAGCGGGCGC	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"""transmembrane protein 28"", ""chromosome X open reading frame 63"""	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.115C>A	chrX.hg19:g.68725240C>A		54.0	0.0		55.0	4.0	NM_015686	B1ALV6|B9EGK1|D3DVU1	Silent	SNP	ENST00000252338.4	hg19	CCDS35317.1																																																																																			.	.		0.701	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686	
ARR3	407	hgsc.bcm.edu	37	X	69496000	69496000	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:69496000C>T	ENST00000307959.8	+	6	265	c.214C>T	c.(214-216)Cga>Tga	p.R72*	ARR3_ENST00000374495.3_Nonsense_Mutation_p.R72*	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	72					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						TCTGACGTTCCGAAAAGATCT	0.537																																					p.R72X		Atlas-SNP	.											.	ARR3	41	.	0			c.C214T						.						113.0	79.0	90.0					X																	69496000		2203	4300	6503	SO:0001587	stop_gained	407	exon6			ACGTTCCGAAAAG		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"""arrestin 4"""	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.214C>T	chrX.hg19:g.69496000C>T	ENSP00000311538:p.Arg72*	166.0	0.0		99.0	4.0	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Nonsense_Mutation	SNP	ENST00000307959.8	hg19	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.942918	0.53079	.	.	ENSG00000120500	ENST00000374495;ENST00000374480;ENST00000480877;ENST00000307959	.	.	.	4.23	1.43	0.22495	.	0.151709	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2853	4.3483	0.11143	0.4395:0.3706:0.0:0.19	.	.	.	.	X	72;72;21;72	.	ENSP00000311538:R72X	R	+	1	2	ARR3	69412725	0.936000	0.31750	0.693000	0.30195	0.429000	0.31625	0.147000	0.16202	-0.047000	0.13423	-0.283000	0.09986	CGA	.	.		0.537	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312	
SNX12	29934	hgsc.bcm.edu	37	X	70282707	70282707	+	Silent	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:70282707G>A	ENST00000374274.3	-	2	374	c.258C>T	c.(256-258)agC>agT	p.S86S	SNX12_ENST00000465030.1_5'UTR|SNX12_ENST00000276105.3_Silent_p.S82S	NM_001256185.1|NM_001256188.1|NM_013346.3	NP_001243114.1|NP_001243117.1|NP_037478.2	Q9UMY4	SNX12_HUMAN	sorting nexin 12	86	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of protein transport (GO:0051224)|regulation of endocytosis (GO:0030100)	early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	Renal(35;0.156)					GCCATACCTTGCTATCTCTCT	0.483																																					p.S86S		Atlas-SNP	.											.	SNX12	18	.	0			c.C258T						.						105.0	81.0	89.0					X																	70282707		2203	4300	6503	SO:0001819	synonymous_variant	29934	exon3			TACCTTGCTATCT	AF171229	CCDS14405.1, CCDS59169.1	Xq13.1	2008-03-11			ENSG00000147164	ENSG00000147164		"""Sorting nexins"""	14976	protein-coding gene	gene with protein product		300883					Standard	NM_013346		Approved		uc004dyr.2	Q9UMY4	OTTHUMG00000021786	ENST00000374274.3:c.258C>T	chrX.hg19:g.70282707G>A		128.0	0.0		87.0	19.0	NM_001256185	F8W8K5|Q8WUG9	Silent	SNP	ENST00000374274.3	hg19	CCDS14405.1																																																																																			.	.		0.483	SNX12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057094.1	NM_013346	
PHKA1	5255	hgsc.bcm.edu	37	X	71915637	71915637	+	Silent	SNP	C	C	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:71915637C>T	ENST00000373542.4	-	4	534	c.375G>A	c.(373-375)gtG>gtA	p.V125V	PHKA1_ENST00000541944.1_Silent_p.V125V|PHKA1_ENST00000373539.3_Silent_p.V125V|PHKA1_ENST00000373545.3_Silent_p.V125V|PHKA1-AS1_ENST00000420998.1_RNA|PHKA1_ENST00000339490.3_Silent_p.V125V	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	125					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GATCATCACCCACTACAGTGG	0.458																																					p.V125V		Atlas-SNP	.											.	PHKA1	129	.	0			c.G375A						.						157.0	133.0	141.0					X																	71915637		2202	4280	6482	SO:0001819	synonymous_variant	5255	exon4			ATCACCCACTACA		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.375G>A	chrX.hg19:g.71915637C>T		1274.0	1.0		886.0	223.0	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Silent	SNP	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.458	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1		
KIAA2022	340533	hgsc.bcm.edu	37	X	73960460	73960460	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:73960460C>A	ENST00000055682.6	-	3	4543	c.3932G>T	c.(3931-3933)cGg>cTg	p.R1311L		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1311					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGAAATTCCCGTTGGTCATC	0.532																																					p.R1311L		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G3932T						.						124.0	115.0	118.0					X																	73960460		2203	4300	6503	SO:0001583	missense	340533	exon3			AATTCCCGTTGGT		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3932G>T	chrX.hg19:g.73960460C>A	ENSP00000055682:p.Arg1311Leu	127.0	0.0		77.0	5.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966002	0.74131	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.35236	1.32;1.32	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55205	-0.8177	10	0.87932	D	0	-8.1691	18.525	0.90968	0.0:1.0:0.0:0.0	.	1311	Q5QGS0	K2022_HUMAN	L	1311	ENSP00000362567:R1311L;ENSP00000055682:R1311L	ENSP00000055682:R1311L	R	-	2	0	KIAA2022	73877185	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.487000	0.81328	2.317000	0.78254	0.544000	0.68410	CGG	.	.		0.532	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
DRP2	1821	hgsc.bcm.edu	37	X	100513518	100513518	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:100513518A>G	ENST00000395209.3	+	22	3138	c.2611A>G	c.(2611-2613)Agg>Ggg	p.R871G	DRP2_ENST00000402866.1_Missense_Mutation_p.R871G|DRP2_ENST00000538510.1_Missense_Mutation_p.R871G|DRP2_ENST00000541709.1_Missense_Mutation_p.R793G	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	871					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GCAGCGTCTGAGGGAGCTTCT	0.607																																					p.R871G		Atlas-SNP	.											.	DRP2	98	.	0			c.A2611G						.						10.0	9.0	9.0					X																	100513518		2181	4257	6438	SO:0001583	missense	1821	exon22			CGTCTGAGGGAGC	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2611A>G	chrX.hg19:g.100513518A>G	ENSP00000378635:p.Arg871Gly	92.0	0.0		97.0	4.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	hg19	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069855	0.76301	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.09723	3.02;3.02;2.95;3.02	5.39	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.32615	0.0835	M	0.84082	2.675	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.09930	-1.0652	10	0.87932	D	0	-12.7117	10.4037	0.44243	0.8386:0.1614:0.0:0.0	.	871	Q13474	DRP2_HUMAN	G	871;871;793;871	ENSP00000385038:R871G;ENSP00000378635:R871G;ENSP00000444752:R793G;ENSP00000441051:R871G	ENSP00000378635:R871G	R	+	1	2	DRP2	100400174	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.270000	0.51600	1.798000	0.52647	0.441000	0.28932	AGG	.	.		0.607	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939	
BHLHB9	80823	hgsc.bcm.edu	37	X	102004395	102004395	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:102004395G>T	ENST00000372735.1	+	4	1057	c.472G>T	c.(472-474)Gat>Tat	p.D158Y	BHLHB9_ENST00000447531.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000457056.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000448867.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000361229.4_Missense_Mutation_p.D158Y			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	158					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGCTGGGGCCGATTGCAAACC	0.483																																					p.D158Y		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G472T						.						81.0	86.0	84.0					X																	102004395		2203	4299	6502	SO:0001583	missense	80823	exon2			GGGGCCGATTGCA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.472G>T	chrX.hg19:g.102004395G>T	ENSP00000361820:p.Asp158Tyr	145.0	0.0		110.0	5.0	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	hg19	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	1.495	-0.553643	0.03996	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	4.38	0.812	0.18744	.	1.046050	0.07568	N	0.918073	T	0.06096	0.0158	N	0.08118	0	0.09310	N	1	P	0.39576	0.679	B	0.35510	0.204	T	0.35226	-0.9797	9	.	.	.	-16.1094	5.6751	0.17743	0.6143:0.0:0.3857:0.0	.	158	Q6PI77	BHLH9_HUMAN	Y	158	ENSP00000403226:D158Y;ENSP00000354675:D158Y;ENSP00000405893:D158Y;ENSP00000391722:D158Y;ENSP00000361820:D158Y	.	D	+	1	0	BHLHB9	101891051	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.014000	0.13333	0.033000	0.15463	-0.395000	0.06472	GAT	.	.		0.483	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
IRS4	8471	hgsc.bcm.edu	37	X	107979422	107979422	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:107979422C>A	ENST00000372129.2	-	1	229	c.153G>T	c.(151-153)ccG>ccT	p.P51P	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	51					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						ACATGGCTCCCGGACAAGACG	0.672																																					p.P51P		Atlas-SNP	.											.	IRS4	253	.	0			c.G153T						.						20.0	24.0	23.0					X																	107979422		2170	4211	6381	SO:0001819	synonymous_variant	8471	exon1			GGCTCCCGGACAA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.153G>T	chrX.hg19:g.107979422C>A		173.0	0.0		121.0	6.0	NM_003604		Silent	SNP	ENST00000372129.2	hg19	CCDS14544.1																																																																																			.	.		0.672	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
ALG13	79868	hgsc.bcm.edu	37	X	110980011	110980011	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:110980011G>T	ENST00000394780.3	+	23	2611	c.2599G>T	c.(2599-2601)Ggt>Tgt	p.G867C	ALG13_ENST00000470971.1_3'UTR|ALG13_ENST00000251943.4_Missense_Mutation_p.G763C	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	867					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						CTTATCTAACGGTGCAGCGGC	0.453																																					p.G867C		Atlas-SNP	.											.	ALG13	230	.	0			c.G2599T						.						221.0	188.0	198.0					X																	110980011		1568	3582	5150	SO:0001583	missense	79868	exon23			TCTAACGGTGCAG	AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2599G>T	chrX.hg19:g.110980011G>T	ENSP00000378260:p.Gly867Cys	262.0	0.0		166.0	7.0	NM_001099922	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Missense_Mutation	SNP	ENST00000394780.3	hg19	CCDS55477.1	.	.	.	.	.	.	.	.	.	.	G	1.646	-0.515106	0.04200	.	.	ENSG00000101901	ENST00000251943;ENST00000394780;ENST00000436609	T;T	0.74106	1.59;-0.81	5.49	0.135	0.14775	.	0.517332	0.21477	N	0.073895	T	0.35480	0.0933	N	0.00436	-1.5	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.40327	-0.9569	10	0.39692	T	0.17	-0.0745	6.5785	0.22581	0.2464:0.0:0.2588:0.4948	.	789;867;763	Q9NP73-3;Q9NP73;Q9NP73-4	.;ALG13_HUMAN;.	C	763;867;500	ENSP00000251943:G763C;ENSP00000378260:G867C	ENSP00000251943:G763C	G	+	1	0	ALG13	110866667	0.155000	0.22806	0.087000	0.20705	0.066000	0.16364	0.890000	0.28295	-0.249000	0.09569	-0.328000	0.08392	GGT	.	.		0.453	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466	
GLUD2	2747	hgsc.bcm.edu	37	X	120181981	120181981	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:120181981G>A	ENST00000328078.1	+	1	520	c.443G>A	c.(442-444)gGa>gAa	p.G148E		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	148					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CCCTGCAAGGGAGGTATCCGT	0.577																																					p.G148E		Atlas-SNP	.											.	GLUD2	89	.	0			c.G443A						.						94.0	67.0	76.0					X																	120181981		2203	4300	6503	SO:0001583	missense	2747	exon1			GCAAGGGAGGTAT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"""glutamate dehydrogenase pseudogene 1"""	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.443G>A	chrX.hg19:g.120181981G>A	ENSP00000327589:p.Gly148Glu	246.0	0.0		147.0	38.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498790	0.64298	.	.	ENSG00000182890	ENST00000328078	D	0.99685	-6.4	1.8	1.8	0.24995	Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain (1);	0.124053	0.53938	N	0.000048	D	0.99832	0.9924	H	0.99697	4.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97061	0.9771	10	0.87932	D	0	.	9.1461	0.36933	0.0:0.0:1.0:0.0	.	148	P49448	DHE4_HUMAN	E	148	ENSP00000327589:G148E	ENSP00000327589:G148E	G	+	2	0	GLUD2	120009662	1.000000	0.71417	0.835000	0.33067	0.842000	0.47809	6.236000	0.72339	1.228000	0.43614	0.472000	0.43445	GGA	.	.		0.577	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084	
ZIC3	7547	hgsc.bcm.edu	37	X	136649847	136649847	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:136649847C>A	ENST00000287538.5	+	1	1547	c.997C>A	c.(997-999)Ccg>Acg	p.P333T	ZIC3_ENST00000370606.3_Missense_Mutation_p.P333T	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	333	Nuclear localization signal.				anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					ATGCCCCTTCCCGGGCTGCGG	0.597																																					p.P333T		Atlas-SNP	.											.	ZIC3	93	.	0			c.C997A						.						67.0	73.0	71.0					X																	136649847		2202	4299	6501	SO:0001583	missense	7547	exon1			CCCTTCCCGGGCT	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.997C>A	chrX.hg19:g.136649847C>A	ENSP00000287538:p.Pro333Thr	199.0	0.0		125.0	5.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	hg19	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.798537	0.70567	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	D;D	0.91124	-2.79;-2.79	4.96	4.96	0.65561	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.052480	0.85682	D	0.000000	D	0.91436	0.7297	L	0.41415	1.275	0.80722	D	1	P	0.39737	0.685	P	0.51777	0.679	D	0.92506	0.6012	10	0.87932	D	0	.	16.2665	0.82581	0.0:1.0:0.0:0.0	.	333	O60481	ZIC3_HUMAN	T	333	ENSP00000287538:P333T;ENSP00000359638:P333T	ENSP00000287538:P333T	P	+	1	0	ZIC3	136477513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.837000	0.69381	2.299000	0.77371	0.596000	0.82720	CCG	.	.		0.597	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
SLITRK2	84631	hgsc.bcm.edu	37	X	144905572	144905572	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:144905572G>T	ENST00000370490.1	+	1	5884	c.1629G>T	c.(1627-1629)tgG>tgT	p.W543C	SLITRK2_ENST00000413937.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000447897.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000434188.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000428560.2_Missense_Mutation_p.W543C			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	543	LRRCT 2.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TGAAAGACTGGACAGAACATG	0.512																																					p.W543C		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G1629T						.						71.0	65.0	67.0					X																	144905572		2203	4300	6503	SO:0001583	missense	84631	exon5			AGACTGGACAGAA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1629G>T	chrX.hg19:g.144905572G>T	ENSP00000359521:p.Trp543Cys	163.0	0.0		97.0	4.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368903	0.61624	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47	5.84	5.84	0.93424	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80053	0.4553	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85242	0.1039	10	0.87932	D	0	-4.5593	16.2774	0.82651	0.0:0.0:1.0:0.0	.	543	Q9H156	SLIK2_HUMAN	C	543	ENSP00000334374:W543C;ENSP00000411681:W543C;ENSP00000359521:W543C;ENSP00000397015:W543C;ENSP00000407347:W543C;ENSP00000412010:W543C	ENSP00000334374:W543C	W	+	3	0	SLITRK2	144713264	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.869000	0.99810	2.448000	0.82819	0.600000	0.82982	TGG	.	.		0.512	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
AFF2	2334	hgsc.bcm.edu	37	X	148037651	148037651	+	Silent	SNP	C	C	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:148037651C>A	ENST00000370460.2	+	11	2555	c.2076C>A	c.(2074-2076)ccC>ccA	p.P692P	AFF2_ENST00000286437.5_Silent_p.P333P|AFF2_ENST00000370457.5_Silent_p.P659P|AFF2_ENST00000342251.3_Silent_p.P659P	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	692					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CTTTGGCTCCCGAGAAGAAGA	0.498																																					p.P692P		Atlas-SNP	.											.	AFF2	679	.	0			c.C2076A						.						89.0	93.0	91.0					X																	148037651		2203	4300	6503	SO:0001819	synonymous_variant	2334	exon11			GGCTCCCGAGAAG	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2076C>A	chrX.hg19:g.148037651C>A		100.0	0.0		85.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.498	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
ZNF185	7739	hgsc.bcm.edu	37	X	152128427	152128427	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:152128427A>G	ENST00000370268.4	+	17	1628	c.1591A>G	c.(1591-1593)Agc>Ggc	p.S531G	ZNF185_ENST00000539731.1_Missense_Mutation_p.S534G|ZNF185_ENST00000370270.2_Missense_Mutation_p.S563G|ZNF185_ENST00000535861.1_Missense_Mutation_p.S563G|ZNF185_ENST00000324823.6_Missense_Mutation_p.S299G|ZNF185_ENST00000318504.7_Missense_Mutation_p.S472G|ZNF185_ENST00000454925.1_Missense_Mutation_p.S169G|ZNF185_ENST00000318529.8_Missense_Mutation_p.S310G|ZNF185_ENST00000449285.2_Missense_Mutation_p.S532G			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	531						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CAGACGAGAGAGCTGCACCAG	0.572																																					p.S563G		Atlas-SNP	.											.	ZNF185	92	.	0			c.A1687G						.						37.0	40.0	39.0					X																	152128427		2079	4185	6264	SO:0001583	missense	7739	exon18			CGAGAGAGCTGCA	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"""Zinc fingers, C2H2-type"""	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1591A>G	chrX.hg19:g.152128427A>G	ENSP00000359291:p.Ser531Gly	73.0	0.0		53.0	4.0	NM_001178106	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.247|9.247	1.039815|1.039815	0.19669|0.19669	.|.	.|.	ENSG00000147394|ENSG00000147394	ENST00000426821|ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000370268;ENST00000318529;ENST00000370270	.|T;T;T;T;T	.|0.51071	.|0.73;0.72;0.74;0.74;0.74	4.14|4.14	-3.64|-3.64	0.04515|0.04515	.|.	.|0.566443	.|0.16697	.|N	.|0.203312	T|T	0.55577|0.55577	0.1929|0.1929	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	.|B;B;B;P;B;B;B;D;B	.|0.61697	.|0.161;0.161;0.002;0.907;0.28;0.161;0.037;0.99;0.162	.|B;B;B;P;B;B;B;D;B	.|0.72982	.|0.05;0.05;0.003;0.648;0.143;0.05;0.103;0.979;0.102	T|T	0.55964|0.55964	-0.8057|-0.8057	5|10	.|0.62326	.|D	.|0.03	-0.7509|-0.7509	12.7073|12.7073	0.57067|0.57067	0.246:0.0:0.754:0.0|0.246:0.0:0.754:0.0	.|.	.|532;472;502;534;563;531;169;310;294	.|O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231;Q8N1R8;F8W8V7;O15231-2	.|.;.;.;.;.;ZN185_HUMAN;.;.;.	G|G	316|563;534;532;472;366;299;531;310;294	.|ENSP00000440847:S563G;ENSP00000444367:S534G;ENSP00000395228:S532G;ENSP00000312782:S472G;ENSP00000359291:S531G	.|ENSP00000312782:S472G	E|S	+|+	2|1	0|0	ZNF185|ZNF185	151879083|151879083	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-0.722000|-0.722000	0.04958|0.04958	-0.979000|-0.979000	0.03529|0.03529	-0.424000|-0.424000	0.05967|0.05967	GAG|AGC	.	.		0.572	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150	
PLXNB3	5365	hgsc.bcm.edu	37	X	153032892	153032892	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:153032892G>T	ENST00000361971.5	+	3	724	c.610G>T	c.(610-612)Gcc>Tcc	p.A204S	PLXNB3_ENST00000538543.1_Intron|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A227S|U52111.14_ENST00000416854.1_RNA|PLXNB3_ENST00000538282.1_Intron|PLXNB3_ENST00000538776.1_Intron	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	204	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GCCACCCCTGGCCATCCGCCA	0.711																																					p.A227S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G679T						.						10.0	10.0	10.0					X																	153032892		2165	4249	6414	SO:0001583	missense	5365	exon4			CCCCTGGCCATCC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.610G>T	chrX.hg19:g.153032892G>T	ENSP00000355378:p.Ala204Ser	50.0	0.0		66.0	10.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	6.317	0.426546	0.11987	.	.	ENSG00000198753	ENST00000538966;ENST00000361971	T;T	0.10668	2.85;2.85	4.79	0.894	0.19242	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	3.310250	0.01446	N	0.015302	T	0.04363	0.0120	N	0.02315	-0.6	0.19300	N	0.999976	B;B	0.14012	0.009;0.002	B;B	0.15052	0.012;0.007	T	0.37267	-0.9713	10	0.02654	T	1	.	7.8823	0.29629	0.7283:0.0:0.2717:0.0	.	227;204	F5H773;Q9ULL4	.;PLXB3_HUMAN	S	227;204	ENSP00000442736:A227S;ENSP00000355378:A204S	ENSP00000355378:A204S	A	+	1	0	PLXNB3	152686086	0.375000	0.25089	0.193000	0.23327	0.788000	0.44548	1.395000	0.34520	-0.197000	0.10350	-0.374000	0.07098	GCC	.	.		0.711	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
MT-ND3	4537	hgsc.bcm.edu	37	M	10197	10197	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrM:10197G>A	ENST00000361227.2	+	1	139	c.139G>A	c.(139-141)Gcc>Acc	p.A47T	MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	47			A -> T (in LS and MT-C1D). {ECO:0000269|PubMed:17152068, ECO:0000269|PubMed:20818383}.		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)										CTATATCCCCCGCCCGCGTCC	0.423																																					p.A47T		Atlas-SNP	.											.	.	.	.	0			c.G139A						.																																			SO:0001583	missense	0	exon1			TCCCCCGCCCGCG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.139G>A	chrM.hg19:g.10197G>A	ENSP00000355206:p.Ala47Thr	10.0	0.0		11.0	11.0	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	hg19																																																																																				.	.		0.423	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
SLC9C1	285335	hgsc.bcm.edu	37	3	111985087	111985089	+	In_Frame_Del	DEL	AAG	AAG	-	rs557883834	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:111985087_111985089delAAG	ENST00000305815.5	-	8	1126_1128	c.874_876delCTT	c.(874-876)cttdel	p.L292del	SLC9C1_ENST00000487372.1_In_Frame_Del_p.L292del	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	292					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCACTTACTCAAGAAGAAGTGTT	0.315														4	0.000798722	0.003	0.0	5008	,	,		14903	0.0		0.0	False		,,,				2504	0.0				p.292_293del		Pindel	.											.	.	.	.	0			c.875_877del						.																																			SO:0001651	inframe_deletion	285335	exon8			.	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.874_876delCTT	chr3.hg19:g.111985093_111985095delAAG	ENSP00000306627:p.Leu292del	420.0	0.0		423.0	87.0	NM_183061	Q6ZRP4|Q7RTP2	In_Frame_Del	DEL	ENST00000305815.5	hg19	CCDS33817.1																																																																																			.	.		0.315	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
WDR7	23335	hgsc.bcm.edu	37	18	54349915	54349915	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:54349915delC	ENST00000254442.3	+	5	562	c.351delC	c.(349-351)tacfs	p.Y117fs	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Frame_Shift_Del_p.Y117fs	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	117					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGTAGTTCTACCAGTTCTCTG	0.368																																					p.Y117fs		Pindel	.											.	WDR7	166	.	0			c.350delA						.						147.0	135.0	139.0					18																	54349915		2203	4300	6503	SO:0001589	frameshift_variant	23335	exon5			.	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.351delC	chr18.hg19:g.54349915delC	ENSP00000254442:p.Tyr117fs	227.0	0.0		169.0	31.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Frame_Shift_Del	DEL	ENST00000254442.3	hg19	CCDS11962.1																																																																																			.	.		0.368	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		
BACE1	23621	hgsc.bcm.edu	37	11	117161738	117161739	+	Frame_Shift_Ins	INS	-	-	C			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117161738_117161739insC	ENST00000313005.6	-	7	1429_1430	c.969_970insG	c.(967-972)tggctafs	p.L324fs	BACE1_ENST00000513780.1_Frame_Shift_Ins_p.L299fs|BACE1_ENST00000445823.2_Frame_Shift_Ins_p.L280fs|BACE1_ENST00000428381.2_Frame_Shift_Ins_p.L255fs|BACE1_ENST00000392937.6_Frame_Shift_Ins_p.L224fs|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000510630.1_Frame_Shift_Ins_p.L199fs|BACE1_ENST00000528053.1_Frame_Shift_Ins_p.L290fs	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	324					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	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;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		TGCTCTCCTAGCCAGAAACCAT	0.505																																					p.L324fs		Pindel	.											.	BACE1	33	.	0			c.970_971insG						.																																			SO:0001589	frameshift_variant	23621	exon7			.	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.970dupG	chr11.hg19:g.117161740_117161740dupC	ENSP00000318585:p.Leu324fs	145.0	0.0		72.0	17.0	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Frame_Shift_Ins	INS	ENST00000313005.6	hg19	CCDS8383.1																																																																																			.	.		0.505	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
NCOA3	8202	hgsc.bcm.edu	37	20	46265318	46265320	+	In_Frame_Del	DEL	AAG	AAG	-	rs149716562		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:46265318_46265320delAAG	ENST00000371998.3	+	12	2379_2381	c.2188_2190delAAG	c.(2188-2190)aagdel	p.K732del	NCOA3_ENST00000341724.6_In_Frame_Del_p.K742del|NCOA3_ENST00000372004.3_In_Frame_Del_p.K732del|NCOA3_ENST00000371997.3_In_Frame_Del_p.K742del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	732					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTAAGTCCTAAGAAGAAGGAGA	0.468																																					p.739_740del		Pindel	.											.	NCOA3	156	.	0			c.2217_2219del						.																																			SO:0001651	inframe_deletion	8202	exon12			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2188_2190delAAG	chr20.hg19:g.46265324_46265326delAAG	ENSP00000361066:p.Lys732del	200.0	0.0		207.0	23.0	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.468	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
SETD8	387893	hgsc.bcm.edu	37	12	123880916	123880924	+	In_Frame_Del	DEL	TCGCAAACT	TCGCAAACT	-	rs148212570|rs372757608|rs77198130	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	TCGCAAACT	TCGCAAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:123880916_123880924delTCGCAAACT	ENST00000402868.3	+	5	960_968	c.534_542delTCGCAAACT	c.(532-543)aatcgcaaactt>aat	p.RKL179del	SETD8_ENST00000478781.2_3'UTR|SETD8_ENST00000330479.4_In_Frame_Del_p.RKL179del			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	220					histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CGCAACAGAATCGCAAACTTACGGATTTC	0.502																																					p.178_181del		Pindel	.											.	SETD8	35	.	0			c.533_541del						.																																			SO:0001651	inframe_deletion	387893	exon5			.	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.534_542delTCGCAAACT	chr12.hg19:g.123880916_123880924delTCGCAAACT	ENSP00000384629:p.Arg179_Leu181del	102.0	0.0		63.0	17.0	NM_020382	A8K9D0|Q86W83|Q8TD09	In_Frame_Del	DEL	ENST00000402868.3	hg19	CCDS9247.1																																																																																			.	.		0.502	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
