#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
ITGA10	8515	hgsc.bcm.edu	37	1	145532515	145532515	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:145532515G>A	ENST00000369304.3	+	9	1143	c.968G>A	c.(967-969)aGa>aAa	p.R323K	ITGA10_ENST00000538811.1_Missense_Mutation_p.R192K|ITGA10_ENST00000539363.1_Missense_Mutation_p.R180K|ITGA10_ENST00000481236.1_3'UTR	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	323	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGAGAAATTAGAACTATTGCC	0.473																																					p.R323K		Atlas-SNP	.											.	ITGA10	131	.	0			c.G968A						PASS	.						144.0	138.0	140.0					1																	145532515		2203	4300	6503	SO:0001583	missense	8515	exon9			AAATTAGAACTAT	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.968G>A	chr1.hg19:g.145532515G>A	ENSP00000358310:p.Arg323Lys	143.0	0.0	.		170.0	66.0	.	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	7.649	0.682583	0.14907	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	D;D;D	0.83914	-1.78;-1.78;-1.78	5.27	4.34	0.51931	von Willebrand factor, type A (3);	0.060779	0.64402	D	0.000004	T	0.34600	0.0903	N	0.01771	-0.73	0.35261	D	0.779612	B;B;B;B	0.18741	0.024;0.024;0.024;0.03	B;B;B;B	0.23150	0.021;0.021;0.044;0.036	T	0.39292	-0.9621	10	0.02654	T	1	.	7.3767	0.26833	0.1809:0.0:0.8191:0.0	.	289;192;180;323	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	K	323;289;180;192	ENSP00000358310:R323K;ENSP00000439894:R180K;ENSP00000440011:R192K	ENSP00000358310:R323K	R	+	2	0	ITGA10	144243872	1.000000	0.71417	0.974000	0.42286	0.966000	0.64601	5.786000	0.69006	2.653000	0.90120	0.561000	0.74099	AGA	.	.	.	none		0.473	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
SEMA6C	10500	hgsc.bcm.edu	37	1	151109386	151109386	+	Silent	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:151109386C>T	ENST00000341697.3	-	11	2612	c.921G>A	c.(919-921)gtG>gtA	p.V307V				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	307	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATGCAGGTTCACAGGCCCAG	0.542																																					p.V307V		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G921A						PASS	.						101.0	108.0	106.0					1																	151109386		2203	4300	6503	SO:0001819	synonymous_variant	10500	exon11			CAGGTTCACAGGC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.921G>A	chr1.hg19:g.151109386C>T		184.0	0.0	.		165.0	47.0	.	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	hg19	CCDS984.1																																																																																			.	.	.	none		0.542	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
PEAR1	375033	hgsc.bcm.edu	37	1	156877993	156877993	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:156877993C>T	ENST00000338302.3	+	10	1201	c.976C>T	c.(976-978)Cgt>Tgt	p.R326C	PEAR1_ENST00000292357.7_Missense_Mutation_p.R326C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	326	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCGGACGCCCGTTGCTTCCC	0.692																																					p.R326C		Atlas-SNP	.											.	PEAR1	118	.	0			c.C976T						PASS	.						21.0	26.0	24.0					1																	156877993		2202	4296	6498	SO:0001583	missense	375033	exon9			GACGCCCGTTGCT	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.976C>T	chr1.hg19:g.156877993C>T	ENSP00000344465:p.Arg326Cys	31.0	0.0	.		22.0	11.0	.	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373658	0.82573	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.18016	2.24;2.24	4.33	4.33	0.51752	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.152429	0.30920	N	0.008604	T	0.30603	0.0770	M	0.72479	2.2	0.58432	D	0.999999	D;D	0.76494	0.998;0.999	D;D	0.70016	0.953;0.967	T	0.05582	-1.0876	10	0.62326	D	0.03	.	14.3643	0.66795	0.0:1.0:0.0:0.0	.	127;326	Q8N780;Q5VY43	.;PEAR1_HUMAN	C	326	ENSP00000344465:R326C;ENSP00000292357:R326C	ENSP00000292357:R326C	R	+	1	0	PEAR1	155144617	0.978000	0.34361	1.000000	0.80357	0.896000	0.52359	2.495000	0.45337	2.230000	0.72887	0.561000	0.74099	CGT	.	.	.	none		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
DUSP27	92235	hgsc.bcm.edu	37	1	167096129	167096129	+	Silent	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:167096129A>G	ENST00000361200.2	+	6	1927	c.1761A>G	c.(1759-1761)acA>acG	p.T587T	DUSP27_ENST00000271385.5_Silent_p.T587T|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Silent_p.T587T			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	587					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						TCAGCCTGACAGCCTACCAGG	0.597																																					p.T587T		Atlas-SNP	.											.	DUSP27	235	.	0			c.A1761G						PASS	.						45.0	45.0	45.0					1																	167096129		2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			CCTGACAGCCTAC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1761A>G	chr1.hg19:g.167096129A>G		68.0	0.0	.		63.0	29.0	.	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	hg19	CCDS30932.1																																																																																			.	.	.	none		0.597	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
C1orf112	55732	hgsc.bcm.edu	37	1	169806133	169806133	+	Silent	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169806133C>T	ENST00000286031.6	+	17	2305	c.1605C>T	c.(1603-1605)tcC>tcT	p.S535S	C1orf112_ENST00000359326.4_Silent_p.S535S|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	535										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AACATATTTCCTTCCAGGCGT	0.438																																					p.S535S		Atlas-SNP	.											.	C1orf112	74	.	0			c.C1605T						PASS	.						73.0	69.0	71.0					1																	169806133		2203	4300	6503	SO:0001819	synonymous_variant	55732	exon17			TATTTCCTTCCAG	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1605C>T	chr1.hg19:g.169806133C>T		63.0	0.0	.		65.0	23.0	.	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	hg19	CCDS1285.1																																																																																			.	.	.	none		0.438	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
PPFIA4	8497	hgsc.bcm.edu	37	1	203025587	203025587	+	Silent	SNP	C	C	A	rs549873910		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:203025587C>A	ENST00000447715.2	+	23	2566	c.2125C>A	c.(2125-2127)Cgg>Agg	p.R709R	PPFIA4_ENST00000295706.4_Silent_p.R225R|PPFIA4_ENST00000414050.2_Silent_p.R438R|PPFIA4_ENST00000367240.2_Silent_p.R710R|PPFIA4_ENST00000599966.1_Silent_p.R225R|PPFIA4_ENST00000272198.6_Silent_p.R225R			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	709					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.R856W(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CAGGACGCTGCGGCTAGAGAA	0.567																																					p.R225R		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,0,3	PPFIA4	139	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673A						PASS	.						37.0	43.0	41.0					1																	203025587		2040	4173	6213	SO:0001819	synonymous_variant	8497	exon5			ACGCTGCGGCTAG	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2125C>A	chr1.hg19:g.203025587C>A		51.0	0.0	.		47.0	3.0	.	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	hg19																																																																																				.	.	.	none		0.567	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
EMILIN1	11117	hgsc.bcm.edu	37	2	27306240	27306240	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:27306240C>A	ENST00000380320.4	+	4	2300	c.1801C>A	c.(1801-1803)Cgc>Agc	p.R601S		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	601					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTGTGGAGCGCTGCTCCTG	0.697																																					p.R601S		Atlas-SNP	.											.	EMILIN1	75	.	0			c.C1801A						PASS	.						31.0	38.0	36.0					2																	27306240		2181	4280	6461	SO:0001583	missense	11117	exon4			GTGGAGCGCTGCT	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"""EMI domain containing"""	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.1801C>A	chr2.hg19:g.27306240C>A	ENSP00000369677:p.Arg601Ser	98.0	0.0	.		88.0	4.0	.	NM_007046	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Missense_Mutation	SNP	ENST00000380320.4	hg19	CCDS1733.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504285	0.44558	.	.	ENSG00000138080	ENST00000380320	T	0.62364	0.03	4.73	4.73	0.59995	.	0.252874	0.30859	N	0.008737	T	0.40322	0.1112	N	0.08118	0	0.31742	N	0.635692	B	0.29646	0.253	B	0.31290	0.127	T	0.43556	-0.9384	10	0.15066	T	0.55	-16.6262	13.0709	0.59061	0.0:1.0:0.0:0.0	.	601	Q9Y6C2	EMIL1_HUMAN	S	601	ENSP00000369677:R601S	ENSP00000369677:R601S	R	+	1	0	EMILIN1	27159744	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.045000	0.30341	2.456000	0.83038	0.561000	0.74099	CGC	.	.	.	none		0.697	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046	
EIF2AK2	5610	hgsc.bcm.edu	37	2	37365711	37365711	+	Silent	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:37365711G>A	ENST00000233057.4	-	7	856	c.534C>T	c.(532-534)tcC>tcT	p.S178S	EIF2AK2_ENST00000405334.1_Silent_p.S178S|EIF2AK2_ENST00000395127.2_Silent_p.S178S	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	178					activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				AAGAACCAGAGGACAGGTAGT	0.363																																					p.S178S		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.C534T						PASS	.						90.0	93.0	92.0					2																	37365711		2203	4300	6503	SO:0001819	synonymous_variant	5610	exon5			ACCAGAGGACAGG	BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 83"""	176871	"""protein kinase, interferon-inducible double stranded RNA dependent"""	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.534C>T	chr2.hg19:g.37365711G>A		75.0	0.0	.		71.0	32.0	.	NM_001135652	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	hg19	CCDS1786.1																																																																																			.	.	.	none		0.363	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759	
KIAA1841	84542	hgsc.bcm.edu	37	2	61310382	61310382	+	Missense_Mutation	SNP	C	C	A	rs140620846	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:61310382C>A	ENST00000402291.1	+	8	1064	c.823C>A	c.(823-825)Cgt>Agt	p.R275S	KIAA1841_ENST00000356719.2_Missense_Mutation_p.R275S|KIAA1841_ENST00000295031.5_Missense_Mutation_p.R275S|KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000453873.1_Missense_Mutation_p.R275S	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	275										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			TCTTCTCACACGTATAGCTGA	0.303																																					p.R275S		Atlas-SNP	.											KIAA1841_ENST00000402291,colon,carcinoma,0,2	KIAA1841	95	.	0			c.C823A						PASS	.						104.0	88.0	94.0					2																	61310382		2203	4299	6502	SO:0001583	missense	84542	exon8			CTCACACGTATAG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.823C>A	chr2.hg19:g.61310382C>A	ENSP00000385579:p.Arg275Ser	48.0	0.0	.		45.0	2.0	.	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975234	0.74360	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.48	-0.618	0.11576	.	0.109289	0.64402	D	0.000006	T	0.63674	0.2531	M	0.83223	2.63	0.43936	D	0.99659	D;P;D	0.57571	0.963;0.902;0.98	P;P;P	0.52881	0.677;0.637;0.712	T	0.62445	-0.6853	9	0.87932	D	0	-4.9877	6.0162	0.19605	0.1151:0.5612:0.0:0.3237	.	275;275;275	Q6NSI8-2;Q6NSI8;Q6NSI8-4	.;K1841_HUMAN;.	S	275	.	ENSP00000295031:R275S	R	+	1	0	KIAA1841	61163886	0.999000	0.42202	0.895000	0.35142	0.966000	0.64601	3.890000	0.56220	-0.342000	0.08363	-0.119000	0.15052	CGT	.	C|0.999;T|0.001	.	alt		0.303	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506	
GPAT2	150763	hgsc.bcm.edu	37	2	96687959	96687959	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:96687959A>T	ENST00000434632.1	-	23	2795	c.2336T>A	c.(2335-2337)cTg>cAg	p.L779Q	GPAT2_ENST00000359548.4_Missense_Mutation_p.L779Q|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000453542.1_Missense_Mutation_p.L708Q|GPAT2_ENST00000377137.3_3'UTR			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	779					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.L779Q(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTGATTGTCCAGGCTGGCAAA	0.567																																					p.L779Q		Atlas-SNP	.											GPAT2,trunk,malignant_melanoma,0,2	GPAT2	46	.	2	Substitution - Missense(2)	skin(2)	c.T2336A						PASS	.						30.0	30.0	30.0					2																	96687959		1847	4102	5949	SO:0001583	missense	150763	exon22			TTGTCCAGGCTGG	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"""cancer/testis antigen 123"""					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.2336T>A	chr2.hg19:g.96687959A>T	ENSP00000389395:p.Leu779Gln	34.0	0.0	.		35.0	2.0	.	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	hg19	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	t	0.005	-2.199373	0.00299	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	T;T;T	0.74526	-0.85;-0.85;0.16	4.97	-1.85	0.07784	.	.	.	.	.	T	0.31857	0.0810	N	0.00483	-1.445	0.09310	N	0.999997	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39187	-0.9626	9	0.02654	T	1	-26.1951	5.7343	0.18057	0.1497:0.2636:0.0:0.5866	.	708;785;779;708	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	Q	779;779;708	ENSP00000352547:L779Q;ENSP00000389395:L779Q;ENSP00000393770:L708Q	ENSP00000352547:L779Q	L	-	2	0	GPAT2	96051686	0.001000	0.12720	0.375000	0.26029	0.081000	0.17604	-0.019000	0.12546	-0.483000	0.06772	-0.751000	0.03497	CTG	.	.	.	none		0.567	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328	
CNNM4	26504	hgsc.bcm.edu	37	2	97428127	97428127	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:97428127A>G	ENST00000377075.2	+	1	1489	c.1391A>G	c.(1390-1392)gAg>gGg	p.E464G		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	464	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						ATGCTGGAGGAGTTCAAGAAG	0.517																																					p.E464G		Atlas-SNP	.											.	CNNM4	48	.	0			c.A1391G						PASS	.						87.0	83.0	85.0					2																	97428127		2203	4300	6503	SO:0001583	missense	26504	exon1			TGGAGGAGTTCAA	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1391A>G	chr2.hg19:g.97428127A>G	ENSP00000366275:p.Glu464Gly	82.0	0.0	.		81.0	36.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937929	0.73557	.	.	ENSG00000158158	ENST00000377075	D	0.93712	-3.27	5.26	5.26	0.73747	Cystathionine beta-synthase, core (2);	0.000000	0.85682	D	0.000000	D	0.96623	0.8898	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97084	0.9786	10	0.66056	D	0.02	-1.1101	14.1805	0.65572	1.0:0.0:0.0:0.0	.	464	Q6P4Q7	CNNM4_HUMAN	G	464	ENSP00000366275:E464G	ENSP00000366275:E464G	E	+	2	0	CNNM4	96791854	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.281000	0.95811	1.996000	0.58369	0.533000	0.62120	GAG	.	.	.	none		0.517	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
TMEM131	23505	hgsc.bcm.edu	37	2	98413329	98413329	+	Silent	SNP	T	T	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:98413329T>A	ENST00000186436.5	-	27	3219	c.2991A>T	c.(2989-2991)gcA>gcT	p.A997A		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	997						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CTTTTAACAATGCTTCCGTGA	0.393																																					p.A997A		Atlas-SNP	.											.	TMEM131	258	.	0			c.A2991T						PASS	.						109.0	108.0	109.0					2																	98413329		1899	4122	6021	SO:0001819	synonymous_variant	23505	exon27			TAACAATGCTTCC	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.2991A>T	chr2.hg19:g.98413329T>A		59.0	0.0	.		65.0	23.0	.	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	.	.	none		0.393	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
COL6A3	1293	hgsc.bcm.edu	37	2	238280361	238280361	+	Intron	SNP	C	C	T	rs373893821		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:238280361C>T	ENST00000295550.4	-	9	4738				COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000392003.2_Silent_p.A1026A|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392004.3_Silent_p.A1227A|COL6A3_ENST00000472056.1_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A1227A(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GAACCTCCGACGCCCCCATCT	0.473																																					p.A1227A		Atlas-SNP	.											.	COL6A3	608	.	1	Substitution - coding silent(1)	lung(1)	c.G3681A						PASS	.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	69.0	78.0	75.0		,3078,3681,,	-1.3	0.0	2		75	0,8600		0,0,4300	no	intron,coding-synonymous,coding-synonymous,intron,intron	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	,1026/1037,1227/1238,,	238280361	1,13005	2203	4300	6503	SO:0001627	intron_variant	1293	exon8			CTCCGACGCCCCC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4285+13G>A	chr2.hg19:g.238280361C>T		147.0	0.0	.		171.0	54.0	.	NM_057165	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.	.	weak		0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CAPN7	23473	hgsc.bcm.edu	37	3	15288921	15288921	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:15288921A>G	ENST00000253693.2	+	19	2414	c.2161A>G	c.(2161-2163)Ata>Gta	p.I721V		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	721	Domain N.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCAATTCCATATAGAAAAGAC	0.363																																					p.I721V		Atlas-SNP	.											.	CAPN7	63	.	0			c.A2161G						PASS	.						84.0	84.0	84.0					3																	15288921		2203	4300	6503	SO:0001583	missense	23473	exon19			TTCCATATAGAAA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"""calpain like protease"", ""homolog of Aspergillus Nidulans PALB"""	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2161A>G	chr3.hg19:g.15288921A>G	ENSP00000253693:p.Ile721Val	121.0	0.0	.		116.0	46.0	.	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	A	7.495	0.651423	0.14516	.	.	ENSG00000131375	ENST00000253693	D	0.85629	-2.01	5.57	-3.39	0.04868	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.669254	0.16098	N	0.229700	T	0.62816	0.2459	N	0.16266	0.395	0.21105	N	0.999789	B	0.02656	0.0	B	0.12837	0.008	T	0.49244	-0.8960	10	0.15066	T	0.55	-2.6499	1.3262	0.02126	0.3616:0.1918:0.2926:0.154	.	721	Q9Y6W3	CAN7_HUMAN	V	721	ENSP00000253693:I721V	ENSP00000253693:I721V	I	+	1	0	CAPN7	15263925	0.062000	0.20869	0.564000	0.28396	0.978000	0.69477	-0.068000	0.11561	-0.127000	0.11661	0.533000	0.62120	ATA	.	.	.	none		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296	
ACAA1	30	hgsc.bcm.edu	37	3	38168151	38168151	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:38168151T>G	ENST00000333167.8	-	8	839	c.667A>C	c.(667-669)Att>Ctt	p.I223L	ACAA1_ENST00000444607.2_3'UTR|ACAA1_ENST00000301810.7_Missense_Mutation_p.I190L|ACAA1_ENST00000544624.1_Missense_Mutation_p.I71L|ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000450296.1_Missense_Mutation_p.I182L|Y_RNA_ENST00000365095.1_RNA	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	223					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		ACAGGCACAATCTCAGCTTGG	0.612																																					p.I223L		Atlas-SNP	.											.	ACAA1	32	.	0			c.A667C						PASS	.						146.0	120.0	129.0					3																	38168151		2203	4300	6503	SO:0001583	missense	30	exon8			GCACAATCTCAGC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.667A>C	chr3.hg19:g.38168151T>G	ENSP00000333664:p.Ile223Leu	117.0	0.0	.		125.0	54.0	.	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.183188|5.183188	0.94885|0.94885	.|.	.|.	ENSG00000060971|ENSG00000060971	ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122;ENST00000544624|ENST00000452171;ENST00000421218	D;D;D;D|.	0.93547|.	-3.11;-3.11;-3.24;-3.24|.	5.46|5.46	5.46|5.46	0.80206|0.80206	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78892|0.78892	0.4355|0.4355	M|M	0.84585|0.84585	2.705|2.705	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.71674|.	0.911;0.997;0.998;0.993|.	D;D;D;D|.	0.85130|.	0.926;0.914;0.997;0.956|.	T|T	0.81484|0.81484	-0.0912|-0.0912	10|5	0.87932|.	D|.	0|.	-10.3475|-10.3475	15.5417|15.5417	0.76057|0.76057	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	155;182;190;223|.	F5GXL8;C9JDE9;G5E935;P09110|.	.;.;.;THIK_HUMAN|.	L|S	223;190;182;155;71|95;112	ENSP00000333664:I223L;ENSP00000301810:I190L;ENSP00000395183:I182L;ENSP00000445710:I71L|.	ENSP00000301810:I190L|.	I|R	-|-	1|3	0|2	ACAA1|ACAA1	38143155|38143155	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.998000|0.998000	0.95712|0.95712	6.148000|6.148000	0.71788|0.71788	2.072000|2.072000	0.62099|0.62099	0.533000|0.533000	0.62120|0.62120	ATT|AGA	.	.	.	none		0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
TGM4	7047	hgsc.bcm.edu	37	3	44926858	44926858	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:44926858G>T	ENST00000296125.4	+	2	129	c.61G>T	c.(61-63)Gcc>Tcc	p.A21S		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	21					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	TCAGGACAACGCCGTTTCTCA	0.522																																					p.A21S		Atlas-SNP	.											.	TGM4	82	.	0			c.G61T						PASS	.						102.0	93.0	96.0					3																	44926858		2203	4300	6503	SO:0001583	missense	7047	exon2			GACAACGCCGTTT	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.61G>T	chr3.hg19:g.44926858G>T	ENSP00000296125:p.Ala21Ser	48.0	0.0	.		44.0	13.0	.	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	9.481	1.098065	0.20552	.	.	ENSG00000163810	ENST00000296125	D	0.84873	-1.91	2.77	-1.63	0.08345	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.329666	0.20233	U	0.096458	T	0.70850	0.3271	L	0.33245	0.995	0.09310	N	1	B;P	0.36027	0.448;0.533	B;B	0.37047	0.24;0.1	T	0.62296	-0.6884	10	0.10902	T	0.67	.	6.6582	0.22998	0.4424:0.0:0.5576:0.0	.	21;21	P49221;B4YUQ1	TGM4_HUMAN;.	S	21	ENSP00000296125:A21S	ENSP00000296125:A21S	A	+	1	0	TGM4	44901862	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.711000	0.05019	-0.425000	0.07371	0.467000	0.42956	GCC	.	.	.	none		0.522	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
SETD2	29072	hgsc.bcm.edu	37	3	47127778	47127778	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:47127778C>A	ENST00000409792.3	-	11	5346	c.5304G>T	c.(5302-5304)aaG>aaT	p.K1768N	SETD2_ENST00000492397.1_5'Flank|snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1768					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCAGAAAGGACTTCAGGCAGG	0.512			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.K1768N		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G5304T						PASS	.						127.0	110.0	116.0					3																	47127778		2203	4300	6503	SO:0001583	missense	29072	exon11			AAAGGACTTCAGG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5304G>T	chr3.hg19:g.47127778C>A	ENSP00000386759:p.Lys1768Asn	72.0	0.0	.		57.0	22.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988848	0.74589	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.90504	-2.68	5.47	4.52	0.55395	.	0.000000	0.56097	D	0.000025	D	0.93220	0.7840	M	0.62723	1.935	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.91914	0.5542	10	0.42905	T	0.14	.	9.269	0.37659	0.0:0.8236:0.0:0.1764	.	1768;1768	F2Z317;Q9BYW2	.;SETD2_HUMAN	N	1768	ENSP00000386759:K1768N	ENSP00000386759:K1768N	K	-	3	2	SETD2	47102782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.865000	0.39479	1.167000	0.42706	0.650000	0.86243	AAG	.	.	.	none		0.512	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
TMEM175	84286	hgsc.bcm.edu	37	4	947053	947053	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:947053C>G	ENST00000264771.4	+	8	723	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	TMEM175_ENST00000515740.1_Missense_Mutation_p.L64V|TMEM175_ENST00000508204.1_Missense_Mutation_p.L98V|TMEM175_ENST00000504180.1_3'UTR	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	180						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCACAGGGCTCTGTACCGACG	0.617																																					p.L180V		Atlas-SNP	.											.	TMEM175	44	.	0			c.C538G						PASS	.						120.0	100.0	107.0					4																	947053		2203	4300	6503	SO:0001583	missense	84286	exon8			AGGGCTCTGTACC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.538C>G	chr4.hg19:g.947053C>G	ENSP00000264771:p.Leu180Val	52.0	0.0	.		65.0	33.0	.	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	hg19	CCDS3341.1	.	.	.	.	.	.	.	.	.	.	c	0.044	-1.272845	0.01421	.	.	ENSG00000127419	ENST00000264771;ENST00000514453;ENST00000515492;ENST00000359768;ENST00000509508;ENST00000515740;ENST00000508204;ENST00000510493	T;T;T;T	0.46819	1.44;0.94;1.49;0.86	4.71	-0.169	0.13339	.	0.217286	0.39083	N	0.001461	T	0.31263	0.0791	L	0.54323	1.7	0.09310	N	1	B;B;B	0.20887	0.001;0.049;0.031	B;B;B	0.19666	0.001;0.026;0.005	T	0.11251	-1.0595	10	0.15499	T	0.54	-27.4926	1.8457	0.03158	0.1956:0.2847:0.3858:0.1339	.	98;180;98	D6RBE5;Q9BSA9;B3KR27	.;TM175_HUMAN;.	V	180;167;98;98;86;64;98;98	ENSP00000264771:L180V;ENSP00000425181:L167V;ENSP00000427039:L64V;ENSP00000423669:L98V	ENSP00000264771:L180V	L	+	1	2	TMEM175	937053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.647000	0.24812	0.040000	0.15660	-0.322000	0.08575	CTG	.	.	.	none		0.617	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	
FGFR3	2261	hgsc.bcm.edu	37	4	1805487	1805487	+	Silent	SNP	C	C	T	rs370530264		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:1805487C>T	ENST00000260795.2	+	7	1101	c.999C>T	c.(997-999)gaC>gaT	p.D333D	FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000340107.4_Intron|FGFR3_ENST00000481110.2_Silent_p.D333D|FGFR3_ENST00000440486.2_Silent_p.D333D|FGFR3_ENST00000412135.2_Intron			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	333	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CCTTTGAGGACGCCGGGGAGT	0.592		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																												p.D333D		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3,colon,carcinoma,0,1	FGFR3	3320	.	0			c.C999T						PASS	.	C	,,	0,4406		0,0,2203	101.0	99.0	100.0		999,,	-1.1	1.0	4		100	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,intron,intron	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,	333/807,,	1805487	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2261	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	TGAGGACGCCGGG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.999C>T	chr4.hg19:g.1805487C>T		65.0	0.0	.		70.0	3.0	.	NM_000142	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.	.	weak		0.592	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
HGFAC	3083	hgsc.bcm.edu	37	4	3443800	3443800	+	Silent	SNP	G	G	C	rs372137428		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:3443800G>C	ENST00000382774.3	+	1	187	c.72G>C	c.(70-72)ctG>ctC	p.L24L	HGFAC_ENST00000511533.1_Silent_p.L24L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	24					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTGCTGCTGCTGC	0.716													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13355	0.0		0.0	False		,,,				2504	0.0				p.L24L		Atlas-SNP	.											.	HGFAC	69	.	0			c.G72C						PASS	.	G		5,3433		0,5,1714	13.0	16.0	15.0		72	0.1	1.0	4		15	0,7164		0,0,3582	no	coding-synonymous	HGFAC	NM_001528.2		0,5,5296	CC,CG,GG		0.0,0.1454,0.0472		24/656	3443800	5,10597	1719	3582	5301	SO:0001819	synonymous_variant	3083	exon1			CCTCCTGCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.72G>C	chr4.hg19:g.3443800G>C		39.0	0.0	.		55.0	5.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.	.	weak		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
DRD5	1816	hgsc.bcm.edu	37	4	9784197	9784197	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:9784197A>T	ENST00000304374.2	+	1	940	c.544A>T	c.(544-546)Agg>Tgg	p.R182W		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	182					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CAACTGGCACAGGGACCAGGC	0.617																																					p.R182W		Atlas-SNP	.											.	DRD5	119	.	0			c.A544T						PASS	.						35.0	36.0	35.0					4																	9784197		2203	4299	6502	SO:0001583	missense	1816	exon1			TGGCACAGGGACC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.544A>T	chr4.hg19:g.9784197A>T	ENSP00000306129:p.Arg182Trp	92.0	0.0	.		84.0	33.0	.	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	hg19	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	a	16.35	3.098148	0.56183	.	.	ENSG00000169676	ENST00000304374	T	0.73047	-0.71	4.53	-6.0	0.02206	GPCR, rhodopsin-like superfamily (1);	0.214762	0.44483	D	0.000455	T	0.80088	0.4559	M	0.74881	2.28	0.37769	D	0.926595	D	0.71674	0.998	D	0.70935	0.971	T	0.82639	-0.0358	10	0.87932	D	0	.	17.6446	0.88145	0.2761:0.7239:0.0:0.0	.	182	P21918	DRD5_HUMAN	W	182	ENSP00000306129:R182W	ENSP00000306129:R182W	R	+	1	2	DRD5	9393295	1.000000	0.71417	0.162000	0.22713	0.673000	0.39480	3.173000	0.50839	-1.286000	0.02384	-0.973000	0.02599	AGG	.	.	.	none		0.617	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
ANK2	287	hgsc.bcm.edu	37	4	114232517	114232517	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:114232517T>A	ENST00000357077.4	+	24	2708	c.2655T>A	c.(2653-2655)aaT>aaA	p.N885K	ANK2_ENST00000264366.6_Missense_Mutation_p.N885K|ANK2_ENST00000394537.3_Missense_Mutation_p.N885K|ANK2_ENST00000509550.1_Missense_Mutation_p.N94K|ANK2_ENST00000506722.1_Missense_Mutation_p.N864K	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	885					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATGGTATGAATTACCTGCGAT	0.438																																					p.N885K		Atlas-SNP	.											.	ANK2	576	.	0			c.T2655A						PASS	.						163.0	134.0	144.0					4																	114232517		2203	4300	6503	SO:0001583	missense	287	exon24			TATGAATTACCTG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2655T>A	chr4.hg19:g.114232517T>A	ENSP00000349588:p.Asn885Lys	95.0	0.0	.		73.0	39.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.511662	0.27036	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	T;T;T;T;T;T;T;T	0.75154	-0.04;0.07;-0.13;-0.04;-0.12;-0.17;-0.2;-0.91	5.15	-2.52	0.06346	.	0.000000	0.53938	D	0.000056	T	0.53932	0.1827	L	0.27053	0.805	0.80722	D	1	B;P;B;P;B;B	0.44627	0.0;0.839;0.372;0.835;0.026;0.288	B;B;B;B;B;B	0.36719	0.001;0.231;0.058;0.228;0.029;0.081	T	0.51810	-0.8658	10	0.21014	T	0.42	.	14.3697	0.66830	0.0:0.6687:0.0:0.3313	.	94;885;885;885;864;864	E9PCH6;Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	.;ANK2_HUMAN;.;.;.;.	K	864;831;864;900;885;885;885;864;94	ENSP00000423799:N864K;ENSP00000421011:N831K;ENSP00000421067:N864K;ENSP00000424722:N900K;ENSP00000378044:N885K;ENSP00000349588:N885K;ENSP00000264366:N885K;ENSP00000426944:N94K	ENSP00000264366:N885K	N	+	3	2	ANK2	114451966	0.711000	0.27906	0.990000	0.47175	0.999000	0.98932	-0.123000	0.10611	-0.397000	0.07691	0.533000	0.62120	AAT	.	.	.	none		0.438	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
TRPC3	7222	hgsc.bcm.edu	37	4	122825594	122825594	+	Missense_Mutation	SNP	A	A	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:122825594A>C	ENST00000379645.3	-	8	2209	c.2136T>G	c.(2134-2136)gaT>gaG	p.D712E	TRPC3_ENST00000264811.5_Missense_Mutation_p.D639E|TRPC3_ENST00000513531.1_Missense_Mutation_p.D584E	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	627					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TGAATTTGTGATCATATTTGA	0.308																																					p.D712E		Atlas-SNP	.											.	TRPC3	201	.	0			c.T2136G						PASS	.						89.0	86.0	87.0					4																	122825594		2203	4298	6501	SO:0001583	missense	7222	exon8			TTTGTGATCATAT	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2136T>G	chr4.hg19:g.122825594A>C	ENSP00000368966:p.Asp712Glu	74.0	0.0	.		52.0	20.0	.	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.982982	0.53827	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.75938	-0.76;-0.98;-0.92	5.77	0.478	0.16789	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.59622	0.2207	L	0.35487	1.065	0.43187	D	0.995017	B;B;B	0.19935	0.002;0.018;0.04	B;B;B	0.30716	0.057;0.057;0.119	T	0.39121	-0.9629	10	0.10111	T	0.7	-24.2756	9.899	0.41335	0.7445:0.0:0.2555:0.0	.	627;584;712	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	E	639;712;584	ENSP00000264811:D639E;ENSP00000368966:D712E;ENSP00000426899:D584E	ENSP00000264811:D639E	D	-	3	2	TRPC3	123045044	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.041000	0.30291	-0.050000	0.13356	0.533000	0.62120	GAT	.	.	.	none		0.308	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
GFM2	84340	hgsc.bcm.edu	37	5	74026107	74026107	+	Silent	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74026107G>T	ENST00000296805.3	-	17	2161	c.1704C>A	c.(1702-1704)atC>atA	p.I568I	GFM2_ENST00000509430.1_Silent_p.I568I|GFM2_ENST00000345239.2_Silent_p.I521I|GFM2_ENST00000515125.1_Intron	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CTGAGTTTAGGATGGTCTCTC	0.413																																					p.I568I		Atlas-SNP	.											.	GFM2	38	.	0			c.C1704A						PASS	.						106.0	100.0	102.0					5																	74026107		2203	4300	6503	SO:0001819	synonymous_variant	84340	exon17			GTTTAGGATGGTC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1704C>A	chr5.hg19:g.74026107G>T		69.0	0.0	.		114.0	32.0	.	NM_032380		Silent	SNP	ENST00000296805.3	hg19	CCDS4023.1																																																																																			.	.	.	none		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
POC5	134359	hgsc.bcm.edu	37	5	74981182	74981182	+	Silent	SNP	G	G	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74981182G>C	ENST00000428202.2	-	10	1446	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	POC5_ENST00000510798.1_Silent_p.S302S|POC5_ENST00000514838.2_Silent_p.S391S|POC5_ENST00000380475.2_Silent_p.S302S|POC5_ENST00000446329.2_Silent_p.S394S	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	419					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CGGCTGGTGGGGATGGCAGCA	0.557																																					p.S419S		Atlas-SNP	.											.	POC5	82	.	0			c.C1257G						PASS	.						100.0	118.0	112.0					5																	74981182		2058	4209	6267	SO:0001819	synonymous_variant	134359	exon10			TGGTGGGGATGGC	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1257C>G	chr5.hg19:g.74981182G>C		120.0	0.0	.		199.0	47.0	.	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Silent	SNP	ENST00000428202.2	hg19	CCDS47236.1																																																																																			.	.	.	none		0.557	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
CHD1	1105	hgsc.bcm.edu	37	5	98195710	98195710	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:98195710T>C	ENST00000284049.3	-	32	4639	c.4490A>G	c.(4489-4491)tAt>tGt	p.Y1497C		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1497					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AGCATGCTTATATAATTTATG	0.274																																					p.Y1497C		Atlas-SNP	.											.	CHD1	137	.	0			c.A4490G						PASS	.						37.0	42.0	40.0					5																	98195710		2193	4275	6468	SO:0001583	missense	1105	exon32			TGCTTATATAATT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4490A>G	chr5.hg19:g.98195710T>C	ENSP00000284049:p.Tyr1497Cys	62.0	0.0	.		67.0	42.0	.	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.048523	0.75846	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.97041	-4.22	5.09	5.09	0.68999	.	0.000000	0.31233	U	0.008011	D	0.98378	0.9461	M	0.83384	2.64	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99620	1.0983	10	0.87932	D	0	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	1497	O14646	CHD1_HUMAN	C	87;1497	ENSP00000284049:Y1497C	ENSP00000284049:Y1497C	Y	-	2	0	CHD1	98223610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.671000	0.83941	2.036000	0.60181	0.533000	0.62120	TAT	.	.	.	none		0.274	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140724210	140724210	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:140724210A>T	ENST00000253812.6	+	1	610	c.610A>T	c.(610-612)Aaa>Taa	p.K204*	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	204	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGTGAGAAAAAAGAAAT	0.537																																					p.K204X		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.A610T						PASS	.						48.0	51.0	50.0					5																	140724210		2151	4270	6421	SO:0001587	stop_gained	56112	exon1			CGTGAGAAAAAAG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.610A>T	chr5.hg19:g.140724210A>T	ENSP00000253812:p.Lys204*	111.0	0.0	.		136.0	39.0	.	NM_032011	Q9Y5D4	Nonsense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	16.89	3.246840	0.59103	.	.	ENSG00000254245	ENST00000253812	.	.	.	5.65	1.35	0.21983	.	0.498029	0.14302	U	0.328230	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	5.4155	0.16372	0.3545:0.1525:0.4931:0.0	.	.	.	.	X	204	.	ENSP00000253812:K204X	K	+	1	0	PCDHGA3	140704394	0.000000	0.05858	0.941000	0.38009	0.356000	0.29392	0.140000	0.16056	0.282000	0.22254	0.533000	0.62120	AAA	.	.	.	none		0.537	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
PCDH1	5097	hgsc.bcm.edu	37	5	141233788	141233788	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:141233788C>T	ENST00000287008.3	-	5	3680	c.3533G>A	c.(3532-3534)cGg>cAg	p.R1178Q	PCDH1_ENST00000503492.1_3'UTR	NM_032420.2	NP_115796.2	Q08174	PCDH1_HUMAN	protocadherin 1	0					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TTTGGTGTTCCGGTCTTCCGG	0.652																																					p.R1178Q	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											PCDH1,NS,carcinoma,0,1	PCDH1	119	.	0			c.G3533A						PASS	.						20.0	22.0	21.0					5																	141233788		2202	4299	6501	SO:0001583	missense	5097	exon5			GTGTTCCGGTCTT	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000287008.3:c.3533G>A	chr5.hg19:g.141233788C>T	ENSP00000287008:p.Arg1178Gln	18.0	0.0	.		39.0	3.0	.	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000287008.3	hg19	CCDS4267.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.490764	0.44249	.	.	ENSG00000156453	ENST00000287008	T	0.53423	0.62	4.78	3.9	0.45041	.	1.032420	0.07798	U	0.956009	T	0.40886	0.1135	L	0.40543	1.245	0.80722	D	1	P	0.50443	0.935	B	0.38755	0.281	T	0.20472	-1.0274	10	0.41790	T	0.15	.	13.0535	0.58967	0.0:0.8367:0.1633:0.0	.	1178	Q08174-2	.	Q	1178	ENSP00000287008:R1178Q	ENSP00000287008:R1178Q	R	-	2	0	PCDH1	141213972	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.887000	0.48586	1.131000	0.42111	0.448000	0.29417	CGG	.	.	.	none		0.652	PCDH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320587.2	NM_032420	
SLC22A7	10864	hgsc.bcm.edu	37	6	43266249	43266249	+	Silent	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:43266249G>A	ENST00000372585.5	+	1	248	c.153G>A	c.(151-153)ctG>ctA	p.L51L	SLC22A7_ENST00000372574.3_Silent_p.L51L|SLC22A7_ENST00000372589.3_Silent_p.L51L|SLC22A7_ENST00000487175.1_Intron	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	51					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GATGTGCCCTGCCGGGTGCCC	0.662																																					p.L51L		Atlas-SNP	.											SLC22A7,NS,carcinoma,0,1	SLC22A7	69	.	0			c.G153A						PASS	.						51.0	51.0	51.0					6																	43266249		2203	4300	6503	SO:0001819	synonymous_variant	10864	exon1			TGCCCTGCCGGGT	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"""Solute carriers"""	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.153G>A	chr6.hg19:g.43266249G>A		116.0	0.0	.		89.0	35.0	.	NM_006672	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	hg19	CCDS4893.2																																																																																			.	.	.	none		0.662	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		
LRRC1	55227	hgsc.bcm.edu	37	6	53660212	53660212	+	Splice_Site	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:53660212A>T	ENST00000370888.1	+	1	435	c.158A>T	c.(157-159)gAg>gTg	p.E53V	RP13-476E20.1_ENST00000429053.1_RNA|LRRC1_ENST00000370882.1_Splice_Site_p.E53V	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	53						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GAGCTGCCCGAGGTAAGGGTC	0.682																																					p.E53V		Atlas-SNP	.											.	LRRC1	59	.	0			c.A158T						PASS	.						28.0	28.0	28.0					6																	53660212		2203	4300	6503	SO:0001630	splice_region_variant	55227	exon1			TGCCCGAGGTAAG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.159+1A>T	chr6.hg19:g.53660212A>T		26.0	0.0	.		31.0	9.0	.	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737840	0.69304	.	.	ENSG00000137269	ENST00000370888;ENST00000370882	T;T	0.58797	0.31;0.31	4.88	3.68	0.42216	.	0.264852	0.37623	N	0.002013	T	0.35008	0.0917	N	0.25380	0.74	0.39279	D	0.96452	B	0.32467	0.372	B	0.42319	0.383	T	0.38373	-0.9664	10	0.87932	D	0	.	9.613	0.39674	0.914:0.0:0.086:0.0	.	53	Q9BTT6	LRRC1_HUMAN	V	53	ENSP00000359925:E53V;ENSP00000359919:E53V	ENSP00000359919:E53V	E	+	2	0	LRRC1	53768171	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	8.227000	0.89787	0.660000	0.30964	0.460000	0.39030	GAG	.	.	.	none		0.682	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	Missense_Mutation
CD109	135228	hgsc.bcm.edu	37	6	74407130	74407130	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:74407130T>C	ENST00000287097.5	+	2	194	c.82T>C	c.(82-84)Ttt>Ctt	p.F28L	CD109_ENST00000437994.2_Missense_Mutation_p.F28L|RP11-553A21.3_ENST00000428865.2_RNA|CD109_ENST00000422508.2_Missense_Mutation_p.F28L			Q6YHK3	CD109_HUMAN	CD109 molecule	28					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAGGCCTCGGTTTCTGGTGAC	0.507																																					p.F28L		Atlas-SNP	.											.	CD109	170	.	0			c.T82C						PASS	.						103.0	101.0	102.0					6																	74407130		2203	4300	6503	SO:0001583	missense	135228	exon2			CCTCGGTTTCTGG	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.82T>C	chr6.hg19:g.74407130T>C	ENSP00000287097:p.Phe28Leu	113.0	0.0	.		118.0	49.0	.	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192857	0.78902	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.35421	1.86;1.31;1.86	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000004	T	0.29850	0.0746	N	0.19112	0.55	0.23555	N	0.997424	D;D;D;D	0.69078	0.965;0.997;0.986;0.985	P;D;P;P	0.66716	0.63;0.946;0.84;0.873	T	0.19516	-1.0303	10	0.72032	D	0.01	.	12.8889	0.58058	0.0:0.0:0.0:1.0	.	28;28;28;28	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	L	28	ENSP00000388062:F28L;ENSP00000404475:F28L;ENSP00000287097:F28L	ENSP00000287097:F28L	F	+	1	0	CD109	74463851	0.998000	0.40836	0.964000	0.40570	0.607000	0.37147	4.263000	0.58853	2.243000	0.73865	0.533000	0.62120	TTT	.	.	.	none		0.507	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
PHIP	55023	hgsc.bcm.edu	37	6	79724879	79724879	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:79724879G>A	ENST00000275034.4	-	15	1611	c.1444C>T	c.(1444-1446)Ctc>Ttc	p.L482F		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	482					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GCAGAAAAGAGAACTCTAGGA	0.358																																					p.L482F		Atlas-SNP	.											.	PHIP	177	.	0			c.C1444T						PASS	.						101.0	94.0	96.0					6																	79724879		2203	4300	6503	SO:0001583	missense	55023	exon15			AAAAGAGAACTCT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1444C>T	chr6.hg19:g.79724879G>A	ENSP00000275034:p.Leu482Phe	93.0	0.0	.		82.0	10.0	.	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033289	0.75504	.	.	ENSG00000146247	ENST00000275034	T	0.68479	-0.33	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.52532	D	0.000061	T	0.60586	0.2280	N	0.21194	0.64	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.61093	-0.7132	9	.	.	.	-5.5196	11.6141	0.51078	0.0821:0.0:0.9179:0.0	.	482;482	A7J992;Q8WWQ0	.;PHIP_HUMAN	F	482	ENSP00000275034:L482F	.	L	-	1	0	PHIP	79781598	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.663000	0.54518	2.586000	0.87340	0.460000	0.39030	CTC	.	.	.	none		0.358	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
GPNMB	10457	hgsc.bcm.edu	37	7	23306207	23306207	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:23306207C>A	ENST00000381990.2	+	7	1287	c.1126C>A	c.(1126-1128)Cac>Aac	p.H376N	GPNMB_ENST00000453162.2_Missense_Mutation_p.H318N|GPNMB_ENST00000258733.4_Missense_Mutation_p.H364N|GPNMB_ENST00000539136.1_Missense_Mutation_p.H265N	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	376					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			CAGATATGGCCACTTTCAAGC	0.478																																					p.H376N		Atlas-SNP	.											.	GPNMB	88	.	0			c.C1126A						PASS	.						82.0	71.0	75.0					7																	23306207		2203	4300	6503	SO:0001583	missense	10457	exon7			TATGGCCACTTTC	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1126C>A	chr7.hg19:g.23306207C>A	ENSP00000371420:p.His376Asn	52.0	0.0	.		52.0	19.0	.	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	hg19	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	6.226	0.409829	0.11812	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.13657	2.58;2.58;2.57;2.58	5.89	-0.668	0.11392	PKD/Chitinase domain (1);	0.606085	0.16307	N	0.220182	T	0.12518	0.0304	L	0.47716	1.5	0.09310	N	0.999998	D;P;P;P	0.53745	0.962;0.82;0.913;0.744	B;B;B;B	0.43990	0.438;0.351;0.345;0.275	T	0.29212	-1.0019	10	0.22706	T	0.39	-12.8359	11.5467	0.50698	0.0:0.5539:0.0:0.4461	.	265;318;376;364	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	N	364;411;376;259;265;318	ENSP00000258733:H364N;ENSP00000371420:H376N;ENSP00000445266:H265N;ENSP00000405586:H318N	ENSP00000258733:H364N	H	+	1	0	GPNMB	23272732	0.759000	0.28416	0.042000	0.18584	0.021000	0.10359	1.106000	0.31098	-0.061000	0.13110	-0.781000	0.03364	CAC	.	.	.	none		0.478	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
GLI3	2737	hgsc.bcm.edu	37	7	42063171	42063171	+	Missense_Mutation	SNP	C	C	T	rs35488756	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:42063171C>T	ENST00000395925.3	-	10	1477	c.1393G>A	c.(1393-1395)Ggg>Agg	p.G465R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	465					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TCTTTGTCCCCTTCCTCCTTG	0.542									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.G465R		Atlas-SNP	.											.	GLI3	312	.	0			c.G1393A						PASS	.						152.0	118.0	129.0					7																	42063171		2203	4300	6503	SO:0001583	missense	2737	exon10	Familial Cancer Database	;	TGTCCCCTTCCTC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1393G>A	chr7.hg19:g.42063171C>T	ENSP00000379258:p.Gly465Arg	103.0	0.0	.		102.0	41.0	.	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727028	0.69074	.	.	ENSG00000106571	ENST00000395925	T	0.69306	-0.39	5.81	5.81	0.92471	.	0.043845	0.85682	D	0.000000	T	0.66713	0.2817	L	0.57536	1.79	0.80722	D	1	B	0.16396	0.017	B	0.14023	0.01	T	0.60762	-0.7199	10	0.42905	T	0.14	.	20.0912	0.97820	0.0:1.0:0.0:0.0	.	465	P10071	GLI3_HUMAN	R	465	ENSP00000379258:G465R	ENSP00000379258:G465R	G	-	1	0	GLI3	42029696	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.975000	0.70475	2.746000	0.94184	0.591000	0.81541	GGG	.	C|0.997;G|0.003	.	alt		0.542	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121651018	121651018	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:121651018G>C	ENST00000393386.2	+	12	2329	c.1918G>C	c.(1918-1920)Gaa>Caa	p.E640Q	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E640Q	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	640					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATCAGGTTCAGAAGAATCACT	0.418																																					p.E640Q		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G1918C						PASS	.						60.0	58.0	59.0					7																	121651018		2203	4300	6503	SO:0001583	missense	5803	exon12			GGTTCAGAAGAAT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1918G>C	chr7.hg19:g.121651018G>C	ENSP00000377047:p.Glu640Gln	113.0	0.0	.		105.0	45.0	.	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952906	0.34471	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.50548	0.8;0.74	5.87	5.87	0.94306	.	0.470308	0.21679	N	0.070741	T	0.61274	0.2334	M	0.67953	2.075	0.27751	N	0.944151	P;P;D	0.63880	0.779;0.671;0.993	B;B;P	0.55713	0.277;0.143;0.782	T	0.60182	-0.7313	10	0.59425	D	0.04	.	14.976	0.71273	0.0:0.0:0.8573:0.1427	.	640;640;640	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	Q	640	ENSP00000377047:E640Q;ENSP00000410000:E640Q	ENSP00000377047:E640Q	E	+	1	0	PTPRZ1	121438254	0.993000	0.37304	0.945000	0.38365	0.967000	0.64934	3.265000	0.51561	2.778000	0.95560	0.655000	0.94253	GAA	.	.	.	none		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
EPPK1	83481	hgsc.bcm.edu	37	8	144942527	144942527	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:144942527C>G	ENST00000525985.1	-	2	4966	c.4895G>C	c.(4894-4896)gGa>gCa	p.G1632A				P58107	EPIPL_HUMAN	epiplakin 1	1632						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCCGAACATTCCTGCTTTGAA	0.627																																					p.G1632A		Atlas-SNP	.											.	EPPK1	199	.	0			c.G4895C						PASS	.						74.0	83.0	80.0					8																	144942527		2037	4184	6221	SO:0001583	missense	83481	exon1			AACATTCCTGCTT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4895G>C	chr8.hg19:g.144942527C>G	ENSP00000436337:p.Gly1632Ala	104.0	0.0	.		128.0	42.0	.	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.25	2.180920	0.38511	.	.	ENSG00000227184	ENST00000525985	D	0.85411	-1.98	4.41	4.41	0.53225	.	.	.	.	.	D	0.93798	0.8017	M	0.92317	3.295	0.09310	N	1	D	0.89917	1.0	D	0.72338	0.977	D	0.87143	0.2204	9	0.72032	D	0.01	.	14.5607	0.68133	0.0:1.0:0.0:0.0	.	1632	E9PPU0	.	A	1632	ENSP00000436337:G1632A	ENSP00000436337:G1632A	G	-	2	0	EPPK1	145014515	0.004000	0.15560	0.114000	0.21550	0.403000	0.30841	1.625000	0.37029	2.280000	0.76307	0.591000	0.81541	GGA	.	.	.	none		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
CNTRL	11064	hgsc.bcm.edu	37	9	123900898	123900898	+	Missense_Mutation	SNP	T	T	G	rs566495778		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:123900898T>G	ENST00000373855.1	+	16	2538	c.2278T>G	c.(2278-2280)Ttc>Gtc	p.F760V	CNTRL_ENST00000373850.1_Missense_Mutation_p.F208V|CNTRL_ENST00000238341.5_Missense_Mutation_p.F760V|CNTRL_ENST00000373847.1_Missense_Mutation_p.F208V			Q7Z7A1	CNTRL_HUMAN	centriolin	760					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AAAAGCCCAGTTCTCAGAAGA	0.418																																					p.F760V		Atlas-SNP	.											.	CNTRL	161	.	0			c.T2278G						PASS	.						97.0	98.0	98.0					9																	123900898		2203	4300	6503	SO:0001583	missense	11064	exon14			GCCCAGTTCTCAG	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.2278T>G	chr9.hg19:g.123900898T>G	ENSP00000362962:p.Phe760Val	93.0	0.0	.		101.0	42.0	.	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248769	0.39797	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.76	2.4	0.29515	.	.	.	.	.	T	0.24236	0.0587	N	0.14661	0.345	0.23731	N	0.996993	B;B;B	0.24483	0.049;0.082;0.104	B;B;B	0.21708	0.016;0.036;0.024	T	0.20338	-1.0278	9	0.27082	T	0.32	.	8.6368	0.33953	0.0:0.3003:0.0:0.6997	.	760;760;760	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	V	760;760;760;242;208;208	ENSP00000362962:F760V;ENSP00000238341:F760V;ENSP00000362956:F208V;ENSP00000362953:F208V	ENSP00000238341:F760V	F	+	1	0	CNTRL	122940719	0.982000	0.34865	0.996000	0.52242	0.970000	0.65996	0.049000	0.14099	0.269000	0.21961	0.533000	0.62120	TTC	.	.	.	none		0.418	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136305499	136305499	+	Silent	SNP	G	G	T	rs371209152		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:136305499G>T	ENST00000371929.3	+	16	2265	c.1821G>T	c.(1819-1821)ggG>ggT	p.G607G	ADAMTS13_ENST00000536611.1_Silent_p.G279G|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.G576G|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Silent_p.G607G	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	607	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCGTGGCTGGGAAGATGAGCA	0.642																																					p.G607G		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G1821T						PASS	.						138.0	98.0	111.0					9																	136305499		2203	4300	6503	SO:0001819	synonymous_variant	11093	exon16			GGCTGGGAAGATG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1821G>T	chr9.hg19:g.136305499G>T		107.0	0.0	.		103.0	32.0	.	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	hg19	CCDS6970.1																																																																																			.	.	.	alt		0.642	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SLC18A3	6572	hgsc.bcm.edu	37	10	50819621	50819621	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:50819621G>C	ENST00000374115.3	+	1	1275	c.835G>C	c.(835-837)Ggc>Cgc	p.G279R	CHAT_ENST00000339797.1_Intron|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000351556.3_5'Flank|CHAT_ENST00000395559.2_5'Flank	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3	279					acetylcholine transport (GO:0015870)|cation transmembrane transport (GO:0098655)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)			endometrium(6)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	43						CCTGCCAGTGGGCACTCCCAT	0.647																																					p.G279R		Atlas-SNP	.											.	SLC18A3	100	.	0			c.G835C						PASS	.						45.0	42.0	43.0					10																	50819621		2202	4300	6502	SO:0001583	missense	6572	exon1			CCAGTGGGCACTC	BC007765	CCDS7231.1	10q11.2	2013-07-18	2013-07-18		ENSG00000187714	ENSG00000187714		"""Solute carriers"""	10936	protein-coding gene	gene with protein product		600336				8071310	Standard	NM_003055		Approved	VACHT	uc001jhw.3	Q16572	OTTHUMG00000018196	ENST00000374115.3:c.835G>C	chr10.hg19:g.50819621G>C	ENSP00000363229:p.Gly279Arg	120.0	0.0	.		126.0	31.0	.	NM_003055	B2R7S1	Missense_Mutation	SNP	ENST00000374115.3	hg19	CCDS7231.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749750	0.89753	.	.	ENSG00000187714	ENST00000374115	T	0.80393	-1.37	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	U	0.000001	D	0.91408	0.7289	M	0.86420	2.815	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.92566	0.6062	10	0.87932	D	0	0.7852	19.2158	0.93778	0.0:0.0:1.0:0.0	.	279	Q16572	VACHT_HUMAN	R	279	ENSP00000363229:G279R	ENSP00000363229:G279R	G	+	1	0	SLC18A3	50489627	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.824000	0.99380	2.552000	0.86080	0.561000	0.74099	GGC	.	.	.	none		0.647	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	NM_003055	
TET1	80312	hgsc.bcm.edu	37	10	70450862	70450862	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:70450862T>G	ENST00000373644.4	+	12	5911	c.5702T>G	c.(5701-5703)aTt>aGt	p.I1901S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1901					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GGCCCTGGCATTTCACAGCTT	0.572																																					p.I1901S		Atlas-SNP	.											.	TET1	255	.	0			c.T5702G						PASS	.						70.0	66.0	67.0					10																	70450862		2203	4300	6503	SO:0001583	missense	80312	exon12			CTGGCATTTCACA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5702T>G	chr10.hg19:g.70450862T>G	ENSP00000362748:p.Ile1901Ser	118.0	0.0	.		167.0	91.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	9.058	0.993658	0.19043	.	.	ENSG00000138336	ENST00000373644	T	0.06849	3.25	5.34	2.89	0.33648	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	5.533840	0.00166	N	0.000001	T	0.11024	0.0269	L	0.41710	1.295	0.09310	N	1	P	0.38729	0.644	B	0.40329	0.326	T	0.22382	-1.0218	10	0.49607	T	0.09	.	5.5383	0.17023	0.0:0.152:0.1458:0.7022	.	1901	Q8NFU7	TET1_HUMAN	S	1901	ENSP00000362748:I1901S	ENSP00000362748:I1901S	I	+	2	0	TET1	70120868	0.002000	0.14202	0.006000	0.13384	0.050000	0.14768	0.124000	0.15728	0.300000	0.22699	0.533000	0.62120	ATT	.	.	.	none		0.572	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
H2AFY2	55506	hgsc.bcm.edu	37	10	71868875	71868875	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:71868875C>A	ENST00000373255.4	+	8	1129	c.865C>A	c.(865-867)Cag>Aag	p.Q289K	AIFM2_ENST00000373248.1_Intron	NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	289	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						ATGTGAAGAACAGCTTGAAGA	0.557																																					p.Q289K		Atlas-SNP	.											.	H2AFY2	30	.	0			c.C865A						PASS	.						89.0	82.0	84.0					10																	71868875		2203	4300	6503	SO:0001583	missense	55506	exon8			GAAGAACAGCTTG	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"""Histones / Replication-independent"""	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.865C>A	chr10.hg19:g.71868875C>A	ENSP00000362352:p.Gln289Lys	92.0	0.0	.		167.0	24.0	.	NM_018649	Q5SQT2	Missense_Mutation	SNP	ENST00000373255.4	hg19	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119095	0.77323	.	.	ENSG00000099284	ENST00000373255;ENST00000395046;ENST00000455786	T;T	0.21031	2.03;2.03	6.03	6.03	0.97812	Appr-1-p processing (2);	0.000000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.17723	0.515	0.80722	D	1	P	0.43231	0.801	B	0.38842	0.283	T	0.02553	-1.1142	10	0.25751	T	0.34	.	20.177	0.98182	0.0:1.0:0.0:0.0	.	289	Q9P0M6	H2AW_HUMAN	K	289;223;223	ENSP00000362352:Q289K;ENSP00000404584:Q223K	ENSP00000362352:Q289K	Q	+	1	0	H2AFY2	71538881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.830000	0.62745	2.854000	0.98071	0.655000	0.94253	CAG	.	.	.	none		0.557	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649	
TRIM8	81603	hgsc.bcm.edu	37	10	104415049	104415049	+	Silent	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:104415049G>A	ENST00000302424.7	+	3	1001	c.879G>A	c.(877-879)acG>acA	p.T293T	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	293					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TTGATAAGACGGAGGATGTCA	0.597																																					p.T293T		Atlas-SNP	.											.	TRIM8	35	.	0			c.G879A						PASS	.						31.0	34.0	33.0					10																	104415049		2202	4300	6502	SO:0001819	synonymous_variant	81603	exon3			TAAGACGGAGGAT	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15579	protein-coding gene	gene with protein product	"""glioblastoma expressed ring finger protein"""	606125	"""ring finger protein 27"", ""tripartite motif-containing 8"""	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.879G>A	chr10.hg19:g.104415049G>A		74.0	0.0	.		92.0	8.0	.	NM_030912	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	hg19	CCDS31274.1																																																																																			.	.	.	none		0.597	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912	
NRAP	4892	hgsc.bcm.edu	37	10	115372127	115372127	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:115372127C>G	ENST00000359988.3	-	30	3608	c.3364G>C	c.(3364-3366)Gcc>Ccc	p.A1122P	NRAP_ENST00000369358.4_Missense_Mutation_p.A1130P|NRAP_ENST00000360478.3_Missense_Mutation_p.A1087P|NRAP_ENST00000369360.3_Missense_Mutation_p.A1095P	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.A1122T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGCACCAGGGCGGCCATGTCC	0.532																																					p.A1122P		Atlas-SNP	.											NRAP,caecum,carcinoma,0,1	NRAP	208	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3364C						PASS	.						106.0	93.0	97.0					10																	115372127		2203	4300	6503	SO:0001583	missense	4892	exon30			CCAGGGCGGCCAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3364G>C	chr10.hg19:g.115372127C>G	ENSP00000353078:p.Ala1122Pro	99.0	0.0	.		157.0	44.0	.	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467717	0.26335	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.62	4.42	0.53409	.	0.222981	0.47852	D	0.000215	T	0.18923	0.0454	L	0.27053	0.805	0.19775	N	0.999954	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.16335	-1.0406	10	0.30078	T	0.28	.	6.6353	0.22879	0.0:0.0846:0.2726:0.6428	.	1122;1087;1122	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	P	1130;1095;1122;1087	ENSP00000358365:A1130P;ENSP00000358367:A1095P;ENSP00000353078:A1122P;ENSP00000353666:A1087P	ENSP00000353078:A1122P	A	-	1	0	NRAP	115362117	0.827000	0.29292	0.788000	0.31933	0.559000	0.35586	1.269000	0.33074	0.978000	0.38470	-0.345000	0.07892	GCC	.	.	.	none		0.532	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
NELL1	4745	hgsc.bcm.edu	37	11	21594920	21594920	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:21594920A>T	ENST00000357134.5	+	19	2499	c.2347A>T	c.(2347-2349)Atg>Ttg	p.M783L	NELL1_ENST00000298925.5_Missense_Mutation_p.M811L|NELL1_ENST00000532434.1_Missense_Mutation_p.M736L|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Missense_Mutation_p.M726L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	783					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGTGTGGACGATGGCTGGATC	0.488																																					p.M783L		Atlas-SNP	.											.	NELL1	179	.	0			c.A2347T						PASS	.						165.0	145.0	152.0					11																	21594920		2203	4300	6503	SO:0001583	missense	4745	exon19			TGGACGATGGCTG	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.2347A>T	chr11.hg19:g.21594920A>T	ENSP00000349654:p.Met783Leu	211.0	0.0	.		211.0	75.0	.	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	5.365	0.252558	0.10185	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78481	-1.18;-1.15;-1.07;-1.06	5.73	4.59	0.56863	.	0.047962	0.85682	N	0.000000	T	0.66655	0.2811	L	0.46157	1.445	0.34190	D	0.671993	P;B;B;B;P	0.37370	0.592;0.0;0.001;0.001;0.457	B;B;B;B;B	0.33254	0.16;0.0;0.002;0.007;0.077	T	0.68561	-0.5376	10	0.10636	T	0.68	-16.3644	12.2052	0.54348	0.872:0.0:0.0:0.1279	.	726;811;328;736;783	F5H6I3;B3KXR2;Q8N9Z6;Q92832-2;Q92832	.;.;.;.;NELL1_HUMAN	L	811;783;726;736	ENSP00000298925:M811L;ENSP00000349654:M783L;ENSP00000317837:M726L;ENSP00000437170:M736L	ENSP00000298925:M811L	M	+	1	0	NELL1	21551496	1.000000	0.71417	0.995000	0.50966	0.203000	0.24098	5.967000	0.70403	0.983000	0.38602	0.454000	0.30748	ATG	.	.	.	none		0.488	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
IMMP1L	196294	hgsc.bcm.edu	37	11	31482191	31482191	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:31482191T>C	ENST00000278200.1	-	4	371	c.176A>G	c.(175-177)cAt>cGt	p.H59R	IMMP1L_ENST00000532287.1_Missense_Mutation_p.H59R|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000528161.1_Intron|IMMP1L_ENST00000533642.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	59					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					ACCATAAAAATGTCGACTAAG	0.318																																					p.H59R		Atlas-SNP	.											.	IMMP1L	16	.	0			c.A176G						PASS	.						67.0	69.0	68.0					11																	31482191		2202	4295	6497	SO:0001583	missense	196294	exon4			TAAAAATGTCGAC		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.176A>G	chr11.hg19:g.31482191T>C	ENSP00000278200:p.His59Arg	59.0	0.0	.		36.0	11.0	.	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	hg19	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	8.728	0.915998	0.17907	.	.	ENSG00000148950	ENST00000532287;ENST00000278200;ENST00000529749;ENST00000530023	.	.	.	5.58	5.58	0.84498	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.046287	0.85682	D	0.000000	T	0.32102	0.0818	N	0.02403	-0.565	0.80722	D	1	P;B	0.38300	0.626;0.0	P;B	0.45232	0.474;0.006	T	0.36187	-0.9758	9	0.02654	T	1	-14.2458	16.0334	0.80603	0.0:0.0:0.0:1.0	.	59;59	E9PIG6;Q96LU5	.;IMP1L_HUMAN	R	59	.	ENSP00000278200:H59R	H	-	2	0	IMMP1L	31438767	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.245000	0.65405	2.243000	0.73865	0.533000	0.62120	CAT	.	.	.	none		0.318	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
CCDC73	493860	hgsc.bcm.edu	37	11	32676507	32676507	+	Silent	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:32676507T>C	ENST00000335185.5	-	10	700	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	219										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CTGAGGCTGCTTTTTTTAGTT	0.303																																					p.D219E		Atlas-SNP	.											CCDC73,NS,carcinoma,-2,1	CCDC73	136	.	0			c.T657G						PASS	.						80.0	67.0	71.0					11																	32676507		1809	4051	5860	SO:0001819	synonymous_variant	493860	exon10			GGCTGCTTTTTTT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.657A>G	chr11.hg19:g.32676507T>C		42.0	0.0	.		25.0	2.0	.	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.	.	none		0.303	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
PRR5L	79899	hgsc.bcm.edu	37	11	36472765	36472765	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:36472765C>T	ENST00000378867.3	+	9	947	c.592C>T	c.(592-594)Cac>Tac	p.H198Y	PRR5L_ENST00000311599.5_Missense_Mutation_p.H125Y|PRR5L_ENST00000527487.1_Intron|PRR5L_ENST00000530639.1_Missense_Mutation_p.H198Y|PRR5L_ENST00000389693.3_3'UTR	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	198					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)	p.H198Y(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						CCAGAGTGTTCACGAGCCCAC	0.502																																					p.H198Y		Atlas-SNP	.											PRR5L,NS,carcinoma,0,1	PRR5L	35	.	1	Substitution - Missense(1)	cervix(1)	c.C592T						PASS	.						170.0	157.0	162.0					11																	36472765		2202	4298	6500	SO:0001583	missense	79899	exon9			AGTGTTCACGAGC		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"""protein observed with Rictor-2"""	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.592C>T	chr11.hg19:g.36472765C>T	ENSP00000368144:p.His198Tyr	145.0	0.0	.		156.0	67.0	.	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	hg19	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049026	0.75846	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867	T;T;T	0.36157	1.27;1.5;1.27	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.80982	2.52	0.58432	D	0.999995	D;D	0.71674	0.989;0.998	D;D	0.77557	0.979;0.99	T	0.69815	-0.5043	10	0.87932	D	0	-17.9831	17.9793	0.89136	0.0:1.0:0.0:0.0	.	70;198	Q6MZQ0-3;Q6MZQ0	.;PRR5L_HUMAN	Y	198;125;198	ENSP00000435050:H198Y;ENSP00000310103:H125Y;ENSP00000368144:H198Y	ENSP00000310103:H125Y	H	+	1	0	PRR5L	36429341	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.758000	0.68776	2.345000	0.79718	0.313000	0.20887	CAC	.	.	.	none		0.502	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
AAMDC	28971	hgsc.bcm.edu	37	11	77580812	77580812	+	Silent	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:77580812G>A	ENST00000526415.1	+	4	350	c.177G>A	c.(175-177)gaG>gaA	p.E59E	AAMDC_ENST00000532481.1_Silent_p.E59E|AAMDC_ENST00000304716.8_Silent_p.E59E|RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000393427.2_Silent_p.E59E|AAMDC_ENST00000533193.1_Silent_p.E105E|AAMDC_ENST00000527134.1_Silent_p.E59E|AAMDC_ENST00000525409.1_Intron|AAMDC_ENST00000525034.1_Silent_p.E78E|RP11-91P24.7_ENST00000525594.1_RNA			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	59	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)											AAGTTGTTGAGAAGGGTGTAC	0.493																																					p.E59E		Atlas-SNP	.											.	.	.	.	0			c.G177A						PASS	.						349.0	322.0	331.0					11																	77580812		2200	4292	6492	SO:0001819	synonymous_variant	28971	exon3			TGTTGAGAAGGGT	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.177G>A	chr11.hg19:g.77580812G>A		338.0	0.0	.		264.0	91.0	.	NM_024684	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	hg19	CCDS8254.1																																																																																			.	.	.	none		0.493	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
PCF11	51585	hgsc.bcm.edu	37	11	82877724	82877724	+	Silent	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:82877724A>G	ENST00000298281.4	+	5	2237	c.1785A>G	c.(1783-1785)aaA>aaG	p.K595K		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	595					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AGTCTGCCAAAAGATGGAAAT	0.348																																					p.K595K		Atlas-SNP	.											.	PCF11	220	.	0			c.A1785G						PASS	.						73.0	75.0	74.0					11																	82877724		1755	3856	5611	SO:0001819	synonymous_variant	51585	exon5			TGCCAAAAGATGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1785A>G	chr11.hg19:g.82877724A>G		142.0	0.0	.		125.0	55.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.	.	none		0.348	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128840894	128840894	+	Missense_Mutation	SNP	C	C	T	rs530219324		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:128840894C>T	ENST00000310343.9	-	22	4171	c.4172G>A	c.(4171-4173)cGg>cAg	p.R1391Q	ARHGAP32_ENST00000527272.1_Missense_Mutation_p.R1042Q|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.R1042Q|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1391	Interaction with GAB2.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CAGCGGGACCCGGGCACCGTC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17039	0.0		0.001	False		,,,				2504	0.0				p.R1391Q		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.G4172A						PASS	.						45.0	47.0	47.0					11																	128840894		2201	4297	6498	SO:0001583	missense	9743	exon22			GGGACCCGGGCAC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.4172G>A	chr11.hg19:g.128840894C>T	ENSP00000310561:p.Arg1391Gln	58.0	0.0	.		61.0	25.0	.	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168938	0.78339	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.11712	2.77;2.75;2.75	5.71	5.71	0.89125	.	0.112572	0.56097	D	0.000024	T	0.19805	0.0476	M	0.69823	2.125	0.32214	N	0.576128	D	0.58620	0.983	P	0.44422	0.449	T	0.09207	-1.0685	10	0.37606	T	0.19	.	19.8599	0.96779	0.0:1.0:0.0:0.0	.	1391	A7KAX9	RHG32_HUMAN	Q	1391;1042;1042	ENSP00000310561:R1391Q;ENSP00000376425:R1042Q;ENSP00000432862:R1042Q	ENSP00000310561:R1391Q	R	-	2	0	ARHGAP32	128346104	0.998000	0.40836	0.932000	0.37286	0.291000	0.27294	3.773000	0.55333	2.710000	0.92621	0.655000	0.94253	CGG	.	.	.	none		0.632	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
AKAP3	10566	hgsc.bcm.edu	37	12	4737430	4737430	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:4737430T>G	ENST00000545990.2	-	5	1162	c.638A>C	c.(637-639)aAa>aCa	p.K213T	AKAP3_ENST00000228850.1_Missense_Mutation_p.K213T|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	213					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GGACTTGTATTTCAAATTTGG	0.468																																					p.K213T		Atlas-SNP	.											.	AKAP3	212	.	0			c.A638C						PASS	.						99.0	99.0	99.0					12																	4737430		2203	4300	6503	SO:0001583	missense	10566	exon4			TTGTATTTCAAAT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.638A>C	chr12.hg19:g.4737430T>G	ENSP00000440994:p.Lys213Thr	173.0	0.0	.		202.0	121.0	.	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.224438	0.39300	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.09255	3.0;3.0	4.87	1.27	0.21489	A-kinase anchor 110kDa, C-terminal (1);	0.332965	0.25968	N	0.027150	T	0.20861	0.0502	M	0.63428	1.95	0.09310	N	1	D	0.63046	0.992	P	0.60415	0.874	T	0.03651	-1.1016	10	0.87932	D	0	-14.2358	6.9349	0.24461	0.0:0.2845:0.0:0.7155	.	213	O75969	AKAP3_HUMAN	T	213	ENSP00000228850:K213T;ENSP00000440994:K213T	ENSP00000228850:K213T	K	-	2	0	AKAP3	4607691	0.949000	0.32298	0.109000	0.21407	0.693000	0.40251	1.094000	0.30951	0.121000	0.18284	0.528000	0.53228	AAA	.	.	.	none		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
GTSF1	121355	hgsc.bcm.edu	37	12	54856511	54856511	+	Splice_Site	SNP	T	T	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:54856511T>A	ENST00000552397.1	-	5	1141		c.e5-2		RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000552395.1_Splice_Site|GTSF1_ENST00000305879.5_Splice_Site|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1							cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				TTTGGTTGACTGCAAGACAAT	0.483																																					.		Atlas-SNP	.											.	GTSF1	15	.	0			c.245-2A>T						PASS	.						92.0	91.0	92.0					12																	54856511		2203	4300	6503	SO:0001630	splice_region_variant	121355	exon6			GTTGACTGCAAGA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"""family with sequence similarity 112, member B"""	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.245-2A>T	chr12.hg19:g.54856511T>A		93.0	0.0	.		168.0	46.0	.	NM_144594	B3KQ60|Q0VGM4|Q8N778	Splice_Site	SNP	ENST00000552397.1	hg19	CCDS8881.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220561	0.22457	.	.	ENSG00000170627	ENST00000552397;ENST00000305879	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3935	0.55373	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTSF1	53142778	1.000000	0.71417	0.971000	0.41717	0.231000	0.25187	4.551000	0.60740	2.183000	0.69458	0.533000	0.62120	.	.	.	.	none		0.483	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594	Intron
WIF1	11197	hgsc.bcm.edu	37	12	65460514	65460514	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:65460514G>T	ENST00000286574.4	-	6	1011	c.637C>A	c.(637-639)Ctt>Att	p.L213I		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	213	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		GGGGTACAAAGGGCTTATAGG	0.433			T	HMGA2	pleomorphic salivary gland adenoma																																p.L213I	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.C637A						PASS	.						75.0	72.0	73.0					12																	65460514		2203	4300	6503	SO:0001583	missense	11197	exon6			TACAAAGGGCTTA	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.637C>A	chr12.hg19:g.65460514G>T	ENSP00000286574:p.Leu213Ile	44.0	0.0	.		54.0	14.0	.	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572822	0.45798	.	.	ENSG00000156076	ENST00000286574	T	0.03035	4.07	5.23	4.34	0.51931	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.068823	0.64402	D	0.000016	T	0.02455	0.0075	N	0.05306	-0.075	0.53688	D	0.999978	B	0.19935	0.04	B	0.25291	0.059	T	0.54675	-0.8258	9	.	.	.	.	14.326	0.66521	0.0722:0.0:0.9278:0.0	.	213	Q9Y5W5	WIF1_HUMAN	I	213	ENSP00000286574:L213I	.	L	-	1	0	WIF1	63746781	1.000000	0.71417	0.998000	0.56505	0.123000	0.20343	4.824000	0.62701	1.530000	0.49136	0.655000	0.94253	CTT	.	.	.	none		0.433	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2		
PTPN11	5781	hgsc.bcm.edu	37	12	112892407	112892407	+	Missense_Mutation	SNP	T	T	G	rs79068130		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:112892407T>G	ENST00000351677.2	+	5	763	c.565T>G	c.(565-567)Tct>Gct	p.S189A	PTPN11_ENST00000392597.1_Missense_Mutation_p.S189A	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	189	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.S189A(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ACGGTTTGATTCTTTGACAGA	0.368			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																												p.S189A		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	PTPN11,NS,carcinoma,0,1	PTPN11	623	.	1	Substitution - Missense(1)	stomach(1)	c.T565G						PASS	.						112.0	105.0	108.0					12																	112892407		2203	4300	6503	SO:0001583	missense	5781	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TTTGATTCTTTGA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.565T>G	chr12.hg19:g.112892407T>G	ENSP00000340944:p.Ser189Ala	72.0	0.0	.		121.0	6.0	.	NM_080601	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.87|17.87	3.494925|3.494925	0.64186|0.64186	.|.	.|.	ENSG00000179295|ENSG00000179295	ENST00000530818|ENST00000392597;ENST00000351677;ENST00000392596	.|T;T	.|0.80824	.|-1.42;-1.42	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.051687	.|0.85682	.|D	.|0.000000	D|D	0.86151|0.86151	0.5864|0.5864	M|M	0.90977|0.90977	3.165|3.165	0.53005|0.53005	D|D	0.99996|0.99996	.|B;B	.|0.22480	.|0.07;0.07	.|B;B	.|0.36845	.|0.234;0.234	D|D	0.84453|0.84453	0.0589|0.0589	5|10	.|0.44086	.|T	.|0.13	.|.	11.0193|11.0193	0.47709|0.47709	0.1389:0.0:0.0:0.8611|0.1389:0.0:0.0:0.8611	.|.	.|189;189	.|Q06124-2;Q06124-3	.|.;.	M|A	33|189	.|ENSP00000376376:S189A;ENSP00000340944:S189A	.|ENSP00000340944:S189A	I|S	+|+	3|1	3|0	PTPN11|PTPN11	111376790|111376790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	4.663000|4.663000	0.61532|0.61532	2.144000|2.144000	0.66660|0.66660	0.397000|0.397000	0.26171|0.26171	ATT|TCT	.	T|0.500;G|0.500	0.500	weak		0.368	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
PTPN11	5781	hgsc.bcm.edu	37	12	112892458	112892458	+	Silent	SNP	T	T	C	rs78376169		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:112892458T>C	ENST00000351677.2	+	5	814	c.616T>C	c.(616-618)Ttg>Ctg	p.L206L	PTPN11_ENST00000392597.1_Silent_p.L206L	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	206	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.L206L(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGTGGAAACATTGGGTACAGT	0.373			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																												p.L206L		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	PTPN11,NS,carcinoma,0,2	PTPN11	623	.	1	Substitution - coding silent(1)	stomach(1)	c.T616C						PASS	.						87.0	82.0	84.0					12																	112892458		2203	4300	6503	SO:0001819	synonymous_variant	5781	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GAAACATTGGGTA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.616T>C	chr12.hg19:g.112892458T>C		60.0	0.0	.		99.0	5.0	.	NM_080601	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	hg19	CCDS9163.1																																																																																			.	.	.	weak		0.373	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
PARP4	143	hgsc.bcm.edu	37	13	25029240	25029240	+	Silent	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:25029240T>C	ENST00000381989.3	-	22	2778	c.2673A>G	c.(2671-2673)acA>acG	p.T891T	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	891	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTTGCAAGAATGTCACACCCT	0.502																																					p.T891T		Atlas-SNP	.											.	PARP4	142	.	0			c.A2673G						PASS	.						261.0	222.0	235.0					13																	25029240		2203	4300	6503	SO:0001819	synonymous_variant	143	exon22			CAAGAATGTCACA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2673A>G	chr13.hg19:g.25029240T>C		257.0	0.0	.		286.0	104.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	hg19	CCDS9307.1																																																																																			.	.	.	none		0.502	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
CPB2	1361	hgsc.bcm.edu	37	13	46658419	46658419	+	Missense_Mutation	SNP	A	A	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:46658419A>C	ENST00000181383.4	-	3	226	c.210T>G	c.(208-210)ttT>ttG	p.F70L	CPB2-AS1_ENST00000606351.1_RNA|CPB2_ENST00000439329.3_Missense_Mutation_p.F70L|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000606243.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	70					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		CATTTACAAAAAAATGGACTT	0.368																																					p.F70L		Atlas-SNP	.											.	CPB2	60	.	0			c.T210G						PASS	.						151.0	139.0	143.0					13																	46658419		2203	4300	6503	SO:0001583	missense	1361	exon3			TACAAAAAAATGG	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"""thrombin-activatable fibrinolysis inhibitor"", ""carboxypeptidase U"", ""plasma carboxypeptidase B"", ""carboxypeptidase R"""	603101	"""carboxypeptidase B2 (plasma, carboxypeptidase U)"""			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.210T>G	chr13.hg19:g.46658419A>C	ENSP00000181383:p.Phe70Leu	166.0	0.0	.		171.0	74.0	.	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	hg19	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.740893	0.49151	.	.	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.13538	2.58;2.58	5.41	-2.81	0.05805	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.050842	0.85682	D	0.000000	T	0.12646	0.0307	L	0.42245	1.32	0.40335	D	0.978972	B;P	0.49253	0.337;0.921	B;P	0.46320	0.162;0.512	T	0.03875	-1.0996	10	0.44086	T	0.13	.	10.4812	0.44695	0.4897:0.0:0.5103:0.0	.	70;70	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	L	70	ENSP00000181383:F70L;ENSP00000400714:F70L	ENSP00000181383:F70L	F	-	3	2	CPB2	45556420	0.999000	0.42202	0.991000	0.47740	0.819000	0.46315	0.355000	0.20163	-0.389000	0.07786	-0.263000	0.10527	TTT	.	.	.	none		0.368	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
AP1G2	8906	hgsc.bcm.edu	37	14	24032848	24032848	+	Splice_Site	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:24032848C>T	ENST00000308724.5	-	12	1988		c.e12-1		RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000556277.1_5'Flank|AP1G2_ENST00000397120.3_Splice_Site	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit						intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TGGAGCAAACCTAGGGGATAT	0.567											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	AP1G2	75	.	0			c.1233-1G>A						PASS	.						138.0	109.0	119.0					14																	24032848		2203	4300	6503	SO:0001630	splice_region_variant	8906	exon14			GCAAACCTAGGGG	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1233-1G>A	chr14.hg19:g.24032848C>T		103.0	0.0	.	768	68.0	46.0	.	NM_003917	D3DS51|O75504	Splice_Site	SNP	ENST00000308724.5	hg19	CCDS9602.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691409	0.48097	.	.	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7542	0.69552	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP1G2	23102688	1.000000	0.71417	0.997000	0.53966	0.613000	0.37349	4.964000	0.63701	2.314000	0.78098	0.557000	0.71058	.	.	.	.	none		0.567	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	Intron
MIS18BP1	55320	hgsc.bcm.edu	37	14	45711249	45711249	+	Silent	SNP	A	A	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:45711249A>C	ENST00000310806.4	-	4	1589	c.1131T>G	c.(1129-1131)ctT>ctG	p.L377L	MIS18BP1_ENST00000492652.1_5'UTR	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	377					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						GATTTTTTTTAAGTCCATTTG	0.308																																					p.L377L		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.T1131G						PASS	.						57.0	66.0	63.0					14																	45711249		2202	4294	6496	SO:0001819	synonymous_variant	55320	exon4			TTTTTTAAGTCCA	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1131T>G	chr14.hg19:g.45711249A>C		110.0	0.0	.		47.0	30.0	.	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	hg19	CCDS9684.1																																																																																			.	.	.	none		0.308	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
SERINC4	619189	hgsc.bcm.edu	37	15	44090645	44090645	+	Silent	SNP	A	A	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr15:44090645A>T	ENST00000319327.6	-	4	750	c.516T>A	c.(514-516)atT>atA	p.I172I	SERINC4_ENST00000249714.3_5'UTR|SERF2_ENST00000594896.1_Intron|HYPK_ENST00000442995.2_5'Flank|HYPK_ENST00000406925.1_5'UTR|SERINC4_ENST00000299969.6_Silent_p.I172I|HYPK_ENST00000458412.1_5'Flank|RP11-296A16.1_ENST00000417761.2_Intron|SERF2_ENST00000600633.1_5'Flank|SERF2_ENST00000409646.1_Intron|SERF2_ENST00000409291.1_Intron	NM_001258031.1	NP_001244960.1	A6NH21	SERC4_HUMAN	serine incorporator 4	172					phospholipid biosynthetic process (GO:0008654)	integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	6		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;7.81e-07)		GCTCATCAGGAATGCAGAAGG	0.483																																					p.I172I		Atlas-SNP	.											.	SERINC4	18	.	0			c.T516A						PASS	.						115.0	106.0	109.0					15																	44090645		2198	4298	6496	SO:0001819	synonymous_variant	619189	exon4			ATCAGGAATGCAG	DQ103711	CCDS58360.1	15q15.3	2013-09-25			ENSG00000184716	ENSG00000184716			32237	protein-coding gene	gene with protein product		614550					Standard	NM_001258031		Approved	FLJ40363	uc031qrp.1	A6NH21	OTTHUMG00000060144	ENST00000319327.6:c.516T>A	chr15.hg19:g.44090645A>T		102.0	0.0	.		91.0	44.0	.	NM_001258031	B2RN41|Q3YL75	Silent	SNP	ENST00000319327.6	hg19	CCDS58360.1																																																																																			.	.	.	none		0.483	SERINC4-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133485.2		
LRRK1	79705	hgsc.bcm.edu	37	15	101529603	101529603	+	Splice_Site	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr15:101529603A>G	ENST00000388948.3	+	6	1121	c.762A>G	c.(760-762)acA>acG	p.T254T	LRRK1_ENST00000532029.2_Silent_p.T254T|LRRK1_ENST00000284395.5_Splice_Site_p.T251T	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGGGAAAAACAGTGAGTAGTC	0.433																																					p.T254T		Atlas-SNP	.											.	LRRK1	310	.	0			c.A762G						PASS	.						80.0	79.0	79.0					15																	101529603		1890	4124	6014	SO:0001630	splice_region_variant	79705	exon6			AAAAACAGTGAGT	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.762+1A>G	chr15.hg19:g.101529603A>G		59.0	0.0	.		64.0	30.0	.	NM_024652		Silent	SNP	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.	.	none		0.433	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	Silent
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570232	570232	+	Silent	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:570232C>T	ENST00000262305.4	+	12	2359	c.1971C>T	c.(1969-1971)cgC>cgT	p.R657R	RAB11FIP3_ENST00000457159.1_Silent_p.R702R|RAB11FIP3_ENST00000450428.1_Silent_p.R361R	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	657					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				ACCACAGCCGCGCCCGGGAGA	0.682																																					p.R657R	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.C1971T						PASS	.						5.0	9.0	8.0					16																	570232		2086	4138	6224	SO:0001819	synonymous_variant	9727	exon12			CAGCCGCGCCCGG	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1971C>T	chr16.hg19:g.570232C>T		8.0	0.0	.		11.0	6.0	.	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.	.	none		0.682	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700	
ARL6IP1	23204	hgsc.bcm.edu	37	16	18810023	18810023	+	Splice_Site	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:18810023A>G	ENST00000304414.7	-	2	381	c.170T>C	c.(169-171)cTg>cCg	p.L57P	ARL6IP1_ENST00000546206.2_Splice_Site_p.L28P|RP11-1035H13.3_ENST00000567078.2_Splice_Site_p.L57P|ARL6IP1_ENST00000562819.1_Intron	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	57					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						GCTCACTTACAGAAACACCAA	0.413																																					p.L57P		Atlas-SNP	.											.	ARL6IP1	23	.	0			c.T170C						PASS	.						132.0	115.0	121.0					16																	18810023		2197	4300	6497	SO:0001630	splice_region_variant	23204	exon2			ACTTACAGAAACA	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"""ADP-ribosylation factor-like 6 interacting protein"""	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.170+1T>C	chr16.hg19:g.18810023A>G		147.0	0.0	.		168.0	63.0	.	NM_015161		Missense_Mutation	SNP	ENST00000304414.7	hg19	CCDS10572.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.394667	0.83011	.	.	ENSG00000170540	ENST00000304414;ENST00000545430;ENST00000546206	T;T	0.52754	0.65;0.65	5.07	5.07	0.68467	.	0.320357	0.30930	N	0.008581	T	0.64182	0.2575	M	0.65498	2.005	0.80722	D	1	D	0.58970	0.984	D	0.64237	0.923	T	0.64841	-0.6312	9	.	.	.	-0.7325	14.7838	0.69787	1.0:0.0:0.0:0.0	.	57	Q15041	AR6P1_HUMAN	P	57;9;28	ENSP00000306788:L57P;ENSP00000440048:L28P	.	L	-	2	0	ARL6IP1	18717524	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.476000	0.81055	2.016000	0.59253	0.533000	0.62120	CTG	.	.	.	none		0.413	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161	Missense_Mutation
PRSS53	339105	hgsc.bcm.edu	37	16	31098021	31098021	+	Silent	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:31098021C>T	ENST00000280606.6	-	4	594	c.441G>A	c.(439-441)caG>caA	p.Q147Q		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	147	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GATGGGCGGGCTGGGGCAGGC	0.657																																					p.Q147Q		Atlas-SNP	.											.	PRSS53	29	.	0			c.G441A						PASS	.						30.0	38.0	35.0					16																	31098021		1927	4114	6041	SO:0001819	synonymous_variant	339105	exon4			GGCGGGCTGGGGC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.441G>A	chr16.hg19:g.31098021C>T		78.0	0.0	.		94.0	44.0	.	NM_001039503		Silent	SNP	ENST00000280606.6	hg19	CCDS42153.1																																																																																			.	.	.	none		0.657	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
DDX19B	11269	hgsc.bcm.edu	37	16	70346536	70346536	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:70346536G>C	ENST00000288071.6	+	2	327	c.82G>C	c.(82-84)Gag>Cag	p.E28Q	DDX19B_ENST00000451014.3_Missense_Mutation_p.E33Q|RP11-529K1.3_ENST00000567706.1_Missense_Mutation_p.E28Q|DDX19B_ENST00000393657.2_Intron|DDX19B_ENST00000568625.1_Intron|DDX19B_ENST00000563392.1_Intron|DDX19B_ENST00000563206.1_Missense_Mutation_p.E33Q|DDX19B_ENST00000570055.1_3'UTR|DDX19B_ENST00000355992.3_Missense_Mutation_p.E28Q	NM_007242.5	NP_009173.1	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B	28	N-terminal lobe.				mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)	9		Ovarian(137;0.0694)				TCTTAAGGAAGAGAAAATCAA	0.378																																					p.E33Q	Esophageal Squamous(26;382 757 1343 9728 15939)	Atlas-SNP	.											RP11-529K1.3,NS,carcinoma,0,2	DDX19B	31	.	0			c.G97C						PASS	.						100.0	94.0	96.0					16																	70346536		2198	4300	6498	SO:0001583	missense	11269	exon2			AAGGAAGAGAAAA	AJ237946	CCDS10888.1, CCDS32475.1, CCDS42187.1, CCDS58478.1	16q22.3	2012-02-23	2012-02-23	2005-07-13	ENSG00000157349	ENSG00000157349		"""DEAD-boxes"""	2742	protein-coding gene	gene with protein product		605812	"""DEAD (Asp-Glu-Ala-As) box polypeptide 19"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (Dbp5, yeast, homolog)"""	DDX19		10428971	Standard	NM_007242		Approved	DBP5	uc002eyo.4	Q9UMR2	OTTHUMG00000137577	ENST00000288071.6:c.82G>C	chr16.hg19:g.70346536G>C	ENSP00000288071:p.Glu28Gln	55.0	0.0	.		35.0	2.0	.	NM_001257172	B3KNE9|B4DXS6|E7EMK4|Q6FIB7|Q6IAE0|Q96KE7|Q9H0U0	Missense_Mutation	SNP	ENST00000288071.6	hg19	CCDS10888.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.714638	0.48622	.	.	ENSG00000157349	ENST00000451014;ENST00000355992;ENST00000288071	T;T;T	0.62639	3.73;0.01;0.01	5.24	5.24	0.73138	.	0.047526	0.85682	D	0.000000	T	0.50360	0.1611	L	0.31845	0.965	0.43000	D	0.994511	B;B;P;B	0.36535	0.085;0.259;0.557;0.006	B;B;B;B	0.33620	0.015;0.11;0.167;0.01	T	0.53436	-0.8439	10	0.42905	T	0.14	.	14.1874	0.65614	0.0:0.0:1.0:0.0	.	33;28;28;28	E7EMK4;Q7Z4W5;Q9UMR2-2;Q9UMR2	.;.;.;DD19B_HUMAN	Q	33;28;28	ENSP00000392639:E33Q;ENSP00000348271:E28Q;ENSP00000288071:E28Q	ENSP00000288071:E28Q	E	+	1	0	DDX19B	68904037	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.261000	0.65496	2.732000	0.93576	0.655000	0.94253	GAG	.	.	.	none		0.378	DDX19B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268965.3	NM_007242	
TXNL4B	54957	hgsc.bcm.edu	37	16	72120699	72120699	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:72120699G>T	ENST00000268483.3	-	4	608	c.287C>A	c.(286-288)tCt>tAt	p.S96Y	RP11-384M15.3_ENST00000561827.1_RNA|TXNL4B_ENST00000423037.1_Missense_Mutation_p.S96Y|TXNL4B_ENST00000426362.2_Missense_Mutation_p.S96Y	NM_001142318.1|NM_017853.2	NP_001135790.1|NP_060323.1	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	96					mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)				cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)	8						GTGATCTGGAGATCTAGACAG	0.358																																					p.S96Y		Atlas-SNP	.											.	TXNL4B	17	.	0			c.C287A						PASS	.						68.0	65.0	66.0					16																	72120699		2198	4300	6498	SO:0001583	missense	54957	exon4			TCTGGAGATCTAG	BC009646	CCDS10906.1	16q22.2	2012-11-19			ENSG00000140830	ENSG00000140830			26041	protein-coding gene	gene with protein product						15161931	Standard	NM_017853		Approved	FLJ20511, DLP, Dim2	uc010vmn.2	Q9NX01	OTTHUMG00000173453	ENST00000268483.3:c.287C>A	chr16.hg19:g.72120699G>T	ENSP00000268483:p.Ser96Tyr	68.0	0.0	.		61.0	26.0	.	NM_001142318	D3DWS6	Missense_Mutation	SNP	ENST00000268483.3	hg19	CCDS10906.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824185	0.90955	.	.	ENSG00000140830	ENST00000268483;ENST00000426362;ENST00000423037	.	.	.	5.87	5.87	0.94306	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.60345	0.873	T	0.66594	-0.5884	9	0.87932	D	0	.	18.0718	0.89410	0.0:0.0:1.0:0.0	.	96	Q9NX01	TXN4B_HUMAN	Y	96	.	ENSP00000268483:S96Y	S	-	2	0	TXNL4B	70678200	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	TCT	.	.	.	none		0.358	TXNL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269007.2	NM_017853	
SLC2A4	6517	hgsc.bcm.edu	37	17	7189210	7189210	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7189210G>C	ENST00000317370.8	+	10	1577	c.1309G>C	c.(1309-1311)Ggt>Cgt	p.G437R	SLC2A4_ENST00000571308.1_Missense_Mutation_p.G437R|SLC2A4_ENST00000424875.2_Missense_Mutation_p.G427R|RP1-4G17.2_ENST00000576271.1_RNA	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	437					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CATTGGCATGGGTTTCCAGTA	0.627																																					p.G437R		Atlas-SNP	.											.	SLC2A4	44	.	0			c.G1309C						PASS	.						88.0	72.0	77.0					17																	7189210		2203	4300	6503	SO:0001583	missense	6517	exon10			GGCATGGGTTTCC	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1309G>C	chr17.hg19:g.7189210G>C	ENSP00000320935:p.Gly437Arg	62.0	0.0	.		71.0	24.0	.	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	hg19	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851854	0.51270	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.74002	-0.8;-0.8	5.09	1.72	0.24424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256239	0.39834	N	0.001255	T	0.72162	0.3426	M	0.67569	2.06	0.46654	D	0.999149	P;P	0.40144	0.539;0.704	P;B	0.48488	0.579;0.443	T	0.65463	-0.6162	10	0.30854	T	0.27	.	3.2542	0.06826	0.2014:0.0:0.4319:0.3667	.	437;427	P14672;F5H081	GTR4_HUMAN;.	R	437;427	ENSP00000320935:G437R;ENSP00000396887:G427R	ENSP00000320935:G437R	G	+	1	0	SLC2A4	7129934	0.224000	0.23674	0.998000	0.56505	0.998000	0.95712	-0.437000	0.06914	0.677000	0.31305	0.563000	0.77884	GGT	.	.	.	none		0.627	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
POLR2A	5430	hgsc.bcm.edu	37	17	7399344	7399344	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7399344C>G	ENST00000322644.6	+	2	577	c.178C>G	c.(178-180)Ccg>Gcg	p.P60A	POLR2A_ENST00000572844.1_Missense_Mutation_p.P60A	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	60					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCTGATGGACCCGAGGCAGGG	0.612																																					p.P60A		Atlas-SNP	.											.	POLR2A	157	.	0			c.C178G						PASS	.						42.0	48.0	46.0					17																	7399344		2202	4299	6501	SO:0001583	missense	5430	exon2			ATGGACCCGAGGC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.178C>G	chr17.hg19:g.7399344C>G	ENSP00000314949:p.Pro60Ala	79.0	0.0	.		100.0	36.0	.	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134164	0.77662	.	.	ENSG00000181222	ENST00000322644	T	0.21734	1.99	5.33	5.33	0.75918	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	T	0.48927	-0.8991	10	0.87932	D	0	.	17.783	0.88529	0.0:1.0:0.0:0.0	.	60;60	P24928;Q6NX41	RPB1_HUMAN;.	A	60	ENSP00000314949:P60A	ENSP00000314949:P60A	P	+	1	0	SLC35G6	7340068	1.000000	0.71417	0.995000	0.50966	0.853000	0.48598	7.142000	0.77339	2.499000	0.84300	0.467000	0.42956	CCG	.	.	.	none		0.612	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
TAF15	8148	hgsc.bcm.edu	37	17	34172014	34172014	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:34172014G>T	ENST00000588240.1	+	15	1826	c.1711G>T	c.(1711-1713)Ggt>Tgt	p.G571C	TAF15_ENST00000311979.3_Missense_Mutation_p.G568C|TAF15_ENST00000592237.1_Missense_Mutation_p.E375D	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AGGAGACCGAGGTGGCTATGG	0.527			T	"""TEC, CHN1, ZNF384"""	"""extraskeletal myxoid chondrosarcomas, ALL"""																																p.G571C		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"""TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"""		"""L, M"""	.	TAF15	46	.	0			c.G1711T						PASS	.						76.0	89.0	85.0					17																	34172014		2203	4300	6503	SO:0001583	missense	8148	exon15			GACCGAGGTGGCT	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"""RNA binding motif (RRM) containing"""	11547	protein-coding gene	gene with protein product		601574	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1711G>T	chr17.hg19:g.34172014G>T	ENSP00000466950:p.Gly571Cys	168.0	0.0	.		165.0	55.0	.	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911288	0.52439	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.94862	-3.54	5.07	4.09	0.47781	.	.	.	.	.	D	0.94424	0.8206	L	0.34521	1.04	0.39114	D	0.961521	D;D	0.89917	1.0;1.0	D;D	0.69479	0.92;0.964	D	0.94444	0.7661	9	0.87932	D	0	-3.2622	10.8882	0.46978	0.0922:0.0:0.9078:0.0	.	571;568	Q92804;Q92804-2	RBP56_HUMAN;.	C	571;374	ENSP00000309558:G571C	ENSP00000309558:G571C	G	+	1	0	TAF15	31196127	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.652000	0.61454	2.520000	0.84964	0.591000	0.81541	GGT	.	.	.	none		0.527	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215	
ACACA	31	hgsc.bcm.edu	37	17	35567392	35567392	+	Silent	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:35567392A>G	ENST00000394406.2	-	30	3775	c.3585T>C	c.(3583-3585)ccT>ccC	p.P1195P	ACACA_ENST00000353139.5_Silent_p.P1232P|ACACA_ENST00000360679.3_Silent_p.P1137P|ACACA_ENST00000335166.5_Silent_p.P1117P	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1195					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TGTTTAGCGTAGGGATGTTCC	0.343																																					p.P1232P	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.T3696C						PASS	.						94.0	95.0	95.0					17																	35567392		2203	4300	6503	SO:0001819	synonymous_variant	31	exon30			TAGCGTAGGGATG	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3585T>C	chr17.hg19:g.35567392A>G		104.0	0.0	.		97.0	4.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.	.	none		0.343	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
LRRC46	90506	hgsc.bcm.edu	37	17	45914207	45914207	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:45914207G>A	ENST00000269025.4	+	8	1050	c.687G>A	c.(685-687)atG>atA	p.M229I		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	229										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGATGGAGATGCAGCCCACCC	0.667																																					p.M229I		Atlas-SNP	.											.	LRRC46	25	.	0			c.G687A						PASS	.						54.0	56.0	55.0					17																	45914207		2203	4300	6503	SO:0001583	missense	90506	exon8			GGAGATGCAGCCC		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.687G>A	chr17.hg19:g.45914207G>A	ENSP00000269025:p.Met229Ile	97.0	0.0	.		132.0	38.0	.	NM_033413	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	hg19	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	G	6.561	0.471736	0.12461	.	.	ENSG00000141294	ENST00000269025	T	0.72167	-0.63	5.53	-11.1	0.00147	.	1.132520	0.06682	N	0.768096	T	0.41558	0.1164	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47623	-0.9103	10	0.37606	T	0.19	0.4736	6.5183	0.22260	0.1084:0.4274:0.3331:0.131	.	229;229	A8K9Q0;Q96FV0	.;LRC46_HUMAN	I	229	ENSP00000269025:M229I	ENSP00000269025:M229I	M	+	3	0	LRRC46	43269206	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.635000	0.00058	-4.674000	0.00036	-1.325000	0.01285	ATG	.	.	.	none		0.667	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413	
ACSF2	80221	hgsc.bcm.edu	37	17	48549793	48549793	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:48549793G>A	ENST00000300441.4	+	12	1432	c.1328G>A	c.(1327-1329)cGg>cAg	p.R443Q	ACSF2_ENST00000504392.1_Missense_Mutation_p.R400Q|ACSF2_ENST00000541920.1_Missense_Mutation_p.R283Q|ACSF2_ENST00000502667.1_Missense_Mutation_p.R430Q|ACSF2_ENST00000506085.1_Intron|ACSF2_ENST00000427954.2_Missense_Mutation_p.R468Q	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	443					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCCCAGGCCCGGATCATGAAC	0.612																																					p.R443Q		Atlas-SNP	.											.	ACSF2	46	.	0			c.G1328A						PASS	.						50.0	48.0	49.0					17																	48549793		2203	4300	6503	SO:0001583	missense	80221	exon12			AGGCCCGGATCAT	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1328G>A	chr17.hg19:g.48549793G>A	ENSP00000300441:p.Arg443Gln	34.0	0.0	.		53.0	31.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.851859	0.32699	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.09	1.7	0.24286	AMP-dependent synthetase/ligase (1);	0.312695	0.37393	N	0.002103	T	0.26810	0.0656	L	0.28192	0.835	0.24361	N	0.994876	B;B;B;B	0.15930	0.003;0.015;0.003;0.003	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.18085	-1.0348	10	0.52906	T	0.07	-5.2723	7.7408	0.28841	0.7438:0.0:0.2562:0.0	.	430;468;400;443	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	Q	443;283;400;468;430	ENSP00000300441:R443Q;ENSP00000437987:R283Q;ENSP00000425964:R400Q;ENSP00000401831:R468Q;ENSP00000421884:R430Q	ENSP00000300441:R443Q	R	+	2	0	ACSF2	45904792	1.000000	0.71417	0.994000	0.49952	0.237000	0.25408	4.324000	0.59228	0.295000	0.22570	-0.378000	0.06908	CGG	.	.	.	none		0.612	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
PITPNC1	26207	hgsc.bcm.edu	37	17	65665781	65665781	+	Splice_Site	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:65665781T>C	ENST00000581322.1	+	7	618		c.e7+2		PITPNC1_ENST00000335257.6_Splice_Site|PITPNC1_ENST00000580974.1_Splice_Site|PITPNC1_ENST00000299954.9_Splice_Site			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1						phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)			breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GTACACAAGGTAAGTGGTCCA	0.468																																					.		Atlas-SNP	.											.	PITPNC1	47	.	0			c.618+2T>C						PASS	.						64.0	68.0	67.0					17																	65665781		1987	4159	6146	SO:0001630	splice_region_variant	26207	exon7			ACAAGGTAAGTGG	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.618+2T>C	chr17.hg19:g.65665781T>C		10.0	0.0	.		20.0	12.0	.	NM_181671	A8K473|J3QR20|Q96I07	Splice_Site	SNP	ENST00000581322.1	hg19	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709581	0.68730	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0556	0.80801	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PITPNC1	63096243	1.000000	0.71417	0.955000	0.39395	0.604000	0.37047	7.880000	0.87243	2.239000	0.73571	0.533000	0.62120	.	.	.	.	none		0.468	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	Intron
DNAH17	8632	hgsc.bcm.edu	37	17	76491997	76491997	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:76491997C>G	ENST00000585328.1	-	38	5972	c.5848G>C	c.(5848-5850)Gga>Cga	p.G1950R	RP11-559N14.5_ENST00000585969.1_RNA|DNAH17-AS1_ENST00000598378.1_5'Flank|DNAH17_ENST00000389840.5_Missense_Mutation_p.G1941R|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1941	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TCCGCGCGTCCGGCGTACCCA	0.557																																					p.G1955R		Atlas-SNP	.											.	DNAH17	347	.	0			c.G5863C						PASS	.						93.0	94.0	94.0					17																	76491997		2059	4237	6296	SO:0001583	missense	8632	exon38			CGCGTCCGGCGTA	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.5848G>C	chr17.hg19:g.76491997C>G	ENSP00000465516:p.Gly1950Arg	77.0	0.0	.		82.0	20.0	.	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	c	16.89	3.247501	0.59103	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.17528	2.27	4.49	4.49	0.54785	.	.	.	.	.	T	0.57902	0.2085	H	0.96833	3.89	0.58432	D	0.999995	.	.	.	.	.	.	T	0.74910	-0.3503	7	0.87932	D	0	.	17.7846	0.88533	0.0:1.0:0.0:0.0	.	.	.	.	R	1950;1941	ENSP00000374490:G1941R	ENSP00000300671:G1950R	G	-	1	0	DNAH17	74003592	1.000000	0.71417	0.121000	0.21740	0.087000	0.18053	7.472000	0.80996	2.501000	0.84356	0.537000	0.68136	GGA	.	.	.	none		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
PNPLA6	10908	hgsc.bcm.edu	37	19	7615223	7615223	+	Silent	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:7615223G>A	ENST00000221249.6	+	18	2168	c.1737G>A	c.(1735-1737)gcG>gcA	p.A579A	PNPLA6_ENST00000545201.2_Silent_p.A553A|PNPLA6_ENST00000600737.1_Silent_p.A618A|PNPLA6_ENST00000450331.3_Silent_p.A579A|PNPLA6_ENST00000414982.3_Silent_p.A627A|PNPLA6_ENST00000594864.1_3'UTR	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	618					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TGAGTGCGGCGCACACGGTGG	0.637																																					p.A627A		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G1881A						PASS	.						61.0	58.0	59.0					19																	7615223		2202	4290	6492	SO:0001819	synonymous_variant	10908	exon17			TGCGGCGCACACG	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1737G>A	chr19.hg19:g.7615223G>A		113.0	0.0	.		149.0	53.0	.	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	hg19	CCDS32891.1																																																																																			.	.	.	none		0.637	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
JUNB	3726	hgsc.bcm.edu	37	19	12902787	12902787	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:12902787T>C	ENST00000302754.4	+	1	478	c.202T>C	c.(202-204)Tac>Cac	p.Y68H		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	68					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|decidualization (GO:0046697)|embryonic process involved in female pregnancy (GO:0060136)|gene expression (GO:0010467)|labyrinthine layer blood vessel development (GO:0060716)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|osteoclast differentiation (GO:0030316)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|kidney(1)|lung(3)	6						TGGCGGCAGCTACTTTTCTGG	0.672																																					p.Y68H		Atlas-SNP	.											.	JUNB	14	.	0			c.T202C						PASS	.						12.0	13.0	13.0					19																	12902787		2200	4294	6494	SO:0001583	missense	3726	exon1			GGCAGCTACTTTT	M29039	CCDS12280.1	19p13.13	2013-01-10				ENSG00000171223		"""basic leucine zipper proteins"""	6205	protein-coding gene	gene with protein product		165161				2513129	Standard	NM_002229		Approved		uc002mvc.3	P17275		ENST00000302754.4:c.202T>C	chr19.hg19:g.12902787T>C	ENSP00000303315:p.Tyr68His	15.0	0.0	.		31.0	13.0	.	NM_002229	Q96GH3	Missense_Mutation	SNP	ENST00000302754.4	hg19	CCDS12280.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192125	0.38707	.	.	ENSG00000171223	ENST00000302754	T	0.29142	1.58	4.97	4.97	0.65823	Jun-like transcription factor (1);	1.243760	0.05788	U	0.609862	T	0.21103	0.0508	N	0.22421	0.69	0.34616	D	0.718126	B	0.18166	0.026	B	0.11329	0.006	T	0.28681	-1.0036	10	0.15499	T	0.54	-6.7954	6.385	0.21556	0.0:0.1805:0.0:0.8195	.	68	P17275	JUNB_HUMAN	H	68	ENSP00000303315:Y68H	ENSP00000303315:Y68H	Y	+	1	0	JUNB	12763787	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.617000	0.36943	1.865000	0.54081	0.448000	0.29417	TAC	.	.	.	none		0.672	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229	
ZNF681	148213	hgsc.bcm.edu	37	19	23927146	23927146	+	Silent	SNP	A	A	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:23927146A>G	ENST00000402377.3	-	4	1347	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	ZNF681_ENST00000395385.3_Silent_p.A333A	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				ACTTGTTAAAAGCTTTGCCAC	0.398																																					p.A402A		Atlas-SNP	.											ZNF681,bladder,carcinoma,0,8	ZNF681	76	.	0			c.T1206C						PASS	.						69.0	74.0	72.0					19																	23927146		2203	4300	6503	SO:0001819	synonymous_variant	148213	exon4			GTTAAAAGCTTTG	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1206T>C	chr19.hg19:g.23927146A>G		53.0	1.0	.		62.0	3.0	.	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.	.	none		0.398	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
LSM14A	26065	hgsc.bcm.edu	37	19	34712486	34712486	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:34712486G>T	ENST00000433627.5	+	9	1286	c.1211G>T	c.(1210-1212)cGt>cTt	p.R404L	LSM14A_ENST00000540746.2_Missense_Mutation_p.R363L|LSM14A_ENST00000544216.3_Missense_Mutation_p.R404L	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	404					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CGTCCAAACCGTGGCCGTGGG	0.507																																					p.R404L		Atlas-SNP	.											.	LSM14A	44	.	0			c.G1211T						PASS	.						96.0	71.0	79.0					19																	34712486		2203	4300	6503	SO:0001583	missense	26065	exon9			CAAACCGTGGCCG	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"""chromosome 19 open reading frame 13"", ""family with sequence similarity 61, member A"", ""LSM14 homolog A (SCD6, S. cerevisiae)"""	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.1211G>T	chr19.hg19:g.34712486G>T	ENSP00000413964:p.Arg404Leu	87.0	0.0	.		63.0	20.0	.	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	hg19	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	g	28.6	4.933243	0.92458	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.18657	2.2;2.2;2.2	5.96	4.93	0.64822	.	0.104479	0.64402	D	0.000004	T	0.40297	0.1111	M	0.76002	2.32	0.80722	D	1	P;D;D	0.56287	0.889;0.958;0.975	B;P;P	0.55824	0.396;0.614;0.785	T	0.26503	-1.0101	10	0.37606	T	0.19	-9.5825	15.0274	0.71680	0.0679:0.0:0.9321:0.0	.	363;404;404	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	L	404;404;363	ENSP00000446271:R404L;ENSP00000413964:R404L;ENSP00000446451:R363L	ENSP00000314768:R404L	R	+	2	0	LSM14A	39404326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.382000	0.97209	1.533000	0.49186	0.655000	0.94253	CGT	.	.	.	none		0.507	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38572702	38572702	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:38572702T>C	ENST00000222345.6	+	3	1006	c.497T>C	c.(496-498)cTt>cCt	p.L166P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	166					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TTCCTCCCCCTTCGGCACCGC	0.711																																					p.L166P		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.T497C						PASS	.						46.0	56.0	53.0					19																	38572702		2203	4299	6502	SO:0001583	missense	23094	exon3			TCCCCCTTCGGCA	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.497T>C	chr19.hg19:g.38572702T>C	ENSP00000222345:p.Leu166Pro	105.0	0.0	.		125.0	52.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.672868	0.67928	.	.	ENSG00000105738	ENST00000222345	T	0.80994	-1.44	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000006	D	0.83737	0.5319	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.85925	0.1448	10	0.87932	D	0	-15.4086	14.0813	0.64925	0.0:0.0:0.0:1.0	.	166	O60292	SI1L3_HUMAN	P	166	ENSP00000222345:L166P	ENSP00000222345:L166P	L	+	2	0	SIPA1L3	43264542	0.433000	0.25562	0.937000	0.37676	0.960000	0.62799	3.929000	0.56514	1.971000	0.57363	0.460000	0.39030	CTT	.	.	.	none		0.711	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
MYL9	10398	hgsc.bcm.edu	37	20	35177592	35177592	+	Silent	SNP	C	C	T			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35177592C>T	ENST00000279022.2	+	4	563	c.459C>T	c.(457-459)aaC>aaT	p.N153N	RP5-977B1.11_ENST00000561134.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA|MYL9_ENST00000346786.2_Silent_p.N99N	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	153	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				AGAAAGGCAACTTCAACTACG	0.592																																					p.N153N		Atlas-SNP	.											.	MYL9	13	.	0			c.C459T						PASS	.						112.0	95.0	101.0					20																	35177592		2203	4300	6503	SO:0001819	synonymous_variant	10398	exon4			AGGCAACTTCAAC	J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"""Myosins / Light chain"", ""EF-hand domain containing"""	15754	protein-coding gene	gene with protein product	"""myosin regulatory light chain 2, smooth muscle isoform"", ""myosin regulatory light chain 1"""	609905	"""myosin, light polypeptide 9, regulatory"""			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.459C>T	chr20.hg19:g.35177592C>T		49.0	0.0	.		69.0	20.0	.	NM_006097	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	hg19	CCDS13276.1																																																																																			.	.	.	none		0.592	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097	
UBA1	7317	hgsc.bcm.edu	37	X	47069022	47069022	+	Splice_Site	SNP	T	T	G			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:47069022T>G	ENST00000335972.6	+	17	2122	c.1939T>G	c.(1939-1941)Tgg>Ggg	p.W647G	UBA1_ENST00000377269.3_Missense_Mutation_p.W95G|UBA1_ENST00000377351.4_Splice_Site_p.W647G	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	647					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CTGTCTGCAGTGGGCTCGGGA	0.498																																					p.W647G		Atlas-SNP	.											.	UBA1	89	.	0			c.T1939G						PASS	.						122.0	93.0	103.0					X																	47069022		2203	4300	6503	SO:0001630	splice_region_variant	7317	exon17			CTGCAGTGGGCTC	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1939-1T>G	chrX.hg19:g.47069022T>G		21.0	0.0	.		32.0	26.0	.	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.009850	0.75046	.	.	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.51817	0.69;0.69;0.69	5.22	5.22	0.72569	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-activating enzyme (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.111594	0.64402	D	0.000003	T	0.79782	0.4505	H	0.98577	4.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86491	0.1797	10	0.87932	D	0	-10.8017	11.8816	0.52579	0.0:0.0:0.0:1.0	.	95;647	Q5JRR6;P22314	.;UBA1_HUMAN	G	647;647;95	ENSP00000366568:W647G;ENSP00000338413:W647G;ENSP00000366481:W95G	ENSP00000338413:W647G	W	+	1	0	UBA1	46953966	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.580000	0.82523	1.860000	0.53959	0.427000	0.28365	TGG	.	.	.	none		0.498	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	Missense_Mutation
PLXNB3	5365	hgsc.bcm.edu	37	X	153037078	153037078	+	Missense_Mutation	SNP	G	G	C	rs375202688		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:153037078G>C	ENST00000361971.5	+	14	2599	c.2485G>C	c.(2485-2487)Gag>Cag	p.E829Q	PLXNB3_ENST00000538776.1_Missense_Mutation_p.E482Q|PLXNB3_ENST00000538966.1_Missense_Mutation_p.E852Q|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E439Q	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	829	PSI 3.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGGGCTGTGGAGCTGCTGTG	0.692																																					p.E852Q		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G2554C						PASS	.						20.0	20.0	20.0					X																	153037078		2180	4292	6472	SO:0001583	missense	5365	exon15			GCTGTGGAGCTGC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.2485G>C	chrX.hg19:g.153037078G>C	ENSP00000355378:p.Glu829Gln	14.0	0.0	.		12.0	12.0	.	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.404697	0.25378	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.66460	5.33;5.29;4.71;-0.21	5.01	-0.321	0.12717	.	.	.	.	.	T	0.59945	0.2231	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.23128	0.001;0.08;0.009;0.003	B;B;B;B	0.17098	0.005;0.017;0.008;0.005	T	0.43718	-0.9374	9	0.12103	T	0.63	.	17.8542	0.88758	0.0:0.6872:0.3128:0.0	.	482;511;852;829	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	Q	852;829;482;439	ENSP00000442736:E852Q;ENSP00000355378:E829Q;ENSP00000445569:E482Q;ENSP00000441919:E439Q	ENSP00000355378:E829Q	E	+	1	0	PLXNB3	152690272	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.736000	0.26130	-0.636000	0.05524	-0.347000	0.07816	GAG	.	.	.	weak		0.692	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
MT-ND1	4535	hgsc.bcm.edu	37	M	3776	3776	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrM:3776G>A	ENST00000361390.2	+	1	470	c.470G>A	c.(469-471)aGt>aAt	p.S157N	MT-TN_ENST00000387400.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-RNR2_ENST00000387347.2_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TA_ENST00000387392.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	157					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)	ATTACTAATAAGTGGCTCCTT	0.443																																					p.S157N		Atlas-SNP	.											.	.	.	.	0			c.G470A						PASS	.																																			SO:0001583	missense	10625	exon1			TAATAAGTGGCTC			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.470G>A	chrM.hg19:g.3776G>A	ENSP00000354687:p.Ser157Asn	1.0	0.0	.		10.0	10.0	.	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	hg19																																																																																				.	.	.	none		0.443	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
MT-ND5	4540	hgsc.bcm.edu	37	M	13814	13814	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrM:13814T>C	ENST00000361567.2	+	1	1478	c.1478T>C	c.(1477-1479)gTc>gCc	p.V493A	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	493					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AGCCCTCGCTGTCACTTTCCT	0.438																																					p.V493A		Atlas-SNP	.											.	.	.	.	0			c.T1478C						PASS	.																																			SO:0001583	missense	0	exon1			TCGCTGTCACTTT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1478T>C	chrM.hg19:g.13814T>C	ENSP00000354813:p.Val493Ala	0.0	0.0	.		15.0	14.0	.	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.	.	none		0.438	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
UEVLD	55293	hgsc.bcm.edu	37	11	18568448	18568448	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:18568448delG	ENST00000396197.3	-	8	893	c.865delC	c.(865-867)ctgfs	p.L290fs	UEVLD_ENST00000543987.1_Frame_Shift_Del_p.L290fs|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000535484.1_Frame_Shift_Del_p.L252fs|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000379387.4_Frame_Shift_Del_p.L268fs|UEVLD_ENST00000320750.6_Frame_Shift_Del_p.L268fs	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GCAACGAGCAGGACACTGTGT	0.403																																					p.L289fs		Atlas-INDEL	.											.	UEVLD	58	.	0			c.866delT						PASS	.						142.0	133.0	136.0					11																	18568448		2199	4293	6492	SO:0001589	frameshift_variant	55293	exon8			.	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.865delC	chr11.hg19:g.18568448delG	ENSP00000379500:p.Leu290fs	125.0	0.0	0		98.0	35.0	0.357143	NM_018314		Frame_Shift_Del	DEL	ENST00000396197.3	hg19	CCDS41624.1																																																																																			.	.	.	none		0.403	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
FAM208B	54906	hgsc.bcm.edu	37	10	5790239	5790239	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:5790239delT	ENST00000328090.5	+	15	5480	c.4855delT	c.(4855-4857)tttfs	p.F1619fs		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1619																	GAACCATCTCTTTCCCGGTGA	0.453																																					p.L1618fs		Atlas-INDEL	.											.	.	.	.	0			c.4854delC						PASS	.						65.0	65.0	65.0					10																	5790239		1964	4151	6115	SO:0001589	frameshift_variant	54906	exon15			.	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.4855delT	chr10.hg19:g.5790239delT	ENSP00000328426:p.Phe1619fs	91.0	0.0	0		133.0	29.0	0.218045	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Frame_Shift_Del	DEL	ENST00000328090.5	hg19	CCDS41485.1																																																																																			.	.	.	none		0.453	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
GALNT5	11227	hgsc.bcm.edu	37	2	158115698	158115699	+	Frame_Shift_Ins	INS	-	-	T	rs141648249		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:158115698_158115699insT	ENST00000259056.4	+	1	1589_1590	c.1104_1105insT	c.(1105-1107)tctfs	p.S369fs		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	369					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						AGATGTCTTCCTCTTCACTTGC	0.416																																					p.S368fs		Atlas-INDEL	.											.	GALNT5	112	.	0			c.1104_1105insT						PASS	.																																			SO:0001589	frameshift_variant	11227	exon1			.	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4127	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 5"""	615129	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"""			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1105dupT	chr2.hg19:g.158115699_158115699dupT	ENSP00000259056:p.Ser369fs	186.0	0.0	0		147.0	49.0	0.333333	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Frame_Shift_Ins	INS	ENST00000259056.4	hg19	CCDS2203.1																																																																																			.	.	.	none		0.416	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568	
ATP1B1	481	hgsc.bcm.edu	37	1	169100749	169100768	+	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENST00000367816.1	+	7	1397_1416	c.868_887delCGTTTTCAGGGACGTTTTGA	c.(868-888)cgttttcagggacgttttgatfs	p.RFQGRFD290fs	ATP1B1_ENST00000367815.4_Frame_Shift_Del_p.RFQGRFD290fs|ATP1B1_ENST00000367813.3_Frame_Shift_Del_p.RFQGRFD282fs|ATP1B1_ENST00000499679.3_Frame_Shift_Del_p.RFQGRFD234fs			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	290	immunoglobulin-like.				blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.R290S(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					TGAGAAAGACCGTTTTCAGGGACGTTTTGATGTAAAAATT	0.4																																					p.289_296del		Atlas-INDEL	.											.	ATP1B1	29	.	1	Substitution - Missense(1)	lung(1)	c.867_886del						PASS	.																																			SO:0001589	frameshift_variant	481	exon6			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"""ATPases / P-type"""	804	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit beta-1"", ""sodium pump subunit beta-1"", ""sodium-potassium ATPase subunit beta 1 (non-catalytic)"""	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.868_887delCGTTTTCAGGGACGTTTTGA	chr1.hg19:g.169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENSP00000356790:p.Arg290fs	113.0	0.0	0		79.0	26.0	0.329114	NM_001677	Q5TGZ3	Frame_Shift_Del	DEL	ENST00000367816.1	hg19	CCDS1276.1																																																																																			.	.	.	none		0.400	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1		
STAG2	10735	hgsc.bcm.edu	37	X	123211859	123211862	+	Frame_Shift_Del	DEL	AGAT	AGAT	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	AGAT	AGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:123211859_123211862delAGAT	ENST00000371160.1	+	27	3016_3019	c.2726_2729delAGAT	c.(2725-2730)cagatafs	p.QI909fs	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371145.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000218089.9_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.QI840fs|STAG2_ENST00000371157.3_Frame_Shift_Del_p.QI909fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	909					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AAAACAAGGCAGATAGACAAAATT	0.314																																					p.909_910del		Atlas-INDEL	.											.	STAG2	309	.	0			c.2725_2728del						PASS	.																																			SO:0001589	frameshift_variant	10735	exon27			.	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2726_2729delAGAT	chrX.hg19:g.123211859_123211862delAGAT	ENSP00000360202:p.Gln909fs	69.0	0.0	0		58.0	45.0	0.775862	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.	.	none		0.314	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
CENPH	64946	hgsc.bcm.edu	37	5	68505552	68505552	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:68505552delA	ENST00000283006.2	+	9	757	c.670delA	c.(670-672)aaafs	p.K224fs	CENPH_ENST00000515001.1_Frame_Shift_Del_p.K205fs	NM_022909.3	NP_075060.1			centromere protein H											kidney(15)|large_intestine(2)|lung(3)	20		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		TTTGGGGAGTAAAGTCAATTG	0.289																																					p.S223fs		Atlas-INDEL	.											.	CENPH	28	.	0			c.669delT						PASS	.						78.0	78.0	78.0					5																	68505552		2203	4300	6503	SO:0001589	frameshift_variant	64946	exon9			.	AB035124	CCDS3998.1	5p15.2	2013-11-05			ENSG00000153044	ENSG00000153044			17268	protein-coding gene	gene with protein product		605607				11092768, 15502821	Standard	NM_022909		Approved		uc003jvp.3	Q9H3R5	OTTHUMG00000097816	ENST00000283006.2:c.670delA	chr5.hg19:g.68505552delA	ENSP00000283006:p.Lys224fs	57.0	0.0	0		57.0	31.0	0.54386	NM_022909		Frame_Shift_Del	DEL	ENST00000283006.2	hg19	CCDS3998.1																																																																																			.	.	.	none		0.289	CENPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215083.1		
ADAM29	11086	hgsc.bcm.edu	37	4	175898831	175898832	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:175898831_175898832insA	ENST00000359240.3	+	5	2825_2826	c.2155_2156insA	c.(2155-2157)gaafs	p.E719fs	ADAM29_ENST00000514159.1_Frame_Shift_Ins_p.E719fs|ADAM29_ENST00000404450.4_Frame_Shift_Ins_p.E719fs|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Frame_Shift_Ins_p.E719fs	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	719					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E719K(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AAAAGAAGAGGAAAAAATTCAG	0.406																																					p.E719fs	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-INDEL	.											ADAM29,NS,malignant_melanoma,0,1	ADAM29	262	.	1	Substitution - Missense(1)	NS(1)	c.2155_2156insA						PASS	.																																			SO:0001589	frameshift_variant	11086	exon5			.	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2161dupA	chr4.hg19:g.175898837_175898837dupA	ENSP00000352177:p.Glu719fs	101.0	0.0	0		73.0	46.0	0.630137	NM_014269	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Frame_Shift_Ins	INS	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.	.	none		0.406	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
UFL1	23376	hgsc.bcm.edu	37	6	96996102	96996102	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:96996102delC	ENST00000369278.4	+	13	1531	c.1465delC	c.(1465-1467)cacfs	p.H489fs		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	489					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										TTTAAGAAAACACATACAAGA	0.308																																					p.K488fs		Atlas-INDEL	.											.	.	.	.	0			c.1464delA						PASS	.						57.0	59.0	58.0					6																	96996102		2202	4300	6502	SO:0001589	frameshift_variant	23376	exon13			.	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1465delC	chr6.hg19:g.96996102delC	ENSP00000358283:p.His489fs	45.0	0.0	0		35.0	17.0	0.485714	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Frame_Shift_Del	DEL	ENST00000369278.4	hg19	CCDS5034.1																																																																																			.	.	.	none		0.308	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
MSH3	4437	hgsc.bcm.edu	37	5	80160742	80160743	+	Frame_Shift_Ins	INS	-	-	GAAA			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:80160742_80160743insGAAA	ENST00000265081.6	+	22	3191_3192	c.3111_3112insGAAA	c.(3112-3114)gaafs	p.-1038fs		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCAGTGAGGATGAAAGCAAACT	0.396								Mismatch excision repair (MMR)																													p.D1037fs	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-INDEL	.											.	MSH3	129	.	0			c.3111_3112insGAAA						PASS	.																																			SO:0001589	frameshift_variant	4437	exon22			.	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.3112_3115dupGAAA	chr5.hg19:g.80160743_80160746dupGAAA	ENSP00000265081:p.Glu1038fs	143.0	0.0	0		171.0	38.0	0.222222	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Ins	INS	ENST00000265081.6	hg19	CCDS34195.1																																																																																			.	.	.	none		0.396	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
TGIF2	60436	hgsc.bcm.edu	37	20	35219568	35219569	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35219568_35219569insA	ENST00000373874.2	+	3	647_648	c.448_449insA	c.(448-450)gagfs	p.E150fs	TGIF2_ENST00000373872.4_Frame_Shift_Ins_p.E150fs|TGIF2-C20orf24_ENST00000558530.1_Intron|RP5-977B1.11_ENST00000561134.1_RNA	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	150	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CCCACGTGGGGAGCTGGAGTCT	0.629																																					p.E150fs		Atlas-INDEL	.											.	TGIF2	26	.	0			c.448_449insA						PASS	.																																			SO:0001589	frameshift_variant	60436	exon3			.	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"""Homeoboxes / TALE class"""	15764	protein-coding gene	gene with protein product		607294	"""TGFB-induced factor 2 (TALE family homeobox)"""			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.449dupA	chr20.hg19:g.35219569_35219569dupA	ENSP00000362981:p.Glu150fs	101.0	0.0	0		104.0	42.0	0.403846	NM_021809	B2R9U3|E1P5T9|H0YNI0	Frame_Shift_Ins	INS	ENST00000373874.2	hg19	CCDS13278.1																																																																																			.	.	.	none		0.629	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809	
SLC26A8	116369	hgsc.bcm.edu	37	6	35923086	35923086	+	Frame_Shift_Del	DEL	T	T	-	rs200648238		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:35923086delT	ENST00000490799.1	-	17	2428	c.2075delA	c.(2074-2076)aacfs	p.N692fs	SLC26A8_ENST00000394602.2_Frame_Shift_Del_p.N587fs|SLC26A8_ENST00000355574.2_Frame_Shift_Del_p.N692fs	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						TGGTGAGCTGTTTCTTGATGA	0.507																																					p.N692fs		Atlas-INDEL	.											.	SLC26A8	95	.	0			c.2076delC						PASS	.						194.0	187.0	190.0					6																	35923086		2203	4300	6503	SO:0001589	frameshift_variant	116369	exon17			.	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2075delA	chr6.hg19:g.35923086delT	ENSP00000417638:p.Asn692fs	122.0	0.0	0		108.0	45.0	0.416667	NM_001193476		Frame_Shift_Del	DEL	ENST00000490799.1	hg19	CCDS4813.1																																																																																			.	.	.	none		0.507	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
NCOA2	10499	hgsc.bcm.edu	37	8	71039066	71039067	+	Frame_Shift_Ins	INS	-	-	AAAC			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:71039066_71039067insAAAC	ENST00000452400.2	-	19	4078_4079	c.3897_3898insGTTT	c.(3895-3900)tttccafs	p.P1300fs	NCOA2_ENST00000267974.4_Frame_Shift_Ins_p.P388fs	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1300					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GGAGGAAATGGAAACTGCTGTG	0.53			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.P1300fs		Atlas-INDEL	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.3898_3899insGTTT						PASS	.																																			SO:0001589	frameshift_variant	10499	exon19			.	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3894_3897dupGTTT	chr8.hg19:g.71039067_71039070dupAAAC	ENSP00000399968:p.Pro1300fs	43.0	0.0	0		50.0	11.0	0.22	NM_006540	Q14CD2	Frame_Shift_Ins	INS	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.	.	none		0.530	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
LGR4	55366	hgsc.bcm.edu	37	11	27412675	27412676	+	In_Frame_Ins	INS	-	-	AAG			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:27412675_27412676insAAG	ENST00000379214.4	-	4	809_810	c.366_367insCTT	c.(364-369)agtgaa>agtCTTgaa	p.122_123SE>SLE	LGR4_ENST00000480977.2_Intron|LGR4_ENST00000389858.4_In_Frame_Ins_p.98_99SE>SLE	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	122					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CGAATGGCTTCACTGGGTACTG	0.366																																					p.E123delinsLE		Atlas-INDEL	.											LGR4,NS,carcinoma,0,1	LGR4	87	.	0			c.367_368insCTT						PASS	.																																			SO:0001652	inframe_insertion	55366	exon4			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.366_367insCTT	chr11.hg19:g.27412675_27412676insAAG	ENSP00000368516:p.Ser122_Glu123insLeu	85.0	0.0	0		83.0	21.0	0.253012	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	In_Frame_Ins	INS	ENST00000379214.4	hg19	CCDS31449.1																																																																																			.	.	.	none		0.366	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
