#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
MACF1	23499	hgsc.bcm.edu	37	1	39550024	39550024	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:39550024G>C	ENST00000372915.3	+	1	221	c.134G>C	c.(133-135)tGg>tCg	p.W45S	MACF1_ENST00000317713.7_Missense_Mutation_p.W45S|MACF1_ENST00000484793.1_Missense_Mutation_p.W45S|MACF1_ENST00000545844.1_Missense_Mutation_p.W45S|MACF1_ENST00000361689.2_Missense_Mutation_p.W45S|MACF1_ENST00000602421.1_Missense_Mutation_p.W45S|MACF1_ENST00000567887.1_Missense_Mutation_p.W45S|MACF1_ENST00000539005.1_Missense_Mutation_p.W45S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	45	Actin-binding.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACCTTGCCCTGGAACCTGCCA	0.617																																					p.W45S		Atlas-SNP	.											.	MACF1	909	.	0			c.G134C						PASS	.						50.0	42.0	45.0					1																	39550024		2203	4300	6503	SO:0001583	missense	23499	exon3			TGCCCTGGAACCT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.134G>C	chr1.hg19:g.39550024G>C	ENSP00000362006:p.Trp45Ser	52.0	0.0	.		44.0	15.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.5	4.540445	0.85917	.	.	ENSG00000127603	ENST00000484793;ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005	T;T;T;T;T	0.64260	-0.06;0.0;-0.06;-0.09;0.1	5.55	5.55	0.83447	.	.	.	.	.	T	0.68091	0.2963	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.71104	-0.4689	9	0.54805	T	0.06	.	17.013	0.86411	0.0:0.0:1.0:0.0	.	45	F8W8Q1	.	S	45;45;45;45;61;45;45	ENSP00000439537:W45S;ENSP00000362006:W45S;ENSP00000354573:W45S;ENSP00000313438:W45S;ENSP00000444364:W45S	ENSP00000313438:W45S	W	+	2	0	MACF1	39322611	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.954000	0.93051	2.611000	0.88343	0.655000	0.94253	TGG	.	.	.	none		0.617	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
ZZZ3	26009	hgsc.bcm.edu	37	1	78034104	78034104	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:78034104T>C	ENST00000370801.3	-	13	2854	c.2379A>G	c.(2377-2379)aaA>aaG	p.K793K	ZZZ3_ENST00000370798.1_Silent_p.K299K|ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	793					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						GTAATAGTTCTTTATATTCAG	0.279																																					p.K793K		Atlas-SNP	.											.	ZZZ3	80	.	0			c.A2379G						PASS	.						63.0	67.0	65.0					1																	78034104		2203	4298	6501	SO:0001819	synonymous_variant	26009	exon13			TAGTTCTTTATAT	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.2379A>G	chr1.hg19:g.78034104T>C		228.0	0.0	.		241.0	114.0	.	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Silent	SNP	ENST00000370801.3	hg19	CCDS677.1																																																																																			.	.	.	none		0.279	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534	
SASS6	163786	hgsc.bcm.edu	37	1	100573051	100573051	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:100573051T>G	ENST00000287482.5	-	11	1345	c.1205A>C	c.(1204-1206)aAa>aCa	p.K402T	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.K235T	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	402					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ATTCTTCAATTTCAACTTACC	0.308																																					p.K402T		Atlas-SNP	.											.	SASS6	61	.	0			c.A1205C						PASS	.						70.0	73.0	72.0					1																	100573051		2201	4290	6491	SO:0001583	missense	163786	exon11			TTCAATTTCAACT	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1205A>C	chr1.hg19:g.100573051T>G	ENSP00000287482:p.Lys402Thr	176.0	0.0	.		181.0	77.0	.	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936841	0.73557	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.32988	1.43;1.43	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.50939	0.1645	M	0.82716	2.605	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.56062	-0.8041	10	0.48119	T	0.1	-11.3163	15.8532	0.78952	0.0:0.0:0.0:1.0	.	402	Q6UVJ0	SAS6_HUMAN	T	402;375;235	ENSP00000287482:K402T;ENSP00000440169:K235T	ENSP00000287482:K402T	K	-	2	0	SASS6	100345639	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	6.990000	0.76225	2.140000	0.66376	0.477000	0.44152	AAA	.	.	.	none		0.308	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292	
WDR77	79084	hgsc.bcm.edu	37	1	111990187	111990187	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:111990187A>T	ENST00000235090.5	-	3	519	c.313T>A	c.(313-315)Ttg>Atg	p.L105M	Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'Flank|ATP5F1_ENST00000483994.1_5'Flank|WDR77_ENST00000411751.2_Intron|WDR77_ENST00000497278.1_5'Flank	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77	105					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA metabolic process (GO:0016070)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|methylosome (GO:0034709)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		AGTTCCCACAATTCAACAGCA	0.428																																					p.L105M		Atlas-SNP	.											.	WDR77	21	.	0			c.T313A						PASS	.						123.0	103.0	110.0					1																	111990187		2203	4300	6503	SO:0001583	missense	79084	exon3			CCCACAATTCAAC	BC016946	CCDS835.1	1p13.2	2013-01-09		2005-08-09	ENSG00000116455	ENSG00000116455		"""WD repeat domain containing"""	29652	protein-coding gene	gene with protein product		611734				11756452, 8619474	Standard	NM_024102		Approved	MEP50	uc001ebb.3	Q9BQA1	OTTHUMG00000011748	ENST00000235090.5:c.313T>A	chr1.hg19:g.111990187A>T	ENSP00000235090:p.Leu105Met	110.0	0.0	.		88.0	27.0	.	NM_024102	B3KMW6|B4DP38|Q3LID2|Q53FU2|Q6JZZ5|Q96GK4|Q9BWY3	Missense_Mutation	SNP	ENST00000235090.5	hg19	CCDS835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.4|21.4	4.147877|4.147877	0.78001|0.78001	.|.	.|.	ENSG00000116455|ENSG00000116455	ENST00000235090|ENST00000449340	T|.	0.35973|.	1.28|.	5.76|5.76	3.4|3.4	0.38934|0.38934	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.129654|.	0.53938|.	D|.	0.000056|.	T|T	0.43545|0.43545	0.1252|0.1252	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	P|.	0.62740|.	0.906|.	T|T	0.44907|0.44907	-0.9297|-0.9297	10|5	0.87932|.	D|.	0|.	-11.3985|-11.3985	4.9088|4.9088	0.13811|0.13811	0.4997:0.0:0.5003:0.0|0.4997:0.0:0.5003:0.0	.|.	105|.	Q9BQA1|.	MEP50_HUMAN|.	M|K	105|41	ENSP00000235090:L105M|.	ENSP00000235090:L105M|.	L|N	-|-	1|3	2|2	WDR77|WDR77	111791710|111791710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	2.746000|2.746000	0.47467|0.47467	1.003000|1.003000	0.39130|0.39130	0.379000|0.379000	0.24179|0.24179	TTG|AAT	.	.	.	none		0.428	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1	NM_024102	
MTMR11	10903	hgsc.bcm.edu	37	1	149907227	149907227	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:149907227T>C	ENST00000439741.2	-	4	540	c.290A>G	c.(289-291)gAt>gGt	p.D97G	MTMR11_ENST00000406732.3_Missense_Mutation_p.D69G|MTMR11_ENST00000361405.6_Missense_Mutation_p.D97G|MTMR11_ENST00000369140.3_Missense_Mutation_p.D25G|MTMR11_ENST00000492824.1_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	97							phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CAGGGCAAAATCGTATTCACT	0.527																																					p.D97G		Atlas-SNP	.											.	MTMR11	136	.	0			c.A290G						PASS	.						98.0	82.0	87.0					1																	149907227		2203	4300	6503	SO:0001583	missense	10903	exon4			GCAAAATCGTATT	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.290A>G	chr1.hg19:g.149907227T>C	ENSP00000391668:p.Asp97Gly	196.0	0.0	.		151.0	52.0	.	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	hg19	CCDS53360.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.644788	0.67358	.	.	ENSG00000014914	ENST00000369140;ENST00000439741;ENST00000361405;ENST00000406732	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.11	5.11	0.69529	.	0.112517	0.64402	D	0.000012	D	0.87434	0.6176	M	0.73962	2.25	0.45554	D	0.998509	D;D;D	0.89917	1.0;0.998;0.997	D;D;D	0.87578	0.998;0.995;0.989	D	0.87975	0.2739	9	.	.	.	.	11.2282	0.48897	0.0:0.0:0.0:1.0	.	69;25;97	A4FU01-6;A4FU01-4;A4FU01	.;.;MTMRB_HUMAN	G	25;97;97;69	ENSP00000358136:D25G;ENSP00000391668:D97G;ENSP00000354941:D97G;ENSP00000383948:D69G	.	D	-	2	0	MTMR11	148173851	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.778000	0.55371	2.145000	0.66743	0.528000	0.53228	GAT	.	.	.	none		0.527	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
BNIPL	149428	hgsc.bcm.edu	37	1	151009216	151009216	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:151009216A>T	ENST00000368931.3	+	1	171	c.15A>T	c.(13-15)caA>caT	p.Q5H	BNIPL_ENST00000295294.7_5'UTR	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	5					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|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)			GAACTATACAAGAGGCAGGAA	0.483																																					p.Q5H		Atlas-SNP	.											.	BNIPL	45	.	0			c.A15T						PASS	.						144.0	140.0	142.0					1																	151009216		1898	4125	6023	SO:0001583	missense	149428	exon1			TATACAAGAGGCA	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.15A>T	chr1.hg19:g.151009216A>T	ENSP00000357927:p.Gln5His	138.0	0.0	.		127.0	43.0	.	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	hg19	CCDS978.2	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180184	0.57800	.	.	ENSG00000163141	ENST00000368931;ENST00000361277	T;T	0.38401	1.15;1.14	4.7	-1.45	0.08828	.	0.594348	0.15154	N	0.277530	T	0.17109	0.0411	M	0.63428	1.95	0.28607	N	0.908861	P	0.37864	0.61	B	0.38712	0.28	T	0.12502	-1.0545	10	0.59425	D	0.04	.	8.6368	0.33953	0.5017:0.0:0.4983:0.0	.	5	Q7Z465	BNIPL_HUMAN	H	5	ENSP00000357927:Q5H;ENSP00000355333:Q5H	ENSP00000355333:Q5H	Q	+	3	2	BNIPL	149275840	0.182000	0.23173	0.101000	0.21167	0.276000	0.26787	-0.720000	0.04969	-0.128000	0.11641	-0.304000	0.09214	CAA	.	.	.	none		0.483	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
SLC27A3	11000	hgsc.bcm.edu	37	1	153751216	153751216	+	Missense_Mutation	SNP	T	T	A	rs141064582		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:153751216T>A	ENST00000368661.3	+	7	1707	c.1642T>A	c.(1642-1644)Tat>Aat	p.Y548N	SLC27A3_ENST00000271857.2_Missense_Mutation_p.Y629N|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	548					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ATTCCTGGGCTATGCTGGCGG	0.622																																					p.Y548N		Atlas-SNP	.											.	SLC27A3	42	.	0			c.T1642A						PASS	.						41.0	42.0	41.0					1																	153751216		2203	4300	6503	SO:0001583	missense	11000	exon7			CTGGGCTATGCTG	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.1642T>A	chr1.hg19:g.153751216T>A	ENSP00000357650:p.Tyr548Asn	38.0	0.0	.		20.0	8.0	.	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.381272	0.82792	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.50813	0.73;0.73	5.14	5.14	0.70334	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.76292	0.3967	H	0.98542	4.26	0.51482	D	0.999923	D	0.76494	0.999	D	0.81914	0.995	D	0.85387	0.1123	10	0.87932	D	0	-14.8688	12.9728	0.58522	0.0:0.0:0.0:1.0	.	548	Q5K4L6	S27A3_HUMAN	N	629;548	ENSP00000271857:Y629N;ENSP00000357650:Y548N	ENSP00000271857:Y629N	Y	+	1	0	SLC27A3	152017840	1.000000	0.71417	0.994000	0.49952	0.801000	0.45260	5.950000	0.70265	2.155000	0.67459	0.460000	0.39030	TAT	.	T|1.000;C|0.000	.	alt		0.622	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
DENND4B	9909	hgsc.bcm.edu	37	1	153903435	153903435	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:153903435A>C	ENST00000361217.4	-	25	4520	c.4102T>G	c.(4102-4104)Tgg>Ggg	p.W1368G	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1368					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)			TGGACCCTCCAGAGCACATAG	0.572																																					p.W1368G		Atlas-SNP	.											.	DENND4B	210	.	0			c.T4102G						PASS	.						29.0	32.0	31.0					1																	153903435		1907	4124	6031	SO:0001583	missense	9909	exon25			CCCTCCAGAGCAC	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.4102T>G	chr1.hg19:g.153903435A>C	ENSP00000354597:p.Trp1368Gly	129.0	0.0	.		107.0	40.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634508	0.47049	.	.	ENSG00000198837	ENST00000361217	T	0.21543	2.0	5.14	4.01	0.46588	.	0.060660	0.64402	N	0.000001	T	0.28532	0.0706	M	0.71871	2.18	0.58432	D	0.999999	D	0.69078	0.997	P	0.60789	0.879	T	0.08806	-1.0704	10	0.87932	D	0	-8.0431	11.3312	0.49477	0.8472:0.1528:0.0:0.0	.	1368	O75064	DEN4B_HUMAN	G	1368	ENSP00000354597:W1368G	ENSP00000354597:W1368G	W	-	1	0	DENND4B	152170059	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.584000	0.82572	0.958000	0.37956	-0.461000	0.05368	TGG	.	.	.	none		0.572	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
HCN3	57657	hgsc.bcm.edu	37	1	155258126	155258126	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:155258126G>A	ENST00000368358.3	+	8	2205	c.2197G>A	c.(2197-2199)Gga>Aga	p.G733R	HCN3_ENST00000496230.1_3'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	733	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGGGCGTAAGGGATCAGGAAG	0.692																																					p.G733R		Atlas-SNP	.											.	HCN3	74	.	0			c.G2197A						PASS	.						31.0	34.0	33.0					1																	155258126		2203	4299	6502	SO:0001583	missense	57657	exon8			CGTAAGGGATCAG	AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.2197G>A	chr1.hg19:g.155258126G>A	ENSP00000357342:p.Gly733Arg	60.0	0.0	.		47.0	21.0	.	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Missense_Mutation	SNP	ENST00000368358.3	hg19	CCDS1108.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692523	0.48202	.	.	ENSG00000143630	ENST00000368358	D	0.97888	-4.59	5.01	4.09	0.47781	.	0.126715	0.36101	N	0.002785	D	0.90752	0.7097	N	0.08118	0	0.36001	D	0.837413	P;P	0.44260	0.83;0.733	P;B	0.44946	0.465;0.346	D	0.91322	0.5083	10	0.40728	T	0.16	.	11.3683	0.49686	0.0887:0.0:0.9113:0.0	.	428;733	B7Z5R8;Q9P1Z3	.;HCN3_HUMAN	R	733	ENSP00000357342:G733R	ENSP00000357342:G733R	G	+	1	0	HCN3	153524750	0.967000	0.33354	1.000000	0.80357	0.964000	0.63967	1.074000	0.30703	1.464000	0.47987	0.557000	0.71058	GGA	.	.	.	none		0.692	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897	
PYHIN1	149628	hgsc.bcm.edu	37	1	158911893	158911893	+	Silent	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:158911893A>C	ENST00000368140.1	+	5	951	c.706A>C	c.(706-708)Aga>Cga	p.R236R	PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Silent_p.R227R|PYHIN1_ENST00000392252.3_Silent_p.R227R|PYHIN1_ENST00000392254.2_Silent_p.R236R	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	236	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AAATGAGCAAAGAAGAATGTT	0.348																																					p.R236R		Atlas-SNP	.											.	PYHIN1	208	.	0			c.A706C						PASS	.						71.0	73.0	72.0					1																	158911893		2203	4300	6503	SO:0001819	synonymous_variant	149628	exon5			GAGCAAAGAAGAA	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.706A>C	chr1.hg19:g.158911893A>C		159.0	0.0	.		217.0	17.0	.	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	hg19	CCDS1178.1																																																																																			.	.	.	none		0.348	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501	
ABCB10	23456	hgsc.bcm.edu	37	1	229684985	229684985	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:229684985A>G	ENST00000344517.4	-	2	756	c.714T>C	c.(712-714)acT>acC	p.T238T	RNA5SP78_ENST00000364622.1_RNA	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	238	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TGTTACCTGAAGTTTGCATGA	0.542																																					p.T238T		Atlas-SNP	.											.	ABCB10	71	.	0			c.T714C						PASS	.						86.0	77.0	80.0					1																	229684985		2203	4300	6503	SO:0001819	synonymous_variant	23456	exon2			ACCTGAAGTTTGC	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.714T>C	chr1.hg19:g.229684985A>G		127.0	0.0	.		124.0	57.0	.	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Silent	SNP	ENST00000344517.4	hg19	CCDS1580.1																																																																																			.	.	.	none		0.542	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089	
ADCY3	109	hgsc.bcm.edu	37	2	25042856	25042856	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:25042856G>A	ENST00000260600.5	-	21	4231	c.3380C>T	c.(3379-3381)aCc>aTc	p.T1127I	CENPO_ENST00000473706.1_3'UTR|CENPO_ENST00000380834.2_3'UTR|ADCY3_ENST00000405392.1_Missense_Mutation_p.T714I	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	1127					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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ATTGGGGAAGGTGGCTAGCTT	0.582																																					p.T1127I		Atlas-SNP	.											.	ADCY3	114	.	0			c.C3380T						PASS	.						58.0	50.0	53.0					2																	25042856		2203	4300	6503	SO:0001583	missense	109	exon21			GGGAAGGTGGCTA	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.3380C>T	chr2.hg19:g.25042856G>A	ENSP00000260600:p.Thr1127Ile	132.0	0.0	.		139.0	56.0	.	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	hg19	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725137	0.30593	.	.	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879	T;T	0.81330	-1.35;-1.48	5.59	4.72	0.59763	.	0.702099	0.14759	N	0.300131	T	0.74718	0.3753	L	0.39898	1.24	0.28882	N	0.894332	B;B;B	0.17268	0.021;0.021;0.001	B;B;B	0.14023	0.01;0.01;0.002	T	0.67393	-0.5682	10	0.41790	T	0.15	.	14.6206	0.68582	0.0711:0.0:0.9289:0.0	.	1128;1127;714	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	I	1127;714;1102	ENSP00000260600:T1127I;ENSP00000384484:T714I	ENSP00000260600:T1127I	T	-	2	0	ADCY3	24896360	1.000000	0.71417	0.788000	0.31933	0.028000	0.11728	6.328000	0.72915	1.499000	0.48617	0.655000	0.94253	ACC	.	.	.	none		0.582	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
BIRC6	57448	hgsc.bcm.edu	37	2	32740321	32740321	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:32740321T>C	ENST00000421745.2	+	55	10967	c.10833T>C	c.(10831-10833)gcT>gcC	p.A3611A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3611					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)					CACATTTGGCTACCCTTGCTT	0.403																																					p.A3611A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T10833C						PASS	.						130.0	129.0	129.0					2																	32740321		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon55			TTTGGCTACCCTT	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.10833T>C	chr2.hg19:g.32740321T>C		80.0	0.0	.		65.0	25.0	.	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.	.	none		0.403	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LIMS1	3987	hgsc.bcm.edu	37	2	109292439	109292439	+	Silent	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:109292439C>T	ENST00000393310.1	+	6	767	c.600C>T	c.(598-600)atC>atT	p.I200I	LIMS1_ENST00000409441.1_Silent_p.I237I|LIMS1_ENST00000338045.3_Silent_p.I200I|LIMS1_ENST00000332345.6_Silent_p.I200I|LIMS1_ENST00000410093.1_Silent_p.I204I|AC010095.5_ENST00000411710.1_RNA|LIMS1_ENST00000542845.1_Silent_p.I262I|LIMS1_ENST00000544547.1_Silent_p.I212I	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	200	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						GACGGCCCATCGAAGGGCGCG	0.547																																					p.I262I		Atlas-SNP	.											.	LIMS1	38	.	0			c.C786T						PASS	.						46.0	41.0	42.0					2																	109292439		2203	4300	6503	SO:0001819	synonymous_variant	3987	exon6			GCCCATCGAAGGG		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983	ENST00000393310.1:c.600C>T	chr2.hg19:g.109292439C>T		199.0	0.0	.		163.0	72.0	.	NM_001193485	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Silent	SNP	ENST00000393310.1	hg19	CCDS2078.1																																																																																			.	.	.	none		0.547	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987	
SP3	6670	hgsc.bcm.edu	37	2	174820712	174820712	+	Silent	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:174820712G>A	ENST00000310015.6	-	4	1058	c.528C>T	c.(526-528)atC>atT	p.I176I	SP3_ENST00000455789.2_Silent_p.I123I|SP3_ENST00000483084.1_5'Flank|SP3_ENST00000418194.2_Silent_p.I108I	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	176	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CTGCTGACTGGATCTGTGGTA	0.403																																					p.I176I		Atlas-SNP	.											.	SP3	82	.	0			c.C528T						PASS	.						247.0	244.0	245.0					2																	174820712		2203	4300	6503	SO:0001819	synonymous_variant	6670	exon4			TGACTGGATCTGT	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.528C>T	chr2.hg19:g.174820712G>A		127.0	0.0	.		104.0	44.0	.	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Silent	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	G	3.289	-0.145284	0.06627	.	.	ENSG00000172845	ENST00000416195	.	.	.	5.95	4.73	0.59995	.	.	.	.	.	T	0.58807	0.2148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55829	-0.8079	4	.	.	.	.	8.0434	0.30534	0.77:0.0:0.23:0.0	.	.	.	.	F	133	.	.	S	-	2	0	SP3	174528958	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.317000	0.33631	1.063000	0.40649	-0.440000	0.05779	TCC	.	.	.	none		0.403	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111	
C2orf54	79919	hgsc.bcm.edu	37	2	241835325	241835325	+	Silent	SNP	C	C	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:241835325C>G	ENST00000388934.4	-	1	248	c.90G>C	c.(88-90)gcG>gcC	p.A30A		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	30										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|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)		GGGCACGCGGCGCCTCCCGGG	0.687																																					p.A30A		Atlas-SNP	.											.	C2orf54	14	.	0			c.G90C						PASS	.						10.0	12.0	12.0					2																	241835325		2081	4195	6276	SO:0001819	synonymous_variant	79919	exon1			ACGCGGCGCCTCC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.90G>C	chr2.hg19:g.241835325C>G		48.0	0.0	.		54.0	23.0	.	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	hg19	CCDS42839.1																																																																																			.	.	.	none		0.687	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
CNTN4	152330	hgsc.bcm.edu	37	3	3095549	3095549	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:3095549C>A	ENST00000397461.1	+	23	3254	c.2870C>A	c.(2869-2871)tCg>tAg	p.S957*	CNTN4_ENST00000358480.3_Nonsense_Mutation_p.S738*|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000397459.2_Nonsense_Mutation_p.S629*|CNTN4_ENST00000448906.2_Nonsense_Mutation_p.S629*|CNTN4_ENST00000418658.1_Nonsense_Mutation_p.S957*|CNTN4_ENST00000427331.1_Nonsense_Mutation_p.S957*	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	957	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		AATAAAACATCGGTGGAGCTT	0.423																																					p.S957X		Atlas-SNP	.											.	CNTN4	335	.	0			c.C2870A						PASS	.						98.0	106.0	103.0					3																	3095549		2203	4300	6503	SO:0001587	stop_gained	152330	exon24			AAACATCGGTGGA	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2870C>A	chr3.hg19:g.3095549C>A	ENSP00000380602:p.Ser957*	148.0	0.0	.		151.0	131.0	.	NM_175607	B2RAX3|Q8IX14|Q8TC35	Nonsense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	C	40	8.002247	0.98605	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	.	.	.	5.14	5.14	0.70334	.	0.067800	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6165	0.91304	0.0:1.0:0.0:0.0	.	.	.	.	X	957;957;957;738;629;629	.	ENSP00000351267:S738X	S	+	2	0	CNTN4	3070549	1.000000	0.71417	0.753000	0.31225	0.999000	0.98932	5.598000	0.67585	2.377000	0.81083	0.655000	0.94253	TCG	.	.	.	none		0.423	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
HDAC11	79885	hgsc.bcm.edu	37	3	13525048	13525048	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:13525048A>C	ENST00000295757.3	+	3	419	c.236A>C	c.(235-237)tAt>tCt	p.Y79S	HDAC11_ENST00000402271.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000404548.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000522202.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000437379.2_Missense_Mutation_p.Y51S|HDAC11_ENST00000433119.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000404040.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000405025.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000446613.2_Intron	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	79	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						ACGAGGCGCTATCTTAATGAG	0.647																																					p.Y79S		Atlas-SNP	.											.	HDAC11	39	.	0			c.A236C						PASS	.						67.0	76.0	73.0					3																	13525048		2203	4300	6503	SO:0001583	missense	79885	exon3			GGCGCTATCTTAA	AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.236A>C	chr3.hg19:g.13525048A>C	ENSP00000295757:p.Tyr79Ser	129.0	0.0	.		114.0	85.0	.	NM_024827	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Missense_Mutation	SNP	ENST00000295757.3	hg19	CCDS2615.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683964	0.88639	.	.	ENSG00000163517	ENST00000433119;ENST00000295757;ENST00000402271;ENST00000404548;ENST00000404040;ENST00000458642;ENST00000405478;ENST00000405025;ENST00000522202;ENST00000418189;ENST00000434848;ENST00000416248;ENST00000455904;ENST00000437379	D;D;D;T;D;D;D;T;D;D;D;D	0.84223	-1.76;-1.82;-1.76;-0.66;-1.76;-1.76;-1.76;-0.96;-1.76;-1.76;-1.76;-1.76	5.91	5.91	0.95273	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.95082	0.8407	H	0.97611	4.04	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;0.999;1.0;1.0	D	0.96466	0.9345	10	0.87932	D	0	0.9856	13.7215	0.62730	1.0:0.0:0.0:0.0	.	51;51;51;79	B4DDK1;Q658J9;B5MCV5;Q96DB2	.;.;.;HDA11_HUMAN	S	51;79;79;79;79;79;51;51;51;98;98;51;51;51	ENSP00000295757:Y79S;ENSP00000384123:Y79S;ENSP00000385528:Y79S;ENSP00000385475:Y79S;ENSP00000405403:Y79S;ENSP00000385252:Y51S;ENSP00000384019:Y51S;ENSP00000429794:Y51S;ENSP00000398651:Y98S;ENSP00000402298:Y51S;ENSP00000396122:Y51S;ENSP00000395188:Y51S	ENSP00000295757:Y79S	Y	+	2	0	HDAC11	13500048	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.260000	0.78391	2.254000	0.74563	0.533000	0.62120	TAT	.	.	.	none		0.647	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827	
FGD5	152273	hgsc.bcm.edu	37	3	14922083	14922083	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:14922083A>G	ENST00000285046.5	+	3	2773	c.2663A>G	c.(2662-2664)gAa>gGa	p.E888G	FGD5_ENST00000543601.1_Missense_Mutation_p.E647G	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	888					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						CCACAGGTGGAAGGACAGTCC	0.527																																					p.E888G		Atlas-SNP	.											.	FGD5	248	.	0			c.A2663G						PASS	.						67.0	67.0	67.0					3																	14922083		2071	4204	6275	SO:0001583	missense	152273	exon3			AGGTGGAAGGACA	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.2663A>G	chr3.hg19:g.14922083A>G	ENSP00000285046:p.Glu888Gly	105.0	0.0	.		99.0	4.0	.	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.681534	0.47991	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.77358	-1.09;-0.93	4.99	4.99	0.66335	Dbl homology (DH) domain (1);	0.232426	0.29822	N	0.011101	T	0.71239	0.3316	L	0.57536	1.79	0.39731	D	0.971604	P;B	0.41475	0.751;0.205	B;B	0.34536	0.185;0.032	T	0.75085	-0.3442	10	0.45353	T	0.12	-13.8278	12.9328	0.58296	1.0:0.0:0.0:0.0	.	647;888	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	G	888;647	ENSP00000285046:E888G;ENSP00000445949:E647G	ENSP00000285046:E888G	E	+	2	0	FGD5	14897087	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.065000	0.57513	1.874000	0.54306	0.260000	0.18958	GAA	.	.	.	none		0.527	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
SEC22C	9117	hgsc.bcm.edu	37	3	42594897	42594897	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:42594897A>G	ENST00000264454.3	-	7	898	c.755T>C	c.(754-756)gTg>gCg	p.V252A	SEC22C_ENST00000417572.1_Intron|SEC22C_ENST00000423701.2_Intron|SEC22C_ENST00000273156.7_Intron|SEC22C_ENST00000536332.1_Intron			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	252					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		CATAAGCACCACCTTCATAGT	0.453																																					p.V252A		Atlas-SNP	.											.	SEC22C	27	.	0			c.T755C						PASS	.						97.0	95.0	96.0					3																	42594897		2203	4300	6503	SO:0001583	missense	9117	exon7			AGCACCACCTTCA	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.755T>C	chr3.hg19:g.42594897A>G	ENSP00000264454:p.Val252Ala	65.0	0.0	.		82.0	71.0	.	NM_032970	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	hg19	CCDS2700.1	.	.	.	.	.	.	.	.	.	.	A	9.808	1.182327	0.21870	.	.	ENSG00000093183	ENST00000264454	T	0.16324	2.35	4.25	3.09	0.35607	.	0.345862	0.29594	N	0.011709	T	0.07954	0.0199	N	0.12182	0.205	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.24870	-1.0148	10	0.20046	T	0.44	-23.3351	6.6199	0.22798	0.7104:0.0:0.2896:0.0	.	252	Q9BRL7	SC22C_HUMAN	A	252	ENSP00000264454:V252A	ENSP00000264454:V252A	V	-	2	0	SEC22C	42569901	0.989000	0.36119	1.000000	0.80357	0.995000	0.86356	1.955000	0.40372	0.790000	0.33803	0.482000	0.46254	GTG	.	.	.	none		0.453	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48718979	48718979	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:48718979G>C	ENST00000294129.2	-	5	952	c.833C>G	c.(832-834)aCt>aGt	p.T278S	NCKIPSD_ENST00000416649.2_Missense_Mutation_p.T271S|NCKIPSD_ENST00000341520.4_Missense_Mutation_p.T278S	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	278					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGTTGTACCAGTTGCCACTTC	0.642																																					p.T278S		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C833G						PASS	.						82.0	73.0	76.0					3																	48718979		2203	4300	6503	SO:0001583	missense	51517	exon5			GTACCAGTTGCCA	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.833C>G	chr3.hg19:g.48718979G>C	ENSP00000294129:p.Thr278Ser	69.0	0.0	.		62.0	52.0	.	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	hg19	CCDS2776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.037|0.037	-1.300432|-1.300432	0.01364|0.01364	.|.	.|.	ENSG00000213672|ENSG00000213672	ENST00000415281|ENST00000341520;ENST00000416649;ENST00000294129;ENST00000439518;ENST00000453349;ENST00000426678	.|T;T;T;T	.|0.41065	.|1.01;1.62;1.64;1.66	5.27|5.27	-4.4|-4.4	0.03600|0.03600	.|.	.|1.160740	.|0.06523	.|U	.|0.739951	T|T	0.16085|0.16085	0.0387|0.0387	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.0;0.0;0.001	T|T	0.27434|0.27434	-1.0074|-1.0074	5|10	.|0.06365	.|T	.|0.9	.|.	5.1942|5.1942	0.15227|0.15227	0.1384:0.1345:0.5335:0.1936|0.1384:0.1345:0.5335:0.1936	.|.	.|278;278;271	.|C9JSC3;Q9NZQ3;Q9NZQ3-3	.|.;SPN90_HUMAN;.	K|S	13|278;271;278;278;200;162	.|ENSP00000342621:T278S;ENSP00000389059:T271S;ENSP00000294129:T278S;ENSP00000409675:T278S	.|ENSP00000294129:T278S	N|T	-|-	3|2	2|0	NCKIPSD|NCKIPSD	48693983|48693983	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.275000|0.275000	0.26752|0.26752	-0.325000|-0.325000	0.07976|0.07976	-0.772000|-0.772000	0.04602|0.04602	-0.471000|-0.471000	0.05019|0.05019	AAC|ACT	.	.	.	none		0.642	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
WDFY3	23001	hgsc.bcm.edu	37	4	85716133	85716133	+	Splice_Site	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:85716133C>T	ENST00000295888.4	-	20	3575		c.e20-1		WDFY3_ENST00000322366.6_Splice_Site	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3						aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AAAAAGACATCTATTAAAGAA	0.398																																					.		Atlas-SNP	.											.	WDFY3	314	.	0			c.3168-1G>A						PASS	.						58.0	57.0	58.0					4																	85716133		2203	4300	6503	SO:0001630	splice_region_variant	23001	exon21			AGACATCTATTAA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3168-1G>A	chr4.hg19:g.85716133C>T		367.0	0.0	.		387.0	134.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Splice_Site	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632744	0.67015	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6264	0.95679	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDFY3	85935157	1.000000	0.71417	0.996000	0.52242	0.455000	0.32408	7.445000	0.80570	2.717000	0.92951	0.655000	0.94253	.	.	.	.	none		0.398	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	Intron
ARHGAP24	83478	hgsc.bcm.edu	37	4	86916381	86916381	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:86916381A>C	ENST00000395184.1	+	9	2040	c.1574A>C	c.(1573-1575)cAg>cCg	p.Q525P	ARHGAP24_ENST00000264343.4_Missense_Mutation_p.Q432P|ARHGAP24_ENST00000395183.2_Missense_Mutation_p.Q430P	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	525					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GAGTTAGGCCAGCACAACAGA	0.488																																					p.Q525P		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A1574C						PASS	.						141.0	120.0	127.0					4																	86916381		2203	4300	6503	SO:0001583	missense	83478	exon9			TAGGCCAGCACAA	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1574A>C	chr4.hg19:g.86916381A>C	ENSP00000378611:p.Gln525Pro	87.0	0.0	.		113.0	44.0	.	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	18.85	3.710859	0.68730	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.14516	2.84;2.5;2.5;2.5	5.87	5.87	0.94306	.	0.167043	0.53938	D	0.000042	T	0.30293	0.0760	L	0.54323	1.7	0.58432	D	0.999997	D;P;D	0.67145	0.995;0.934;0.996	P;P;P	0.59703	0.862;0.767;0.794	T	0.00939	-1.1507	10	0.66056	D	0.02	.	16.2567	0.82522	1.0:0.0:0.0:0.0	.	430;432;525	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	P	525;430;440;432	ENSP00000378611:Q525P;ENSP00000378610:Q430P;ENSP00000425589:Q440P;ENSP00000264343:Q432P	ENSP00000264343:Q432P	Q	+	2	0	ARHGAP24	87135405	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.581000	0.74045	2.242000	0.73789	0.482000	0.46254	CAG	.	.	.	none		0.488	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
POU4F2	5458	hgsc.bcm.edu	37	4	147560484	147560484	+	Silent	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:147560484C>A	ENST00000281321.3	+	1	440	c.192C>A	c.(190-192)ggC>ggA	p.G64G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	64	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					gcggcggcggcggcggcggag	0.771																																					p.G64G		Atlas-SNP	.											.	POU4F2	83	.	0			c.C192A						PASS	.						3.0	5.0	5.0					4																	147560484		1329	2897	4226	SO:0001819	synonymous_variant	5458	exon1			CGGCGGCGGCGGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.192C>A	chr4.hg19:g.147560484C>A		72.0	0.0	.		88.0	7.0	.	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.	.	none		0.771	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
KIAA0922	23240	hgsc.bcm.edu	37	4	154523827	154523827	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:154523827C>T	ENST00000409663.3	+	23	2636	c.2584C>T	c.(2584-2586)Cca>Tca	p.P862S	KIAA0922_ENST00000409959.3_Missense_Mutation_p.P863S|KIAA0922_ENST00000440693.1_Missense_Mutation_p.P779S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	862						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				AGACGTGGTTCCAGGACCCAG	0.512																																					p.P863S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C2587T						PASS	.						178.0	172.0	174.0					4																	154523827		2203	4300	6503	SO:0001583	missense	23240	exon23			GTGGTTCCAGGAC	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2584C>T	chr4.hg19:g.154523827C>T	ENSP00000386574:p.Pro862Ser	110.0	0.0	.		111.0	55.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	28.7	4.944424	0.92593	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.24723	2.09;1.84;2.08;1.85	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.58637	0.2136	M	0.86268	2.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.997	T	0.63580	-0.6605	10	0.72032	D	0.01	-16.3383	19.6869	0.95982	0.0:1.0:0.0:0.0	.	779;863;862	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	S	862;779;863;640	ENSP00000386574:P862S;ENSP00000409663:P779S;ENSP00000386787:P863S;ENSP00000240487:P640S	ENSP00000240487:P640S	P	+	1	0	KIAA0922	154743277	1.000000	0.71417	0.883000	0.34634	0.994000	0.84299	7.398000	0.79919	2.726000	0.93360	0.655000	0.94253	CCA	.	.	.	none		0.512	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
AGA	175	hgsc.bcm.edu	37	4	178354476	178354476	+	Nonsense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:178354476T>A	ENST00000264595.2	-	8	959	c.832A>T	c.(832-834)Aga>Tga	p.R278*	AGA_ENST00000506853.1_5'Flank	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	278					protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)			endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TCTTCTCCTCTTCTCATGTAT	0.388																																					p.R278X		Atlas-SNP	.											.	AGA	39	.	0			c.A832T						PASS	.						160.0	157.0	158.0					4																	178354476		2203	4300	6503	SO:0001587	stop_gained	175	exon8			CTCCTCTTCTCAT	X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"""glycosylasparaginase"", ""N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"""	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.832A>T	chr4.hg19:g.178354476T>A	ENSP00000264595:p.Arg278*	117.0	0.0	.		72.0	27.0	.	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Nonsense_Mutation	SNP	ENST00000264595.2	hg19	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327041	0.81690	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	.	.	.	5.98	-9.32	0.00643	.	1.744170	0.02144	N	0.057429	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-18.6433	7.5456	0.27764	0.0:0.3083:0.2807:0.411	.	.	.	.	X	278;135	.	ENSP00000264595:R278X	R	-	1	2	AGA	178591470	0.000000	0.05858	0.004000	0.12327	0.964000	0.63967	-0.368000	0.07543	-1.547000	0.01715	-1.171000	0.01739	AGA	.	.	.	none		0.388	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027	
FAT1	2195	hgsc.bcm.edu	37	4	187539964	187539964	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:187539964A>G	ENST00000441802.2	-	10	7985	c.7776T>C	c.(7774-7776)aaT>aaC	p.N2592N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2592	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATTGTGGTGCATTGTCATTGT	0.463										HNSCC(5;0.00058)																											p.N2592N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T7776C						PASS	.						58.0	56.0	56.0					4																	187539964		1994	4153	6147	SO:0001819	synonymous_variant	2195	exon10			TGGTGCATTGTCA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7776T>C	chr4.hg19:g.187539964A>G		95.0	0.0	.		73.0	29.0	.	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CLPTM1L	81037	hgsc.bcm.edu	37	5	1338066	1338066	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:1338066G>A	ENST00000320895.5	-	5	888	c.631C>T	c.(631-633)Ccc>Tcc	p.P211S	CLPTM1L_ENST00000507807.1_Missense_Mutation_p.P78S|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.P211S	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	211					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		AACAGGATGGGCAGGTAATGC	0.527																																					p.P211S		Atlas-SNP	.											.	CLPTM1L	60	.	0			c.C631T						PASS	.						132.0	107.0	116.0					5																	1338066		2203	4297	6500	SO:0001583	missense	81037	exon5			GGATGGGCAGGTA	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"""cisplatin resistance related protein"""	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.631C>T	chr5.hg19:g.1338066G>A	ENSP00000313854:p.Pro211Ser	94.0	0.0	.		92.0	32.0	.	NM_030782	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	hg19	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680386	0.88542	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.76448	-0.5;-0.5;-1.02	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.90758	0.7099	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93044	0.6460	10	0.87932	D	0	-28.9216	16.6738	0.85273	0.0:0.0:1.0:0.0	.	211;78	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	S	211;78;211	ENSP00000313854:P211S;ENSP00000423321:P78S;ENSP00000315196:P211S	ENSP00000313854:P211S	P	-	1	0	CLPTM1L	1391066	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.128000	0.89595	2.339000	0.79563	0.655000	0.94253	CCC	.	.	.	none		0.527	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782	
RAI14	26064	hgsc.bcm.edu	37	5	34757673	34757673	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:34757673C>T	ENST00000265109.3	+	3	424	c.137C>T	c.(136-138)gCc>gTc	p.A46V	RAI14_ENST00000515799.1_Missense_Mutation_p.A49V|RAI14_ENST00000506376.1_Missense_Mutation_p.A38V|RAI14_ENST00000428746.2_Missense_Mutation_p.A46V|RAI14_ENST00000512629.1_Missense_Mutation_p.A46V|RAI14_ENST00000503673.1_Missense_Mutation_p.A46V|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000397449.1_Missense_Mutation_p.A39V	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	46						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GGGGCCAGTGCCACCAAACAC	0.537																																					p.A49V		Atlas-SNP	.											.	RAI14	100	.	0			c.C146T						PASS	.						72.0	69.0	70.0					5																	34757673		2203	4300	6503	SO:0001583	missense	26064	exon5			CCAGTGCCACCAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.137C>T	chr5.hg19:g.34757673C>T	ENSP00000265109:p.Ala46Val	45.0	0.0	.		41.0	18.0	.	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	C	36	5.647579	0.96714	.	.	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.72	5.72	0.89469	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.52322	0.1727	N	0.02391	-0.57	0.58432	D	0.999999	D;D;D;D	0.67145	0.972;0.978;0.995;0.996	P;P;P;D	0.63597	0.797;0.871;0.864;0.916	T	0.61811	-0.6986	9	0.26408	T	0.33	-12.1349	19.8937	0.96942	0.0:1.0:0.0:0.0	.	38;46;49;46	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	V	46;46;46;46;46;46;46;46;46;46;49;46;46;38;39	ENSP00000265109:A46V;ENSP00000424879:A46V;ENSP00000422112:A46V;ENSP00000422377:A46V;ENSP00000388725:A46V;ENSP00000421424:A46V;ENSP00000422942:A46V;ENSP00000422515:A46V;ENSP00000422114:A46V;ENSP00000424502:A46V;ENSP00000427123:A49V;ENSP00000426770:A46V;ENSP00000425115:A46V;ENSP00000423854:A38V;ENSP00000380591:A39V	ENSP00000265109:A46V	A	+	2	0	RAI14	34793430	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.052000	0.71080	2.716000	0.92895	0.650000	0.86243	GCC	.	.	.	none		0.537	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
CMYA5	202333	hgsc.bcm.edu	37	5	79034827	79034827	+	Silent	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:79034827T>A	ENST00000446378.2	+	2	10270	c.10239T>A	c.(10237-10239)cgT>cgA	p.R3413R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3413					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)		AGAGGCTCCGTAATAGCCCTG	0.433																																					p.R3413R		Atlas-SNP	.											.	CMYA5	643	.	0			c.T10239A						PASS	.						86.0	83.0	84.0					5																	79034827		1900	4105	6005	SO:0001819	synonymous_variant	202333	exon2			GCTCCGTAATAGC	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.10239T>A	chr5.hg19:g.79034827T>A		117.0	0.0	.		109.0	45.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ANKRD34B	340120	hgsc.bcm.edu	37	5	79854839	79854839	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:79854839G>T	ENST00000338682.3	-	5	1672	c.1000C>A	c.(1000-1002)Caa>Aaa	p.Q334K		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	334						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TCAATGCATTGCTGATTTCCT	0.393																																					p.Q334K		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.C1000A						PASS	.						77.0	77.0	77.0					5																	79854839		2203	4300	6503	SO:0001583	missense	340120	exon5			TGCATTGCTGATT		CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"""Ankyrin repeat domain containing"""	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.1000C>A	chr5.hg19:g.79854839G>T	ENSP00000339802:p.Gln334Lys	58.0	0.0	.		51.0	27.0	.	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	hg19	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	G	5.706	0.314760	0.10789	.	.	ENSG00000189127	ENST00000338682	T	0.19806	2.12	5.74	3.95	0.45737	.	1.624130	0.04344	U	0.354534	T	0.21145	0.0509	L	0.44542	1.39	0.22571	N	0.998977	B	0.06786	0.001	B	0.04013	0.001	T	0.25572	-1.0128	10	0.33940	T	0.23	-0.2737	7.2927	0.26374	0.0775:0.0:0.5171:0.4055	.	334	A5PLL1	AN34B_HUMAN	K	334	ENSP00000339802:Q334K	ENSP00000339802:Q334K	Q	-	1	0	ANKRD34B	79890595	0.000000	0.05858	0.836000	0.33094	0.988000	0.76386	0.449000	0.21744	0.765000	0.33221	0.655000	0.94253	CAA	.	.	.	none		0.393	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95119657	95119657	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:95119657A>C	ENST00000379982.3	+	10	2121	c.1613A>C	c.(1612-1614)aAa>aCa	p.K538T	GLRX_ENST00000508780.1_Intron|RHOBTB3_ENST00000504179.1_Missense_Mutation_p.K169T|GLRX_ENST00000507605.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	538	Interaction with Rab9.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		GACCTGCTTAAAAAGGCCAAG	0.358																																					p.K538T		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A1613C						PASS	.						82.0	74.0	76.0					5																	95119657		2203	4300	6503	SO:0001583	missense	22836	exon10			TGCTTAAAAAGGC	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1613A>C	chr5.hg19:g.95119657A>C	ENSP00000369318:p.Lys538Thr	74.0	0.0	.		66.0	19.0	.	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	hg19	CCDS4077.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	12.44|12.44|12.44	1.939487|1.939487|1.939487	0.34189|0.34189|0.34189	.|.|.	.|.|.	ENSG00000164292|ENSG00000164292|ENSG00000164292	ENST00000510313|ENST00000379982;ENST00000504179|ENST00000503737	T|T;T|.	0.80909|0.75154|.	-1.43|-0.16;-0.91|.	5.71|5.71|5.71	4.53|4.53|4.53	0.55603|0.55603|0.55603	.|.|.	0.165681|0.165681|.	0.51477|0.51477|.	D|D|.	0.000098|0.000098|.	T|T|.	0.50956|0.50956|.	0.1646|0.1646|.	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B|.	.|0.27351|.	.|0.176|.	.|B|.	.|0.19148|.	.|0.024|.	T|T|.	0.42766|0.42766|.	-0.9432|-0.9432|.	8|10|.	0.14656|0.16420|.	T|T|.	0.56|0.52|.	-17.4539|-17.4539|-17.4539	8.0259|8.0259|8.0259	0.30436|0.30436|0.30436	0.7769:0.0:0.2231:0.0|0.7769:0.0:0.2231:0.0|0.7769:0.0:0.2231:0.0	.|.|.	.|538|.	.|O94955|.	.|RHBT3_HUMAN|.	Q|T|Y	120|538;169|40	ENSP00000424844:K120Q|ENSP00000369318:K538T;ENSP00000422360:K169T|.	ENSP00000424844:K120Q|ENSP00000369318:K538T|.	K|K|X	+|+|+	1|2|3	0|0|2	RHOBTB3|RHOBTB3|RHOBTB3	95145413|95145413|95145413	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.808000|0.808000|0.808000	0.45660|0.45660|0.45660	3.440000|3.440000|3.440000	0.52886|0.52886|0.52886	0.952000|0.952000|0.952000	0.37798|0.37798|0.37798	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	AAA|AAA|TAA	.	.	.	none		0.358	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
PCSK1	5122	hgsc.bcm.edu	37	5	95761539	95761539	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:95761539A>G	ENST00000311106.3	-	3	618	c.381T>C	c.(379-381)aaT>aaC	p.N127N	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Silent_p.N80N	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	127					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	ACCATTGCTGATTCCACATGG	0.408																																					p.N127N		Atlas-SNP	.											.	PCSK1	93	.	0			c.T381C						PASS	.						156.0	134.0	141.0					5																	95761539		2203	4300	6503	SO:0001819	synonymous_variant	5122	exon3			TTGCTGATTCCAC		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.381T>C	chr5.hg19:g.95761539A>G		65.0	0.0	.		49.0	16.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Silent	SNP	ENST00000311106.3	hg19	CCDS4081.1																																																																																			.	.	.	none		0.408	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
FEM1C	56929	hgsc.bcm.edu	37	5	114860326	114860326	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:114860326A>G	ENST00000274457.3	-	3	2094	c.1533T>C	c.(1531-1533)acT>acC	p.T511T		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	511					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TCAGTATTGCAGTAACTTGTA	0.453																																					p.T511T		Atlas-SNP	.											.	FEM1C	50	.	0			c.T1533C						PASS	.						186.0	175.0	179.0					5																	114860326		2202	4300	6502	SO:0001819	synonymous_variant	56929	exon3			TATTGCAGTAACT		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1533T>C	chr5.hg19:g.114860326A>G		100.0	0.0	.		65.0	26.0	.	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	ENST00000274457.3	hg19	CCDS4118.1																																																																																			.	.	.	none		0.453	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177	
DAAM2	23500	hgsc.bcm.edu	37	6	39824224	39824224	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:39824224A>G	ENST00000398904.2	+	2	328	c.146A>G	c.(145-147)aAc>aGc	p.N49S	DAAM2_ENST00000274867.4_Missense_Mutation_p.N49S|DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000405961.3_Missense_Mutation_p.N49S|DAAM2_ENST00000538976.1_Missense_Mutation_p.N49S			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	49	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GAGGAGCTCAACATCCGCTTT	0.607																																					p.N49S		Atlas-SNP	.											.	DAAM2	101	.	0			c.A146G						PASS	.						40.0	43.0	42.0					6																	39824224		2034	4199	6233	SO:0001583	missense	23500	exon2			AGCTCAACATCCG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.146A>G	chr6.hg19:g.39824224A>G	ENSP00000381876:p.Asn49Ser	105.0	0.0	.		133.0	49.0	.	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189591	0.78789	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976;ENST00000405961	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.99	5.99	0.97316	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.096890	0.64402	D	0.000001	D	0.87014	0.6072	L	0.59436	1.845	0.44366	D	0.99726	B;B;P	0.52463	0.341;0.393;0.953	B;B;P	0.54759	0.116;0.185;0.76	D	0.85729	0.1330	10	0.31617	T	0.26	.	15.4718	0.75446	1.0:0.0:0.0:0.0	.	49;49;49	G5EA45;Q86T65;F2Z2Q2	.;DAAM2_HUMAN;.	S	49	ENSP00000274867:N49S;ENSP00000381876:N49S;ENSP00000437808:N49S;ENSP00000384637:N49S	ENSP00000274867:N49S	N	+	2	0	DAAM2	39932202	0.998000	0.40836	0.064000	0.19789	0.780000	0.44128	8.760000	0.91671	2.296000	0.77279	0.533000	0.62120	AAC	.	.	.	none		0.607	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
SNX14	57231	hgsc.bcm.edu	37	6	86303311	86303311	+	Silent	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:86303311G>T	ENST00000314673.3	-	1	302	c.126C>A	c.(124-126)tcC>tcA	p.S42S	SNX14_ENST00000369627.2_Silent_p.S42S|SNX14_ENST00000513865.1_Silent_p.S42S|SNX14_ENST00000346348.3_Silent_p.S42S|RP11-321N4.5_ENST00000503906.1_Intron|SNX14_ENST00000505648.1_Intron	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	42					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TAAGAAGCAGGGAGGCGGCGC	0.672																																					p.S42S		Atlas-SNP	.											.	SNX14	58	.	0			c.C126A						PASS	.						28.0	26.0	27.0					6																	86303311		2202	4299	6501	SO:0001819	synonymous_variant	57231	exon1			AAGCAGGGAGGCG	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.126C>A	chr6.hg19:g.86303311G>T		126.0	0.0	.		136.0	54.0	.	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Silent	SNP	ENST00000314673.3	hg19	CCDS5004.1																																																																																			.	.	.	none		0.672	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
NR2E1	7101	hgsc.bcm.edu	37	6	108492734	108492734	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:108492734G>A	ENST00000368986.4	+	2	806	c.98G>A	c.(97-99)tGc>tAc	p.C33Y	NR2E1_ENST00000368983.3_Missense_Mutation_p.C70Y	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	33					aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		GTCTACGCCTGCGACGGCTGC	0.562																																					p.C33Y		Atlas-SNP	.											.	NR2E1	57	.	0			c.G98A						PASS	.						120.0	131.0	127.0					6																	108492734		2203	4300	6503	SO:0001583	missense	7101	exon2			ACGCCTGCGACGG	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"""Nuclear hormone receptors"""	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.98G>A	chr6.hg19:g.108492734G>A	ENSP00000357982:p.Cys33Tyr	88.0	0.0	.		80.0	26.0	.	NM_003269	Q6ZMP8	Missense_Mutation	SNP	ENST00000368986.4	hg19	CCDS5063.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750777	0.89753	.	.	ENSG00000112333	ENST00000368986;ENST00000368983	D;D	0.99828	-6.99;-6.99	5.39	5.39	0.77823	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.084915	0.85682	D	0.000000	D	0.99923	0.9964	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95984	0.8980	10	0.87932	D	0	.	18.7646	0.91866	0.0:0.0:1.0:0.0	.	33	Q9Y466	NR2E1_HUMAN	Y	33;70	ENSP00000357982:C33Y;ENSP00000357979:C70Y	ENSP00000357979:C70Y	C	+	2	0	NR2E1	108599427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.542000	0.85734	0.561000	0.74099	TGC	.	.	.	none		0.562	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2		
THEMIS	387357	hgsc.bcm.edu	37	6	128134425	128134425	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:128134425C>T	ENST00000368248.2	-	4	1509	c.1361G>A	c.(1360-1362)cGt>cAt	p.R454H	THEMIS_ENST00000537166.1_Missense_Mutation_p.R419H|THEMIS_ENST00000368250.1_Missense_Mutation_p.R375H|THEMIS_ENST00000543064.1_Missense_Mutation_p.R454H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	454	CABIT 2.				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						GAAGGGCAAACGGAACTGTTT	0.483																																					p.R454H		Atlas-SNP	.											.	THEMIS	168	.	0			c.G1361A						PASS	.						86.0	90.0	88.0					6																	128134425		2203	4300	6503	SO:0001583	missense	387357	exon4			GGCAAACGGAACT	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.1361G>A	chr6.hg19:g.128134425C>T	ENSP00000357231:p.Arg454His	92.0	0.0	.		81.0	33.0	.	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	9.748	1.166588	0.21621	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.16597	2.33;2.33;2.33;2.33	5.69	-4.82	0.03171	.	0.926991	0.09311	N	0.819555	T	0.02649	0.0080	N	0.12182	0.205	0.09310	N	1	B;B	0.16166	0.016;0.004	B;B	0.08055	0.003;0.003	T	0.47315	-0.9127	10	0.48119	T	0.1	1.4237	9.9298	0.41514	0.0:0.5558:0.1306:0.3135	.	454;454	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	375;454;454;419	ENSP00000357233:R375H;ENSP00000439594:R454H;ENSP00000357231:R454H;ENSP00000439863:R419H	ENSP00000357231:R454H	R	-	2	0	THEMIS	128176118	0.001000	0.12720	0.051000	0.19133	0.848000	0.48234	-2.321000	0.01119	-0.481000	0.06792	0.563000	0.77884	CGT	.	.	.	none		0.483	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923	
ADAP1	11033	hgsc.bcm.edu	37	7	959664	959664	+	Missense_Mutation	SNP	C	C	T	rs373846581		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:959664C>T	ENST00000265846.5	-	4	548	c.329G>A	c.(328-330)cGg>cAg	p.R110Q	ADAP1_ENST00000539900.1_Missense_Mutation_p.R121Q|ADAP1_ENST00000449296.2_Missense_Mutation_p.R38Q|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	110	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)	p.R110Q(1)		endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						GTACTTGGCCCGGATCCACTG	0.682													C|||	1	0.000199681	0.0008	0.0	5008	,	,		8018	0.0		0.0	False		,,,				2504	0.0				p.R110Q		Atlas-SNP	.											ADAP1,mouth,carcinoma,0,1	ADAP1	23	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G329A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	38.0	35.0	36.0		329	4.5	1.0	7		36	1,8591	1.2+/-3.3	0,1,4295	no	missense	ADAP1	NM_006869.2	43	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	110/375	959664	1,12995	2202	4296	6498	SO:0001583	missense	11033	exon4			TTGGCCCGGATCC	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.329G>A	chr7.hg19:g.959664C>T	ENSP00000265846:p.Arg110Gln	26.0	0.0	.		32.0	3.0	.	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	hg19	CCDS5318.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.084852|5.084852	0.94100|0.94100	0.0|0.0	1.16E-4|1.16E-4	ENSG00000105963|ENSG00000105963	ENST00000446141;ENST00000437486;ENST00000453823|ENST00000265846;ENST00000449296;ENST00000538188;ENST00000539900;ENST00000435943	.|T;T;T;T	.|0.47528	.|0.84;0.85;0.84;0.84	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.112189	.|0.56097	.|D	.|0.000024	T|T	0.68796|0.68796	0.3040|0.3040	M|M	0.80332|0.80332	2.49|2.49	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.70716	.|0.969;0.97	T|T	0.74562|0.74562	-0.3624|-0.3624	5|10	.|0.87932	.|D	.|0	-33.1793|-33.1793	14.5163|14.5163	0.67821|0.67821	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|15;110	.|B4DUZ7;O75689	.|.;ADAP1_HUMAN	R|Q	93;44;53|110;38;15;121;97	.|ENSP00000265846:R110Q;ENSP00000407267:R38Q;ENSP00000442682:R121Q;ENSP00000394973:R97Q	.|ENSP00000265846:R110Q	G|R	-|-	1|2	0|0	ADAP1|ADAP1	926190|926190	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.816000|0.816000	0.46133|0.46133	4.105000|4.105000	0.57797|0.57797	2.215000|2.215000	0.71742|0.71742	0.549000|0.549000	0.68633|0.68633	GGG|CGG	.	.	.	weak		0.682	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	
FBXL18	80028	hgsc.bcm.edu	37	7	5541280	5541280	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:5541280G>A	ENST00000382368.3	-	3	743	c.620C>T	c.(619-621)aCg>aTg	p.T207M	FBXL18_ENST00000453700.3_Missense_Mutation_p.T207M	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	207									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GCCCTCGCGCGTGCGGTCCAG	0.657																																					p.T207M		Atlas-SNP	.											.	FBXL18	99	.	0			c.C620T						PASS	.						23.0	28.0	26.0					7																	5541280		2059	4209	6268	SO:0001583	missense	80028	exon3			TCGCGCGTGCGGT	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.620C>T	chr7.hg19:g.5541280G>A	ENSP00000371805:p.Thr207Met	118.0	0.0	.		123.0	5.0	.	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000382368.3	hg19	CCDS43546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.94|19.94	3.920520|3.920520	0.73213|0.73213	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000458142|ENST00000382368;ENST00000312577;ENST00000453700	.|T;T	.|0.51071	.|0.75;0.72	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.159486	.|0.53938	.|D	.|0.000047	T|T	0.54382|0.54382	0.1855|0.1855	N|N	0.19112|0.19112	0.55|0.55	0.47476|0.47476	D|D	0.999437|0.999437	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.69824	.|0.966;0.942	T|T	0.53760|0.53760	-0.8393|-0.8393	5|10	.|0.35671	.|T	.|0.21	.|.	18.1629|18.1629	0.89716|0.89716	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|207;207	.|F5H4Z4;Q96ME1-4	.|.;.	C|M	91|207	.|ENSP00000371805:T207M;ENSP00000444797:T207M	.|ENSP00000311990:T207M	R|T	-|-	1|2	0|0	FBXL18|FBXL18	5507806|5507806	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.898000|0.898000	0.52572|0.52572	5.561000|5.561000	0.67339|0.67339	2.528000|2.528000	0.85240|0.85240	0.655000|0.655000	0.94253|0.94253	CGC|ACG	.	.	.	none		0.657	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
SP4	6671	hgsc.bcm.edu	37	7	21468306	21468306	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:21468306G>A	ENST00000222584.3	+	2	237	c.19G>A	c.(19-21)Gag>Aag	p.E7K		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	7	Poly-Glu.				regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						TCAGAAGAAGGAGGAGGAGGA	0.512																																					p.E7K		Atlas-SNP	.											SP4,colon,carcinoma,0,1	SP4	91	.	0			c.G19A						PASS	.						20.0	20.0	20.0					7																	21468306		2171	4251	6422	SO:0001583	missense	6671	exon2			AAGAAGGAGGAGG		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.19G>A	chr7.hg19:g.21468306G>A	ENSP00000222584:p.Glu7Lys	84.0	1.0	.		141.0	8.0	.	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318989	0.41096	.	.	ENSG00000105866	ENST00000222584;ENST00000446800	T	0.09911	2.93	4.5	4.5	0.54988	.	0.061123	0.64402	N	0.000005	T	0.10937	0.0267	L	0.36672	1.1	0.44142	D	0.996934	P	0.34587	0.458	B	0.39152	0.292	T	0.20907	-1.0261	10	0.23891	T	0.37	.	12.5742	0.56355	0.0:0.0:1.0:0.0	.	7	Q02446	SP4_HUMAN	K	7	ENSP00000222584:E7K	ENSP00000222584:E7K	E	+	1	0	SP4	21434831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.555000	0.73928	2.345000	0.79718	0.563000	0.77884	GAG	.	.	.	none		0.512	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112	
CPVL	54504	hgsc.bcm.edu	37	7	29135788	29135788	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:29135788G>T	ENST00000409850.1	-	8	980	c.334C>A	c.(334-336)Ccg>Acg	p.P112T	CPVL_ENST00000265394.5_Missense_Mutation_p.P112T|CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Missense_Mutation_p.P112T			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	112						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						GAACCTCCCGGCCCACCCTGT	0.468																																					p.P112T		Atlas-SNP	.											.	CPVL	60	.	0			c.C334A						PASS	.						138.0	129.0	132.0					7																	29135788		2203	4300	6503	SO:0001583	missense	54504	exon4			CTCCCGGCCCACC	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.334C>A	chr7.hg19:g.29135788G>T	ENSP00000387164:p.Pro112Thr	111.0	0.0	.		146.0	77.0	.	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	hg19	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415714	0.62511	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000409850;ENST00000448959;ENST00000447426	D;D;D;D;D	0.99245	-5.62;-5.62;-5.62;-5.62;-5.62	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.99691	0.9883	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97328	0.9948	10	0.87932	D	0	0.0175	13.4872	0.61373	0.0773:0.0:0.9227:0.0	.	112	Q9H3G5	CPVL_HUMAN	T	112;112;112;42;42	ENSP00000265394:P112T;ENSP00000379572:P112T;ENSP00000387164:P112T;ENSP00000409036:P42T;ENSP00000395690:P42T	ENSP00000265394:P112T	P	-	1	0	CPVL	29102313	1.000000	0.71417	0.937000	0.37676	0.458000	0.32498	6.755000	0.74914	2.519000	0.84933	0.491000	0.48974	CCG	.	.	.	none		0.468	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
POLD2	5425	hgsc.bcm.edu	37	7	44156052	44156052	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:44156052C>T	ENST00000406581.2	-	8	1487	c.838G>A	c.(838-840)Gat>Aat	p.D280N	POLD2_ENST00000223361.3_Missense_Mutation_p.D280N|POLD2_ENST00000452185.1_Missense_Mutation_p.D280N	NM_001256879.1	NP_001243808.1	P49005	DPOD2_HUMAN	polymerase (DNA directed), delta 2, accessory subunit	280					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	12						AGGATCTCATCCAGCATCTTA	0.597																																					p.D315N		Atlas-SNP	.											.	POLD2	62	.	0			c.G943A						PASS	.						59.0	47.0	51.0					7																	44156052		2203	4299	6502	SO:0001583	missense	5425	exon7			TCTCATCCAGCAT		CCDS5477.1, CCDS75586.1	7p13	2012-05-18	2012-05-18		ENSG00000106628	ENSG00000106628		"""DNA polymerases"""	9176	protein-coding gene	gene with protein product	"""Pol delta B subunit (p50)"", ""DNA polymerase delta subunit p50"""	600815	"""polymerase (DNA directed), delta 2, regulatory subunit (50kD)"", ""polymerase (DNA directed), delta 2, regulatory subunit 50kDa"""			8530069	Standard	NM_001127218		Approved		uc003tkf.5	P49005	OTTHUMG00000022909	ENST00000406581.2:c.838G>A	chr7.hg19:g.44156052C>T	ENSP00000386105:p.Asp280Asn	53.0	0.0	.		84.0	31.0	.	NM_006230	A4D2J4|B2R5S4	Missense_Mutation	SNP	ENST00000406581.2	hg19	CCDS5477.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139271	0.94560	.	.	ENSG00000106628	ENST00000406581;ENST00000223361;ENST00000452185;ENST00000436400;ENST00000436844	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	5.84	5.84	0.93424	DNA polymerase alpha/epsilon, subunit B (1);	0.000000	0.85682	D	0.000000	T	0.70116	0.3187	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.70716	0.873;0.97	T	0.78298	-0.2258	10	0.66056	D	0.02	-13.0784	14.3287	0.66537	0.0:0.9273:0.0:0.0726	.	280;280	P49005;F8W8R3	DPOD2_HUMAN;.	N	280;280;280;20;198	ENSP00000386105:D280N;ENSP00000223361:D280N;ENSP00000395231:D280N;ENSP00000416203:D198N	ENSP00000223361:D280N	D	-	1	0	POLD2	44122577	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.355000	0.59424	2.778000	0.95560	0.655000	0.94253	GAT	.	.	.	none		0.597	POLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250994.2	NM_001127218	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106685477	106685477	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:106685477A>C	ENST00000265717.4	+	1	384	c.125A>C	c.(124-126)gAg>gCg	p.E42A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	42	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						CTGCAGCAGGAGAACGAGCGC	0.716																																					p.E42A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A125C						PASS	.						5.0	6.0	6.0					7																	106685477		2082	4111	6193	SO:0001583	missense	5577	exon1			AGCAGGAGAACGA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.125A>C	chr7.hg19:g.106685477A>C	ENSP00000265717:p.Glu42Ala	66.0	0.0	.		80.0	54.0	.	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381480	0.24944	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	T	0.79454	-1.27	3.91	3.91	0.45181	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (3);	1.313690	0.04903	N	0.451690	T	0.53174	0.1780	N	0.01250	-0.93	0.35233	D	0.777118	B	0.02656	0.0	B	0.14023	0.01	T	0.49093	-0.8975	10	0.20519	T	0.43	-13.5013	9.0772	0.36529	0.8148:0.1852:0.0:0.0	.	42	P31323	KAP3_HUMAN	A	42	ENSP00000265717:E42A	ENSP00000265717:E42A	E	+	2	0	PRKAR2B	106472713	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.293000	0.43558	1.652000	0.50683	0.374000	0.22700	GAG	.	.	.	none		0.716	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
C9orf85	138241	hgsc.bcm.edu	37	9	74586475	74586475	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:74586475A>G	ENST00000377031.3	+	3	454	c.264A>G	c.(262-264)ccA>ccG	p.P88P	C9orf85_ENST00000486911.2_Intron|C9orf85_ENST00000334731.2_Silent_p.P88P			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	88										kidney(2)|large_intestine(1)|lung(4)	7						TGTGCAGGCCATGTGCCTGTG	0.303																																					p.P88P		Atlas-SNP	.											.	C9orf85	28	.	0			c.A264G						PASS	.						145.0	134.0	137.0					9																	74586475		2203	4300	6503	SO:0001819	synonymous_variant	138241	exon3			CAGGCCATGTGCC	BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.264A>G	chr9.hg19:g.74586475A>G		58.0	0.0	.		54.0	17.0	.	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Silent	SNP	ENST00000377031.3	hg19																																																																																				.	.	.	none		0.303	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505	
SVEP1	79987	hgsc.bcm.edu	37	9	113212406	113212406	+	Missense_Mutation	SNP	C	C	T	rs376449068	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:113212406C>T	ENST00000401783.2	-	24	4372	c.4036G>A	c.(4036-4038)Gtc>Atc	p.V1346I	SVEP1_ENST00000374469.1_Missense_Mutation_p.V1323I|SVEP1_ENST00000302728.8_Missense_Mutation_p.V1346I|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1346	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CACTCATCGACGTTCTTTCCA	0.453													C|||	2	0.000399361	0.0	0.0	5008	,	,		19558	0.0		0.0	False		,,,				2504	0.002				p.V1346I		Atlas-SNP	.											.	SVEP1	326	.	0			c.G4036A						PASS	.	C	ILE/VAL	0,3788		0,0,1894	259.0	241.0	247.0		4036	-10.9	0.0	9		247	2,8236		0,2,4117	no	missense	SVEP1	NM_153366.3	29	0,2,6011	TT,TC,CC		0.0243,0.0,0.0166	benign	1346/3572	113212406	2,12024	1894	4119	6013	SO:0001583	missense	79987	exon24			CATCGACGTTCTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4036G>A	chr9.hg19:g.113212406C>T	ENSP00000384917:p.Val1346Ile	90.0	0.0	.		112.0	51.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	4.180	0.032029	0.08101	0.0	2.43E-4	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	D;D;D	0.87103	-2.21;-2.21;-2.21	5.44	-10.9	0.00192	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.010870	0.07909	N	0.974027	T	0.56232	0.1971	N	0.03194	-0.395	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.04013	0.001;0.001	T	0.54918	-0.8221	10	0.02654	T	1	.	2.8122	0.05445	0.1765:0.3925:0.1795:0.2514	.	1346;1346	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	I	1346;1323;1346	ENSP00000384917:V1346I;ENSP00000363593:V1323I;ENSP00000304118:V1346I	ENSP00000304118:V1346I	V	-	1	0	SVEP1	112252227	0.078000	0.21339	0.000000	0.03702	0.198000	0.23893	-0.651000	0.05372	-1.719000	0.01382	-0.482000	0.04802	GTC	.	.	.	weak		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RAB14	51552	hgsc.bcm.edu	37	9	123954485	123954485	+	Nonsense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:123954485T>A	ENST00000373840.4	-	3	307	c.70A>T	c.(70-72)Aaa>Taa	p.K24*		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family	24					embryo development (GO:0009790)|endocytic recycling (GO:0032456)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi to endosome transport (GO:0006895)|GTP catabolic process (GO:0006184)|intracellular transport (GO:0046907)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AAGCAAGATTTTCCTACTCCC	0.303																																					p.K24X		Atlas-SNP	.											.	RAB14	14	.	0			c.A70T						PASS	.						141.0	143.0	142.0					9																	123954485		2203	4292	6495	SO:0001587	stop_gained	51552	exon3			AAGATTTTCCTAC	AF152463	CCDS6827.1	9q32-q34.11	2008-07-21			ENSG00000119396	ENSG00000119396		"""RAB, member RAS oncogene"""	16524	protein-coding gene	gene with protein product	"""F protein-binding protein 1"", ""bA165P4.3 (member RAS oncogene family)"", ""small GTP binding protein RAB14"""	612673				9792283, 15004230	Standard	NM_016322		Approved	FBP, RAB-14	uc004blc.3	P61106	OTTHUMG00000020582	ENST00000373840.4:c.70A>T	chr9.hg19:g.123954485T>A	ENSP00000362946:p.Lys24*	30.0	0.0	.		30.0	14.0	.	NM_016322	B3KR31|P35287|Q5JVD4|Q6Q7K5|Q969L0|Q9UI11	Nonsense_Mutation	SNP	ENST00000373840.4	hg19	CCDS6827.1	.	.	.	.	.	.	.	.	.	.	T	38	6.999408	0.97990	.	.	ENSG00000119396	ENST00000373840;ENST00000451303	.	.	.	5.83	5.83	0.93111	.	0.089556	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	.	.	.	X	24	.	ENSP00000362946:K24X	K	-	1	0	RAB14	122994306	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.870000	0.87175	2.216000	0.71823	0.460000	0.39030	AAA	.	.	.	none		0.303	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	NM_016322	
COL5A1	1289	hgsc.bcm.edu	37	9	137694764	137694764	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:137694764G>T	ENST00000371817.3	+	39	3451	c.3037G>T	c.(3037-3039)Gag>Tag	p.E1013*		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1013	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCAATGGGTGAGCGTGGCCA	0.597																																					p.E1013X		Atlas-SNP	.											.	COL5A1	323	.	0			c.G3037T						PASS	.						24.0	28.0	27.0					9																	137694764		2198	4298	6496	SO:0001587	stop_gained	1289	exon39			ATGGGTGAGCGTG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.3037G>T	chr9.hg19:g.137694764G>T	ENSP00000360882:p.Glu1013*	108.0	0.0	.		82.0	37.0	.	NM_000093	Q15094|Q5SUX4	Nonsense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	46	12.371230	0.99661	.	.	ENSG00000130635	ENST00000371817	.	.	.	4.39	4.39	0.52855	.	0.135437	0.48767	U	0.000174	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.3375	0.87286	0.0:0.0:1.0:0.0	.	.	.	.	X	1013	.	ENSP00000360882:E1013X	E	+	1	0	COL5A1	136834585	1.000000	0.71417	0.942000	0.38095	0.908000	0.53690	9.579000	0.98204	2.158000	0.67659	0.551000	0.68910	GAG	.	.	.	none		0.597	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
OLFM1	10439	hgsc.bcm.edu	37	9	138011750	138011750	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:138011750C>T	ENST00000371793.3	+	6	1435	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	OLFM1_ENST00000252854.4_Missense_Mutation_p.T377M|OLFM1_ENST00000371796.3_Missense_Mutation_p.T368M	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	395	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		ACCTGGAACACGAGCTACCCC	0.632																																					p.T377M		Atlas-SNP	.											.	OLFM1	57	.	0			c.C1130T						PASS	.						70.0	59.0	63.0					9																	138011750		2203	4300	6503	SO:0001583	missense	10439	exon6			GGAACACGAGCTA	AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"""pancortin"""	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.1184C>T	chr9.hg19:g.138011750C>T	ENSP00000360858:p.Thr395Met	74.0	0.0	.		71.0	29.0	.	NM_014279	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	hg19		.	.	.	.	.	.	.	.	.	.	C	23.8	4.459036	0.84317	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.92397	-3.03;-3.03;-3.03	4.7	4.7	0.59300	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.048581	0.85682	D	0.000000	D	0.97349	0.9133	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98883	1.0770	10	0.87932	D	0	.	17.6361	0.88122	0.0:1.0:0.0:0.0	.	395;377	Q99784;Q6IMJ8	NOE1_HUMAN;.	M	377;368;395	ENSP00000252854:T377M;ENSP00000360861:T368M;ENSP00000360858:T395M	ENSP00000252854:T377M	T	+	2	0	OLFM1	137151571	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.590000	0.82653	2.166000	0.68216	0.491000	0.48974	ACG	.	.	.	none		0.632	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279	
INPP5E	56623	hgsc.bcm.edu	37	9	139333176	139333176	+	Missense_Mutation	SNP	G	G	T	rs536052945		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:139333176G>T	ENST00000371712.3	-	1	1098	c.696C>A	c.(694-696)agC>agA	p.S232R	SEC16A_ENST00000467838.1_5'Flank	NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		GGCCCAGGCTGCTGTGGGCCC	0.687																																					p.S232R		Atlas-SNP	.											.	INPP5E	18	.	0			c.C696A						PASS	.						9.0	12.0	11.0					9																	139333176		2166	4259	6425	SO:0001583	missense	56623	exon1			CAGGCTGCTGTGG	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.696C>A	chr9.hg19:g.139333176G>T	ENSP00000360777:p.Ser232Arg	100.0	0.0	.		103.0	39.0	.	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	hg19	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.134472	0.37630	.	.	ENSG00000148384	ENST00000371712	D	0.97710	-4.5	3.8	0.925	0.19424	.	0.453580	0.22328	N	0.061505	D	0.94032	0.8088	L	0.43923	1.385	0.35619	D	0.809293	B;B	0.31318	0.319;0.132	B;B	0.30105	0.111;0.017	D	0.90931	0.4790	10	0.29301	T	0.29	-36.6616	8.7927	0.34861	0.274:0.0:0.726:0.0	.	232;232	Q9NRR6-2;Q9NRR6	.;INP5E_HUMAN	R	232	ENSP00000360777:S232R	ENSP00000360777:S232R	S	-	3	2	INPP5E	138452997	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	2.991000	0.49409	0.396000	0.25283	-0.251000	0.11542	AGC	.	.	.	none		0.687	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
DIP2C	22982	hgsc.bcm.edu	37	10	387190	387190	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:387190A>G	ENST00000280886.6	-	29	3620	c.3533T>C	c.(3532-3534)aTc>aCc	p.I1178T		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1178						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GTCCAGGCAGATGGCCACTTC	0.483																																					p.I1178T		Atlas-SNP	.											.	DIP2C	195	.	0			c.T3533C						PASS	.						156.0	129.0	138.0					10																	387190		2203	4300	6503	SO:0001583	missense	22982	exon29			AGGCAGATGGCCA	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3533T>C	chr10.hg19:g.387190A>G	ENSP00000280886:p.Ile1178Thr	124.0	0.0	.		116.0	54.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.656310	0.67586	.	.	ENSG00000151240	ENST00000280886;ENST00000535541;ENST00000381503	T	0.39787	1.06	5.53	5.53	0.82687	AMP-dependent synthetase/ligase (1);	0.048817	0.85682	D	0.000000	T	0.42944	0.1225	L	0.47716	1.5	0.80722	D	1	P	0.37015	0.578	P	0.46208	0.507	T	0.25293	-1.0136	10	0.02654	T	1	-37.9788	15.6619	0.77193	1.0:0.0:0.0:0.0	.	1178	Q9Y2E4	DIP2C_HUMAN	T	1178;103;27	ENSP00000280886:I1178T	ENSP00000280886:I1178T	I	-	2	0	DIP2C	377190	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.287000	0.95975	2.106000	0.64143	0.528000	0.53228	ATC	.	.	.	none		0.483	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
DIP2C	22982	hgsc.bcm.edu	37	10	390824	390826	+	Missense_Mutation	TNP	GCA	GCA	ATG			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G|C|A	G|C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:390824_390826GCA>ATG	ENST00000280886.6	-	28	3463_3465	c.3376_3378TGC>CAT	c.(3376-3378)TGC>CAT	p.C1126H		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1126						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TGCAAGGTTTGCAGATCTGGGCA	0.567																																					p.C1126C|p.C1126Y|p.C1126R		Atlas-SNP	.											.	DIP2C	195	.	0			c.C3378T|c.G3377A|c.T3376C						PASS	.																																			SO:0001583	missense	22982	exon28			AGGTTTGCAGATC|GGTTTGCAGATCT|GTTTGCAGATCTG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3376_3378TGC>CAT	chr10.hg19:g.390824GCA>ATG	ENSP00000280886:p.Cys1126His	108.0|111.0|111.0	0.0	.		66.0|65.0|64.0	25.0	.	NM_014974	B4DPI5|Q5SS78	Silent|Missense_Mutation|Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1																																																																																			.	.	.	none		0.567	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
BICC1	80114	hgsc.bcm.edu	37	10	60560020	60560020	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:60560020C>A	ENST00000373886.3	+	13	1796	c.1792C>A	c.(1792-1794)Cac>Aac	p.H598N	BICC1_ENST00000263103.1_Missense_Mutation_p.H224N	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	598					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						GAGTGCAAATCACGGGGATCC	0.403																																					p.H598N		Atlas-SNP	.											.	BICC1	121	.	0			c.C1792A						PASS	.						48.0	45.0	46.0					10																	60560020		2203	4300	6503	SO:0001583	missense	80114	exon13			GCAAATCACGGGG	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.1792C>A	chr10.hg19:g.60560020C>A	ENSP00000362993:p.His598Asn	347.0	0.0	.		354.0	159.0	.	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	C	8.488	0.861398	0.17178	.	.	ENSG00000122870	ENST00000373886;ENST00000263103	T;T	0.48522	1.68;0.81	6.02	6.02	0.97574	.	0.099783	0.64402	D	0.000001	T	0.49864	0.1582	L	0.46157	1.445	0.45806	D	0.99868	D;D	0.55385	0.971;0.971	P;B	0.45712	0.491;0.265	T	0.36138	-0.9760	10	0.33141	T	0.24	-15.3338	20.5407	0.99260	0.0:1.0:0.0:0.0	.	518;598	E7EU62;Q9H694	.;BICC1_HUMAN	N	598;224	ENSP00000362993:H598N;ENSP00000263103:H224N	ENSP00000263103:H224N	H	+	1	0	BICC1	60230026	1.000000	0.71417	0.647000	0.29507	0.124000	0.20399	5.335000	0.65929	2.865000	0.98341	0.655000	0.94253	CAC	.	.	.	none		0.403	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	
ANK3	288	hgsc.bcm.edu	37	10	61824009	61824009	+	Silent	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:61824009G>A	ENST00000280772.2	-	39	12548	c.12357C>T	c.(12355-12357)atC>atT	p.I4119I	ANK3_ENST00000503366.1_Silent_p.I1507I|ANK3_ENST00000373827.2_Silent_p.I1500I|ANK3_ENST00000355288.2_Silent_p.I640I	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4119	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTATTTGATTGATTTCATCCA	0.328																																					p.I4119I		Atlas-SNP	.											.	ANK3	703	.	0			c.C12357T						PASS	.						76.0	80.0	78.0					10																	61824009		2203	4298	6501	SO:0001819	synonymous_variant	288	exon39			TTGATTGATTTCA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12357C>T	chr10.hg19:g.61824009G>A		56.0	0.0	.		51.0	23.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	9.439	1.087582	0.20390	.	.	ENSG00000151150	ENST00000514197;ENST00000511043	.	.	.	5.4	4.5	0.54988	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52888	-0.8515	4	.	.	.	.	5.1251	0.14880	0.1458:0.0:0.523:0.3312	.	.	.	.	L	13;66	.	.	S	-	2	0	ANK3	61494015	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.138000	0.42140	1.273000	0.44346	-0.152000	0.13540	TCA	.	.	.	none		0.328	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
STOX1	219736	hgsc.bcm.edu	37	10	70652348	70652348	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:70652348A>G	ENST00000298596.6	+	4	2909	c.2826A>G	c.(2824-2826)acA>acG	p.T942T	STOX1_ENST00000399165.4_Missense_Mutation_p.T223A|STOX1_ENST00000421961.2_Silent_p.T832T|STOX1_ENST00000399162.2_Missense_Mutation_p.H156R|STOX1_ENST00000399169.4_Silent_p.T942T	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	942						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						TCTTTAGGACACAGAGTCTGG	0.353																																					p.T223A		Atlas-SNP	.											.	STOX1	75	.	0			c.A667G						PASS	.						81.0	79.0	80.0					10																	70652348		1836	4096	5932	SO:0001819	synonymous_variant	219736	exon4			TAGGACACAGAGT	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.2826A>G	chr10.hg19:g.70652348A>G		225.0	0.0	.		207.0	82.0	.	NM_001130159	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	hg19	CCDS41535.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.69|13.69	2.313014|2.313014	0.40895|0.40895	.|.	.|.	ENSG00000165730|ENSG00000165730	ENST00000399162|ENST00000399165	D|D	0.82167|0.82255	-1.58|-1.59	5.81|5.81	1.94|1.94	0.25998|0.25998	.|.	.|0.053934	.|0.64402	.|D	.|0.000001	T|T	0.58047|0.58047	0.2095|0.2095	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B	0.09022|0.11235	0.002|0.004	B|B	0.12156|0.09377	0.007|0.004	T|T	0.45542|0.45542	-0.9254|-0.9254	8|9	0.06891|0.07030	T|T	0.86|0.85	.|.	2.5133|2.5133	0.04662|0.04662	0.5545:0.199:0.1391:0.1075|0.5545:0.199:0.1391:0.1075	.|.	156|223	Q6ZVD7-3|Q6ZVD7-2	.|.	R|A	156|223	ENSP00000382115:H156R|ENSP00000382118:T223A	ENSP00000382115:H156R|ENSP00000382118:T223A	H|T	+|+	2|1	0|0	STOX1|STOX1	70322354|70322354	0.968000|0.968000	0.33430|0.33430	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.092000|0.092000	0.15066|0.15066	1.035000|1.035000	0.39972|0.39972	0.533000|0.533000	0.62120|0.62120	CAC|ACA	.	.	.	none		0.353	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
FAM178A	55719	hgsc.bcm.edu	37	10	102719193	102719193	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:102719193C>G	ENST00000238961.4	+	19	3968	c.3426C>G	c.(3424-3426)gaC>gaG	p.D1142E	FAM178A_ENST00000370269.3_Missense_Mutation_p.D1142E	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1142						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.D1142E(1)									AGGTGAAAGACTTGGTCGCCA	0.358																																					p.D1142E		Atlas-SNP	.											C10orf6,NS,carcinoma,0,1	FAM178A	9	.	1	Substitution - Missense(1)	kidney(1)	c.C3426G						PASS	.						188.0	196.0	193.0					10																	102719193		2203	4300	6503	SO:0001583	missense	55719	exon19			GAAAGACTTGGTC	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"""chromosome 10 open reading frame 6"""	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.3426C>G	chr10.hg19:g.102719193C>G	ENSP00000238961:p.Asp1142Glu	93.0	0.0	.		89.0	42.0	.	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	hg19	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382986	0.82792	.	.	ENSG00000119906	ENST00000238961;ENST00000370269	T;T	0.40756	1.03;1.02	5.98	4.99	0.66335	.	0.245484	0.40064	N	0.001183	T	0.50137	0.1598	M	0.62723	1.935	0.44816	D	0.997823	D;D	0.65815	0.991;0.995	P;P	0.55713	0.782;0.782	T	0.52449	-0.8574	10	0.72032	D	0.01	-12.5499	7.0266	0.24944	0.0:0.8615:0.0:0.1385	.	1142;1142	Q8IX21;B1AL17	F178A_HUMAN;.	E	1142	ENSP00000238961:D1142E;ENSP00000359292:D1142E	ENSP00000238961:D1142E	D	+	3	2	FAM178A	102709183	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.744000	0.26245	2.838000	0.97847	0.591000	0.81541	GAC	.	.	.	none		0.358	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3		
DPCD	25911	hgsc.bcm.edu	37	10	103360566	103360566	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:103360566C>T	ENST00000370151.4	+	3	266	c.217C>T	c.(217-219)Ccc>Tcc	p.P73S	MIR3158-1_ENST00000583596.1_RNA|DPCD_ENST00000370147.1_Missense_Mutation_p.P73S|DPCD_ENST00000370148.2_Missense_Mutation_p.P73S	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	73					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						AGACCCAGCGCCCCTAGGAGC	0.587																																					p.P73S		Atlas-SNP	.											.	DPCD	15	.	0			c.C217T						PASS	.						73.0	72.0	72.0					10																	103360566		2203	4300	6503	SO:0001583	missense	25911	exon3			CCAGCGCCCCTAG		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.217C>T	chr10.hg19:g.103360566C>T	ENSP00000359170:p.Pro73Ser	57.0	0.0	.		78.0	25.0	.	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	hg19	CCDS7514.1	.	.	.	.	.	.	.	.	.	.	C	8.646	0.897084	0.17686	.	.	ENSG00000166171	ENST00000370151;ENST00000370147;ENST00000370148;ENST00000370149;ENST00000434727	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.96	-1.19	0.09585	.	0.947984	0.08934	N	0.872625	T	0.16514	0.0397	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	10	0.11485	T	0.65	-20.1397	0.9631	0.01399	0.2025:0.2982:0.2681:0.2312	.	73	Q9BVM2	DPCD_HUMAN	S	73;73;73;38;37	ENSP00000359170:P73S;ENSP00000359166:P73S;ENSP00000359167:P73S;ENSP00000403505:P37S	ENSP00000359166:P73S	P	+	1	0	DPCD	103350556	0.000000	0.05858	0.000000	0.03702	0.448000	0.32197	-1.903000	0.01594	0.094000	0.17404	0.655000	0.94253	CCC	.	.	.	none		0.587	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
DNHD1	144132	hgsc.bcm.edu	37	11	6589765	6589765	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:6589765T>A	ENST00000527990.2	+	36	12620	c.12620T>A	c.(12619-12621)cTt>cAt	p.L4207H	DNHD1_ENST00000254579.6_Missense_Mutation_p.L4207H			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4207					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GATTTTCGTCTTTGGCTTATT	0.488																																					p.L4207H		Atlas-SNP	.											.	DNHD1	198	.	0			c.T12620A						PASS	.						164.0	150.0	154.0					11																	6589765		1944	4151	6095	SO:0001583	missense	144132	exon38			TTCGTCTTTGGCT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.12620T>A	chr11.hg19:g.6589765T>A	ENSP00000436180:p.Leu4207His	50.0	0.0	.		70.0	26.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628693	0.67015	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.17054	2.3;2.3	4.77	4.77	0.60923	Dynein heavy chain (1);	0.000000	0.64402	D	0.000012	T	0.38904	0.1058	M	0.69823	2.125	0.33897	D	0.638033	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	T	0.55811	-0.8082	10	0.87932	D	0	-10.3556	10.8544	0.46789	0.0:0.0:0.0:1.0	.	3295;475;260;4207	B0I1S4;D3DQT9;Q9NSW8;Q96M86	.;.;.;DNHD1_HUMAN	H	4207;4207;475;475	ENSP00000254579:L4207H;ENSP00000436180:L4207H	ENSP00000254579:L4207H	L	+	2	0	DNHD1	6546341	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.149000	0.42244	2.143000	0.66587	0.459000	0.35465	CTT	.	.	.	none		0.488	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ARNTL	406	hgsc.bcm.edu	37	11	13402758	13402758	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:13402758C>T	ENST00000403290.1	+	18	1929	c.1574C>T	c.(1573-1575)aCg>aTg	p.T525M	ARNTL_ENST00000361003.4_Missense_Mutation_p.T407M|ARNTL_ENST00000389708.3_3'UTR|ARNTL_ENST00000403482.3_Missense_Mutation_p.T523M|ARNTL_ENST00000389707.4_Missense_Mutation_p.T524M|ARNTL_ENST00000403510.3_Missense_Mutation_p.T481M|ARNTL_ENST00000401424.1_Missense_Mutation_p.T482M|ARNTL_ENST00000396441.3_Missense_Mutation_p.T524M			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	525	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)		TTGAACATCACGAGTACGCCT	0.473																																					p.T524M		Atlas-SNP	.											.	ARNTL	46	.	0			c.C1571T						PASS	.						143.0	130.0	134.0					11																	13402758		2200	4294	6494	SO:0001583	missense	406	exon17			ACATCACGAGTAC	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.1574C>T	chr11.hg19:g.13402758C>T	ENSP00000384517:p.Thr525Met	66.0	0.0	.		49.0	25.0	.	NM_001030272	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Missense_Mutation	SNP	ENST00000403290.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.02	2.409897	0.42715	.	.	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000403510;ENST00000339640;ENST00000403482	T;T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3;1.3	5.49	5.49	0.81192	.	0.097970	0.64402	D	0.000001	T	0.45617	0.1351	L	0.44542	1.39	0.80722	D	1	B;P;D;D;P	0.69078	0.11;0.942;0.99;0.997;0.904	B;P;P;P;B	0.56474	0.027;0.62;0.556;0.799;0.416	T	0.24693	-1.0153	10	0.46703	T	0.11	.	14.2188	0.65812	0.1494:0.8506:0.0:0.0	.	523;482;525;524;481	O00327-7;O00327-1;O00327;O00327-8;A2I2N6	.;.;BMAL1_HUMAN;.;.	M	524;524;482;525;407;481;481;523	ENSP00000379718:T524M;ENSP00000374357:T524M;ENSP00000385915:T482M;ENSP00000384517:T525M;ENSP00000354278:T407M;ENSP00000385581:T481M;ENSP00000385897:T523M	ENSP00000340289:T481M	T	+	2	0	ARNTL	13359334	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.325000	0.59234	2.731000	0.93534	0.650000	0.86243	ACG	.	.	.	none		0.473	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178	
HARBI1	283254	hgsc.bcm.edu	37	11	46637239	46637239	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:46637239T>C	ENST00000326737.3	-	2	796	c.549A>G	c.(547-549)agA>agG	p.R183R	ATG13_ENST00000524625.1_5'Flank|ATG13_ENST00000528494.1_5'Flank|ATG13_ENST00000359513.4_5'Flank|ATG13_ENST00000434074.1_5'Flank|ATG13_ENST00000530500.1_5'Flank|ATG13_ENST00000529655.1_5'Flank|ATG13_ENST00000312040.4_5'Flank|ATG13_ENST00000451945.1_5'Flank|ATG13_ENST00000526508.1_5'Flank	NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	183						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclease activity (GO:0004518)			large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	3						TTAGTGTCCCTCTAATGTCAC	0.517																																					p.R183R		Atlas-SNP	.											.	HARBI1	19	.	0			c.A549G						PASS	.						164.0	168.0	167.0					11																	46637239		2201	4299	6500	SO:0001819	synonymous_variant	283254	exon2			TGTCCCTCTAATG	AK057237	CCDS7920.1	11p11.2	2008-07-10	2008-07-01	2008-07-01	ENSG00000180423	ENSG00000180423			26522	protein-coding gene	gene with protein product		615086	"""chromosome 11 open reading frame 77"""	C11orf77		15169610, 18339812	Standard	NM_173811		Approved	FLJ32675	uc001ncy.3	Q96MB7	OTTHUMG00000166537	ENST00000326737.3:c.549A>G	chr11.hg19:g.46637239T>C		135.0	0.0	.		104.0	47.0	.	NM_173811	D3DQP9	Silent	SNP	ENST00000326737.3	hg19	CCDS7920.1																																																																																			.	.	.	none		0.517	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1	NM_173811	
SLC3A2	6520	hgsc.bcm.edu	37	11	62650443	62650443	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:62650443A>G	ENST00000377890.2	+	6	1133	c.965A>G	c.(964-966)cAg>cGg	p.Q322R	SLC3A2_ENST00000377891.2_Missense_Mutation_p.Q323R|SLC3A2_ENST00000377889.2_Missense_Mutation_p.Q260R|SLC3A2_ENST00000377892.1_Missense_Mutation_p.Q353R|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000338663.7_Missense_Mutation_p.Q221R|SLC3A2_ENST00000535296.1_Missense_Mutation_p.Q291R	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	322					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)	p.Q353R(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						TTCTCCACTCAGGTTGACACT	0.547																																					p.Q323R		Atlas-SNP	.											SLC3A2,NS,carcinoma,0,1	SLC3A2	55	.	1	Substitution - Missense(1)	kidney(1)	c.A968G						PASS	.						147.0	117.0	127.0					11																	62650443		2201	4298	6499	SO:0001583	missense	6520	exon6			CCACTCAGGTTGA		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.965A>G	chr11.hg19:g.62650443A>G	ENSP00000367122:p.Gln322Arg	66.0	0.0	.		60.0	22.0	.	NM_001012662	Q13543	Missense_Mutation	SNP	ENST00000377890.2	hg19	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	A	15.57	2.872936	0.51695	.	.	ENSG00000168003	ENST00000377892;ENST00000377891;ENST00000377890;ENST00000542007;ENST00000377889;ENST00000535296;ENST00000338663;ENST00000422606	D;D;D;D;D;D	0.98296	-4.85;-4.85;-4.85;-4.85;-4.83;-4.85	4.58	4.58	0.56647	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.897130	0.02113	N	0.054979	D	0.97179	0.9078	M	0.63428	1.95	0.09310	N	1	B;B;B;B;B	0.28470	0.159;0.003;0.017;0.007;0.213	B;B;B;B;B	0.28784	0.036;0.015;0.028;0.008;0.094	D	0.87653	0.2529	10	0.14252	T	0.57	-2.611	12.2242	0.54451	1.0:0.0:0.0:0.0	.	260;291;322;221;353	P08195-3;F5GZS6;P08195;P08195-2;P08195-4	.;.;4F2_HUMAN;.;.	R	353;323;322;323;260;291;221;203	ENSP00000367124:Q353R;ENSP00000367123:Q323R;ENSP00000367122:Q322R;ENSP00000367121:Q260R;ENSP00000444236:Q291R;ENSP00000340815:Q221R	ENSP00000340815:Q221R	Q	+	2	0	SLC3A2	62407019	0.020000	0.18652	0.007000	0.13788	0.515000	0.34225	2.014000	0.40951	1.849000	0.53698	0.459000	0.35465	CAG	.	.	.	none		0.547	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
UCP2	7351	hgsc.bcm.edu	37	11	73689030	73689030	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:73689030T>C	ENST00000310473.3	-	4	1080	c.238A>G	c.(238-240)Aat>Gat	p.N80D	UCP2_ENST00000542615.1_5'Flank|UCP2_ENST00000536983.1_Missense_Mutation_p.N80D	NM_003355.2	NP_003346.2	P55851	UCP2_HUMAN	uncoupling protein 2 (mitochondrial, proton carrier)	80					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to amino acid starvation (GO:0034198)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|female pregnancy (GO:0007565)|liver regeneration (GO:0097421)|mitochondrial transport (GO:0006839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|positive regulation of cell death (GO:0010942)|proton transport (GO:0015992)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				large_intestine(1)|lung(3)|prostate(1)	5	Breast(11;0.000112)					ACCAGCCCATTGTAGAGGCTT	0.607																																					p.N80D	Colon(191;388 2040 43557 45622 48925)	Atlas-SNP	.											.	UCP2	24	.	0			c.A238G						PASS	.						58.0	59.0	59.0					11																	73689030		2200	4293	6493	SO:0001583	missense	7351	exon4			GCCCATTGTAGAG	U76367	CCDS8228.1	11q13	2014-02-12						"""Solute carriers"""	12518	protein-coding gene	gene with protein product		601693	"""body mass index QTL 4"", ""body mass index quantitative trait 4"""	BMIQ4		9196039, 11381268	Standard	NM_003355		Approved	SLC25A8	uc001oup.1	P55851		ENST00000310473.3:c.238A>G	chr11.hg19:g.73689030T>C	ENSP00000312029:p.Asn80Asp	87.0	0.0	.		92.0	20.0	.	NM_003355	Q4PJH8|Q53HM3	Missense_Mutation	SNP	ENST00000310473.3	hg19	CCDS8228.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206483	0.58343	.	.	ENSG00000175567	ENST00000310473;ENST00000536983;ENST00000544615	T;T;T	0.78924	-1.22;-1.22;-1.22	6.07	6.07	0.98685	Mitochondrial carrier domain (2);	0.217573	0.53938	D	0.000045	T	0.80470	0.4629	M	0.69185	2.1	0.46678	D	0.999154	B;B	0.15930	0.013;0.015	B;B	0.34242	0.152;0.178	T	0.77297	-0.2640	10	0.56958	D	0.05	-5.0289	15.4529	0.75290	0.0:0.0:0.0:1.0	.	80;80	F5GX45;P55851	.;UCP2_HUMAN	D	80;80;53	ENSP00000312029:N80D;ENSP00000441147:N80D;ENSP00000439951:N53D	ENSP00000312029:N80D	N	-	1	0	UCP2	73366678	1.000000	0.71417	0.989000	0.46669	0.605000	0.37080	6.246000	0.72405	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.607	UCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398108.1	NM_003355	
ENO2	2026	hgsc.bcm.edu	37	12	7031532	7031532	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:7031532C>T	ENST00000535366.1	+	10	1828	c.1202C>T	c.(1201-1203)tCt>tTt	p.S401F	ENO2_ENST00000534977.1_3'UTR|ENO2_ENST00000545045.2_Missense_Mutation_p.S282F|ENO2_ENST00000544774.1_Missense_Mutation_p.S358F|ENO2_ENST00000538763.1_Missense_Mutation_p.S358F|ENO2_ENST00000229277.1_Missense_Mutation_p.S401F|ENO2_ENST00000541477.1_Missense_Mutation_p.S401F|ATN1_ENST00000356654.4_5'Flank			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	401					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CCGTGCCGTTCTGAACGTCTG	0.547																																					p.S401F		Atlas-SNP	.											.	ENO2	20	.	0			c.C1202T						PASS	.						94.0	84.0	87.0					12																	7031532		2203	4300	6503	SO:0001583	missense	2026	exon11			GCCGTTCTGAACG	M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.1202C>T	chr12.hg19:g.7031532C>T	ENSP00000437402:p.Ser401Phe	101.0	0.0	.		133.0	63.0	.	NM_001975	B7Z2X9|Q96J33	Missense_Mutation	SNP	ENST00000535366.1	hg19	CCDS8570.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590935	0.86851	.	.	ENSG00000111674	ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000535366;ENST00000545045	T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21	4.22	4.22	0.49857	Enolase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82536	0.5058	H	0.95504	3.68	0.80722	D	1	P;D	0.69078	0.566;0.997	P;D	0.71656	0.521;0.974	D	0.88558	0.3121	10	0.72032	D	0.01	-10.0883	17.1386	0.86747	0.0:1.0:0.0:0.0	.	358;401	B7Z2X9;P09104	.;ENOG_HUMAN	F	401;401;358;358;401;282	ENSP00000438873:S401F;ENSP00000229277:S401F;ENSP00000441490:S358F;ENSP00000446195:S358F;ENSP00000437402:S401F;ENSP00000438062:S282F	ENSP00000229277:S401F	S	+	2	0	ENO2	6901793	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	7.651000	0.83577	2.361000	0.80049	0.455000	0.32223	TCT	.	.	.	none		0.547	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49427679	49427679	+	Silent	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:49427679C>T	ENST00000301067.7	-	39	10808	c.10809G>A	c.(10807-10809)caG>caA	p.Q3603Q	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3603	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3603Q(1)|p.Q3333Q(1)									gctgctgctgctgttgttgct	0.582																																					p.Q3603Q		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2	1173	.	2	Substitution - coding silent(2)	endometrium(2)	c.G10809A						PASS	.						10.0	10.0	10.0					12																	49427679		2174	4260	6434	SO:0001819	synonymous_variant	8085	exon39			CTGCTGCTGTTGT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10809G>A	chr12.hg19:g.49427679C>T		52.0	1.0	.		42.0	4.0	.	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.582	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
DIP2B	57609	hgsc.bcm.edu	37	12	51108338	51108338	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:51108338C>A	ENST00000301180.5	+	23	2844	c.2810C>A	c.(2809-2811)aCa>aAa	p.T937K		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	937						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						TGCCCCCATACATGTGTGACA	0.463																																					p.T937K		Atlas-SNP	.											.	DIP2B	167	.	0			c.C2810A						PASS	.						110.0	102.0	105.0					12																	51108338		2203	4300	6503	SO:0001583	missense	57609	exon23			CCCATACATGTGT	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2810C>A	chr12.hg19:g.51108338C>A	ENSP00000301180:p.Thr937Lys	68.0	0.0	.		56.0	27.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574553	0.86542	.	.	ENSG00000066084	ENST00000301180	T	0.37235	1.21	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.45458	0.1343	M	0.78801	2.425	0.80722	D	1	P	0.45428	0.858	P	0.45794	0.493	T	0.39663	-0.9603	10	0.08837	T	0.75	-13.4949	18.5538	0.91075	0.0:1.0:0.0:0.0	.	937	Q9P265	DIP2B_HUMAN	K	937	ENSP00000301180:T937K	ENSP00000301180:T937K	T	+	2	0	DIP2B	49394605	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	ACA	.	.	.	none		0.463	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
DYRK2	8445	hgsc.bcm.edu	37	12	68051341	68051341	+	Silent	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:68051341G>T	ENST00000344096.3	+	3	1067	c.654G>T	c.(652-654)gtG>gtT	p.V218V	DYRK2_ENST00000393555.3_Silent_p.V145V|RP11-335O4.3_ENST00000425371.2_RNA	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	218					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		ACGATCACGTGGCTTACAGGT	0.547																																					p.V218V		Atlas-SNP	.											.	DYRK2	63	.	0			c.G654T						PASS	.						72.0	56.0	61.0					12																	68051341		2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			TCACGTGGCTTAC	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.654G>T	chr12.hg19:g.68051341G>T		46.0	0.0	.		50.0	25.0	.	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	hg19	CCDS8978.1																																																																																			.	.	.	none		0.547	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
PTPRB	5787	hgsc.bcm.edu	37	12	71016317	71016317	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:71016317A>T	ENST00000550358.1	-	3	586	c.561T>A	c.(559-561)aaT>aaA	p.N187K	PTPRB_ENST00000551525.1_Missense_Mutation_p.N186K|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.N187K			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CCTCTGTGGTATTCCTAATAA	0.478																																					p.N187K		Atlas-SNP	.											.	PTPRB	676	.	0			c.T561A						PASS	.						68.0	73.0	71.0					12																	71016317		1915	4126	6041	SO:0001583	missense	5787	exon3			TGTGGTATTCCTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.561T>A	chr12.hg19:g.71016317A>T	ENSP00000448058:p.Asn187Lys	85.0	0.0	.		83.0	34.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000550358.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.59	3.166622	0.57476	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.04275	4.17;4.13;3.66	5.72	-9.02	0.00741	.	.	.	.	.	T	0.07954	0.0199	L	0.27053	0.805	0.20307	N	0.999914	D;D;P;P	0.69078	0.997;0.972;0.873;0.873	P;P;B;B	0.58331	0.837;0.621;0.306;0.306	T	0.10314	-1.0635	9	0.40728	T	0.16	.	17.5824	0.87972	0.7669:0.0:0.2331:0.0	.	187;186;187;187	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	K	187;187;187;186	ENSP00000334928:N187K;ENSP00000448058:N187K;ENSP00000448349:N186K	ENSP00000334928:N187K	N	-	3	2	PTPRB	69302584	0.066000	0.20996	0.074000	0.20217	0.002000	0.02628	-0.965000	0.03829	-1.631000	0.01543	-0.904000	0.02843	AAT	.	.	.	none		0.478	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1		
ACSS3	79611	hgsc.bcm.edu	37	12	81627129	81627129	+	Splice_Site	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:81627129G>A	ENST00000548058.1	+	13	2508	c.1598G>A	c.(1597-1599)gGa>gAa	p.G533E	ACSS3_ENST00000261206.3_Splice_Site_p.G532E|ACSS3_ENST00000548324.1_Splice_Site_p.G215E			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	533						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TGTTTTCAGGGATATTATGAT	0.308																																					p.G533E		Atlas-SNP	.											.	ACSS3	118	.	0			c.G1598A						PASS	.						214.0	213.0	213.0					12																	81627129		2203	4300	6503	SO:0001630	splice_region_variant	79611	exon13			TTCAGGGATATTA		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1597-1G>A	chr12.hg19:g.81627129G>A		101.0	0.0	.		96.0	39.0	.	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	hg19	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914047	0.92178	.	.	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.60040	2.07;2.07;0.22	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.82360	0.5020	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	D	0.85234	0.1034	10	0.72032	D	0.01	-9.1533	19.7715	0.96367	0.0:0.0:1.0:0.0	.	215;533	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	E	533;532;215	ENSP00000449535:G533E;ENSP00000261206:G532E;ENSP00000448965:G215E	ENSP00000261206:G532E	G	+	2	0	ACSS3	80151260	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.282000	0.95840	2.777000	0.95525	0.650000	0.86243	GGA	.	.	.	none		0.308	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	Missense_Mutation
SYCP3	50511	hgsc.bcm.edu	37	12	102127402	102127402	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:102127402T>C	ENST00000392927.3	-	6	535	c.404A>G	c.(403-405)cAg>cGg	p.Q135R	SYCP3_ENST00000392924.1_Missense_Mutation_p.Q135R|SYCP3_ENST00000266743.2_Missense_Mutation_p.Q135R	NM_001177948.1|NM_001177949.1|NM_153694.4	NP_001171419.1|NP_001171420.1|NP_710161.1	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	135	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TAAATCCCACTGCTGAAACAA	0.323																																					p.Q135R		Atlas-SNP	.											.	SYCP3	19	.	0			c.A404G						PASS	.						146.0	135.0	138.0					12																	102127402		2203	4300	6503	SO:0001583	missense	50511	exon6			TCCCACTGCTGAA	AF492003, AI075991	CCDS9087.1	12q23.2	2007-02-05			ENSG00000139351	ENSG00000139351			18130	protein-coding gene	gene with protein product		604759				12213195, 10854409	Standard	NM_153694		Approved		uc001tis.3	Q8IZU3	OTTHUMG00000150132	ENST00000392927.3:c.404A>G	chr12.hg19:g.102127402T>C	ENSP00000376658:p.Gln135Arg	47.0	0.0	.		36.0	11.0	.	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	hg19	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.552521	0.27739	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.95	5.95	0.96441	.	0.128110	0.53938	D	0.000053	T	0.49966	0.1588	L	0.39326	1.205	0.48452	D	0.99965	P	0.36010	0.532	B	0.39590	0.304	T	0.48352	-0.9043	9	0.30854	T	0.27	-9.351	10.7032	0.45939	0.0:0.0708:0.0:0.9292	.	135	Q8IZU3	SYCP3_HUMAN	R	135	.	ENSP00000266743:Q135R	Q	-	2	0	SYCP3	100651533	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	3.569000	0.53827	2.272000	0.75746	0.460000	0.39030	CAG	.	.	.	none		0.323	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694	
ANAPC7	51434	hgsc.bcm.edu	37	12	110825587	110825587	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:110825587A>T	ENST00000455511.3	-	5	733	c.733T>A	c.(733-735)Ttt>Att	p.F245I	RP11-478C19.2_ENST00000550231.1_RNA|ANAPC7_ENST00000450008.2_Missense_Mutation_p.F245I	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	245					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 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)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						GTGTGCACAAAAGCATACGCT	0.473																																					p.F245I		Atlas-SNP	.											.	ANAPC7	68	.	0			c.T733A						PASS	.						137.0	109.0	118.0					12																	110825587		2203	4300	6503	SO:0001583	missense	51434	exon5			GCACAAAAGCATA	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.733T>A	chr12.hg19:g.110825587A>T	ENSP00000394394:p.Phe245Ile	91.0	0.0	.		88.0	27.0	.	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386589	0.82902	.	.	ENSG00000196510;ENSG00000196510;ENSG00000258210	ENST00000455511;ENST00000450008;ENST00000550231	T;T	0.63913	-0.07;0.95	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.66896	0.2836	N	0.22421	0.69	0.80722	D	1	D;B	0.57899	0.981;0.207	D;B	0.69142	0.962;0.05	T	0.64045	-0.6499	10	0.25106	T	0.35	-11.8755	16.6245	0.84952	1.0:0.0:0.0:0.0	.	245;245	Q9UJX3-2;Q9UJX3	.;APC7_HUMAN	I	245;245;144	ENSP00000394394:F245I;ENSP00000402314:F245I	ENSP00000402314:F245I	F	-	1	0	RP11-478C19.2;ANAPC7	109309970	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.958000	0.93099	2.323000	0.78572	0.528000	0.53228	TTT	.	.	.	none		0.473	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238	
HECTD4	283450	hgsc.bcm.edu	37	12	112664523	112664523	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:112664523T>C	ENST00000430131.2	-	43	6773	c.5628A>G	c.(5626-5628)ttA>ttG	p.L1876L	HECTD4_ENST00000550722.1_Silent_p.L2152L|HECTD4_ENST00000377560.5_Silent_p.L2126L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1876					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CTTCACAAAATAAGCTGTCTT	0.388																																					p.L2164L		Atlas-SNP	.											.	.	.	.	0			c.A6492G						PASS	.						84.0	81.0	82.0					12																	112664523		1869	4124	5993	SO:0001819	synonymous_variant	283450	exon44			ACAAAATAAGCTG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.5628A>G	chr12.hg19:g.112664523T>C		40.0	0.0	.		36.0	9.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.769	1.172289	0.21704	.	.	ENSG00000173064	ENST00000550968	.	.	.	5.24	-1.38	0.09027	.	.	.	.	.	T	0.57417	0.2052	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54118	-0.8341	4	.	.	.	.	10.8882	0.46978	0.0:0.47:0.0:0.53	.	.	.	.	C	43	.	.	Y	-	2	0	C12orf51	111148906	0.090000	0.21635	0.994000	0.49952	0.996000	0.88848	-0.647000	0.05397	-0.195000	0.10382	0.383000	0.25322	TAT	.	.	.	none		0.388	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
PRPF39	55015	hgsc.bcm.edu	37	14	45578916	45578916	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:45578916A>T	ENST00000355765.6	+	8	1279	c.1109A>T	c.(1108-1110)gAa>gTa	p.E370V	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	370					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GGGACTCATGAACGAGTTGTG	0.338																																					p.E370V		Atlas-SNP	.											.	PRPF39	46	.	0			c.A1109T						PASS	.						75.0	70.0	72.0					14																	45578916		2203	4300	6503	SO:0001583	missense	55015	exon8			CTCATGAACGAGT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1109A>T	chr14.hg19:g.45578916A>T	ENSP00000348010:p.Glu370Val	104.0	0.0	.		91.0	47.0	.	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	18.44	3.625017	0.66901	.	.	ENSG00000185246	ENST00000355765	T	0.35421	1.31	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	L	0.45285	1.41	0.80722	D	1	P	0.50272	0.933	P	0.52672	0.706	T	0.31447	-0.9943	10	0.48119	T	0.1	-4.5178	14.5457	0.68030	1.0:0.0:0.0:0.0	.	370	Q86UA1	PRP39_HUMAN	V	370	ENSP00000348010:E370V	ENSP00000348010:E370V	E	+	2	0	PRPF39	44648666	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.114000	0.94329	2.124000	0.65301	0.383000	0.25322	GAA	.	.	.	none		0.338	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
TMEM30B	161291	hgsc.bcm.edu	37	14	61747022	61747022	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:61747022C>T	ENST00000555868.1	-	1	1536	c.844G>A	c.(844-846)Gcc>Acc	p.A282T	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Missense_Mutation_p.A282T	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	282					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		ACGCGGTAGGCGCCCCGCGGC	0.667																																					p.A282T		Atlas-SNP	.											.	TMEM30B	13	.	0			c.G844A						PASS	.						39.0	40.0	40.0					14																	61747022		2202	4300	6502	SO:0001583	missense	161291	exon1			GGTAGGCGCCCCG	AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.844G>A	chr14.hg19:g.61747022C>T	ENSP00000450842:p.Ala282Thr	54.0	0.0	.		62.0	26.0	.	NM_001017970	B3KR84|Q14D00	Missense_Mutation	SNP	ENST00000555868.1	hg19	CCDS32093.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049475	0.36181	.	.	ENSG00000182107	ENST00000555868;ENST00000355702	.	.	.	4.67	-2.8	0.05823	.	0.667620	0.14557	N	0.312287	T	0.03136	0.0092	N	0.00201	-1.865	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34279	-0.9835	9	0.02654	T	1	-16.991	1.474	0.02422	0.1438:0.2798:0.1415:0.4349	.	282	Q3MIR4	CC50B_HUMAN	T	282	.	ENSP00000347930:A282T	A	-	1	0	TMEM30B	60816775	0.001000	0.12720	0.025000	0.17156	0.923000	0.55619	-0.871000	0.04223	-0.491000	0.06697	0.650000	0.86243	GCC	.	.	.	none		0.667	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552294	102552294	+	Silent	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:102552294G>A	ENST00000216281.8	-	3	535	c.330C>T	c.(328-330)atC>atT	p.I110I	HSP90AA1_ENST00000441629.2_Intron|HSP90AA1_ENST00000334701.7_Silent_p.I232I	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	110					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	CAGACTTGGCGATAGTACCAA	0.423																																					p.I232I		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.C696T						PASS	.						67.0	67.0	67.0					14																	102552294		2203	4297	6500	SO:0001819	synonymous_variant	3320	exon4			CTTGGCGATAGTA	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.330C>T	chr14.hg19:g.102552294G>A		169.0	0.0	.		152.0	64.0	.	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.	.	none		0.423	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
INO80	54617	hgsc.bcm.edu	37	15	41387985	41387985	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:41387985T>C	ENST00000361937.3	-	3	709	c.285A>G	c.(283-285)acA>acG	p.T95T	INO80_ENST00000401393.3_Silent_p.T95T			Q9ULG1	INO80_HUMAN	INO80 complex subunit	95	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TCAGAGAATATGTGTTTAACA	0.428																																					p.T95T		Atlas-SNP	.											INOC1,right_upper_lobe,carcinoma,0,2	INO80	122	.	0			c.A285G						PASS	.						70.0	75.0	73.0					15																	41387985		2203	4300	6503	SO:0001819	synonymous_variant	54617	exon3			AGAATATGTGTTT	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.285A>G	chr15.hg19:g.41387985T>C		73.0	1.0	.		73.0	22.0	.	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	hg19	CCDS10071.1																																																																																			.	.	.	none		0.428	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
ATP8B4	79895	hgsc.bcm.edu	37	15	50168660	50168660	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:50168660G>T	ENST00000284509.6	-	25	2983	c.2842C>A	c.(2842-2844)Ctg>Atg	p.L948M	ATP8B4_ENST00000559829.1_Missense_Mutation_p.L948M	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	948						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TTAAAAAGCAGATTCAGCTGT	0.433																																					p.L948M		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C2842A						PASS	.						107.0	104.0	105.0					15																	50168660		2196	4295	6491	SO:0001583	missense	79895	exon25			AAAGCAGATTCAG	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.2842C>A	chr15.hg19:g.50168660G>T	ENSP00000284509:p.Leu948Met	55.0	0.0	.		61.0	31.0	.	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479600	0.44044	.	.	ENSG00000104043	ENST00000284509	T	0.71698	-0.59	5.86	2.95	0.34219	.	0.148044	0.45606	D	0.000351	T	0.76205	0.3955	L	0.56199	1.76	0.38832	D	0.955877	D;P	0.58620	0.983;0.632	D;B	0.70716	0.97;0.291	T	0.73512	-0.3959	10	0.44086	T	0.13	.	7.022	0.24920	0.1502:0.0:0.7096:0.1402	.	26;948	Q6PG43;Q8TF62	.;AT8B4_HUMAN	M	948	ENSP00000284509:L948M	ENSP00000284509:L948M	L	-	1	2	ATP8B4	47955952	1.000000	0.71417	0.993000	0.49108	0.856000	0.48823	5.705000	0.68355	0.374000	0.24650	-0.150000	0.13652	CTG	.	.	.	none		0.433	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
MYO9A	4649	hgsc.bcm.edu	37	15	72176078	72176078	+	Splice_Site	SNP	C	C	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:72176078C>G	ENST00000356056.5	-	28	5728		c.e28-1		MYO9A_ENST00000444904.1_Splice_Site|MYO9A_ENST00000564571.1_Splice_Site|MYO9A_ENST00000424560.1_Splice_Site	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TCTCTGAGGTCTGTTTAAAGA	0.368																																					.		Atlas-SNP	.											.	MYO9A	203	.	0			c.5256-1G>C						PASS	.						124.0	123.0	124.0					15																	72176078		2199	4297	6496	SO:0001630	splice_region_variant	4649	exon29			TGAGGTCTGTTTA	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5256-1G>C	chr15.hg19:g.72176078C>G		102.0	0.0	.		85.0	38.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Splice_Site	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736224	0.69189	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0021	0.86384	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYO9A	69963132	1.000000	0.71417	0.996000	0.52242	0.944000	0.59088	6.736000	0.74811	2.061000	0.61500	0.557000	0.71058	.	.	.	.	none		0.368	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	Intron
EDC3	80153	hgsc.bcm.edu	37	15	74925259	74925260	+	Missense_Mutation	DNP	GA	GA	AG			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:74925259_74925260GA>AG	ENST00000315127.4	-	7	1401_1402	c.1220_1221TC>CT	c.(1219-1221)gTC>gCT	p.V407A	EDC3_ENST00000426797.3_Missense_Mutation_p.V407A|EDC3_ENST00000568176.1_Missense_Mutation_p.V407A	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	407	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGCAGTTGATGACCAGGTCCAC	0.599											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V407V|p.V407A		Atlas-SNP	.											.	EDC3	32	.	0			c.C1221T|c.T1220C						PASS	.																																			SO:0001583	missense	80153	exon8			GTTGATGACCAGG|TTGATGACCAGGT	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"""yjeF domain containing (E.coli)"", ""LSM16 homolog (EDC3, S. cerevisiae)"", ""enhancer of mRNA decapping 3 homolog (S. cerevisiae)"""	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1220_1221delinsAG	chr15.hg19:g.74925259_74925260delinsAG	ENSP00000320503:p.Val407Ala	64.0|63.0	0.0	.	1156	71.0|72.0	33.0	.	NM_001142444	B3KPH0|D3DW61|Q9H797	Silent|Missense_Mutation	SNP	ENST00000315127.4	hg19	CCDS10267.1																																																																																			.	.	.	none		0.599	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083	
FURIN	5045	hgsc.bcm.edu	37	15	91424718	91424718	+	Silent	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:91424718C>T	ENST00000268171.3	+	16	2274	c.1995C>T	c.(1993-1995)caC>caT	p.H665H	FES_ENST00000414248.2_5'Flank|FES_ENST00000328850.3_5'Flank|FES_ENST00000394302.1_5'Flank	NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	665					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GCCCCAGCCACGCCTCCTTGG	0.706																																					p.H665H		Atlas-SNP	.											.	FURIN	85	.	0			c.C1995T						PASS	.						24.0	27.0	26.0					15																	91424718		2195	4285	6480	SO:0001819	synonymous_variant	5045	exon16			CAGCCACGCCTCC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1995C>T	chr15.hg19:g.91424718C>T		66.0	0.0	.		62.0	28.0	.	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.	.	none		0.706	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
PDIA2	64714	hgsc.bcm.edu	37	16	335403	335403	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:335403G>A	ENST00000219406.6	+	6	905	c.887G>A	c.(886-888)gGc>gAc	p.G296D	PDIA2_ENST00000404312.1_Missense_Mutation_p.G293D|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	296					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CTCCTAGCGGGCTTTGGGGAG	0.667																																					p.G296D		Atlas-SNP	.											.	PDIA2	51	.	0			c.G887A						PASS	.						23.0	26.0	25.0					16																	335403		1918	4116	6034	SO:0001583	missense	64714	exon6			TAGCGGGCTTTGG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.887G>A	chr16.hg19:g.335403G>A	ENSP00000219406:p.Gly296Asp	45.0	0.0	.		52.0	36.0	.	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	hg19	CCDS42089.1	.	.	.	.	.	.	.	.	.	.	g	0.082	-1.181702	0.01633	.	.	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.28069	1.63;1.63	4.03	2.0	0.26442	Thioredoxin-like fold (1);	0.602380	0.17134	N	0.185729	T	0.19167	0.0460	L	0.36672	1.1	0.09310	N	0.99999	B	0.06786	0.001	B	0.11329	0.006	T	0.31364	-0.9946	10	0.10377	T	0.69	.	7.2649	0.26224	0.2953:0.0:0.7047:0.0	.	296	Q13087	PDIA2_HUMAN	D	296;265;293	ENSP00000219406:G296D;ENSP00000384410:G293D	ENSP00000219406:G296D	G	+	2	0	PDIA2	275404	0.009000	0.17119	0.316000	0.25252	0.017000	0.09413	1.175000	0.31944	0.351000	0.24027	-0.348000	0.07805	GGC	.	.	.	none		0.667	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
ANKS3	124401	hgsc.bcm.edu	37	16	4747050	4747050	+	Silent	SNP	C	C	T	rs369166637		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:4747050C>T	ENST00000304283.4	-	17	2244	c.1950G>A	c.(1948-1950)ggG>ggA	p.G650G	ANKS3_ENST00000585773.1_Silent_p.G577G|ANKS3_ENST00000446014.2_Silent_p.G521G	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	650										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GCCACTTCTTCCCGTTCAGCA	0.652																																					p.G650G		Atlas-SNP	.											.	ANKS3	44	.	0			c.G1950A						PASS	.	C	,	1,4393		0,1,2196	77.0	61.0	66.0		1629,1950	2.4	0.2	16		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ANKS3	NM_001242929.1,NM_133450.3	,	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	,	543/550,650/657	4747050	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	124401	exon17			CTTCTTCCCGTTC	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1950G>A	chr16.hg19:g.4747050C>T		61.0	0.0	.		71.0	17.0	.	NM_133450	B4DWU4|D3DUE2|Q8TF25	Silent	SNP	ENST00000304283.4	hg19	CCDS10520.1																																																																																			.	.	.	weak		0.652	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
SEPT12	124404	hgsc.bcm.edu	37	16	4828111	4828111	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:4828111G>T	ENST00000268231.8	-	9	1114	c.851C>A	c.(850-852)cCt>cAt	p.P284H	SEPT12_ENST00000396693.5_Missense_Mutation_p.P238H	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	284	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						TCTCAGGAGAGGAAATTCACA	0.607																																					p.P284H		Atlas-SNP	.											.	SEPT12	40	.	0			c.C851A						PASS	.						80.0	73.0	75.0					16																	4828111		2197	4300	6497	SO:0001583	missense	124404	exon9			AGGAGAGGAAATT	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.851C>A	chr16.hg19:g.4828111G>T	ENSP00000268231:p.Pro284His	106.0	0.0	.		143.0	39.0	.	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Missense_Mutation	SNP	ENST00000268231.8	hg19	CCDS10522.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936273	0.73442	.	.	ENSG00000140623	ENST00000396693;ENST00000268231	T;T	0.50548	0.74;0.74	4.45	3.2	0.36748	.	0.170411	0.50627	D	0.000102	T	0.52805	0.1757	L	0.37561	1.115	0.31027	N	0.717824	D;D	0.65815	0.995;0.993	D;D	0.64687	0.917;0.928	T	0.57159	-0.7859	10	0.87932	D	0	.	9.1566	0.36996	0.1436:0.0:0.8564:0.0	.	238;284	Q8IYM1-2;Q8IYM1	.;SEP12_HUMAN	H	238;284	ENSP00000379922:P238H;ENSP00000268231:P284H	ENSP00000268231:P284H	P	-	2	0	SEPT12	4768112	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	7.391000	0.79828	0.888000	0.36160	0.561000	0.74099	CCT	.	.	.	none		0.607	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
TNRC6A	27327	hgsc.bcm.edu	37	16	24801182	24801182	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:24801182A>G	ENST00000395799.3	+	6	1348	c.1219A>G	c.(1219-1221)Att>Gtt	p.I407V	TNRC6A_ENST00000315183.7_Missense_Mutation_p.I407V	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	407	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 and AGO4.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CAATCAGAGTATTAACTCTAA	0.443																																					p.I407V		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	.	0			c.A1219G						PASS	.						72.0	74.0	73.0					16																	24801182		2197	4300	6497	SO:0001583	missense	27327	exon6			CAGAGTATTAACT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1219A>G	chr16.hg19:g.24801182A>G	ENSP00000379144:p.Ile407Val	71.0	0.0	.		102.0	57.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	A	5.172	0.217280	0.09810	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11277	2.79;2.79	5.94	3.72	0.42706	.	0.130307	0.56097	D	0.000036	T	0.08714	0.0216	L	0.47716	1.5	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.09377	0.004;0.001;0.001	T	0.18023	-1.0350	10	0.17369	T	0.5	-2.9762	6.564	0.22501	0.7316:0.1316:0.1368:0.0	.	154;407;407	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	V	407	ENSP00000326900:I407V;ENSP00000379144:I407V	ENSP00000326900:I407V	I	+	1	0	TNRC6A	24708683	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.862000	0.48388	1.066000	0.40716	0.460000	0.39030	ATT	.	.	.	none		0.443	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
ZNF778	197320	hgsc.bcm.edu	37	16	89294957	89294957	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:89294957A>T	ENST00000433976.2	+	6	2509	c.2177A>T	c.(2176-2178)gAg>gTg	p.E726V	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Missense_Mutation_p.E684V	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	726					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(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CACACTGATGAGAAACCTTTC	0.393																																					p.E754V		Atlas-SNP	.											.	ZNF778	67	.	0			c.A2261T						PASS	.						54.0	56.0	55.0					16																	89294957		1986	4144	6130	SO:0001583	missense	197320	exon7			CTGATGAGAAACC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.2177A>T	chr16.hg19:g.89294957A>T	ENSP00000405289:p.Glu726Val	163.0	0.0	.		169.0	91.0	.	NM_001201407	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	hg19	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	A	8.492	0.862348	0.17178	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.07688	3.25;3.17	0.868	-0.434	0.12283	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.63843	1.955	0.23816	N	0.996768	B;B	0.18863	0.031;0.018	B;B	0.17722	0.019;0.008	T	0.33523	-0.9865	9	0.66056	D	0.02	.	4.12	0.10101	0.7413:0.0:0.2587:0.0	.	684;726	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	V	726;684	ENSP00000405289:E726V;ENSP00000305203:E684V	ENSP00000305203:E684V	E	+	2	0	ZNF778	87822458	0.993000	0.37304	0.014000	0.15608	0.037000	0.13140	1.505000	0.35736	-0.160000	0.11002	0.254000	0.18369	GAG	.	.	.	none		0.393	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
AP2B1	163	hgsc.bcm.edu	37	17	33977776	33977776	+	Silent	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:33977776T>C	ENST00000262325.7	+	13	2317	c.1764T>C	c.(1762-1764)atT>atC	p.I588I	AP2B1_ENST00000592545.1_Silent_p.I550I|AP2B1_ENST00000537622.2_Silent_p.I588I|AP2B1_ENST00000312678.8_Silent_p.I588I|AP2B1_ENST00000538556.1_Silent_p.I531I|AP2B1_ENST00000589344.1_Silent_p.I588I|AP2B1_ENST00000545922.2_3'UTR	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	588	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GTCATGGAATTCATCGTAAAC	0.438																																					p.I588I		Atlas-SNP	.											.	AP2B1	70	.	0			c.T1764C						PASS	.						134.0	120.0	125.0					17																	33977776		2203	4300	6503	SO:0001819	synonymous_variant	163	exon13			TGGAATTCATCGT	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1764T>C	chr17.hg19:g.33977776T>C		103.0	0.0	.		138.0	38.0	.	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	hg19	CCDS32622.1																																																																																			.	.	.	none		0.438	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		
GPATCH8	23131	hgsc.bcm.edu	37	17	42476884	42476884	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:42476884G>T	ENST00000591680.1	-	8	2591	c.2561C>A	c.(2560-2562)tCa>tAa	p.S854*	GPATCH8_ENST00000434000.1_Nonsense_Mutation_p.S776*	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	854	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GCCAGACCTTGAGCGGCTGCG	0.562																																					p.S854X		Atlas-SNP	.											.	GPATCH8	114	.	0			c.C2561A						PASS	.						143.0	128.0	133.0					17																	42476884		2203	4300	6503	SO:0001587	stop_gained	23131	exon8			GACCTTGAGCGGC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2561C>A	chr17.hg19:g.42476884G>T	ENSP00000467556:p.Ser854*	62.0	0.0	.		71.0	46.0	.	NM_001002909	B9EGP9|O60300|Q8TB99	Nonsense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087860	0.94100	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	.	.	.	5.21	5.21	0.72293	.	0.144795	0.48286	D	0.000183	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-10.9423	18.5485	0.91055	0.0:0.0:1.0:0.0	.	.	.	.	X	854;776	.	ENSP00000335486:S854X	S	-	2	0	GPATCH8	39832410	1.000000	0.71417	0.876000	0.34364	0.419000	0.31324	8.899000	0.92544	2.716000	0.92895	0.561000	0.74099	TCA	.	.	.	none		0.562	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
WNT9B	7484	hgsc.bcm.edu	37	17	44952668	44952668	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:44952668C>T	ENST00000290015.2	+	3	589	c.536C>T	c.(535-537)tCc>tTc	p.S179F	WNT9B_ENST00000393461.2_Missense_Mutation_p.S179F	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	179					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			TTCCTGGGGTCCAAGAGAGGA	0.627																																					p.S179F		Atlas-SNP	.											.	WNT9B	37	.	0			c.C536T						PASS	.						60.0	52.0	55.0					17																	44952668		2203	4300	6503	SO:0001583	missense	7484	exon3			TGGGGTCCAAGAG	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.536C>T	chr17.hg19:g.44952668C>T	ENSP00000290015:p.Ser179Phe	204.0	0.0	.		230.0	10.0	.	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	hg19	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441637	0.63067	.	.	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.76839	-1.05;-1.05	4.91	4.91	0.64330	.	0.113119	0.64402	D	0.000010	T	0.70596	0.3242	L	0.52905	1.665	0.26796	N	0.969307	P;B	0.39157	0.662;0.026	B;B	0.34590	0.186;0.084	T	0.69950	-0.5006	10	0.56958	D	0.05	.	11.2092	0.48788	0.3126:0.6874:0.0:0.0	.	179;179	E7EPC3;O14905	.;WNT9B_HUMAN	F	173;179;179	ENSP00000377105:S179F;ENSP00000290015:S179F	ENSP00000290015:S179F	S	+	2	0	WNT9B	42307667	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.914000	0.56401	2.550000	0.86006	0.462000	0.41574	TCC	.	.	.	none		0.627	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
ACSF2	80221	hgsc.bcm.edu	37	17	48540788	48540788	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:48540788C>A	ENST00000300441.4	+	8	1025	c.921C>A	c.(919-921)aaC>aaA	p.N307K	ACSF2_ENST00000427954.2_Missense_Mutation_p.N332K|ACSF2_ENST00000541920.1_Missense_Mutation_p.N147K|ACSF2_ENST00000502667.1_Missense_Mutation_p.N294K|ACSF2_ENST00000504392.1_Missense_Mutation_p.N264K	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	307					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCCTGCCCAACCCCCTGTACC	0.582																																					p.N307K		Atlas-SNP	.											.	ACSF2	46	.	0			c.C921A						PASS	.						104.0	89.0	94.0					17																	48540788		2203	4300	6503	SO:0001583	missense	80221	exon8			GCCCAACCCCCTG	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.921C>A	chr17.hg19:g.48540788C>A	ENSP00000300441:p.Asn307Lys	84.0	0.0	.		124.0	33.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.971738	0.34754	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	4.8	0.521	0.17046	AMP-dependent synthetase/ligase (1);	0.622353	0.17251	N	0.181166	T	0.36908	0.0984	M	0.61703	1.905	0.20196	N	0.999923	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.25759	0.063;0.063;0.063;0.063	T	0.39663	-0.9603	10	0.87932	D	0	-1.458	5.5213	0.16933	0.0:0.3735:0.225:0.4015	.	294;332;264;307	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	K	307;147;264;332;294	ENSP00000300441:N307K;ENSP00000437987:N147K;ENSP00000425964:N264K;ENSP00000401831:N332K;ENSP00000421884:N294K	ENSP00000300441:N307K	N	+	3	2	ACSF2	45895787	0.007000	0.16637	0.169000	0.22859	0.866000	0.49608	-0.285000	0.08410	-0.007000	0.14345	0.655000	0.94253	AAC	.	.	.	none		0.582	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
PSMD12	5718	hgsc.bcm.edu	37	17	65343241	65343241	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:65343241T>A	ENST00000356126.3	-	7	893	c.786A>T	c.(784-786)aaA>aaT	p.K262N	PSMD12_ENST00000357146.4_Missense_Mutation_p.K242N	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	262	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CCTGCTGCCATTTTTCACTTT	0.328																																					p.K262N		Atlas-SNP	.											.	PSMD12	32	.	0			c.A786T						PASS	.						112.0	107.0	108.0					17																	65343241		2202	4297	6499	SO:0001583	missense	5718	exon7			CTGCCATTTTTCA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"""Proteasome (prosome, macropain) subunits"""	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.786A>T	chr17.hg19:g.65343241T>A	ENSP00000348442:p.Lys262Asn	62.0	0.0	.		80.0	46.0	.	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.548664	0.65311	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.06294	3.32;3.32	5.96	3.99	0.46301	.	0.084304	0.85682	D	0.000000	T	0.14227	0.0344	M	0.83953	2.67	0.80722	D	1	P;P	0.49358	0.923;0.923	P;P	0.47827	0.558;0.558	T	0.01015	-1.1480	10	0.48119	T	0.1	-21.8516	8.416	0.32672	0.0:0.7053:0.0:0.2947	.	242;262	A6NP15;O00232	.;PSD12_HUMAN	N	262;242	ENSP00000348442:K262N;ENSP00000349667:K242N	ENSP00000348442:K262N	K	-	3	2	PSMD12	62773703	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.422000	0.34826	0.849000	0.35215	-0.242000	0.12053	AAA	.	.	.	none		0.328	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
UNC13D	201294	hgsc.bcm.edu	37	17	73826558	73826558	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:73826558T>G	ENST00000207549.4	-	29	3094	c.2715A>C	c.(2713-2715)gaA>gaC	p.E905D	UNC13D_ENST00000412096.2_Missense_Mutation_p.E905D	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	905					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGAGGTGGTTTCTGCCTGGG	0.697									Familial Hemophagocytic Lymphohistiocytosis		OREG0024741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E905D		Atlas-SNP	.											.	UNC13D	68	.	0			c.A2715C						PASS	.						26.0	28.0	28.0					17																	73826558		2184	4296	6480	SO:0001583	missense	201294	exon29	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGTGGTTTCTGCC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2715A>C	chr17.hg19:g.73826558T>G	ENSP00000207549:p.Glu905Asp	62.0	0.0	.	1148	98.0	52.0	.	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	T	8.808	0.934637	0.18206	.	.	ENSG00000092929	ENST00000207549;ENST00000412096	T;T	0.70986	-0.51;-0.53	4.71	1.21	0.21127	.	0.403193	0.24722	N	0.036133	T	0.38799	0.1054	N	0.08118	0	0.33043	D	0.531752	B	0.06786	0.001	B	0.04013	0.001	T	0.14090	-1.0485	10	0.16420	T	0.52	-3.4552	0.9409	0.01355	0.1436:0.268:0.2583:0.3301	.	905	Q70J99	UN13D_HUMAN	D	905	ENSP00000207549:E905D;ENSP00000388093:E905D	ENSP00000207549:E905D	E	-	3	2	UNC13D	71338153	0.000000	0.05858	0.982000	0.44146	0.659000	0.38960	-0.243000	0.08915	0.852000	0.35287	0.379000	0.24179	GAA	.	.	.	none		0.697	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6870695	6870695	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:6870695G>T	ENST00000383472.4	+	7	1022	c.918G>T	c.(916-918)aaG>aaT	p.K306N	ARHGAP28_ENST00000532996.1_Missense_Mutation_p.K129N|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.K147N|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.K254N|RP11-146G7.2_ENST00000583659.1_RNA|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.K142N|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.K306N|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.K147N|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.K147N			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	306					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				ATAAACTTAAGAAATCAGAGA	0.343																																					p.K147N		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.G441T						PASS	.						68.0	78.0	74.0					18																	6870695		2203	4300	6503	SO:0001583	missense	79822	exon6			ACTTAAGAAATCA	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.918G>T	chr18.hg19:g.6870695G>T	ENSP00000372964:p.Lys306Asn	257.0	0.0	.		237.0	88.0	.	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.45	2.836053	0.50951	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.08807	3.2;3.15;3.14;3.12;3.14;3.05	5.22	3.03	0.35002	.	0.543333	0.21383	N	0.075434	T	0.12347	0.0300	L	0.50333	1.59	0.29821	N	0.830846	B;B;B;P	0.52577	0.158;0.057;0.364;0.954	B;B;B;P	0.53809	0.035;0.016;0.192;0.735	T	0.04294	-1.0962	10	0.39692	T	0.17	.	4.3594	0.11194	0.4628:0.0:0.5372:0.0	.	306;138;147;254	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	N	306;254;147;142;147;147;138;129	ENSP00000382963:K306N;ENSP00000262227:K254N;ENSP00000392660:K147N;ENSP00000437262:K142N;ENSP00000313506:K147N;ENSP00000406907:K147N	ENSP00000262227:K254N	K	+	3	2	ARHGAP28	6860695	1.000000	0.71417	0.933000	0.37362	0.975000	0.68041	2.199000	0.42715	1.332000	0.45431	0.655000	0.94253	AAG	.	.	.	none		0.343	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6870698	6870698	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:6870698A>T	ENST00000383472.4	+	7	1025	c.921A>T	c.(919-921)aaA>aaT	p.K307N	ARHGAP28_ENST00000532996.1_Missense_Mutation_p.K130N|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.K148N|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.K255N|RP11-146G7.2_ENST00000583659.1_RNA|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.K143N|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.K307N|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.K148N|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.K148N			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	307					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				AACTTAAGAAATCAGAGATTA	0.348																																					p.K148N		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A444T						PASS	.						68.0	78.0	74.0					18																	6870698		2203	4299	6502	SO:0001583	missense	79822	exon6			TAAGAAATCAGAG	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.921A>T	chr18.hg19:g.6870698A>T	ENSP00000372964:p.Lys307Asn	253.0	0.0	.		242.0	88.0	.	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.85	2.954762	0.53293	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.08720	3.22;3.18;3.14;3.14;3.14;3.06	5.22	-2.37	0.06643	.	0.143359	0.64402	D	0.000007	T	0.09379	0.0231	L	0.27053	0.805	0.32678	N	0.51592	D;B;B;B	0.58620	0.983;0.012;0.02;0.01	P;B;B;B	0.55713	0.782;0.014;0.032;0.01	T	0.11867	-1.0570	10	0.15952	T	0.53	.	13.072	0.59068	0.7418:0.0:0.2582:0.0	.	307;139;148;255	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	N	307;255;148;143;148;148;139;130	ENSP00000382963:K307N;ENSP00000262227:K255N;ENSP00000392660:K148N;ENSP00000437262:K143N;ENSP00000313506:K148N;ENSP00000406907:K148N	ENSP00000262227:K255N	K	+	3	2	ARHGAP28	6860698	0.910000	0.30920	0.633000	0.29310	0.960000	0.62799	-0.038000	0.12144	-0.308000	0.08792	-0.242000	0.12053	AAA	.	.	.	none		0.348	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14852332	14852332	+	Silent	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:14852332A>G	ENST00000358984.4	+	36	4212	c.4032A>G	c.(4030-4032)ctA>ctG	p.L1344L		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1344										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AACGTCATCTAAACGAGAAAA	0.318																																					p.L1344L		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.A4032G						PASS	.						4.0	2.0	3.0					18																	14852332		592	1263	1855	SO:0001819	synonymous_variant	374860	exon36			TCATCTAAACGAG	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.4032A>G	chr18.hg19:g.14852332A>G		178.0	0.0	.		194.0	81.0	.	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	hg19	CCDS54182.1																																																																																			.	.	.	none		0.318	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60036643	60036643	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:60036643A>G	ENST00000586569.1	+	9	1531	c.1493A>G	c.(1492-1494)gAt>gGt	p.D498G	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	498					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				GATGGGGCTGATGGGAGGCTC	0.637																																					p.D498G		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.A1493G						PASS	.						38.0	42.0	41.0					18																	60036643		1924	3761	5685	SO:0001583	missense	8792	exon9			GGGCTGATGGGAG	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.1493A>G	chr18.hg19:g.60036643A>G	ENSP00000465500:p.Asp498Gly	47.0	0.0	.		33.0	12.0	.	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	hg19	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.606631	0.28623	.	.	ENSG00000141655	ENST00000269485	.	.	.	4.51	1.98	0.26296	.	1.695040	0.03041	N	0.153332	T	0.37404	0.1002	L	0.51422	1.61	0.09310	N	1	B	0.18741	0.03	B	0.13407	0.009	T	0.15065	-1.0450	8	.	.	.	-3.3746	4.8605	0.13581	0.6714:0.1652:0.1634:0.0	.	498	Q9Y6Q6	TNR11_HUMAN	G	498	.	.	D	+	2	0	TNFRSF11A	58187623	0.054000	0.20591	0.002000	0.10522	0.046000	0.14306	0.964000	0.29306	0.744000	0.32741	0.460000	0.39030	GAT	.	.	.	none		0.637	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
DOT1L	84444	hgsc.bcm.edu	37	19	2194549	2194549	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:2194549G>A	ENST00000398665.3	+	7	660	c.624G>A	c.(622-624)tgG>tgA	p.W208*		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	208	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		GGATGAAATGGTATGGAAAAA	0.607																																					p.W208X		Atlas-SNP	.											.	DOT1L	205	.	0			c.G624A						PASS	.						104.0	108.0	107.0					19																	2194549		1949	4144	6093	SO:0001587	stop_gained	84444	exon7			GAAATGGTATGGA	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.624G>A	chr19.hg19:g.2194549G>A	ENSP00000381657:p.Trp208*	52.0	0.0	.		40.0	18.0	.	NM_032482	O60379|Q96JL1	Nonsense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	37	6.521979	0.97633	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	.	.	.	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.6037	15.8524	0.78943	0.0:0.0:1.0:0.0	.	.	.	.	X	208;208;184	.	ENSP00000221482:W208X	W	+	3	0	DOT1L	2145549	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.122000	0.94380	2.216000	0.71823	0.462000	0.41574	TGG	.	.	.	none		0.607	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
CHERP	10523	hgsc.bcm.edu	37	19	16643886	16643886	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:16643886T>A	ENST00000198939.6	-	4	494	c.458A>T	c.(457-459)gAc>gTc	p.D153V	CHERP_ENST00000546361.2_Missense_Mutation_p.D153V|CTD-3222D19.2_ENST00000409035.1_Intron					calcium homeostasis endoplasmic reticulum protein											endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						CTCGTTCATGTCTAGCTGGGT	0.642																																					p.D153V		Atlas-SNP	.											.	CHERP	70	.	0			c.A458T						PASS	.						95.0	115.0	108.0					19																	16643886		2152	4250	6402	SO:0001583	missense	10523	exon4			TTCATGTCTAGCT	U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"""G patch domain containing"""	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.458A>T	chr19.hg19:g.16643886T>A	ENSP00000198939:p.Asp153Val	69.0	0.0	.		64.0	30.0	.	NM_006387		Missense_Mutation	SNP	ENST00000198939.6	hg19		.	.	.	.	.	.	.	.	.	.	T	16.10	3.026403	0.54683	.	.	ENSG00000085872	ENST00000546361;ENST00000198939	T;T	0.26518	1.73;1.76	5.08	5.08	0.68730	ENTH/VHS (1);RNA polymerase II, large subunit, CTD (1);	.	.	.	.	T	0.40196	0.1107	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.08785	-1.0705	9	0.30854	T	0.27	-28.7397	14.0179	0.64536	0.0:0.0:0.0:1.0	.	153	Q8IWX8	CHERP_HUMAN	V	153	ENSP00000439856:D153V;ENSP00000198939:D153V	ENSP00000198939:D153V	D	-	2	0	CHERP	16504886	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	5.952000	0.70282	1.922000	0.55676	0.402000	0.26972	GAC	.	.	.	none		0.642	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387	
UNC13A	23025	hgsc.bcm.edu	37	19	17766949	17766949	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:17766949C>A	ENST00000519716.2	-	10	1025	c.1026G>T	c.(1024-1026)gaG>gaT	p.E342D	UNC13A_ENST00000551649.1_Missense_Mutation_p.E342D|UNC13A_ENST00000252773.7_Missense_Mutation_p.E342D|UNC13A_ENST00000552293.1_Missense_Mutation_p.E342D|UNC13A_ENST00000550896.1_Missense_Mutation_p.E342D|UNC13A_ENST00000428389.2_Missense_Mutation_p.E430D	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	342	Glu-rich.				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						cctccagctcctcctcatctt	0.592																																					p.E342D		Atlas-SNP	.											.	UNC13A	299	.	0			c.G1026T						PASS	.						33.0	37.0	36.0					19																	17766949		2097	4132	6229	SO:0001583	missense	23025	exon10			CAGCTCCTCCTCA	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.1026G>T	chr19.hg19:g.17766949C>A	ENSP00000429562:p.Glu342Asp	39.0	0.0	.		61.0	22.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	8.553	0.875969	0.17395	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;T;T;D	0.82433	-1.58;-1.61;-1.58;-1.45;-1.44;-1.57	4.56	2.36	0.29203	.	0.284950	0.21761	U	0.069513	T	0.57315	0.2045	N	0.08118	0	0.22317	N	0.999201	B	0.02656	0.0	B	0.01281	0.0	T	0.44742	-0.9308	10	0.05833	T	0.94	-9.3465	4.585	0.12279	0.0:0.5972:0.1803:0.2226	.	342	Q9UPW8	UN13A_HUMAN	D	342;430;342;342;342;342	ENSP00000429562:E342D;ENSP00000400409:E430D;ENSP00000252773:E342D;ENSP00000447236:E342D;ENSP00000447572:E342D;ENSP00000446831:E342D	ENSP00000252773:E342D	E	-	3	2	UNC13A	17627949	0.000000	0.05858	0.996000	0.52242	0.941000	0.58515	0.549000	0.23329	0.849000	0.35215	0.491000	0.48974	GAG	.	.	.	none		0.592	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
RYR1	6261	hgsc.bcm.edu	37	19	39052079	39052079	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:39052079G>C	ENST00000359596.3	+	90	12609	c.12609G>C	c.(12607-12609)caG>caC	p.Q4203H	RYR1_ENST00000360985.3_Missense_Mutation_p.Q4198H|RYR1_ENST00000355481.4_Missense_Mutation_p.Q4198H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4203					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)	ACCGCGCCCAGTGGGAGATGC	0.662																																					p.Q4203H		Atlas-SNP	.											.	RYR1	708	.	0			c.G12609C						PASS	.						38.0	32.0	34.0					19																	39052079		2202	4300	6502	SO:0001583	missense	6261	exon90			CGCCCAGTGGGAG	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.12609G>C	chr19.hg19:g.39052079G>C	ENSP00000352608:p.Gln4203His	25.0	0.0	.		26.0	8.0	.	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487943	0.26686	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97553	-4.43;-4.43;-4.43	3.43	2.39	0.29439	.	0.000000	0.64402	U	0.000004	D	0.98333	0.9447	M	0.90542	3.125	0.47819	D	0.999523	D;D;D	0.64830	0.994;0.994;0.99	D;D;D	0.78314	0.991;0.991;0.979	D	0.98411	1.0572	10	0.87932	D	0	.	10.5699	0.45194	0.0988:0.0:0.9012:0.0	.	4198;4198;4203	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	H	4203;4198;4198	ENSP00000352608:Q4203H;ENSP00000347667:Q4198H;ENSP00000354254:Q4198H	ENSP00000347667:Q4198H	Q	+	3	2	RYR1	43743919	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	4.668000	0.61568	0.816000	0.34421	0.298000	0.19748	CAG	.	.	.	none		0.662	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
SCAF1	58506	hgsc.bcm.edu	37	19	50155522	50155522	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50155522A>T	ENST00000360565.3	+	7	2000	c.1876A>T	c.(1876-1878)Agg>Tgg	p.R626W		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	626	Arg-rich.|Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		GTCGTCCTCGAGGCGCGAGCG	0.751																																					p.R626W		Atlas-SNP	.											.	SCAF1	78	.	0			c.A1876T						PASS	.						2.0	2.0	2.0					19																	50155522		1455	3069	4524	SO:0001583	missense	58506	exon7			TCCTCGAGGCGCG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.1876A>T	chr19.hg19:g.50155522A>T	ENSP00000353769:p.Arg626Trp	32.0	0.0	.		43.0	22.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	5.477	0.273021	0.10349	.	.	ENSG00000126461	ENST00000360565	T	0.39229	1.09	3.95	-1.19	0.09585	.	0.000000	0.39475	N	0.001357	T	0.44456	0.1294	L	0.27053	0.805	0.09310	N	0.999997	D	0.71674	0.998	D	0.72338	0.977	T	0.45498	-0.9257	9	.	.	.	-21.7886	11.8881	0.52615	0.3307:0.6693:0.0:0.0	.	626	Q9H7N4	SFR19_HUMAN	W	626	ENSP00000353769:R626W	.	R	+	1	2	SCAF1	54847334	0.854000	0.29725	0.019000	0.16419	0.340000	0.28889	0.835000	0.27531	-0.551000	0.06175	0.459000	0.35465	AGG	.	.	.	none		0.751	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
CPT1C	126129	hgsc.bcm.edu	37	19	50209661	50209661	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50209661G>C	ENST00000392518.4	+	12	1706	c.1334G>C	c.(1333-1335)gGc>gCc	p.G445A	CPT1C_ENST00000598293.1_Missense_Mutation_p.G445A|CPT1C_ENST00000354199.5_Missense_Mutation_p.G445A|CPT1C_ENST00000323446.5_Missense_Mutation_p.G445A|CPT1C_ENST00000405931.2_Missense_Mutation_p.G434A	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	445					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GCCGGCCGGGGCCATGATCGG	0.637																																					p.G445A		Atlas-SNP	.											.	CPT1C	93	.	0			c.G1334C						PASS	.						10.0	12.0	12.0					19																	50209661		2184	4276	6460	SO:0001583	missense	126129	exon12			GCCGGGGCCATGA	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1334G>C	chr19.hg19:g.50209661G>C	ENSP00000376303:p.Gly445Ala	52.0	0.0	.		49.0	22.0	.	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	hg19	CCDS12779.1	.	.	.	.	.	.	.	.	.	.	G	2.139	-0.397238	0.04899	.	.	ENSG00000169169	ENST00000392518;ENST00000354199;ENST00000405931;ENST00000323446;ENST00000295404	D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73	4.36	3.3	0.37823	.	0.000000	0.48767	D	0.000179	D	0.92984	0.7767	L	0.61218	1.895	0.44652	D	0.997633	D;D;D;D	0.89917	0.999;1.0;0.984;0.988	D;D;P;D	0.91635	0.967;0.999;0.868;0.919	D	0.90301	0.4330	10	0.14656	T	0.56	-29.4364	13.1346	0.59402	0.0:0.1628:0.8372:0.0	.	316;445;434;445	C9IY45;Q8TCG5-3;Q8TCG5-2;Q8TCG5	.;.;.;CPT1C_HUMAN	A	445;445;434;445;316	ENSP00000376303:G445A;ENSP00000346138:G445A;ENSP00000384465:G434A;ENSP00000319343:G445A	ENSP00000295404:G316A	G	+	2	0	CPT1C	54901473	1.000000	0.71417	0.240000	0.24138	0.004000	0.04260	8.802000	0.91910	1.040000	0.40099	-0.181000	0.13052	GGC	.	.	.	none		0.637	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
AKT1S1	84335	hgsc.bcm.edu	37	19	50374877	50374877	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50374877G>T	ENST00000391833.1	-	3	2543	c.554C>A	c.(553-555)cCt>cAt	p.P185H	AKT1S1_ENST00000344175.5_Missense_Mutation_p.P185H|AKT1S1_ENST00000391835.1_Missense_Mutation_p.P205H|AKT1S1_ENST00000391834.2_Missense_Mutation_p.P185H|AKT1S1_ENST00000391831.1_Missense_Mutation_p.P185H|AKT1S1_ENST00000391832.3_Missense_Mutation_p.P185H	NM_001278160.1	NP_001265089.1			AKT1 substrate 1 (proline-rich)											kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CACAGACACAGGCAGGGACTT	0.657																																					p.P205H		Atlas-SNP	.											.	AKT1S1	16	.	0			c.C614A						PASS	.						82.0	88.0	86.0					19																	50374877		2203	4300	6503	SO:0001583	missense	84335	exon4			GACACAGGCAGGG	BC022241	CCDS12784.1, CCDS59410.1	19q13.33	2008-02-05			ENSG00000204673	ENSG00000204673			28426	protein-coding gene	gene with protein product	"""proline-rich Akt substrate, 40 kDa"""	610221				12524439	Standard	NM_032375		Approved	PRAS40, MGC2865, Lobe	uc031rmg.1	Q96B36	OTTHUMG00000150246	ENST00000391833.1:c.554C>A	chr19.hg19:g.50374877G>T	ENSP00000375709:p.Pro185His	55.0	0.0	.		35.0	11.0	.	NM_032375		Missense_Mutation	SNP	ENST00000391833.1	hg19	CCDS12784.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200977	0.79015	.	.	ENSG00000204673	ENST00000391833;ENST00000344175;ENST00000391832;ENST00000391834;ENST00000391835;ENST00000391831	D;D;D;D;D;D	0.82711	-1.61;-1.61;-1.61;-1.61;-1.64;-1.61	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.88764	0.6525	L	0.60067	1.865	0.58432	D	0.999993	D	0.89917	1.0	D	0.87578	0.998	D	0.89888	0.4035	10	0.87932	D	0	-10.2665	14.2818	0.66219	0.0:0.0:1.0:0.0	.	185	Q96B36	AKTS1_HUMAN	H	185;185;185;185;205;185	ENSP00000375709:P185H;ENSP00000341698:P185H;ENSP00000375708:P185H;ENSP00000375710:P185H;ENSP00000375711:P205H;ENSP00000375707:P185H	ENSP00000341698:P185H	P	-	2	0	AKT1S1	55066689	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	5.823000	0.69272	2.305000	0.77605	0.655000	0.94253	CCT	.	.	.	none		0.657	AKT1S1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317073.1	NM_032375	
PCK1	5105	hgsc.bcm.edu	37	20	56139426	56139426	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:56139426A>G	ENST00000319441.4	+	7	1327	c.1163A>G	c.(1162-1164)aAt>aGt	p.N388S	PCK1_ENST00000535860.1_Missense_Mutation_p.N256S|PCK1_ENST00000543666.1_Missense_Mutation_p.N71S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	388					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCCTGGAAGAATAAGGAGTGG	0.577																																					p.N388S		Atlas-SNP	.											.	PCK1	95	.	0			c.A1163G						PASS	.						84.0	75.0	78.0					20																	56139426		2203	4300	6503	SO:0001583	missense	5105	exon7			GGAAGAATAAGGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1163A>G	chr20.hg19:g.56139426A>G	ENSP00000319814:p.Asn388Ser	143.0	0.0	.		165.0	42.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.056807	0.36277	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.04049	3.72;3.72;3.72	5.2	4.1	0.47936	.	0.080070	0.85682	D	0.000000	T	0.07863	0.0197	M	0.67397	2.05	0.58432	D	0.999995	B;B	0.11235	0.004;0.002	B;B	0.11329	0.006;0.002	T	0.05146	-1.0903	10	0.87932	D	0	-27.5119	10.481	0.44693	0.9211:0.0:0.0789:0.0	.	71;388	B4DT64;P35558	.;PCKGC_HUMAN	S	70;388;71;256	ENSP00000319814:N388S;ENSP00000445767:N71S;ENSP00000444342:N256S	ENSP00000319814:N388S	N	+	2	0	PCK1	55572832	1.000000	0.71417	0.988000	0.46212	0.324000	0.28378	4.873000	0.63057	0.918000	0.36919	0.533000	0.62120	AAT	.	.	.	none		0.577	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
OGFR	11054	hgsc.bcm.edu	37	20	61436359	61436359	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:61436359G>C	ENST00000290291.6	+	1	173	c.148G>C	c.(148-150)Gcg>Ccg	p.A50P	OGFR_ENST00000370461.1_5'Flank|OGFR-AS1_ENST00000431361.1_RNA	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	50				AAR -> GPE (in Ref. 2). {ECO:0000305}.|DAGDEDEESEEPRAARPSSFQSRMTGSRNWRATRDMCRYRH NYP -> GARRALGVLGQPGGLQMRLPERHGGPQGSLCLMD PCCPLSLALQ (in Ref. 5). {ECO:0000305}.	opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					GGAGCCGCGGGCGGCGCGGCC	0.801																																					p.A50P		Atlas-SNP	.											.	OGFR	63	.	0			c.G148C						PASS	.						8.0	12.0	11.0					20																	61436359		1504	2710	4214	SO:0001583	missense	11054	exon1			CCGCGGGCGGCGC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.148G>C	chr20.hg19:g.61436359G>C	ENSP00000290291:p.Ala50Pro	42.0	0.0	.		59.0	15.0	.	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	hg19	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	G	5.458	0.269520	0.10349	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163	T;T	0.47177	1.84;0.85	2.24	1.25	0.21368	.	1.107710	0.07007	N	0.824466	T	0.32734	0.0839	N	0.14661	0.345	0.20307	N	0.999915	D	0.61080	0.989	P	0.47573	0.55	T	0.17048	-1.0382	10	0.28530	T	0.3	.	4.5217	0.11962	0.0:0.2882:0.4714:0.2404	.	50	Q9NZT2	OGFR_HUMAN	P	50	ENSP00000290291:A50P;ENSP00000359499:A50P	ENSP00000290291:A50P	A	+	1	0	OGFR	60906804	0.026000	0.19158	0.007000	0.13788	0.045000	0.14185	0.706000	0.25690	0.469000	0.27268	-0.333000	0.08304	GCG	.	.	.	none		0.801	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
EEF1A2	1917	hgsc.bcm.edu	37	20	62126370	62126370	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:62126370C>T	ENST00000298049.7	-	3	479	c.409G>A	c.(409-411)Gcc>Acc	p.A137T	EEF1A2_ENST00000217182.3_Missense_Mutation_p.A137T			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	137	tr-type G.				positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			GCCAGCAGGGCATGCTCCCGC	0.657																																					p.A137T		Atlas-SNP	.											.	EEF1A2	60	.	0			c.G409A						PASS	.						94.0	85.0	88.0					20																	62126370		2203	4300	6503	SO:0001583	missense	1917	exon4			GCAGGGCATGCTC	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"""statin-like"", ""statin"""	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.409G>A	chr20.hg19:g.62126370C>T	ENSP00000298049:p.Ala137Thr	64.0	0.0	.		96.0	62.0	.	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Missense_Mutation	SNP	ENST00000298049.7	hg19	CCDS13522.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461676	0.63513	.	.	ENSG00000101210	ENST00000298049;ENST00000217182	T;T	0.71341	-0.56;-0.56	3.88	2.93	0.34026	Protein synthesis factor, GTP-binding (1);	0.125571	0.52532	N	0.000078	T	0.76926	0.4056	L	0.45285	1.41	0.58432	D	0.999999	D;B	0.69078	0.997;0.187	D;B	0.79108	0.992;0.332	T	0.77744	-0.2473	10	0.87932	D	0	-1.4932	11.838	0.52338	0.0:0.9122:0.0:0.0878	.	113;137	Q59GP5;Q05639	.;EF1A2_HUMAN	T	137	ENSP00000298049:A137T;ENSP00000217182:A137T	ENSP00000217182:A137T	A	-	1	0	EEF1A2	61596814	1.000000	0.71417	0.982000	0.44146	0.586000	0.36452	5.950000	0.70265	0.766000	0.33244	-0.671000	0.03813	GCC	.	.	.	none		0.657	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958	
MYT1	4661	hgsc.bcm.edu	37	20	62843443	62843443	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:62843443G>A	ENST00000328439.1	+	9	1833	c.1469G>A	c.(1468-1470)gGc>gAc	p.G490D	MYT1_ENST00000536311.1_Missense_Mutation_p.G490D|MYT1_ENST00000360149.4_Missense_Mutation_p.G192D	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CCCACTCCTGGCTGCACAGGC	0.627																																					p.G490D	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G1469A						PASS	.						140.0	129.0	132.0					20																	62843443		2203	4300	6503	SO:0001583	missense	4661	exon9			CTCCTGGCTGCAC	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1469G>A	chr20.hg19:g.62843443G>A	ENSP00000327465:p.Gly490Asp	27.0	0.0	.		59.0	19.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531388	0.64972	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.68331	-0.13;-0.32;1.64	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87870	0.2670	10	0.87932	D	0	-31.1382	17.4965	0.87719	0.0:0.0:1.0:0.0	.	490;490;192	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	D	192;490;490	ENSP00000353269:G192D;ENSP00000327465:G490D;ENSP00000442412:G490D	ENSP00000327465:G490D	G	+	2	0	MYT1	62313887	1.000000	0.71417	0.998000	0.56505	0.757000	0.42996	9.725000	0.98778	2.187000	0.69744	0.557000	0.71058	GGC	.	.	.	none		0.627	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
UMODL1	89766	hgsc.bcm.edu	37	21	43505510	43505510	+	Silent	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr21:43505510T>A	ENST00000408910.2	+	4	591	c.591T>A	c.(589-591)ctT>ctA	p.L197L	UMODL1_ENST00000408989.2_Silent_p.L197L|UMODL1_ENST00000400427.1_Silent_p.L125L|UMODL1_ENST00000400424.2_Silent_p.L125L	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	197					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						ACATGCGCCTTCTGCATTCCT	0.607																																					p.L197L	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T591A						PASS	.						138.0	142.0	141.0					21																	43505510		1939	4137	6076	SO:0001819	synonymous_variant	89766	exon4			GCGCCTTCTGCAT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.591T>A	chr21.hg19:g.43505510T>A		52.0	0.0	.		51.0	28.0	.	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	hg19	CCDS42936.1																																																																																			.	.	.	none		0.607	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462120	37462120	+	Nonstop_Mutation	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:37462120T>C	ENST00000346753.3	-	18	2552	c.2436A>G	c.(2434-2436)tgA>tgG	p.*812W	TMPRSS6_ENST00000406856.1_Nonstop_Mutation_p.*825W|TMPRSS6_ENST00000381792.2_Nonstop_Mutation_p.*825W|TMPRSS6_ENST00000406725.1_Nonstop_Mutation_p.*803W	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	0					angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GGGCAGTTCCTCAGGTCACCA	0.647																																					p.X812W		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.A2436G						PASS	.						48.0	52.0	51.0					22																	37462120		2203	4300	6503	SO:0001578	stop_lost	164656	exon18			AGTTCCTCAGGTC	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.2436A>G	chr22.hg19:g.37462120T>C	ENSP00000334962:p.*812Cysext*96	72.0	0.0	.		75.0	31.0	.	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	hg19	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.824874	0.32237	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3168	0.66457	0.0:0.0:0.0:1.0	.	.	.	.	W	825;812;803;825	.	.	X	-	3	0	TMPRSS6	35792066	1.000000	0.71417	0.994000	0.49952	0.458000	0.32498	5.142000	0.64820	1.837000	0.53436	0.482000	0.46254	TGA	.	.	.	none		0.647	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
FBLN1	2192	hgsc.bcm.edu	37	22	45931203	45931203	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:45931203T>A	ENST00000327858.6	+	8	1003	c.908T>A	c.(907-909)cTa>cAa	p.L303Q	FBLN1_ENST00000442170.2_Missense_Mutation_p.L303Q|FBLN1_ENST00000402984.3_Missense_Mutation_p.L341Q|FBLN1_ENST00000262722.7_Missense_Mutation_p.L303Q|FBLN1_ENST00000340923.5_Missense_Mutation_p.L303Q|FBLN1_ENST00000348697.2_Missense_Mutation_p.L303Q	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	303	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAAGATGCTCTAGGCAACTGT	0.537																																					p.L303Q		Atlas-SNP	.											.	FBLN1	143	.	0			c.T908A						PASS	.						79.0	71.0	74.0					22																	45931203		2203	4300	6503	SO:0001583	missense	2192	exon8			ATGCTCTAGGCAA		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.908T>A	chr22.hg19:g.45931203T>A	ENSP00000331544:p.Leu303Gln	78.0	0.0	.		70.0	32.0	.	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	t	17.75	3.466305	0.63625	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.15;-2.89;-2.89	5.47	5.47	0.80525	EGF-like calcium-binding (2);	0.070231	0.64402	D	0.000017	D	0.90800	0.7111	N	0.12637	0.245	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;0.999;0.998;0.999	D;D;D;D	0.77557	0.99;0.985;0.971;0.971	D	0.88285	0.2939	10	0.13470	T	0.59	.	15.6182	0.76784	0.0:0.0:0.0:1.0	.	341;303;303;303	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	Q	303;341;303;303;303;303	ENSP00000262723:L303Q;ENSP00000385521:L341Q;ENSP00000262722:L303Q;ENSP00000331544:L303Q;ENSP00000393812:L303Q;ENSP00000342212:L303Q	ENSP00000262722:L303Q	L	+	2	0	FBLN1	44309867	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.463000	0.66712	2.101000	0.63845	0.445000	0.29226	CTA	.	.	.	none		0.537	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	
MLC1	23209	hgsc.bcm.edu	37	22	50502534	50502534	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:50502534T>C	ENST00000311597.5	-	11	1594	c.988A>G	c.(988-990)Aag>Gag	p.K330E	MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Missense_Mutation_p.K296E|MLC1_ENST00000431262.2_Missense_Mutation_p.K300E|MLC1_ENST00000450140.2_Missense_Mutation_p.K278E|MLC1_ENST00000395876.2_Missense_Mutation_p.K330E|MLC1_ENST00000535444.1_Missense_Mutation_p.K251E	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	330					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GCACTGACCTTGAAGCGCACG	0.677																																					p.K330E		Atlas-SNP	.											.	MLC1	48	.	0			c.A988G						PASS	.						50.0	46.0	47.0					22																	50502534		2203	4300	6503	SO:0001583	missense	23209	exon11			TGACCTTGAAGCG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.988A>G	chr22.hg19:g.50502534T>C	ENSP00000310375:p.Lys330Glu	69.0	0.0	.		72.0	25.0	.	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	hg19	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	t	16.64	3.178544	0.57692	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140	D;D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4;-3.4	3.99	2.9	0.33743	.	0.098520	0.64402	D	0.000002	D	0.94997	0.8381	M	0.68952	2.095	0.49389	D	0.999786	D;D;D;D	0.71674	0.996;0.998;0.996;0.998	D;D;D;D	0.78314	0.987;0.991;0.987;0.991	D	0.93639	0.6963	10	0.87932	D	0	-29.1483	7.6427	0.28303	0.0:0.0:0.2162:0.7838	.	296;300;278;330	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	E	330;330;296;300;251;278	ENSP00000379216:K330E;ENSP00000310375:K330E;ENSP00000445805:K296E;ENSP00000415877:K300E;ENSP00000438910:K251E;ENSP00000412448:K278E	ENSP00000310375:K330E	K	-	1	0	MLC1	48844661	0.753000	0.28349	0.958000	0.39756	0.472000	0.32918	0.549000	0.23329	0.616000	0.30141	0.454000	0.30748	AAG	.	.	.	none		0.677	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
LRP2	4036	hgsc.bcm.edu	37	2	170058161	170058163	+	In_Frame_Del	DEL	TTA	TTA	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:170058161_170058163delTTA	ENST00000263816.3	-	44	8712_8714	c.8427_8429delTAA	c.(8425-8430)aataac>aac	p.2809_2810NN>N		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2809	LDL-receptor class A 18. {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)"""	ATCTGAAGTGTTATTATCATGGC	0.379																																					p.2810_2810del		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.8428_8430del						PASS	.																																			SO:0001651	inframe_deletion	4036	exon44			.		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.8427_8429delTAA	chr2.hg19:g.170058164_170058166delTTA	ENSP00000263816:p.Asn2810del	57.0	0.0	0		49.0	25.0	0.510204	NM_004525	O00711|Q16215	In_Frame_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.379	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
RGL2	5863	hgsc.bcm.edu	37	6	33262758	33262758	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:33262758delC	ENST00000497454.1	-	10	1769	c.1274delG	c.(1273-1275)ggtfs	p.G427fs	PFDN6_ENST00000463584.1_Intron|RGL2_ENST00000444031.2_Frame_Shift_Del_p.G345fs|RGL2_ENST00000437840.2_5'UTR	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	427	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						ACTCACCCCACCCCGGGAGCC	0.597																																					p.G425fs		Atlas-Indel,Pindel	.											.	RGL2	58	.	0			c.1275delT						PASS	.						21.0	23.0	22.0					6																	33262758		2182	4275	6457	SO:0001589	frameshift_variant	5863	exon10			.		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"""RAB2, member RAS oncogene family-like"""	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.1274delG	chr6.hg19:g.33262758delC	ENSP00000420211:p.Gly427fs	134.0	0.0	0		130.0	52.0	0.4	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Frame_Shift_Del	DEL	ENST00000497454.1	hg19	CCDS4774.1																																																																																			.	.	.	none		0.597	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2		
NOTCH4	4855	hgsc.bcm.edu	37	6	32168924	32168937	+	Frame_Shift_Del	DEL	AGGGGCTGCGTTTG	AGGGGCTGCGTTTG	-	rs204987	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	AGGGGCTGCGTTTG	AGGGGCTGCGTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:32168924_32168937delAGGGGCTGCGTTTG	ENST00000375023.3	-	22	4234_4247	c.4096_4109delCAAACGCAGCCCCT	c.(4096-4110)caaacgcagcccctgfs	p.QTQPL1366fs		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1366					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CTCCTTGCCCAGGGGCTGCGTTTGAGGGGCTGCT	0.598																																					p.1366_1370del		Atlas-Indel,Pindel	.											.	NOTCH4	201	.	0			c.4097_4110del						PASS	.																																			SO:0001589	frameshift_variant	4855	exon22			.		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4096_4109delCAAACGCAGCCCCT	chr6.hg19:g.32168924_32168937delAGGGGCTGCGTTTG	ENSP00000364163:p.Gln1366fs	100.0	0.0	0		99.0	24.0	0.242424	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Frame_Shift_Del	DEL	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.	.	none		0.598	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
PDLIM4	8572	hgsc.bcm.edu	37	5	131606622	131606622	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:131606622delA	ENST00000253754.3	+	4	406	c.342delA	c.(340-342)acafs	p.T115fs	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Frame_Shift_Del_p.T115fs	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	115							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGCCCAACAACCAGCAGGC	0.622																																					p.T114fs		Atlas-Indel,Pindel	.											PDLIM4,NS,carcinoma,0,1	PDLIM4	22	.	0			c.341delC						PASS	.						75.0	84.0	81.0					5																	131606622		2203	4300	6503	SO:0001589	frameshift_variant	8572	exon4			.	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.342delA	chr5.hg19:g.131606622delA	ENSP00000253754:p.Thr115fs	155.0	0.0	0		152.0	72.0	0.473684	NM_001131027	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Frame_Shift_Del	DEL	ENST00000253754.3	hg19	CCDS4152.1																																																																																			.	.	.	none		0.622	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
GPATCH8	23131	hgsc.bcm.edu	37	17	42476886	42476891	+	In_Frame_Del	DEL	GCGGCT	GCGGCT	-	rs111563656	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	GCGGCT	GCGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:42476886_42476891delGCGGCT	ENST00000591680.1	-	8	2584_2589	c.2554_2559delAGCCGC	c.(2554-2559)agccgcdel	p.SR854del	GPATCH8_ENST00000434000.1_In_Frame_Del_p.SR776del	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	854	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		CAGACCTTGAGCGGCTGCGGGAATGC	0.553																																					p.852_854del		Atlas-Indel,Pindel	.											.	GPATCH8	114	.	0			c.2555_2560del						PASS	.																																			SO:0001651	inframe_deletion	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2554_2559delAGCCGC	chr17.hg19:g.42476886_42476891delGCGGCT	ENSP00000467556:p.Ser854_Arg855del	63.0	0.0	0		66.0	35.0	0.530303	NM_001002909	B9EGP9|O60300|Q8TB99	In_Frame_Del	DEL	ENST00000591680.1	hg19	CCDS32666.1																																																																																			.	.	.	none		0.553	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
MAP2	4133	hgsc.bcm.edu	37	2	210561373	210561373	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:210561373delC	ENST00000360351.4	+	8	4794	c.4288delC	c.(4288-4290)cctfs	p.P1430fs	MAP2_ENST00000475600.1_3'UTR|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Frame_Shift_Del_p.P1426fs|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1430					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AAAAGAAAAGCCTTTTAAAAC	0.403																																					p.K1429fs	Pancreas(27;423 979 28787 29963)	Atlas-Indel,Pindel	.											.	MAP2	372	.	0			c.4287delG						PASS	.						60.0	66.0	64.0					2																	210561373		2203	4300	6503	SO:0001589	frameshift_variant	4133	exon8			.		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4288delC	chr2.hg19:g.210561373delC	ENSP00000353508:p.Pro1430fs	400.0	0.0	0		341.0	151.0	0.442815	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Frame_Shift_Del	DEL	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.	.	none		0.403	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
SLC7A9	11136	hgsc.bcm.edu	37	19	33350836	33350836	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:33350836delG	ENST00000023064.4	-	8	975	c.784delC	c.(784-786)ctgfs	p.L262fs	SLC7A9_ENST00000590341.1_Frame_Shift_Del_p.L262fs|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Frame_Shift_Del_p.L262fs	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	262					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	GCCGTCACCAGGGGGATCCCG	0.612																																					p.L262fs	GBM(181;1335 2108 9644 44178 46689)	Atlas-Indel,Pindel	.											.	SLC7A9	78	.	0			c.785delT						PASS	.						99.0	81.0	87.0					19																	33350836		2203	4300	6503	SO:0001589	frameshift_variant	11136	exon8			.	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.784delC	chr19.hg19:g.33350836delG	ENSP00000023064:p.Leu262fs	157.0	0.0	0		158.0	56.0	0.35443	NM_001243036	B2R9A6	Frame_Shift_Del	DEL	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.	.	none		0.612	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
DNAAF2	55172	hgsc.bcm.edu	37	14	50100020	50100024	+	Frame_Shift_Del	DEL	GTTTA	GTTTA	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	GTTTA	GTTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:50100020_50100024delGTTTA	ENST00000298292.8	-	1	1924_1928	c.1844_1848delTAAAC	c.(1843-1848)gtaaacfs	p.VN615fs	DNAAF2_ENST00000406043.3_Frame_Shift_Del_p.VN615fs	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	615					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						AAGAATCGTTGTTTACACCATAATA	0.429																																					p.615_617del		Atlas-Indel,Pindel	.											.	DNAAF2	47	.	0			c.1845_1849del						PASS	.																																			SO:0001589	frameshift_variant	55172	exon1			.	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"""kintoun"""	612517	"""chromosome 14 open reading frame 104"""	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.1844_1848delTAAAC	chr14.hg19:g.50100020_50100024delGTTTA	ENSP00000298292:p.Val615fs	131.0	0.0	0		98.0	40.0	0.408163	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Frame_Shift_Del	DEL	ENST00000298292.8	hg19	CCDS9691.2																																																																																			.	.	.	none		0.429	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1		
PDK2	5164	hgsc.bcm.edu	37	17	48184183	48184187	+	Frame_Shift_Del	DEL	CCCAG	CCCAG	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	CCCAG	CCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:48184183_48184187delCCCAG	ENST00000503176.1	+	5	704_708	c.543_547delCCCAG	c.(541-549)aacccagccfs	p.PA182fs	PDK2_ENST00000007708.3_Frame_Shift_Del_p.PA118fs	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	182	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.P182S(1)		central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GCAGCACCAACCCAGCCCATCCCAA	0.629									Autosomal Dominant Polycystic Kidney Disease																												p.181_182del		Atlas-Indel,Pindel	.											.	PDK2	41	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.542_546del						PASS	.																																			SO:0001589	frameshift_variant	5164	exon5	Familial Cancer Database	ADPKD	.	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.543_547delCCCAG	chr17.hg19:g.48184183_48184187delCCCAG	ENSP00000420927:p.Pro182fs	119.0	0.0	0		172.0	40.0	0.232558	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Frame_Shift_Del	DEL	ENST00000503176.1	hg19	CCDS11559.1																																																																																			.	.	.	none		0.629	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
PNKD	25953	hgsc.bcm.edu	37	2	219205495	219205496	+	Frame_Shift_Ins	INS	-	-	G			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:219205495_219205496insG	ENST00000273077.4	+	5	561_562	c.510_511insG	c.(511-513)actfs	p.T171fs	PNKD_ENST00000258362.3_Frame_Shift_Ins_p.T147fs|AC021016.8_ENST00000411433.1_RNA|PNKD_ENST00000436005.2_Frame_Shift_Ins_p.T111fs	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	171					glutathione biosynthetic process (GO:0006750)|neuromuscular process controlling posture (GO:0050884)|regulation of dopamine metabolic process (GO:0042053)|regulation of synaptic transmission, dopaminergic (GO:0032225)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCATTCTGTGTACTCACAAGCA	0.604																																					p.C170fs		Atlas-Indel,Pindel	.											.	PNKD	58	.	0			c.510_511insG						PASS	.																																			SO:0001589	frameshift_variant	25953	exon5			.		CCDS2411.1, CCDS2413.1, CCDS42816.1	2q35	2011-01-21	2007-07-12		ENSG00000127838	ENSG00000127838			9153	protein-coding gene	gene with protein product	"""myofibrillogenesis regulator 1"""	609023	"""paroxysmal nonkinesiogenic dyskinesia"""			8659518	Standard	NM_015488		Approved	DYT8, PDC, DKFZp564N1362, FPD1, MR-1, BRP17, FKSG19, TAHCCP2, KIAA1184, KIPP1184, MGC31943, PKND1	uc002vhn.3	Q8N490	OTTHUMG00000133110	Exception_encountered	chr2.hg19:g.219205495_219205496insG	ENSP00000273077:p.Thr171fs	66.0	0.0	0		61.0	24.0	0.393443	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Frame_Shift_Ins	INS	ENST00000273077.4	hg19	CCDS2411.1																																																																																			.	.	.	none		0.604	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2		
PXDNL	137902	hgsc.bcm.edu	37	8	52412274	52412274	+	Frame_Shift_Del	DEL	A	A	-	rs372013787		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr8:52412274delA	ENST00000356297.4	-	5	537	c.437delT	c.(436-438)ctgfs	p.L146fs	PXDNL_ENST00000543296.1_Frame_Shift_Del_p.L146fs	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	146					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CTCTAATCTCAGAAGGTCTCC	0.433																																					p.L146fs		Atlas-Indel,Pindel	.											.	PXDNL	414	.	0			c.438delG						PASS	.						182.0	175.0	177.0					8																	52412274		1869	4105	5974	SO:0001589	frameshift_variant	137902	exon5			.		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.437delT	chr8.hg19:g.52412274delA	ENSP00000348645:p.Leu146fs	57.0	0.0	0		68.0	39.0	0.573529	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Frame_Shift_Del	DEL	ENST00000356297.4	hg19	CCDS47855.1																																																																																			.	.	.	none		0.433	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
ELN	2006	hgsc.bcm.edu	37	7	73470631	73470631	+	Frame_Shift_Del	DEL	T	T	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:73470631delT	ENST00000252034.7	+	20	1580	c.1181delT	c.(1180-1182)attfs	p.I394fs	ELN_ENST00000380553.4_Frame_Shift_Del_p.I277fs|ELN_ENST00000380575.4_Frame_Shift_Del_p.I384fs|ELN_ENST00000414324.1_Frame_Shift_Del_p.I389fs|ELN_ENST00000466878.1_3'UTR|ELN_ENST00000320399.6_Frame_Shift_Del_p.I394fs|ELN_ENST00000445912.1_Frame_Shift_Del_p.I394fs|ELN_ENST00000357036.5_Frame_Shift_Del_p.I399fs|ELN_ENST00000380562.4_Frame_Shift_Del_p.I394fs|ELN_ENST00000320492.7_Frame_Shift_Del_p.I358fs|ELN_ENST00000380584.4_Frame_Shift_Del_p.I380fs|ELN_ENST00000380576.5_Frame_Shift_Del_p.I394fs|ELN_ENST00000429192.1_Frame_Shift_Del_p.I399fs|ELN_ENST00000358929.4_Frame_Shift_Del_p.I394fs|ELN_ENST00000458204.1_Frame_Shift_Del_p.I384fs	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	394	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GTTGGAGGCATTCCTACTTAC	0.627			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																														p.I399fs		Atlas-Indel,Pindel	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.1195delA						PASS	.						97.0	104.0	102.0					7																	73470631		2203	4300	6503	SO:0001589	frameshift_variant	2006	exon20			.		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1181delT	chr7.hg19:g.73470631delT	ENSP00000252034:p.Ile394fs	105.0	0.0	0		142.0	85.0	0.598592	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Frame_Shift_Del	DEL	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.	.	none		0.627	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
BTAF1	9044	hgsc.bcm.edu	37	10	93722390	93722390	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:93722390delA	ENST00000265990.6	+	12	1667	c.1359delA	c.(1357-1359)tcafs	p.S453fs	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	453					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CTGCAGCATCATTAGTGCCTG	0.333																																					p.S453fs		Pindel	.											.	BTAF1	148	.	0			c.1358delC						PASS	.						59.0	57.0	57.0					10																	93722390		2203	4300	6503	SO:0001589	frameshift_variant	9044	exon12			.	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"""Mot1 homolog (S. cerevisiae)"""	605191	"""BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"""			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.1359delA	chr10.hg19:g.93722390delA	ENSP00000265990:p.Ser453fs	397.0	0.0	.		349.0	87.0	0.249	NM_003972	B4E0W6|O43578	Frame_Shift_Del	DEL	ENST00000265990.6	hg19	CCDS7419.1																																																																																			.	.	.	none		0.333	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972	
