#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
COL11A1	1301	hgsc.bcm.edu	37	1	103470193	103470193	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:103470193G>C	ENST00000370096.3	-	19	2182	c.1870C>G	c.(1870-1872)Cca>Gca	p.P624A	COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000512756.1_Missense_Mutation_p.P508A|COL11A1_ENST00000353414.4_Missense_Mutation_p.P585A|COL11A1_ENST00000358392.2_Missense_Mutation_p.P636A	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	624	Collagen-like 3.|Collagen-like 4.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGAGGACCTGGAGGACCTTGA	0.328																																					p.P636A		Atlas-SNP	.											.	COL11A1	972	.	0			c.C1906G						PASS	.						40.0	36.0	38.0					1																	103470193		2203	4300	6503	SO:0001583	missense	1301	exon19			GACCTGGAGGACC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1870C>G	chr1.hg19:g.103470193G>C	ENSP00000359114:p.Pro624Ala	501.0	0.0	.		504.0	112.0	.	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615873	0.87359	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32	5.83	5.83	0.93111	.	0.115539	0.64402	D	0.000013	D	0.96380	0.8819	M	0.76328	2.33	0.80722	D	1	D;D;D;D	0.89917	0.997;0.996;1.0;1.0	D;D;D;D	0.87578	0.992;0.987;0.997;0.998	D	0.95297	0.8400	10	0.48119	T	0.1	.	20.1162	0.97934	0.0:0.0:1.0:0.0	.	508;585;636;624	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	A	624;636;585;508	ENSP00000359114:P624A;ENSP00000351163:P636A;ENSP00000302551:P585A;ENSP00000426533:P508A	ENSP00000302551:P585A	P	-	1	0	COL11A1	103242781	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.562000	0.67346	2.756000	0.94617	0.655000	0.94253	CCA	.	.	.	none		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
NPR1	4881	hgsc.bcm.edu	37	1	153651789	153651789	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:153651789C>T	ENST00000368680.3	+	1	677	c.205C>T	c.(205-207)Cgc>Tgc	p.R69C		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	69					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	GGTGAAGGCGCGCCCCGACTT	0.736																																					p.R69C	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.C205T						PASS	.						3.0	4.0	4.0					1																	153651789		1837	3626	5463	SO:0001583	missense	4881	exon1			AAGGCGCGCCCCG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.205C>T	chr1.hg19:g.153651789C>T	ENSP00000357669:p.Arg69Cys	60.0	0.0	.		48.0	12.0	.	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	hg19	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.762841	0.31228	.	.	ENSG00000169418	ENST00000368680	D	0.83335	-1.71	3.73	2.8	0.32819	Extracellular ligand-binding receptor (1);	0.471967	0.20468	N	0.091747	T	0.58906	0.2155	N	0.22421	0.69	0.19300	N	0.99997	P	0.44816	0.844	P	0.44359	0.447	T	0.54655	-0.8261	10	0.72032	D	0.01	.	6.4211	0.21744	0.2105:0.5851:0.2044:0.0	.	69	P16066	ANPRA_HUMAN	C	69	ENSP00000357669:R69C	ENSP00000357669:R69C	R	+	1	0	NPR1	151918413	0.024000	0.19004	0.905000	0.35620	0.811000	0.45836	0.786000	0.26844	0.738000	0.32606	0.462000	0.41574	CGC	.	.	.	none		0.736	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
IQGAP3	128239	hgsc.bcm.edu	37	1	156524143	156524143	+	Silent	SNP	G	G	T	rs370248624		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:156524143G>T	ENST00000361170.2	-	13	1342	c.1332C>A	c.(1330-1332)ctC>ctA	p.L444L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	444					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACAGCTGAGAGCATCTCCA	0.612																																					p.L444L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C1332A						PASS	.						43.0	43.0	43.0					1																	156524143		2203	4300	6503	SO:0001819	synonymous_variant	128239	exon13			AGCTGAGAGCATC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1332C>A	chr1.hg19:g.156524143G>T		177.0	0.0	.		160.0	24.0	.	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.	.	none		0.612	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
CACNA1S	779	hgsc.bcm.edu	37	1	201030418	201030418	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:201030418T>G	ENST00000362061.3	-	25	3458	c.3232A>C	c.(3232-3234)Aac>Cac	p.N1078H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.N1078H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1078					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCTCACAGTTCTTGTACTCA	0.552																																					p.N1078H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.A3232C						PASS	.						131.0	105.0	114.0					1																	201030418		2203	4300	6503	SO:0001583	missense	779	exon25			CACAGTTCTTGTA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.3232A>C	chr1.hg19:g.201030418T>G	ENSP00000355192:p.Asn1078His	102.0	0.0	.		76.0	14.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516695	0.64634	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96365	-3.99;-3.91	5.21	4.07	0.47477	.	0.129861	0.64402	D	0.000001	D	0.97870	0.9300	M	0.90922	3.16	0.43740	D	0.996231	P	0.44521	0.837	P	0.58577	0.841	D	0.97740	1.0208	10	0.87932	D	0	.	9.0753	0.36517	0.0:0.1511:0.0:0.8489	.	1078	Q13698	CAC1S_HUMAN	H	1078	ENSP00000355192:N1078H;ENSP00000356307:N1078H	ENSP00000355192:N1078H	N	-	1	0	CACNA1S	199297041	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.036000	0.41165	0.914000	0.36822	0.459000	0.35465	AAC	.	.	.	none		0.552	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
NVL	4931	hgsc.bcm.edu	37	1	224424263	224424263	+	Missense_Mutation	SNP	C	C	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:224424263C>A	ENST00000281701.6	-	20	2570	c.2311G>T	c.(2311-2313)Gat>Tat	p.D771Y	NVL_ENST00000391875.2_Missense_Mutation_p.D665Y|NVL_ENST00000482491.1_Missense_Mutation_p.D495Y|NVL_ENST00000340871.4_Missense_Mutation_p.D582Y|NVL_ENST00000361463.3_3'UTR|NVL_ENST00000469075.1_Missense_Mutation_p.D680Y	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	771						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ACATCTGCATCCAGTGGTGGT	0.408																																					p.D771Y		Atlas-SNP	.											.	NVL	74	.	0			c.G2311T						PASS	.						145.0	137.0	140.0					1																	224424263		2203	4300	6503	SO:0001583	missense	4931	exon20			CTGCATCCAGTGG	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"""ATPases / AAA-type"""	8070	protein-coding gene	gene with protein product	"""Nuclear valosin-containing protein-like"", ""nuclear VCP-like protein"""	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.2311G>T	chr1.hg19:g.224424263C>A	ENSP00000281701:p.Asp771Tyr	191.0	0.0	.		169.0	51.0	.	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	hg19	CCDS1541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.50|16.50	3.141513|3.141513	0.57044|0.57044	.|.	.|.	ENSG00000143748|ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871|ENST00000469968	D;D;D;D;D|.	0.95001|.	-3.58;-3.58;-3.58;-3.58;-3.58|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.199823|.	0.52532|.	D|.	0.000077|.	T|T	0.78419|0.78419	0.4280|0.4280	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	P;P;P|.	0.45283|.	0.855;0.699;0.855|.	B;B;B|.	0.43052|.	0.242;0.162;0.406|.	T|T	0.79329|0.79329	-0.1848|-0.1848	10|5	0.52906|.	T|.	0.07|.	-8.2467|-8.2467	15.5999|15.5999	0.76616|0.76616	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	582;680;771|.	B4DMC4;B4DP98;O15381|.	.;.;NVL_HUMAN|.	Y|V	771;665;680;495;582|653	ENSP00000281701:D771Y;ENSP00000375747:D665Y;ENSP00000417826:D680Y;ENSP00000417213:D495Y;ENSP00000341362:D582Y|.	ENSP00000281701:D771Y|.	D|G	-|-	1|2	0|0	NVL|NVL	222490886|222490886	0.998000|0.998000	0.40836|0.40836	0.994000|0.994000	0.49952|0.49952	0.908000|0.908000	0.53690|0.53690	4.387000|4.387000	0.59626|0.59626	2.831000|2.831000	0.97527|0.97527	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.	.	.	none		0.408	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125405388	125405388	+	Missense_Mutation	SNP	C	C	T	rs200795882		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:125405388C>T	ENST00000431078.1	+	13	2291	c.1927C>T	c.(1927-1929)Cgg>Tgg	p.R643W		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	643	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GACCCGAGTGCGGGGCGCTAA	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19738	0.0		0.0	False		,,,				2504	0.0				p.R643W		Atlas-SNP	.											CNTNAP5,caecum,carcinoma,0,2	CNTNAP5	405	.	0			c.C1927T						PASS	.	C	TRP/ARG	3,4167		0,3,2082	39.0	41.0	41.0		1927	2.2	0.0	2		41	3,8413		0,3,4205	yes	missense	CNTNAP5	NM_130773.2	101	0,6,6287	TT,TC,CC		0.0356,0.0719,0.0477	probably-damaging	643/1307	125405388	6,12580	2085	4208	6293	SO:0001583	missense	129684	exon13			CGAGTGCGGGGCG	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1927C>T	chr2.hg19:g.125405388C>T	ENSP00000399013:p.Arg643Trp	297.0	0.0	.		273.0	72.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376451	0.42105	7.19E-4	3.56E-4	ENSG00000155052	ENST00000431078	T	0.11385	2.78	5.2	2.17	0.27698	.	0.624103	0.14114	N	0.340507	T	0.15176	0.0366	M	0.61703	1.905	0.09310	N	1	D	0.58620	0.983	B	0.43018	0.405	T	0.11641	-1.0579	10	0.72032	D	0.01	.	13.8889	0.63726	0.3906:0.6093:0.0:0.0	.	643	Q8WYK1	CNTP5_HUMAN	W	643	ENSP00000399013:R643W	ENSP00000399013:R643W	R	+	1	2	CNTNAP5	125121858	0.380000	0.25131	0.012000	0.15200	0.339000	0.28857	1.823000	0.39062	0.661000	0.30985	0.561000	0.74099	CGG	.	.	.	weak		0.562	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
LRP1B	53353	hgsc.bcm.edu	37	2	141598582	141598582	+	Silent	SNP	C	C	T	rs373983727		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:141598582C>T	ENST00000389484.3	-	30	5990	c.5019G>A	c.(5017-5019)acG>acA	p.T1673T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1673					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CATTAATTTGCGTTTCATCAA	0.418										TSP Lung(27;0.18)																											p.T1673T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G5019A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	135.0	121.0	126.0		5019	-10.9	1.0	2		126	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1673/4600	141598582	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon30			AATTTGCGTTTCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5019G>A	chr2.hg19:g.141598582C>T		109.0	0.0	.		86.0	13.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.	.	weak		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ANKRD44	91526	hgsc.bcm.edu	37	2	197870520	197870520	+	Missense_Mutation	SNP	C	C	T	rs150303870		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:197870520C>T	ENST00000328737.2	-	21	2246	c.2170G>A	c.(2170-2172)Gcc>Acc	p.A724T	ANKRD44_ENST00000337207.5_Missense_Mutation_p.A724T|ANKRD44_ENST00000450567.1_Missense_Mutation_p.A724T|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A741T			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	749										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGCCACGTGGCGTGGCCACGA	0.527																																					p.A749T		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G2245A						PASS	.	C	THR/ALA	0,4406		0,0,2203	154.0	150.0	151.0		2245	5.3	1.0	2	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANKRD44	NM_001195144.1	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	749/994	197870520	1,13005	2203	4300	6503	SO:0001583	missense	91526	exon21			ACGTGGCGTGGCC	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.2170G>A	chr2.hg19:g.197870520C>T	ENSP00000331516:p.Ala724Thr	183.0	0.0	.		160.0	40.0	.	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.35	2.210902	0.39102	0.0	1.16E-4	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.62804	0.2458	N	0.16130	0.375	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61691	-0.7011	10	0.34782	T	0.22	.	12.4427	0.55634	0.0:0.9242:0.0:0.0758	.	767	Q8N8A2-2	.	T	564;741;724;724;724	ENSP00000403415:A564T;ENSP00000282272:A741T;ENSP00000331516:A724T;ENSP00000402420:A724T;ENSP00000338794:A724T	ENSP00000282272:A741T	A	-	1	0	ANKRD44	197578765	0.960000	0.32886	0.994000	0.49952	0.986000	0.74619	2.068000	0.41471	2.767000	0.95098	0.655000	0.94253	GCC	.	C|1.000;T|0.000	0.000	weak		0.527	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
GIGYF2	26058	hgsc.bcm.edu	37	2	233651983	233651983	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:233651983G>T	ENST00000409547.1	+	11	967	c.656G>T	c.(655-657)gGt>gTt	p.G219V	GIGYF2_ENST00000373566.3_Missense_Mutation_p.G241V|GIGYF2_ENST00000452341.2_Missense_Mutation_p.G50V|GIGYF2_ENST00000373563.4_Missense_Mutation_p.G219V|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G241V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.G241V|GIGYF2_ENST00000409196.3_Missense_Mutation_p.G219V	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	219	Arg-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GAAGATGGAGGTTGGCGACTA	0.463																																					p.G241V		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G722T						PASS	.						124.0	126.0	125.0					2																	233651983		2203	4300	6503	SO:0001583	missense	26058	exon11			ATGGAGGTTGGCG	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.656G>T	chr2.hg19:g.233651983G>T	ENSP00000386537:p.Gly219Val	136.0	0.0	.		123.0	37.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117800	0.77323	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000445650;ENST00000452341;ENST00000421778	T;T;T;T;T;T;T;T;T;T	0.79247	-0.96;-0.91;-0.96;-0.91;-0.99;-0.91;-0.96;-1.07;-1.25;-0.73	5.93	5.05	0.67936	.	0.054310	0.85682	D	0.000000	D	0.85301	0.5665	L	0.52573	1.65	0.80722	D	1	D;P;P;P	0.76494	0.999;0.757;0.912;0.573	D;B;B;B	0.78314	0.991;0.341;0.255;0.168	D	0.86420	0.1754	10	0.59425	D	0.04	-13.7649	17.2528	0.87047	0.0:0.1256:0.8744:0.0	.	50;241;219;219	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	V	241;168;219;241;219;219;168;219;241;219;50;50;46	ENSP00000362667:G241V;ENSP00000362664:G219V;ENSP00000386765:G241V;ENSP00000386537:G219V;ENSP00000404195:G168V;ENSP00000387070:G219V;ENSP00000387170:G241V;ENSP00000410297:G219V;ENSP00000392218:G50V;ENSP00000411505:G50V	ENSP00000362664:G219V	G	+	2	0	GIGYF2	233360227	1.000000	0.71417	0.982000	0.44146	0.915000	0.54546	9.230000	0.95299	1.493000	0.48517	-0.165000	0.13383	GGT	.	.	.	none		0.463	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
UGT1A10	54575	hgsc.bcm.edu	37	2	234545301	234545301	+	Missense_Mutation	SNP	G	G	A	rs371430642		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:234545301G>A	ENST00000344644.5	+	1	202	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Missense_Mutation_p.V45M	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	45					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	GCAGTCGGTGGTGGAGAAACT	0.522																																					p.V45M		Atlas-SNP	.											.	UGT1A10	71	.	0			c.G133A						PASS	.						97.0	81.0	86.0					2																	234545301		2203	4297	6500	SO:0001583	missense	54575	exon1			TCGGTGGTGGAGA	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.133G>A	chr2.hg19:g.234545301G>A	ENSP00000343838:p.Val45Met	115.0	0.0	.		77.0	22.0	.	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	hg19	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757072	0.49468	.	.	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.62364	0.03;0.03	3.67	2.77	0.32553	.	.	.	.	.	T	0.74898	0.3777	M	0.75150	2.29	0.32795	N	0.500625	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.992	T	0.78277	-0.2266	9	0.72032	D	0.01	.	8.077	0.30722	0.0918:0.1602:0.748:0.0	.	45;45	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	M	45	ENSP00000343838:V45M;ENSP00000362544:V45M	ENSP00000343838:V45M	V	+	1	0	UGT1A10	234210040	0.000000	0.05858	0.722000	0.30670	0.806000	0.45545	-0.506000	0.06359	0.885000	0.36088	0.405000	0.27470	GTG	.	.	.	alt		0.522	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
C4orf3	401152	hgsc.bcm.edu	37	4	120221731	120221731	+	5'UTR	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr4:120221731T>C	ENST00000504110.1	-	0	345				C4orf3_ENST00000399075.4_Missense_Mutation_p.H120R	NM_001001701.3	NP_001001701.2	Q8WVX3	CD003_HUMAN	chromosome 4 open reading frame 3							integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(4)	6						AAACCGAAAATGCTTAAGTTC	0.622																																					p.H120R		Atlas-SNP	.											.	C4orf3	16	.	0			c.A359G						PASS	.						67.0	71.0	70.0					4																	120221731		1938	4123	6061	SO:0001623	5_prime_UTR_variant	401152	exon2			CGAAAATGCTTAA		CCDS43266.1, CCDS54798.1	4q26	2012-02-24			ENSG00000164096	ENSG00000164096			19225	protein-coding gene	gene with protein product	"""HCV F-transactivated protein 1"""						Standard	NM_001001701		Approved		uc021xrf.1	Q8WVX3	OTTHUMG00000161333	ENST00000504110.1:c.-41A>G	chr4.hg19:g.120221731T>C		69.0	0.0	.		53.0	8.0	.	NM_001170330	Q6J203	Missense_Mutation	SNP	ENST00000504110.1	hg19	CCDS43266.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.283765	0.40394	.	.	ENSG00000164096	ENST00000399075	T	0.35236	1.32	4.69	-9.37	0.00626	.	.	.	.	.	T	0.22513	0.0543	.	.	.	0.09310	N	1.0	.	.	.	.	.	.	T	0.40534	-0.9558	5	0.72032	D	0.01	3.2825	1.6478	0.02765	0.1686:0.1153:0.2784:0.4377	.	.	.	.	R	120	ENSP00000382026:H120R	ENSP00000382026:H120R	H	-	2	0	C4orf3	120441179	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.183000	0.01255	-1.509000	0.01798	-1.100000	0.02121	CAT	.	.	.	none		0.622	C4orf3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364576.3	NM_001001701	
NNT	23530	hgsc.bcm.edu	37	5	43624161	43624161	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:43624161G>A	ENST00000264663.5	+	6	936	c.715G>A	c.(715-717)Ggg>Agg	p.G239R	NNT_ENST00000512996.2_Missense_Mutation_p.G108R|NNT_ENST00000344920.4_Missense_Mutation_p.G239R	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	239					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TGGTGTTGCTGGGCTTGCTTC	0.408																																					p.G239R		Atlas-SNP	.											.	NNT	92	.	0			c.G715A						PASS	.						358.0	327.0	338.0					5																	43624161		2203	4300	6503	SO:0001583	missense	23530	exon6			GTTGCTGGGCTTG	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.715G>A	chr5.hg19:g.43624161G>A	ENSP00000264663:p.Gly239Arg	123.0	0.0	.		95.0	22.0	.	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	35	5.538687	0.96474	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.97665	-4.48;-4.48;-4.48	6.04	6.04	0.98038	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 (1);Alanine dehydrogenase/PNT, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99492	0.9819	H	0.99985	5.235	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97472	1.0041	10	0.87932	D	0	-10.7542	20.5792	0.99380	0.0:0.0:1.0:0.0	.	239	Q13423	NNTM_HUMAN	R	239;239;108	ENSP00000264663:G239R;ENSP00000343873:G239R;ENSP00000426343:G108R	ENSP00000264663:G239R	G	+	1	0	NNT	43659918	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.334000	0.96470	2.873000	0.98535	0.561000	0.74099	GGG	.	.	.	none		0.408	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
HNRNPA0	10949	hgsc.bcm.edu	37	5	137088931	137088931	+	Silent	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:137088931G>A	ENST00000314940.4	-	1	1108	c.825C>T	c.(823-825)ggC>ggT	p.G275G		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	275	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)	p.G275G(1)		large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			Tgcctccaccgccgccgccgc	0.632																																					p.G275G		Atlas-SNP	.											HNRNPA0,colon,carcinoma,0,1	HNRNPA0	17	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T						PASS	.						9.0	13.0	11.0					5																	137088931		1925	3891	5816	SO:0001819	synonymous_variant	10949	exon1			TCCACCGCCGCCG	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"""RNA binding motif (RRM) containing"""	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.825C>T	chr5.hg19:g.137088931G>A		97.0	0.0	.		80.0	4.0	.	NM_006805	Q6IB18	Silent	SNP	ENST00000314940.4	hg19	CCDS4193.1																																																																																			.	.	.	none		0.632	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626523	140626523	+	Silent	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:140626523C>T	ENST00000231173.3	+	1	1377	c.1377C>T	c.(1375-1377)ttC>ttT	p.F459F		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	459	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACACCCTGTTCGTCCGCGAGA	0.627																																					p.F459F		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1377T						PASS	.						83.0	87.0	86.0					5																	140626523		2203	4297	6500	SO:0001819	synonymous_variant	56121	exon1			CCTGTTCGTCCGC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1377C>T	chr5.hg19:g.140626523C>T		121.0	0.0	.		91.0	19.0	.	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	hg19	CCDS4257.1																																																																																			.	.	.	none		0.627	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
C5orf45	51149	hgsc.bcm.edu	37	5	179267940	179267940	+	Missense_Mutation	SNP	C	C	T	rs112467347		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:179267940C>T	ENST00000292586.6	-	6	559	c.469G>A	c.(469-471)Gtc>Atc	p.V157I	C5orf45_ENST00000523084.1_Missense_Mutation_p.V23I|C5orf45_ENST00000518219.1_Missense_Mutation_p.V157I|C5orf45_ENST00000403396.2_Missense_Mutation_p.V199I|C5orf45_ENST00000376931.2_Missense_Mutation_p.V102I|C5orf45_ENST00000520698.1_Missense_Mutation_p.V102I|C5orf45_ENST00000523267.1_Intron|C5orf45_ENST00000521333.1_Intron|C5orf45_ENST00000518235.1_Missense_Mutation_p.V157I	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	157										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAGGCTGGACGGTGCTCCTG	0.632																																					p.V157I		Atlas-SNP	.											C5orf45,NS,carcinoma,0,1	C5orf45	23	.	0			c.G469A						PASS	.	C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	51.0	42.0	45.0		304,469	1.7	0.0	5	dbSNP_132	45	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	102/289,157/344	179267940	1,13005	2203	4300	6503	SO:0001583	missense	51149	exon6			GCTGGACGGTGCT		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.469G>A	chr5.hg19:g.179267940C>T	ENSP00000292586:p.Val157Ile	84.0	0.0	.		76.0	20.0	.	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	hg19	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	C	2.766	-0.256704	0.05829	0.0	1.16E-4	ENSG00000161010	ENST00000403396;ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000523084;ENST00000292586	T;T;T;T;T;T;T	0.35789	1.78;1.84;1.69;2.06;1.86;1.29;3.02	2.61	1.74	0.24563	.	1.280390	0.05906	N	0.630909	T	0.19565	0.0470	N	0.17674	0.51	0.09310	N	1	B;B;B;B;B	0.20780	0.005;0.005;0.003;0.003;0.048	B;B;B;B;B	0.08055	0.002;0.003;0.002;0.003;0.003	T	0.20773	-1.0265	10	0.06365	T	0.9	0.2268	5.6775	0.17757	0.0:0.8445:0.0:0.1555	.	102;157;102;157;199	E7EMV9;B7Z1T6;E9PAK6;Q6NTE8;Q6NTE8-2	.;.;.;CE045_HUMAN;.	I	199;157;102;102;157;23;157	ENSP00000384599:V199I;ENSP00000430298:V157I;ENSP00000427849:V102I;ENSP00000366130:V102I;ENSP00000428460:V157I;ENSP00000429107:V23I;ENSP00000292586:V157I	ENSP00000292586:V157I	V	-	1	0	C5orf45	179200546	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.217000	0.09253	0.685000	0.31468	-0.263000	0.10527	GTC	.	C|0.500;T|0.500	0.500	weak		0.632	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
HIVEP1	3096	hgsc.bcm.edu	37	6	12163682	12163682	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:12163682G>A	ENST00000379388.2	+	9	7477	c.7145G>A	c.(7144-7146)aGc>aAc	p.S2382N	HIVEP1_ENST00000541134.1_Missense_Mutation_p.S247N	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2382					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CATTTGTTTAGCCACCTTCCT	0.522																																					p.S2382N		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G7145A						PASS	.						96.0	103.0	101.0					6																	12163682		2081	4225	6306	SO:0001583	missense	3096	exon9			TGTTTAGCCACCT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.7145G>A	chr6.hg19:g.12163682G>A	ENSP00000368698:p.Ser2382Asn	93.0	0.0	.		77.0	10.0	.	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	33	5.249744	0.95305	.	.	ENSG00000095951	ENST00000379388;ENST00000541134;ENST00000542327	T;T	0.62105	1.47;0.05	6.03	6.03	0.97812	.	0.000000	0.40640	N	0.001057	T	0.78020	0.4218	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78102	-0.2335	10	0.72032	D	0.01	-21.0673	20.5666	0.99351	0.0:0.0:1.0:0.0	.	2382	P15822	ZEP1_HUMAN	N	2382;247;364	ENSP00000368698:S2382N;ENSP00000445617:S247N	ENSP00000368698:S2382N	S	+	2	0	HIVEP1	12271668	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	9.041000	0.93788	2.854000	0.98071	0.655000	0.94253	AGC	.	.	.	none		0.522	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
DAXX	1616	hgsc.bcm.edu	37	6	33289303	33289303	+	Silent	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:33289303C>T	ENST00000374542.5	-	3	453	c.249G>A	c.(247-249)gaG>gaA	p.E83E	DAXX_ENST00000414083.2_Silent_p.E8E|DAXX_ENST00000266000.6_Silent_p.E83E|DAXX_ENST00000477162.1_Intron	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	83	Necessary for interaction with USP7 and ATRX.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						ATGGGACCACCTCAGGGTGGT	0.547			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.E95E		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.G285A						PASS	.						57.0	62.0	60.0					6																	33289303		2203	4300	6503	SO:0001819	synonymous_variant	1616	exon3			GACCACCTCAGGG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.249G>A	chr6.hg19:g.33289303C>T		109.0	0.0	.		112.0	24.0	.	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	hg19	CCDS4776.1																																																																																			.	.	.	none		0.547	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
ASCC3	10973	hgsc.bcm.edu	37	6	101109798	101109798	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:101109798C>T	ENST00000369162.2	-	16	2931	c.2587G>A	c.(2587-2589)Gaa>Aaa	p.E863K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	863	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		ATTATTCCTTCCCCAAATTTG	0.403																																					p.E863K		Atlas-SNP	.											.	ASCC3	205	.	0			c.G2587A						PASS	.						170.0	164.0	166.0					6																	101109798		2203	4300	6503	SO:0001583	missense	10973	exon16			TTCCTTCCCCAAA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2587G>A	chr6.hg19:g.101109798C>T	ENSP00000358159:p.Glu863Lys	106.0	0.0	.		102.0	21.0	.	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215570	0.79352	.	.	ENSG00000112249	ENST00000369162	D	0.91464	-2.85	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.105493	0.64402	N	0.000005	D	0.91178	0.7221	L	0.55990	1.75	0.80722	D	1	P	0.52316	0.952	P	0.52598	0.703	D	0.90088	0.4175	10	0.48119	T	0.1	.	20.3431	0.98773	0.0:1.0:0.0:0.0	.	863	Q8N3C0	HELC1_HUMAN	K	863	ENSP00000358159:E863K	ENSP00000358159:E863K	E	-	1	0	ASCC3	101216519	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.626000	0.61269	2.880000	0.98712	0.650000	0.86243	GAA	.	.	.	none		0.403	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
COL1A2	1278	hgsc.bcm.edu	37	7	94041426	94041426	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr7:94041426G>T	ENST00000297268.6	+	24	1868	c.1397G>T	c.(1396-1398)gGt>gTt	p.G466V		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	466			Missing (in OI2). {ECO:0000269|PubMed:18996919}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGAAAAGAAGGTCCTGTCGTA	0.368										HNSCC(75;0.22)																											p.G466V		Atlas-SNP	.											.	COL1A2	240	.	0			c.G1397T						PASS	.						93.0	88.0	90.0					7																	94041426		2203	4300	6503	SO:0001583	missense	1278	exon24			AAGAAGGTCCTGT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1397G>T	chr7.hg19:g.94041426G>T	ENSP00000297268:p.Gly466Val	135.0	0.0	.		165.0	32.0	.	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760033	0.49468	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.99186	-5.53	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.99548	0.9838	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98372	1.0554	10	0.87932	D	0	.	20.5471	0.99284	0.0:0.0:1.0:0.0	.	466	P08123	CO1A2_HUMAN	V	466;467	ENSP00000297268:G466V	ENSP00000297268:G466V	G	+	2	0	COL1A2	93879362	1.000000	0.71417	0.977000	0.42913	0.382000	0.30200	9.825000	0.99386	2.941000	0.99782	0.655000	0.94253	GGT	.	.	.	none		0.368	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
TMEM229A	730130	hgsc.bcm.edu	37	7	123672479	123672479	+	Silent	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr7:123672479C>T	ENST00000455783.1	-	1	1044	c.579G>A	c.(577-579)caG>caA	p.Q193Q	RP5-921G16.1_ENST00000484322.1_RNA	NM_001136002.1	NP_001129474.1	B2RXF0	T229A_HUMAN	transmembrane protein 229A	193						host cell nucleus (GO:0042025)|integral component of membrane (GO:0016021)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(3)	6						gctgctgctgctgctgttgct	0.731																																					p.Q193Q		Atlas-SNP	.											.	TMEM229A	31	.	0			c.G579A						PASS	.						2.0	3.0	3.0					7																	123672479		422	1152	1574	SO:0001819	synonymous_variant	730130	exon1			CTGCTGCTGCTGT	BC157828	CCDS47694.1	7q31.32	2009-09-22			ENSG00000234224	ENSG00000234224			37279	protein-coding gene	gene with protein product							Standard	NM_001136002		Approved		uc011kob.2	B2RXF0	OTTHUMG00000154762	ENST00000455783.1:c.579G>A	chr7.hg19:g.123672479C>T		55.0	0.0	.		60.0	5.0	.	NM_001136002	A4D0X6	Silent	SNP	ENST00000455783.1	hg19	CCDS47694.1																																																																																			.	.	.	none		0.731	TMEM229A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336960.3	NM_001136002	
ST18	9705	hgsc.bcm.edu	37	8	53025847	53025847	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr8:53025847T>C	ENST00000276480.7	-	26	3738	c.3055A>G	c.(3055-3057)Atg>Gtg	p.M1019V		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	1019					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGCTGTACATATCTGTGAGT	0.448																																					p.M1019V		Atlas-SNP	.											.	ST18	212	.	0			c.A3055G						PASS	.						159.0	138.0	145.0					8																	53025847		2203	4300	6503	SO:0001583	missense	9705	exon26			TGTACATATCTGT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.3055A>G	chr8.hg19:g.53025847T>C	ENSP00000276480:p.Met1019Val	130.0	0.0	.		80.0	16.0	.	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916209	0.73098	.	.	ENSG00000147488	ENST00000276480	T	0.56103	0.48	5.97	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.69024	0.3065	M	0.67397	2.05	0.58432	D	0.999994	D	0.59767	0.986	D	0.69654	0.965	T	0.71951	-0.4437	10	0.87932	D	0	-17.6121	13.4666	0.61258	0.0:0.0:0.1306:0.8694	.	1019	O60284	ST18_HUMAN	V	1019	ENSP00000276480:M1019V	ENSP00000276480:M1019V	M	-	1	0	ST18	53188400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	1.063000	0.40649	0.477000	0.44152	ATG	.	.	.	none		0.448	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1		
TOPORS	10210	hgsc.bcm.edu	37	9	32542179	32542179	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr9:32542179T>C	ENST00000360538.2	-	3	2460	c.2344A>G	c.(2344-2346)Acc>Gcc	p.T782A	TOPORS_ENST00000379858.1_Missense_Mutation_p.T717A	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	782	Arg-rich.|Interaction with TOP1.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TCAGTCCCGGTAGATGCAGTC	0.443																																					p.T782A		Atlas-SNP	.											.	TOPORS	127	.	0			c.A2344G						PASS	.						105.0	104.0	104.0					9																	32542179		2203	4300	6503	SO:0001583	missense	10210	exon3			TCCCGGTAGATGC	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2344A>G	chr9.hg19:g.32542179T>C	ENSP00000353735:p.Thr782Ala	166.0	0.0	.		134.0	24.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	3.362	-0.130299	0.06753	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.14266	2.52;2.52	6.01	3.7	0.42460	.	0.125216	0.36972	N	0.002314	T	0.04003	0.0112	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41233	-0.9520	10	0.07175	T	0.84	-7.1549	3.2108	0.06682	0.0:0.2476:0.2157:0.5367	.	782	Q9NS56	TOPRS_HUMAN	A	782;717	ENSP00000353735:T782A;ENSP00000369187:T717A	ENSP00000353735:T782A	T	-	1	0	TOPORS	32532179	0.000000	0.05858	0.986000	0.45419	0.940000	0.58332	-0.893000	0.04127	1.115000	0.41800	0.528000	0.53228	ACC	.	.	.	none		0.443	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
SPIN1	10927	hgsc.bcm.edu	37	9	91041456	91041456	+	Start_Codon_SNP	SNP	T	T	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr9:91041456T>A	ENST00000375859.3	+	2	280	c.2T>A	c.(1-3)aTg>aAg	p.M1K	SPIN1_ENST00000469017.2_3'UTR|SPIN1_ENST00000541629.1_Start_Codon_SNP_p.M1K	NM_006717.2	NP_006708.2	Q9Y657	SPIN1_HUMAN	spindlin 1	1					chromatin modification (GO:0016568)|gamete generation (GO:0007276)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of Wnt signaling pathway (GO:0030177)|rRNA transcription (GO:0009303)|Wnt signaling pathway (GO:0016055)	nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle (GO:0005819)	methylated histone binding (GO:0035064)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						TACAGATGAATGAAGACCCCA	0.398																																					p.M1K		Atlas-SNP	.											.	SPIN1	22	.	0			c.T2A						PASS	.						31.0	33.0	32.0					9																	91041456		1828	4076	5904	SO:0001582	initiator_codon_variant	10927	exon2			GATGAATGAAGAC	AF317228	CCDS43843.1	9q22.1	2008-02-05	2007-01-03	2007-01-03	ENSG00000106723	ENSG00000106723			11243	protein-coding gene	gene with protein product		609936	"""spindlin"""	SPIN		16098913	Standard	NM_006717		Approved		uc004apy.3	Q9Y657	OTTHUMG00000020168	ENST00000375859.3:c.2T>A	chr9.hg19:g.91041456T>A	ENSP00000365019:p.Met1Lys	504.0	0.0	.		460.0	120.0	.	NM_006717	A8K0X6|B3KRQ4|Q7KZJ8|Q9GZT2|Q9H0N7	Missense_Mutation	SNP	ENST00000375859.3	hg19	CCDS43843.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228688	0.79576	.	.	ENSG00000106723	ENST00000375859;ENST00000541629	T;T	0.46819	0.86;0.86	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.64283	0.2584	.	.	.	0.80722	D	1	P	0.50156	0.932	P	0.58520	0.84	T	0.70096	-0.4966	9	0.87932	D	0	-8.306	14.4491	0.67372	0.0:0.0:0.0:1.0	.	1	Q9Y657	SPIN1_HUMAN	K	1	ENSP00000365019:M1K;ENSP00000441864:M1K	ENSP00000365019:M1K	M	+	2	0	SPIN1	90231276	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.644000	0.67902	2.160000	0.67779	0.477000	0.44152	ATG	.	.	.	none		0.398	SPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052967.1	NM_006717	Missense_Mutation
CERCAM	51148	hgsc.bcm.edu	37	9	131183331	131183331	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr9:131183331C>T	ENST00000372838.4	+	1	573	c.175C>T	c.(175-177)Ccc>Tcc	p.P59S	CERCAM_ENST00000372842.1_5'UTR|CERCAM_ENST00000493788.1_3'UTR	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	59					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						GCTGGACTACCCCCGGGCCAG	0.721																																					p.P59S		Atlas-SNP	.											.	CERCAM	104	.	0			c.C175T						PASS	.						4.0	8.0	7.0					9																	131183331		654	1516	2170	SO:0001583	missense	51148	exon1			GACTACCCCCGGG	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"""glycosyltransferase 25 domain containing 3"""		"""cerebral cell adhesion molecule"""	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.175C>T	chr9.hg19:g.131183331C>T	ENSP00000361929:p.Pro59Ser	83.0	0.0	.		34.0	9.0	.	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Missense_Mutation	SNP	ENST00000372838.4	hg19	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	C	34	5.403639	0.96051	.	.	ENSG00000167123	ENST00000372838;ENST00000413863	D	0.85484	-1.99	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	D	0.92786	0.7706	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.93976	0.7254	10	0.87932	D	0	1.6041	14.813	0.70010	0.0:1.0:0.0:0.0	.	59	Q5T4B2	GT253_HUMAN	S	59	ENSP00000361929:P59S	ENSP00000361929:P59S	P	+	1	0	CERCAM	130223152	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.807000	0.75201	2.351000	0.79841	0.491000	0.48974	CCC	.	.	.	none		0.721	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174	
PDHX	8050	hgsc.bcm.edu	37	11	35006233	35006233	+	Silent	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:35006233T>C	ENST00000227868.4	+	9	1224	c.1140T>C	c.(1138-1140)gaT>gaC	p.D380D	PDHX_ENST00000477173.3_3'UTR|PDHX_ENST00000448838.3_Silent_p.D365D|PDHX_ENST00000430469.2_Silent_p.D153D			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	380					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCATAAAAGATGCTGCTGCTA	0.393																																					p.D380D		Atlas-SNP	.											.	PDHX	40	.	0			c.T1140C						PASS	.						129.0	126.0	127.0					11																	35006233		2202	4298	6500	SO:0001819	synonymous_variant	8050	exon9			AAAAGATGCTGCT	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.1140T>C	chr11.hg19:g.35006233T>C		145.0	0.0	.		88.0	18.0	.	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	hg19	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	T	2.267	-0.367827	0.05069	.	.	ENSG00000110435	ENST00000526309	.	.	.	5.64	3.35	0.38373	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45205	-0.9277	4	.	.	.	-13.8697	5.4179	0.16384	0.0:0.1506:0.1472:0.7022	.	.	.	.	T	68	.	.	M	+	2	0	PDHX	34962809	1.000000	0.71417	0.996000	0.52242	0.240000	0.25518	0.591000	0.23969	0.434000	0.26340	0.533000	0.62120	ATG	.	.	.	none		0.393	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
GLYAT	10249	hgsc.bcm.edu	37	11	58477502	58477502	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:58477502G>T	ENST00000344743.3	-	6	769	c.628C>A	c.(628-630)Ctg>Atg	p.L210M	GLYAT_ENST00000529732.1_Missense_Mutation_p.L210M	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	210					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TCAGGCCCCAGGAGACAGCAG	0.542																																					p.L210M		Atlas-SNP	.											.	GLYAT	53	.	0			c.C628A						PASS	.						73.0	77.0	76.0					11																	58477502		2201	4295	6496	SO:0001583	missense	10249	exon6			GCCCCAGGAGACA	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.628C>A	chr11.hg19:g.58477502G>T	ENSP00000340200:p.Leu210Met	115.0	0.0	.		118.0	21.0	.	NM_201648	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	hg19	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369214	0.24771	.	.	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.18657	2.2;2.2	6.06	3.17	0.36434	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	0.397208	0.22261	N	0.062407	T	0.44664	0.1304	M	0.83384	2.64	0.09310	N	1	D	0.71674	0.998	D	0.64237	0.923	T	0.37174	-0.9717	10	0.49607	T	0.09	-24.7357	11.5202	0.50546	0.2089:0.0:0.7911:0.0	.	210	Q6IB77	GLYAT_HUMAN	M	210	ENSP00000340200:L210M;ENSP00000431688:L210M	ENSP00000340200:L210M	L	-	1	2	GLYAT	58234078	0.549000	0.26481	0.197000	0.23402	0.004000	0.04260	1.080000	0.30779	0.151000	0.19162	-0.813000	0.03139	CTG	.	.	.	none		0.542	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1		
GPR137	56834	hgsc.bcm.edu	37	11	64056714	64056714	+	Missense_Mutation	SNP	C	C	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:64056714C>A	ENST00000313074.3	+	7	1236	c.1131C>A	c.(1129-1131)caC>caA	p.H377Q	KCNK4_ENST00000394525.2_5'Flank|GPR137_ENST00000539851.1_3'UTR|GPR137_ENST00000438980.2_3'UTR|KCNK4_ENST00000538767.1_5'Flank|GPR137_ENST00000411458.1_Missense_Mutation_p.H435Q|KCNK4_ENST00000422670.2_5'Flank|GPR137_ENST00000377702.4_3'UTR|RP11-783K16.10_ENST00000539086.1_RNA	NM_020155.3	NP_064540.3	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	377						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(4)|skin(1)	10						GTCCCCCTCACCCTAGGCCCC	0.657																																					p.H435Q		Atlas-SNP	.											.	GPR137	52	.	0			c.C1305A						PASS	.						82.0	84.0	83.0					11																	64056714		2201	4297	6498	SO:0001583	missense	56834	exon9			CCCTCACCCTAGG	AJ250392	CCDS8066.1, CCDS53655.1, CCDS53656.1, CCDS53657.1, CCDS53658.1	11q13.1	2014-02-12	2006-01-26		ENSG00000173264	ENSG00000173264		"""GPCR / Unclassified : 7TM orphan receptors"""	24300	protein-coding gene	gene with protein product						10873569, 12732197	Standard	NM_001170726		Approved	C11orf4, GPR137A, TM7SF1L1	uc010rni.2	Q96N19	OTTHUMG00000167817	ENST00000313074.3:c.1131C>A	chr11.hg19:g.64056714C>A	ENSP00000321698:p.His377Gln	123.0	0.0	.		157.0	13.0	.	NM_001170726	B4DTG7|B7Z7M1|Q4G0Y9|Q8N4K6	Missense_Mutation	SNP	ENST00000313074.3	hg19	CCDS8066.1	.	.	.	.	.	.	.	.	.	.	c	3.770	-0.047901	0.07407	.	.	ENSG00000173264	ENST00000411458;ENST00000313074	T;T	0.44482	0.92;0.97	5.27	-10.5	0.00291	.	4.032870	0.00357	N	0.000023	T	0.16599	0.0399	N	0.08118	0	0.09310	N	0.999993	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17961	-1.0352	10	0.66056	D	0.02	-0.3046	0.0787	0.00029	0.2624:0.2081:0.2079:0.3215	.	435;377	B4DTG7;Q96N19	.;G137A_HUMAN	Q	435;377	ENSP00000411827:H435Q;ENSP00000321698:H377Q	ENSP00000321698:H377Q	H	+	3	2	GPR137	63813290	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-2.168000	0.01270	-2.053000	0.00901	-0.215000	0.12644	CAC	.	.	.	none		0.657	GPR137-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396412.1	NM_020155	
TWF1	5756	hgsc.bcm.edu	37	12	44198327	44198327	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:44198327T>C	ENST00000395510.2	-	2	203	c.74A>G	c.(73-75)tAc>tGc	p.Y25C	TWF1_ENST00000547564.1_5'UTR|TWF1_ENST00000552521.1_5'UTR|TWF1_ENST00000325127.4_Missense_Mutation_p.Y59C|TWF1_ENST00000548315.1_Missense_Mutation_p.Y25C	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	25	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		CAGAAGTCTGTACTTTCCATT	0.284																																					p.Y25C		Atlas-SNP	.											TWF1,NS,carcinoma,0,1	TWF1	37	.	0			c.A74G						PASS	.						42.0	46.0	45.0					12																	44198327		2197	4266	6463	SO:0001583	missense	5756	exon2			AGTCTGTACTTTC	U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.74A>G	chr12.hg19:g.44198327T>C	ENSP00000378886:p.Tyr25Cys	501.0	0.0	.		461.0	106.0	.	NM_002822	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Missense_Mutation	SNP	ENST00000395510.2	hg19	CCDS31780.2	.	.	.	.	.	.	.	.	.	.	T	15.99	2.996118	0.54147	.	.	ENSG00000151239	ENST00000395510;ENST00000325127;ENST00000548315;ENST00000546662	T;T;T;T	0.38240	1.39;1.39;1.39;1.15	5.6	4.46	0.54185	Actin-binding, cofilin/tropomyosin type (3);	0.406531	0.30483	N	0.009534	T	0.57051	0.2027	M	0.79475	2.455	0.80722	D	1	D;D	0.63880	0.969;0.993	D;D	0.67725	0.927;0.953	T	0.58233	-0.7672	10	0.51188	T	0.08	-7.5652	10.7348	0.46117	0.0:0.0743:0.0:0.9257	.	25;25	Q12792-3;Q12792	.;TWF1_HUMAN	C	25;59;25;63	ENSP00000378886:Y25C;ENSP00000321058:Y59C;ENSP00000449428:Y25C;ENSP00000448221:Y63C	ENSP00000321058:Y59C	Y	-	2	0	TWF1	42484594	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.146000	0.58072	0.957000	0.37930	0.482000	0.46254	TAC	.	.	.	none		0.284	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
HOXC6	3223	hgsc.bcm.edu	37	12	54422350	54422350	+	Silent	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:54422350C>T	ENST00000243108.4	+	1	209	c.45C>T	c.(43-45)gcC>gcT	p.A15A	RP11-834C11.14_ENST00000512206.1_RNA|HOXC4_ENST00000303406.4_Intron|RP11-834C11.12_ENST00000513209.1_Intron|HOXC6_ENST00000394331.3_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	15					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GCCACCTCGCCGGGGGCCAGG	0.527																																					p.A15A		Atlas-SNP	.											.	HOXC6	30	.	0			c.C45T						PASS	.						75.0	71.0	73.0					12																	54422350		2203	4300	6503	SO:0001819	synonymous_variant	3223	exon1			CCTCGCCGGGGGC		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"""Homeoboxes / ANTP class : HOXL subclass"""	5128	protein-coding gene	gene with protein product		142972	"""homeo box C6"""	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.45C>T	chr12.hg19:g.54422350C>T		164.0	0.0	.		168.0	43.0	.	NM_004503	B2RBV2|Q6DK09	Silent	SNP	ENST00000243108.4	hg19	CCDS8871.1																																																																																			.	.	.	none		0.527	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2		
ERBB3	2065	hgsc.bcm.edu	37	12	56495550	56495550	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:56495550C>T	ENST00000267101.3	+	28	4180	c.3740C>T	c.(3739-3741)cCc>cTc	p.P1247L	RP11-603J24.9_ENST00000548861.1_Intron|PA2G4_ENST00000303305.6_5'Flank|ERBB3_ENST00000450146.2_Missense_Mutation_p.P604L|ERBB3_ENST00000549832.1_Missense_Mutation_p.P367L|RP11-603J24.17_ENST00000548595.1_RNA|ERBB3_ENST00000415288.2_Missense_Mutation_p.P1188L|PA2G4_ENST00000552766.1_5'Flank|ERBB3_ENST00000553131.1_Missense_Mutation_p.P488L	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1247					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CACCCTGTACCCATCATGCCC	0.547																																					p.P1247L		Atlas-SNP	.											.	ERBB3	350	.	0			c.C3740T						PASS	.						87.0	73.0	78.0					12																	56495550		2203	4300	6503	SO:0001583	missense	2065	exon28			CTGTACCCATCAT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3740C>T	chr12.hg19:g.56495550C>T	ENSP00000267101:p.Pro1247Leu	100.0	0.0	.		99.0	21.0	.	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130261	0.56721	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.80824	-1.21;-1.21;-1.2;-1.42;-1.2	5.82	5.82	0.92795	.	0.301833	0.28853	N	0.013924	T	0.73830	0.3637	N	0.19112	0.55	0.46874	D	0.999236	P;P;B	0.45827	0.867;0.79;0.084	B;B;B	0.44085	0.44;0.255;0.051	T	0.76318	-0.3003	10	0.49607	T	0.09	.	17.5929	0.88003	0.0:1.0:0.0:0.0	.	1188;367;1247	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	L	1247;604;1188;370;488;367	ENSP00000267101:P1247L;ENSP00000399178:P604L;ENSP00000408340:P1188L;ENSP00000449129:P488L;ENSP00000448729:P367L	ENSP00000267101:P1247L	P	+	2	0	ERBB3	54781817	0.990000	0.36364	0.957000	0.39632	0.920000	0.55202	3.899000	0.56288	2.752000	0.94435	0.655000	0.94253	CCC	.	.	.	none		0.547	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
STAB2	55576	hgsc.bcm.edu	37	12	104056744	104056744	+	Nonsense_Mutation	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:104056744C>T	ENST00000388887.2	+	18	2194	c.1990C>T	c.(1990-1992)Cga>Tga	p.R664*		NM_017564.9	NP_060034.9			stabilin 2									p.R664*(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TCTGCCCCATCGATGTGATGA	0.468																																					p.R664X		Atlas-SNP	.											STAB2,NS,carcinoma,0,1	STAB2	370	.	1	Substitution - Nonsense(1)	kidney(1)	c.C1990T						PASS	.						131.0	128.0	129.0					12																	104056744		2203	4300	6503	SO:0001587	stop_gained	55576	exon18			CCCCATCGATGTG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1990C>T	chr12.hg19:g.104056744C>T	ENSP00000373539:p.Arg664*	149.0	1.0	.		153.0	51.0	.	NM_017564		Nonsense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	40	8.530526	0.98850	.	.	ENSG00000136011	ENST00000388887	.	.	.	5.31	4.36	0.52297	.	0.063415	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4226	0.21752	0.3716:0.542:0.0:0.0864	.	.	.	.	X	664	.	ENSP00000373539:R664X	R	+	1	2	STAB2	102580874	0.890000	0.30428	0.998000	0.56505	0.699000	0.40488	1.183000	0.32041	2.478000	0.83669	0.655000	0.94253	CGA	.	.	.	none		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
ZNF770	54989	hgsc.bcm.edu	37	15	35275396	35275396	+	Silent	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:35275396A>G	ENST00000356321.4	-	3	584	c.240T>C	c.(238-240)ccT>ccC	p.P80P		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	80					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		TACATTTAAAAGGCAGACTAT	0.353																																					p.P80P		Atlas-SNP	.											.	ZNF770	64	.	0			c.T240C						PASS	.						85.0	85.0	85.0					15																	35275396		2201	4298	6499	SO:0001819	synonymous_variant	54989	exon3			TTTAAAAGGCAGA	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.240T>C	chr15.hg19:g.35275396A>G		65.0	0.0	.		77.0	21.0	.	NM_014106	Q6ZMZ6|Q9NWV2	Silent	SNP	ENST00000356321.4	hg19	CCDS10042.1																																																																																			.	.	.	none		0.353	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
SH3GL3	6457	hgsc.bcm.edu	37	15	84228033	84228033	+	Missense_Mutation	SNP	A	A	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:84228033A>C	ENST00000427482.2	+	2	380	c.74A>C	c.(73-75)gAa>gCa	p.E25A	SH3GL3_ENST00000324537.5_Missense_Mutation_p.E33A|SH3GL3_ENST00000535412.1_Missense_Mutation_p.E25A|SH3GL3_ENST00000434347.1_Missense_Mutation_p.E33A	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	25	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						AGTGGTGCTGAAGGAACTAAA	0.279											OREG0023396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E25A		Atlas-SNP	.											.	SH3GL3	91	.	0			c.A74C						PASS	.						79.0	79.0	79.0					15																	84228033		2203	4299	6502	SO:0001583	missense	6457	exon2			GTGCTGAAGGAAC	AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.74A>C	chr15.hg19:g.84228033A>C	ENSP00000391372:p.Glu25Ala	307.0	0.0	.	1227	325.0	65.0	.	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	hg19	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	A	18.62	3.662604	0.67700	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.63	3.51	0.40186	BAR (3);	0.053790	0.64402	D	0.000001	T	0.60340	0.2261	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	0.982;0.978;0.997;1.0	P;P;D;D	0.78314	0.739;0.621;0.976;0.991	T	0.59679	-0.7409	10	0.51188	T	0.08	-14.5796	8.1715	0.31258	0.9036:0.0:0.0964:0.0	.	25;25;25;33	Q8IVP1;Q99963-4;Q99963;Q99963-3	.;.;SH3G3_HUMAN;.	A	25;25;33;33	ENSP00000391372:E25A;ENSP00000439239:E25A;ENSP00000320092:E33A;ENSP00000397871:E33A	ENSP00000320092:E33A	E	+	2	0	SH3GL3	82019037	1.000000	0.71417	0.928000	0.36995	0.996000	0.88848	7.870000	0.87175	0.805000	0.34159	0.460000	0.39030	GAA	.	.	.	none		0.279	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027	
AGBL1	123624	hgsc.bcm.edu	37	15	87089231	87089231	+	Splice_Site	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:87089231A>G	ENST00000441037.2	+	19	2642		c.e19-1		AGBL1_ENST00000389298.3_Splice_Site|AGBL1_ENST00000421325.2_Splice_Site	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GGGCTATTGTAGGTTTTCTGT	0.428																																					.		Atlas-SNP	.											.	AGBL1	151	.	0			c.2548-2A>G						PASS	.						133.0	121.0	125.0					15																	87089231		1886	4119	6005	SO:0001630	splice_region_variant	123624	exon19			TATTGTAGGTTTT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2548-1A>G	chr15.hg19:g.87089231A>G		99.0	0.0	.		97.0	21.0	.	NM_152336	A1A4X5|A6NJH6|C9JHL5	Splice_Site	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.092020	0.76756	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.981	0.71311	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGBL1	84890235	1.000000	0.71417	0.938000	0.37757	0.821000	0.46438	8.589000	0.90817	2.320000	0.78422	0.528000	0.53228	.	.	.	.	none		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	Intron
RHBDL1	9028	hgsc.bcm.edu	37	16	727363	727363	+	Silent	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:727363G>A	ENST00000219551.2	+	4	885	c.858G>A	c.(856-858)ctG>ctA	p.L286L	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Silent_p.L221L|STUB1_ENST00000565677.1_5'Flank|LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000219548.4_5'Flank			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	286					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				GCATCAGCCTGCTCTACCTGG	0.711																																					p.L286L		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G858A						PASS	.						17.0	14.0	15.0					16																	727363		2180	4267	6447	SO:0001819	synonymous_variant	9028	exon4			CAGCCTGCTCTAC	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"""rhomboid (veinlet, Drosophila)-like"""	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.858G>A	chr16.hg19:g.727363G>A		54.0	0.0	.		73.0	19.0	.	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Silent	SNP	ENST00000219551.2	hg19	CCDS10418.1																																																																																			.	.	.	none		0.711	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961	
DCTPP1	79077	hgsc.bcm.edu	37	16	30435726	30435726	+	Missense_Mutation	SNP	A	A	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:30435726A>T	ENST00000319285.4	-	3	435	c.341T>A	c.(340-342)cTg>cAg	p.L114Q	ZNF771_ENST00000566625.1_Intron|DCTPP1_ENST00000568434.1_5'UTR|DCTPP1_ENST00000568973.1_5'UTR|DCTPP1_ENST00000565758.1_5'UTR|DCTPP1_ENST00000567983.1_Missense_Mutation_p.L15Q	NM_024096.1	NP_077001.1	Q9H773	DCTP1_HUMAN	dCTP pyrophosphatase 1	114					nucleoside triphosphate catabolic process (GO:0009143)|protein homotetramerization (GO:0051289)	cytosol (GO:0005829)	dCTP diphosphatase activity (GO:0047840)|magnesium ion binding (GO:0000287)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|pyrimidine deoxyribonucleotide binding (GO:0032556)			kidney(1)|large_intestine(3)|upper_aerodigestive_tract(1)	5						TGCTAGCGGCAGATCCACACG	0.612																																					p.L114Q		Atlas-SNP	.											.	DCTPP1	12	.	0			c.T341A						PASS	.						62.0	58.0	59.0					16																	30435726		2197	4300	6497	SO:0001583	missense	79077	exon3			AGCGGCAGATCCA	BC001344	CCDS10680.1	16p11.2	2009-02-11			ENSG00000179958	ENSG00000179958	3.6.1.12		28777	protein-coding gene	gene with protein product	"""XTP3-transactivated protein A"""	615840				15740738	Standard	NM_024096		Approved	MGC5627, RS21C6, CDA03, XTP3TPA	uc002dyf.3	Q9H773	OTTHUMG00000132416	ENST00000319285.4:c.341T>A	chr16.hg19:g.30435726A>T	ENSP00000322524:p.Leu114Gln	73.0	0.0	.		66.0	19.0	.	NM_024096		Missense_Mutation	SNP	ENST00000319285.4	hg19	CCDS10680.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277925	0.80692	.	.	ENSG00000179958	ENST00000319285	.	.	.	5.48	5.48	0.80851	NTP pyrophosphohydrolase MazG, putative catalytic core (1);	0.068721	0.56097	D	0.000021	D	0.87649	0.6230	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91634	0.5321	9	0.87932	D	0	-6.6874	14.5404	0.67990	1.0:0.0:0.0:0.0	.	114	Q9H773	DCTP1_HUMAN	Q	114	.	ENSP00000322524:L114Q	L	-	2	0	DCTPP1	30343227	1.000000	0.71417	0.258000	0.24420	0.853000	0.48598	7.565000	0.82337	2.086000	0.62901	0.477000	0.44152	CTG	.	.	.	none		0.612	DCTPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255553.2	NM_024096	
NFATC3	4775	hgsc.bcm.edu	37	16	68248266	68248266	+	Intron	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:68248266A>G	ENST00000346183.3	+	10	3130				NFATC3_ENST00000575270.1_Intron|NFATC3_ENST00000329524.4_Silent_p.S1047S|NFATC3_ENST00000349223.5_Intron|RP11-96D1.5_ENST00000569088.1_RNA|NFATC3_ENST00000535127.2_3'UTR	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3						cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		ACCAGCCATCAGGTTCAGCAG	0.423																																					p.S1047S		Atlas-SNP	.											.	NFATC3	190	.	0			c.A3141G						PASS	.						208.0	169.0	182.0					16																	68248266		2198	4300	6498	SO:0001627	intron_variant	4775	exon10			GCCATCAGGTTCA	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.3107-11987A>G	chr16.hg19:g.68248266A>G		117.0	0.0	.		89.0	22.0	.	NM_004555	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	hg19	CCDS10860.1																																																																																			.	.	.	none		0.423	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
SLC25A11	8402	hgsc.bcm.edu	37	17	4842400	4842400	+	Missense_Mutation	SNP	A	A	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:4842400A>T	ENST00000225665.7	-	2	543	c.203T>A	c.(202-204)cTc>cAc	p.L68H	RNF167_ENST00000575111.1_5'Flank|RNF167_ENST00000572430.1_5'Flank|RNF167_ENST00000576229.1_5'Flank|RNF167_ENST00000262482.6_5'Flank|SLC25A11_ENST00000544061.2_Intron|RNF167_ENST00000571816.1_5'Flank	NM_001165417.1|NM_003562.4	NP_001158889.1|NP_003553.2	Q02978	M2OM_HUMAN	solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11	68					alpha-ketoglutarate transport (GO:0015742)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxoglutarate:malate antiporter activity (GO:0015367)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	10						GATACTGGTGAGGGCATGGAA	0.567																																					p.L68H	Esophageal Squamous(144;1178 2388 18010 48797)	Atlas-SNP	.											.	SLC25A11	22	.	0			c.T203A						PASS	.						135.0	123.0	127.0					17																	4842400		2203	4300	6503	SO:0001583	missense	8402	exon2			CTGGTGAGGGCAT	X66114	CCDS11059.1, CCDS54069.1	17p13.3	2013-05-22			ENSG00000108528	ENSG00000108528		"""Solute carriers"""	10981	protein-coding gene	gene with protein product		604165		SLC20A4		10072597, 1457818	Standard	NM_003562		Approved	OGC	uc002fzo.2	Q02978	OTTHUMG00000099395	ENST00000225665.7:c.203T>A	chr17.hg19:g.4842400A>T	ENSP00000225665:p.Leu68His	111.0	0.0	.		92.0	17.0	.	NM_003562	F5GY65|O75537|Q969P7	Missense_Mutation	SNP	ENST00000225665.7	hg19	CCDS11059.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.074333	0.76415	.	.	ENSG00000108528	ENST00000225665	D	0.81499	-1.5	5.97	4.9	0.64082	Mitochondrial carrier domain (2);	0.230475	0.36815	N	0.002398	D	0.88388	0.6423	M	0.87381	2.88	0.80722	D	1	D;D	0.59767	0.986;0.986	P;P	0.61275	0.886;0.886	D	0.89563	0.3808	10	0.72032	D	0.01	-6.7086	9.5961	0.39576	0.9188:0.0:0.0812:0.0	.	68;68	Q6IBH0;Q02978	.;M2OM_HUMAN	H	68	ENSP00000225665:L68H	ENSP00000225665:L68H	L	-	2	0	SLC25A11	4783145	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.148000	0.71788	2.288000	0.76882	0.533000	0.62120	CTC	.	.	.	none		0.567	SLC25A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216852.4	NM_003562	
TMUB2	79089	hgsc.bcm.edu	37	17	42267972	42267972	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:42267972T>A	ENST00000587989.1	+	4	859	c.706T>A	c.(706-708)Tgt>Agt	p.C236S	TMUB2_ENST00000538716.2_Missense_Mutation_p.C236S|TMUB2_ENST00000319511.6_Missense_Mutation_p.C216S|TMUB2_ENST00000589184.1_Missense_Mutation_p.L50Q|TMUB2_ENST00000592825.1_3'UTR|TMUB2_ENST00000590235.1_3'UTR|TMUB2_ENST00000589785.1_Missense_Mutation_p.C216S|TMUB2_ENST00000357984.3_Missense_Mutation_p.C216S|TMUB2_ENST00000446571.3_Missense_Mutation_p.C179S|TMUB2_ENST00000587172.1_3'UTR			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	236	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TACCGACAACTGTGTGATTCA	0.592																																					p.C236S		Atlas-SNP	.											.	TMUB2	29	.	0			c.T706A						PASS	.						82.0	74.0	77.0					17																	42267972		2203	4300	6503	SO:0001583	missense	79089	exon4			GACAACTGTGTGA		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.706T>A	chr17.hg19:g.42267972T>A	ENSP00000466971:p.Cys236Ser	89.0	0.0	.		100.0	25.0	.	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Missense_Mutation	SNP	ENST00000587989.1	hg19	CCDS54134.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.305926	0.40795	.	.	ENSG00000168591	ENST00000446571;ENST00000357984;ENST00000538716;ENST00000319511	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.77	4.67	0.58626	Ubiquitin supergroup (1);Ubiquitin (2);	0.131169	0.64402	D	0.000001	T	0.18800	0.0451	N	0.01529	-0.815	0.44635	D	0.997618	B;B;B	0.34329	0.449;0.006;0.449	B;B;B	0.38921	0.191;0.008;0.285	T	0.11567	-1.0582	10	0.12430	T	0.62	-9.458	12.0139	0.53303	0.0:0.0:0.1449:0.8551	.	179;216;236	E7ESS3;Q71RG4-2;Q71RG4	.;.;TMUB2_HUMAN	S	179;216;236;216	ENSP00000413127:C179S;ENSP00000350672:C216S;ENSP00000444565:C236S;ENSP00000313214:C216S	ENSP00000313214:C216S	C	+	1	0	TMUB2	39623498	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.592000	0.46171	0.989000	0.38761	0.459000	0.35465	TGT	.	.	.	none		0.592	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441	
TNRC6C	57690	hgsc.bcm.edu	37	17	76089791	76089791	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:76089791C>G	ENST00000588061.1	+	18	4980	c.4253C>G	c.(4252-4254)cCt>cGt	p.P1418R	TNRC6C_ENST00000335749.4_Missense_Mutation_p.P1415R|TNRC6C_ENST00000541771.1_Missense_Mutation_p.P1418R|TNRC6C_ENST00000544502.1_Missense_Mutation_p.P1415R|TNRC6C_ENST00000301624.4_Missense_Mutation_p.P1418R|TNRC6C_ENST00000588847.1_Missense_Mutation_p.P1415R			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1418	Silencing domain; interaction with CNOT1 and PAN3.|Sufficient for translational repression when tethered to a target mRNA.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CCCACTGGGCCTACCATCAAC	0.542																																					p.P1418R		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C4253G						PASS	.						91.0	96.0	95.0					17																	76089791		2166	4277	6443	SO:0001583	missense	57690	exon17			CTGGGCCTACCAT	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4253C>G	chr17.hg19:g.76089791C>G	ENSP00000468647:p.Pro1418Arg	89.0	0.0	.		103.0	31.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135974	0.77662	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.18016	2.24;2.26;2.26;2.24	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.41766	0.1173	M	0.76574	2.34	0.80722	D	1	D;P	0.57257	0.979;0.695	P;B	0.58454	0.839;0.232	T	0.04915	-1.0918	10	0.51188	T	0.08	-15.04	20.6647	0.99678	0.0:1.0:0.0:0.0	.	1415;1418	G3XAB8;Q9HCJ0	.;TNR6C_HUMAN	R	1418;1415;1415;1418;1418;1415	ENSP00000336783:P1415R;ENSP00000301624:P1418R;ENSP00000440310:P1418R;ENSP00000442421:P1415R	ENSP00000301624:P1418R	P	+	2	0	TNRC6C	73601386	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	5.773000	0.68898	2.890000	0.99128	0.655000	0.94253	CCT	.	.	.	none		0.542	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
SETBP1	26040	hgsc.bcm.edu	37	18	42529882	42529882	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr18:42529882T>A	ENST00000282030.5	+	4	873	c.577T>A	c.(577-579)Tat>Aat	p.Y193N		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	193						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AACTCTCCATTATGACACGGG	0.517									Schinzel-Giedion syndrome																												p.Y193N		Atlas-SNP	.											.	SETBP1	577	.	0			c.T577A						PASS	.						66.0	60.0	62.0					18																	42529882		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	CTCCATTATGACA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.577T>A	chr18.hg19:g.42529882T>A	ENSP00000282030:p.Tyr193Asn	77.0	0.0	.		75.0	19.0	.	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686317	0.68157	.	.	ENSG00000152217	ENST00000282030	T	0.70749	-0.51	5.79	5.79	0.91817	.	0.080224	0.53938	D	0.000049	T	0.73329	0.3573	L	0.36672	1.1	0.39128	D	0.961792	D	0.53745	0.962	P	0.54924	0.764	T	0.75777	-0.3198	10	0.46703	T	0.11	.	16.1341	0.81471	0.0:0.0:0.0:1.0	.	193	Q9Y6X0	SETBP_HUMAN	N	193	ENSP00000282030:Y193N	ENSP00000282030:Y193N	Y	+	1	0	SETBP1	40783880	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.244000	0.58728	2.220000	0.72140	0.528000	0.53228	TAT	.	.	.	none		0.517	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
TMX3	54495	hgsc.bcm.edu	37	18	66365251	66365251	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr18:66365251A>G	ENST00000299608.2	-	7	726	c.410T>C	c.(409-411)cTt>cCt	p.L137P	TMX3_ENST00000562706.1_Missense_Mutation_p.L137P|TMX3_ENST00000443099.2_Missense_Mutation_p.L110P	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	137					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TTGACTTGGAAGTGGCCGAAT	0.308																																					p.L137P		Atlas-SNP	.											.	TMX3	44	.	0			c.T410C						PASS	.						86.0	78.0	81.0					18																	66365251		2203	4300	6503	SO:0001583	missense	54495	exon7			CTTGGAAGTGGCC	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.410T>C	chr18.hg19:g.66365251A>G	ENSP00000299608:p.Leu137Pro	55.0	0.0	.		57.0	14.0	.	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083448	0.76642	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T	0.14144	2.53;2.56	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.35451	0.0932	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.08229	-1.0732	10	0.87932	D	0	.	13.5227	0.61576	1.0:0.0:0.0:0.0	.	110;137;137	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	P	137;137;110	ENSP00000299608:L137P;ENSP00000402605:L110P	ENSP00000299608:L137P	L	-	2	0	TMX3	64516231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.992000	0.88273	2.141000	0.66446	0.533000	0.62120	CTT	.	.	.	none		0.308	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
MFSD12	126321	hgsc.bcm.edu	37	19	3544832	3544832	+	Silent	SNP	C	C	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:3544832C>T	ENST00000355415.2	-	9	1564	c.1395G>A	c.(1393-1395)ctG>ctA	p.L465L	MFSD12_ENST00000398558.4_Silent_p.L465L|MFSD12_ENST00000389395.3_Silent_p.L465L|AC005786.7_ENST00000589360.1_RNA	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	465					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						TCGGCCACAGCAGGAGGCTAC	0.662											OREG0025153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L465L		Atlas-SNP	.											.	MFSD12	22	.	0			c.G1395A						PASS	.						32.0	43.0	40.0					19																	3544832		2179	4266	6445	SO:0001819	synonymous_variant	126321	exon9			CCACAGCAGGAGG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 28"""	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1395G>A	chr19.hg19:g.3544832C>T		66.0	0.0	.	612	34.0	19.0	.	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Silent	SNP	ENST00000355415.2	hg19	CCDS42465.1																																																																																			.	.	.	none		0.662	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	
BRD4	23476	hgsc.bcm.edu	37	19	15350822	15350822	+	Missense_Mutation	SNP	C	C	T	rs200902225		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:15350822C>T	ENST00000263377.2	-	15	3402	c.3181G>A	c.(3181-3183)Gaa>Aaa	p.E1061K		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1061	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GAGGGGGCTTCGCGGAGGTGA	0.557			T	C15orf55	lethal midline carcinoma of young people																																p.E1061K		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.G3181A						PASS	.						34.0	37.0	36.0					19																	15350822		2203	4300	6503	SO:0001583	missense	23476	exon15			GGGCTTCGCGGAG	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3181G>A	chr19.hg19:g.15350822C>T	ENSP00000263377:p.Glu1061Lys	63.0	0.0	.		45.0	17.0	.	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938039	0.52972	.	.	ENSG00000141867	ENST00000263377	T	0.34275	1.37	4.41	4.41	0.53225	.	0.000000	0.50627	D	0.000109	T	0.22820	0.0551	L	0.29908	0.895	0.80722	D	1	P	0.49253	0.921	B	0.31390	0.129	T	0.08391	-1.0724	10	0.38643	T	0.18	-8.7097	15.7874	0.78319	0.0:1.0:0.0:0.0	.	1061	O60885	BRD4_HUMAN	K	1061	ENSP00000263377:E1061K	ENSP00000263377:E1061K	E	-	1	0	BRD4	15211822	1.000000	0.71417	0.997000	0.53966	0.936000	0.57629	7.175000	0.77632	1.979000	0.57680	0.561000	0.74099	GAA	.	.	.	weak		0.557	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
AKT2	208	hgsc.bcm.edu	37	19	40743897	40743897	+	Missense_Mutation	SNP	G	G	T	rs150206349		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:40743897G>T	ENST00000392038.2	-	9	1108	c.810C>A	c.(808-810)gaC>gaA	p.D270E	AKT2_ENST00000311278.6_Missense_Mutation_p.D270E|AKT2_ENST00000579047.1_Missense_Mutation_p.D208E|AKT2_ENST00000424901.1_Missense_Mutation_p.D270E	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			GGTATACCACGTCCCGCGAGT	0.592			A		"""ovarian, pancreatic """																																p.D270E		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.C810A						PASS	.						121.0	84.0	96.0					19																	40743897		2203	4300	6503	SO:0001583	missense	208	exon9			TACCACGTCCCGC	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.810C>A	chr19.hg19:g.40743897G>T	ENSP00000375892:p.Asp270Glu	75.0	0.0	.		48.0	13.0	.	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.545765	0.45280	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.24908	1.83;1.83;1.83	5.04	-1.24	0.09435	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.158114	0.56097	D	0.000023	T	0.17238	0.0414	L	0.37507	1.11	0.46113	D	0.99887	B;B;B	0.13145	0.001;0.007;0.0	B;B;B	0.13407	0.002;0.009;0.003	T	0.06826	-1.0805	10	0.44086	T	0.13	.	9.7769	0.40626	0.7366:0.0:0.2634:0.0	.	208;270;270	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	E	270;171;270;270;90	ENSP00000375892:D270E;ENSP00000399532:D270E;ENSP00000309428:D270E	ENSP00000309428:D270E	D	-	3	2	AKT2	45435737	0.149000	0.22717	0.992000	0.48379	0.920000	0.55202	-0.327000	0.07955	-0.005000	0.14395	-0.355000	0.07637	GAC	.	G|1.000;A|0.000	.	alt		0.592	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626	
PRR12	57479	hgsc.bcm.edu	37	19	50104787	50104787	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:50104787C>G	ENST00000418929.2	+	6	4397	c.4385C>G	c.(4384-4386)cCt>cGt	p.P1462R		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		cccactccacctcctgccccg	0.682																																					p.P1462R		Atlas-SNP	.											.	PRR12	157	.	0			c.C4385G						PASS	.						3.0	6.0	5.0					19																	50104787		1546	3424	4970	SO:0001583	missense	57479	exon6			CTCCACCTCCTGC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4385C>G	chr19.hg19:g.50104787C>G	ENSP00000394510:p.Pro1462Arg	126.0	0.0	.		76.0	17.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	6.153	0.396514	0.11638	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	2.41	1.34	0.21922	.	.	.	.	.	T	0.36193	0.0958	.	.	.	0.36279	D	0.855686	P	0.48016	0.904	B	0.42625	0.393	T	0.36915	-0.9728	7	0.38643	T	0.18	-0.189	6.3508	0.21375	0.2937:0.7063:0.0:0.0	.	1462	Q9ULL5-3	.	R	1462;642;642	.	ENSP00000246798:P642R	P	+	2	0	PRR12	54796599	0.002000	0.14202	0.718000	0.30602	0.862000	0.49288	1.602000	0.36783	0.546000	0.28920	0.313000	0.20887	CCT	.	.	.	none		0.682	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
TNNT1	7138	hgsc.bcm.edu	37	19	55656921	55656921	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:55656921G>T	ENST00000588981.1	-	6	323	c.119C>A	c.(118-120)cCc>cAc	p.P40H	TNNT1_ENST00000587465.2_5'UTR|TNNT1_ENST00000592920.1_5'UTR|TNNT1_ENST00000587758.1_Missense_Mutation_p.P29H|TNNT1_ENST00000536926.1_Intron|TNNT1_ENST00000291901.8_Missense_Mutation_p.P40H|TNNT1_ENST00000356783.5_Missense_Mutation_p.P29H|TNNT1_ENST00000585321.2_5'UTR|TNNT1_ENST00000588426.1_Intron	NM_003283.4	NP_003274.3	P13805	TNNT1_HUMAN	troponin T type 1 (skeletal, slow)	40					muscle filament sliding (GO:0030049)|negative regulation of muscle contraction (GO:0045932)|skeletal muscle contraction (GO:0003009)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	cytosol (GO:0005829)|troponin complex (GO:0005861)	tropomyosin binding (GO:0005523)			endometrium(2)|kidney(3)|lung(4)|ovary(1)	10			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		CCTTGGTTTGGGGCGTTCCTC	0.542																																					p.P40H		Atlas-SNP	.											TNNT1,NS,carcinoma,0,2	TNNT1	28	.	0			c.C119A						PASS	.						166.0	173.0	171.0					19																	55656921		2203	4300	6503	SO:0001583	missense	7138	exon6			GGTTTGGGGCGTT		CCDS12917.1, CCDS46185.1, CCDS59421.1	19q13.4	2014-09-17	2005-09-12			ENSG00000105048			11948	protein-coding gene	gene with protein product	"""slow skeletal muscle troponin T"", ""troponin T1, skeletal, slow"", ""nemaline myopathy type 5"""	191041	"""troponin T1, skeletal, slow"""			1505979	Standard	XM_006723343		Approved	ANM, STNT, TNT, TNTS, FLJ98147, MGC104241, NEM5	uc002qjb.4	P13805		ENST00000588981.1:c.119C>A	chr19.hg19:g.55656921G>T	ENSP00000467176:p.Pro40His	106.0	0.0	.		70.0	3.0	.	NM_001126132	O95472|Q16061|Q5U0E1	Missense_Mutation	SNP	ENST00000588981.1	hg19	CCDS12917.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.722866	0.48728	.	.	ENSG00000105048	ENST00000291901;ENST00000356783;ENST00000429737	D;D	0.99880	-7.45;-7.45	3.72	3.72	0.42706	.	0.072594	0.56097	D	0.000035	D	0.99822	0.9921	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.83275	0.99;0.996;0.996;0.99	D	0.96025	0.9012	10	0.72032	D	0.01	-17.4076	13.8205	0.63318	0.0:0.0:1.0:0.0	.	40;29;40;40	Q56R94;P13805-2;P13805-3;P13805	.;.;.;TNNT1_HUMAN	H	40;29;55	ENSP00000291901:P40H;ENSP00000349233:P29H	ENSP00000291901:P40H	P	-	2	0	TNNT1	60348733	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.019000	0.70818	2.006000	0.58801	0.590000	0.80494	CCC	.	.	.	none		0.542	TNNT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451825.2	NM_003283	
RPL28	6158	hgsc.bcm.edu	37	19	55897936	55897936	+	Splice_Site	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:55897936A>G	ENST00000344063.2	+	3	710		c.e3-1		RPL28_ENST00000558815.1_Splice_Site|RPL28_ENST00000559463.1_Splice_Site|RPL28_ENST00000560055.1_Splice_Site|RPL28_ENST00000558752.1_Splice_Site|RPL28_ENST00000558131.1_Splice_Site|RPL28_ENST00000458349.2_Splice_Site|TMEM238_ENST00000444469.3_5'Flank|RPL28_ENST00000428193.2_Splice_Site|RPL28_ENST00000431533.2_Splice_Site|RPL28_ENST00000560583.1_Splice_Site			P46779	RL28_HUMAN	ribosomal protein L28						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCTCCTTCCCAGGAGCCCAAT	0.612																																					.		Atlas-SNP	.											.	RPL28	31	.	0			c.82-2A>G						PASS	.						63.0	65.0	64.0					19																	55897936		2203	4300	6503	SO:0001630	splice_region_variant	6158	exon3			CTTCCCAGGAGCC	U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107		"""L ribosomal proteins"""	10330	protein-coding gene	gene with protein product	"""60S ribosomal protein L28"""	603638				7772601, 9582194	Standard	NM_001136134		Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000344063.2:c.82-1A>G	chr19.hg19:g.55897936A>G		137.0	0.0	.		85.0	23.0	.	NM_001136137	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	Splice_Site	SNP	ENST00000344063.2	hg19	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535153	0.64972	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000428193;ENST00000431533;ENST00000458349	.	.	.	3.37	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.4015	0.44233	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPL28	60589748	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.754000	0.68743	1.791000	0.52520	0.533000	0.62120	.	.	.	.	none		0.612	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	NM_000991	Intron
OGFR	11054	hgsc.bcm.edu	37	20	61443936	61443936	+	Silent	SNP	C	C	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr20:61443936C>A	ENST00000290291.6	+	7	994	c.969C>A	c.(967-969)gcC>gcA	p.A323A	OGFR_ENST00000370461.1_Silent_p.A271A	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	323					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)					ACCACGAGGCCAGCACCCAGG	0.701																																					p.A323A		Atlas-SNP	.											.	OGFR	63	.	0			c.C969A						PASS	.						5.0	6.0	6.0					20																	61443936		2122	4164	6286	SO:0001819	synonymous_variant	11054	exon7			CGAGGCCAGCACC	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.969C>A	chr20.hg19:g.61443936C>A		215.0	0.0	.		177.0	35.0	.	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.	.	none		0.701	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
KRTAP10-8	386681	hgsc.bcm.edu	37	21	46032797	46032797	+	Nonstop_Mutation	SNP	A	A	T			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr21:46032797A>T	ENST00000334662.2	+	1	802	c.780A>T	c.(778-780)tgA>tgT	p.*260C	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	0						keratin filament (GO:0045095)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						tggcctgcTGAGGCCTCTGCT	0.711																																					p.X260C		Atlas-SNP	.											.	KRTAP10-8	34	.	0			c.A780T						PASS	.						29.0	33.0	32.0					21																	46032797		2195	4284	6479	SO:0001578	stop_lost	386681	exon1			CTGCTGAGGCCTC	AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"""Keratin associated proteins"""	20525	protein-coding gene	gene with protein product			"""keratin associated protein 18-8"""	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.780A>T	chr21.hg19:g.46032797A>T	ENSP00000335565:p.*260Cysext*11	48.0	0.0	.		24.0	11.0	.	NM_198695	A0JNW4	Missense_Mutation	SNP	ENST00000334662.2	hg19	CCDS13713.1	.	.	.	.	.	.	.	.	.	.	a	0.016	-1.512184	0.00984	.	.	ENSG00000187766	ENST00000334662	.	.	.	3.5	-1.98	0.07480	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4751	0.11731	0.1872:0.5795:0.0:0.2333	.	.	.	.	C	260	.	.	X	+	3	0	KRTAP10-8	44857225	0.454000	0.25728	0.018000	0.16275	0.002000	0.02628	-0.652000	0.05366	-0.465000	0.06953	-0.644000	0.03951	TGA	.	.	.	none		0.711	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695	
NLGN4X	57502	hgsc.bcm.edu	37	X	5811459	5811459	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrX:5811459T>G	ENST00000381095.3	-	6	2477	c.1850A>C	c.(1849-1851)gAc>gCc	p.D617A	NLGN4X_ENST00000275857.6_Missense_Mutation_p.D617A|NLGN4X_ENST00000538097.1_Missense_Mutation_p.D617A|NLGN4X_ENST00000381093.2_Missense_Mutation_p.D637A|NLGN4X_ENST00000381092.1_Missense_Mutation_p.D617A	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	617					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TGATGTCATGTCTGGTGGAGG	0.493																																					p.D617A		Atlas-SNP	.											.	NLGN4X	191	.	0			c.A1850C						PASS	.						125.0	106.0	112.0					X																	5811459		2203	4297	6500	SO:0001583	missense	57502	exon6			GTCATGTCTGGTG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1850A>C	chrX.hg19:g.5811459T>G	ENSP00000370485:p.Asp617Ala	251.0	1.0	.		216.0	95.0	.	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	T	5.476	0.272923	0.10349	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	4.0	4.0	0.46444	.	0.444374	0.16752	N	0.200994	T	0.54415	0.1857	L	0.46157	1.445	0.58432	D	0.999996	B;B;B	0.16396	0.017;0.017;0.013	B;B;B	0.15484	0.009;0.013;0.012	T	0.51911	-0.8645	10	0.42905	T	0.14	.	11.5189	0.50539	0.0:0.0:0.0:1.0	.	674;617;637	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	A	617;637;617;617;617	ENSP00000370485:D617A;ENSP00000370483:D637A;ENSP00000275857:D617A;ENSP00000370482:D617A;ENSP00000439203:D617A	ENSP00000275857:D617A	D	-	2	0	NLGN4X	5821459	1.000000	0.71417	0.757000	0.31301	0.019000	0.09904	6.912000	0.75753	1.290000	0.44636	0.417000	0.27973	GAC	.	.	.	none		0.493	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49143255	49143255	+	Silent	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrX:49143255G>A	ENST00000055335.6	+	4	2119	c.2103G>A	c.(2101-2103)ggG>ggA	p.G701G	PPP1R3F_ENST00000438316.1_Silent_p.G372G|PPP1R3F_ENST00000466508.1_Silent_p.G355G|PPP1R3F_ENST00000376188.1_Silent_p.G355G|PPP1R3F_ENST00000495799.1_Silent_p.G355G	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	701					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					TTCTGCAGGGGCAAAATCCCA	0.597																																					p.G701G		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G2103A						PASS	.						48.0	30.0	36.0					X																	49143255		2202	4300	6502	SO:0001819	synonymous_variant	89801	exon4			GCAGGGGCAAAAT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.2103G>A	chrX.hg19:g.49143255G>A		102.0	0.0	.		98.0	52.0	.	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.	.	none		0.597	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
MT-ND1	4535	hgsc.bcm.edu	37	M	4136	4136	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrM:4136A>G	ENST00000361390.2	+	1	830	c.830A>G	c.(829-831)tAc>tGc	p.Y277C	MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-ND2_ENST00000361453.3_5'Flank			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	277			Y -> C. {ECO:0000269|PubMed:2018041}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TCGAACAGCATACCCCCGATT	0.433																																					p.Y277C		Atlas-SNP	.											.	.	.	.	0			c.A830G						PASS	.																																			SO:0001583	missense	10625	exon1			CAGCATACCCCCG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.830A>G	chrM.hg19:g.4136A>G	ENSP00000354687:p.Tyr277Cys	25.0	0.0	.		83.0	5.0	.	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	hg19																																																																																				.	.	.	none		0.433	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
MT-ATP6	4508	hgsc.bcm.edu	37	M	8760	8760	+	Silent	SNP	T	T	C			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrM:8760T>C	ENST00000361899.2	+	1	234	c.234T>C	c.(232-234)ttT>ttC	p.F78F	MT-ND3_ENST00000361227.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TY_ENST00000387409.1_RNA			P00846	ATP6_HUMAN	mitochondrially encoded ATP synthase 6	78					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						TTAATCATTTTTATTGCCACA	0.423																																					p.F78F		Atlas-SNP	.											.	.	.	.	0			c.T234C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CATTTTTATTGCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198899	ENSG00000198899		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7414	protein-coding gene	gene with protein product		516060	"""ATP synthase 6"", ""spicular retinitis pigmentosa with dementia, seizures, ataxia, proximal muscle weakness and sensory deficit"""	MTATP6, RP		7219534	Standard			Approved	ATP6, ATPase-6, Su6m		P00846		ENST00000361899.2:c.234T>C	chrM.hg19:g.8760T>C		30.0	0.0	.		92.0	5.0	.	ENST00000361899	Q34772|Q5S8W5|Q5S9E7|Q5S9I6|Q5SA31|Q6RPB7|Q6VHC0|Q6VHE0|Q6WQF4|Q7YCC1|Q7YCF8|Q7YCG1|Q85KU8|Q85KX1|Q85L05|Q8HNQ4|Q8HNQ8|Q8WCX6|Q9B2U5|Q9B2Z2	Silent	SNP	ENST00000361899.2	hg19																																																																																				.	.	.	none		0.423	MT-ATP6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024031	
MT-ND4	4538	hgsc.bcm.edu	37	M	10993	10993	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrM:10993G>A	ENST00000361381.2	+	1	234	c.234G>A	c.(232-234)atG>atA	p.M78I	MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	78					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CTCACAATCATGGCAAGCCAA	0.438																																					p.M78M		Atlas-SNP	.											.	.	.	.	0			c.G234A						PASS	.																																			SO:0001583	missense	0	exon1			AATCATGGCAAGC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.234G>A	chrM.hg19:g.10993G>A	ENSP00000354961:p.Met78Ile	29.0	0.0	.		105.0	14.0	.	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	hg19																																																																																				.	.	.	none		0.438	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SLC46A1	113235	hgsc.bcm.edu	37	17	26729265	26729266	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:26729265_26729266delTC	ENST00000440501.1	-	3	1250_1251	c.1155_1156delGA	c.(1153-1158)gagacafs	p.ET385fs	SLC46A1_ENST00000321666.5_Intron|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	385					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CCCTGCTCTGTCTCTCTCACCA	0.54																																					p.386_386del		Atlas-Indel,Pindel	.											.	SLC46A1	17	.	0			c.1156_1157del						PASS	.																																			SO:0001589	frameshift_variant	113235	exon3			.	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.1155_1156delGA	chr17.hg19:g.26729271_26729272delTC	ENSP00000395653:p.Glu385fs	102.0	0.0	0		87.0	15.0	0.172414	NM_080669	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Frame_Shift_Del	DEL	ENST00000440501.1	hg19																																																																																				.	.	.	none		0.540	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
AGK	55750	hgsc.bcm.edu	37	7	141352709	141352709	+	Frame_Shift_Del	DEL	A	A	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr7:141352709delA	ENST00000355413.4	+	16	1514	c.1254delA	c.(1252-1254)acafs	p.T418fs	RP5-894A10.2_ENST00000467537.1_RNA|AGK_ENST00000473247.1_Frame_Shift_Del_p.T390fs	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	418					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					AGATGCTCACAAGCCCCACCC	0.542																																					p.T418fs		Atlas-Indel,Pindel	.											AGK,NS,carcinoma,0,1	AGK	43	.	0			c.1253delC						PASS	.						82.0	79.0	80.0					7																	141352709		2203	4300	6503	SO:0001589	frameshift_variant	55750	exon16			.	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"""multiple substrate lipid kinase"""	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.1254delA	chr7.hg19:g.141352709delA	ENSP00000347581:p.Thr418fs	74.0	0.0	0		67.0	14.0	0.208955	NM_018238	Q75KN1|Q96GC3|Q9NP48	Frame_Shift_Del	DEL	ENST00000355413.4	hg19	CCDS5865.1																																																																																			.	.	.	none		0.542	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238	
FAM171A2	284069	hgsc.bcm.edu	37	17	42437453	42437453	+	Frame_Shift_Del	DEL	G	G	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:42437453delG	ENST00000293443.7	-	2	326	c.166delC	c.(166-168)ctgfs	p.L56fs		NM_198475.2	NP_940877.2	A8MVW0	F1712_HUMAN	family with sequence similarity 171, member A2	56						integral component of membrane (GO:0016021)											GCCCGGGCCAGGGGCACCAGC	0.617																																					p.L56fs		Atlas-Indel,Pindel	.											.	FAM171A2	13	.	0			c.167delT						PASS	.						23.0	32.0	29.0					17																	42437453		692	1591	2283	SO:0001589	frameshift_variant	284069	exon2			.		CCDS45701.1	17q21.31	2008-06-16			ENSG00000161682	ENSG00000161682			30480	protein-coding gene	gene with protein product						12477932	Standard	NM_198475		Approved	MGC34829	uc002igs.2	A8MVW0	OTTHUMG00000132421	ENST00000293443.7:c.166delC	chr17.hg19:g.42437453delG	ENSP00000293443:p.Leu56fs	161.0	0.0	0		122.0	33.0	0.270492	NM_198475	A8MQB4	Frame_Shift_Del	DEL	ENST00000293443.7	hg19	CCDS45701.1																																																																																			.	.	.	none		0.617	FAM171A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255559.2	NM_198475	
CAMK2N2	94032	hgsc.bcm.edu	37	3	183979036	183979036	+	Frame_Shift_Del	DEL	C	C	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr3:183979036delC	ENST00000296238.3	-	1	215	c.38delG	c.(37-39)ggcfs	p.G13fs	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000402825.3_Intron	NM_033259.2	NP_150284.1	Q96S95	CK2N2_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 2	13						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein kinase inhibitor activity (GO:0008427)					all_cancers(143;1.09e-10)|Ovarian(172;0.0339)		Epithelial(37;2.51e-33)|OV - Ovarian serous cystadenocarcinoma(80;5.69e-22)			GCCGAAGCGGCCCATCTTGTC	0.736																																					p.G13fs		Atlas-Indel,Pindel	.											.	CAMK2N2	2	.	0			c.39delC						PASS	.						22.0	24.0	23.0					3																	183979036		2202	4300	6502	SO:0001589	frameshift_variant	94032	exon1			.	AY037149	CCDS3257.1	3q27.1	2006-03-27			ENSG00000163888	ENSG00000163888			24197	protein-coding gene	gene with protein product		608721				11444830, 9724800	Standard	NM_033259		Approved	CaM-KIIN	uc003fnj.1	Q96S95	OTTHUMG00000156821	ENST00000296238.3:c.38delG	chr3.hg19:g.183979036delC	ENSP00000296238:p.Gly13fs	115.0	0.0	0		105.0	40.0	0.380952	NM_033259		Frame_Shift_Del	DEL	ENST00000296238.3	hg19	CCDS3257.1																																																																																			.	.	.	none		0.736	CAMK2N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346010.1	NM_033259	
TRIM13	10206	hgsc.bcm.edu	37	13	50589218	50589250	+	3'UTR	DEL	AAAAAAAAAAAAAATATATATATATATATATAT	AAAAAAAAAAAAAATATATATATATATATATAT	-	rs2472598|rs59009716|rs12875615|rs9535412|rs60457674|rs71082132		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	AAAAAAAAAAAAAATATATATATATATATATAT	AAAAAAAAAAAAAATATATATATATATATATAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr13:50589218_50589250delAAAAAAAAAAAAAATATATATATATATATATAT	ENST00000378182.3	+	0	3880_3912				KCNRG_ENST00000360473.4_5'Flank|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000478111.1_Intron	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		taataaaaaaaaaaaaaaaaaaaatatatatatatatatatatatatatatat	0.258																																					.		Atlas-INDEL	.											.	TRIM13	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*1950AAAAAAAAAAAAAATATATATATATATATATAT>-	chr13.hg19:g.50589218_50589250delAAAAAAAAAAAAAATATATATATATATATATAT		20.0	0.0	0		22.0	10.0	0.454545	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	DEL	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.	.	none		0.258	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
B4GALT2	8704	hgsc.bcm.edu	37	1	44450687	44450687	+	Frame_Shift_Del	DEL	C	C	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:44450687delC	ENST00000356836.6	+	4	1490	c.700delC	c.(700-702)cccfs	p.P234fs	B4GALT2_ENST00000481924.1_3'UTR|B4GALT2_ENST00000372324.1_Frame_Shift_Del_p.P234fs|B4GALT2_ENST00000309519.7_Frame_Shift_Del_p.P263fs|B4GALT2_ENST00000434555.2_Frame_Shift_Del_p.P168fs	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	234					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	CGGCGACCAACCCCGCCACTT	0.617																																					p.Q262fs		Atlas-INDEL	.											B4GALT2_ENST00000309519,NS,carcinoma,0,2	B4GALT2	35	.	0			c.786delA						PASS	.						55.0	53.0	54.0					1																	44450687		2203	4300	6503	SO:0001589	frameshift_variant	8704	exon4			.	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"""Beta 4-glycosyltransferases"""	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.700delC	chr1.hg19:g.44450687delC	ENSP00000349293:p.Pro234fs	65.0	0.0	0		46.0	11.0	0.23913	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Frame_Shift_Del	DEL	ENST00000356836.6	hg19	CCDS506.1																																																																																			.	.	.	none		0.617	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780	
SPTBN5	51332	hgsc.bcm.edu	37	15	42148681	42148682	+	Frame_Shift_Ins	INS	-	-	G			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:42148681_42148682insG	ENST00000320955.6	-	53	9150_9151	c.8923_8924insC	c.(8923-8925)cagfs	p.Q2975fs		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2975					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTCCAGCTGCTGCACCCGGGCG	0.693																																					p.Q2940fs		Atlas-Indel,Pindel	.											.	SPTBN5	171	.	0			c.8819_8820insC						PASS	.																																			SO:0001589	frameshift_variant	51332	exon53			.	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8924dupC	chr15.hg19:g.42148682_42148682dupG	ENSP00000317790:p.Gln2975fs	80.0	0.0	0		73.0	16.0	0.219178	NM_016642		Frame_Shift_Ins	INS	ENST00000320955.6	hg19																																																																																				.	.	.	none		0.693	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
RELA	5970	hgsc.bcm.edu	37	11	65422254	65422277	+	In_Frame_Del	DEL	AGGGCCTGGGGCTAGGACTGGGAC	AGGGCCTGGGGCTAGGACTGGGAC	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	AGGGCCTGGGGCTAGGACTGGGAC	AGGGCCTGGGGCTAGGACTGGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:65422254_65422277delAGGGCCTGGGGCTAGGACTGGGAC	ENST00000406246.3	-	11	1489_1512	c.1228_1251delGTCCCAGTCCTAGCCCCAGGCCCT	c.(1228-1251)gtcccagtcctagccccaggccctdel	p.VPVLAPGP410del	RELA_ENST00000308639.9_In_Frame_Del_p.VPVLAPGP407del|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	410					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						CAGCCTGAGGAgggcctggggctaggactgggacaggggctggg	0.696																																					p.410_418del		Atlas-Indel,Pindel	.											.	RELA	44	.	0			c.1229_1252del						PASS	.																																			SO:0001651	inframe_deletion	5970	exon11			.	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1228_1251delGTCCCAGTCCTAGCCCCAGGCCCT	chr11.hg19:g.65422254_65422277delAGGGCCTGGGGCTAGGACTGGGAC	ENSP00000384273:p.Val410_Pro417del	146.0	0.0	0		110.0	17.0	0.154545	NM_021975	Q6GTV1|Q6SLK1	In_Frame_Del	DEL	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.	.	none		0.696	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
TOMM40L	84134	hgsc.bcm.edu	37	1	161198533	161198536	+	Frame_Shift_Del	DEL	ACAC	ACAC	-			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	ACAC	ACAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:161198533_161198536delACAC	ENST00000367988.3	+	9	982_985	c.713_716delACAC	c.(712-717)aacacafs	p.NT238fs	TOMM40L_ENST00000545897.1_Frame_Shift_Del_p.NT204fs|TOMM40L_ENST00000367987.1_Frame_Shift_Del_p.NT238fs|TOMM40L_ENST00000474486.1_3'UTR|MIR5187_ENST00000583479.1_RNA|NR1I3_ENST00000479324.1_5'Flank	NM_032174.4	NP_115550.2	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)-like	238					ion transport (GO:0006811)|protein transport (GO:0015031)	mitochondrial outer membrane (GO:0005741)|pore complex (GO:0046930)|protein complex (GO:0043234)	porin activity (GO:0015288)			large_intestine(2)|liver(4)|lung(4)	10	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TTTGAGGCAAACACAAGGCTACAA	0.485																																					p.238_239del		Atlas-Indel,Pindel	.											.	TOMM40L	19	.	0			c.712_715del						PASS	.																																			SO:0001589	frameshift_variant	84134	exon9			.		CCDS1227.1, CCDS65700.1	1q23.3	2008-02-05	2007-01-12		ENSG00000158882	ENSG00000158882			25756	protein-coding gene	gene with protein product			"""translocase of outer mitochondrial membrane 40 homolog-like (yeast)"""				Standard	NM_032174		Approved	FLJ12770, TOMM40B	uc001fzd.3	Q969M1	OTTHUMG00000034345	ENST00000367988.3:c.713_716delACAC	chr1.hg19:g.161198533_161198536delACAC	ENSP00000356967:p.Asn238fs	144.0	0.0	0		109.0	26.0	0.238532	NM_032174	B7Z4U0|D3DVG9	Frame_Shift_Del	DEL	ENST00000367988.3	hg19	CCDS1227.1																																																																																			.	.	.	none		0.485	TOMM40L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083029.1	NM_032174	
DNAH14	127602	hgsc.bcm.edu	37	1	225267076	225267077	+	Frame_Shift_Ins	INS	-	-	ATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:225267076_225267077insATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA	ENST00000445597.2	+	14	2394_2395	c.2394_2395insATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA	c.(2395-2397)attfs	p.-816fs	DNAH14_ENST00000439375.2_Frame_Shift_Ins_p.-882fs|DNAH14_ENST00000430092.1_Frame_Shift_Ins_p.-882fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						ACCAGATCCATATTTCAGAAGA	0.282																																					p.H864fs		Pindel	.											.	DNAH14	300	.	0			c.2592_2593insATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA						PASS	.																																			SO:0001589	frameshift_variant	127602	exon18			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.2395_2447dupATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA	chr1.hg19:g.225267076_225267077insATTTCAGAAGAGCAAATTGCCATATTCCAAGTTCTTCTTCTTAAGTTTAGTCA	ENSP00000409472:p.Gln816fs	422.0	0.0	.		441.0	29.0	0.066	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Ins	INS	ENST00000445597.2	hg19																																																																																				.	.	.	none		0.282	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
