#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
OR10Z1	128368	hgsc.bcm.edu	37	1	158576688	158576688	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158576688C>T	ENST00000361284.1	+	1	460	c.460C>T	c.(460-462)Ctc>Ttc	p.L154F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					GACTGGATACCTCTTTGGACT	0.498																																					p.L154F		Atlas-SNP	.											.	OR10Z1	99	.	0			c.C460T						.						105.0	100.0	102.0					1																	158576688		2203	4300	6503	SO:0001583	missense	128368	exon1			GGATACCTCTTTG	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.460C>T	chr1.hg19:g.158576688C>T	ENSP00000354707:p.Leu154Phe	135.0	0.0		171.0	44.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	C	0.519	-0.862988	0.02610	.	.	ENSG00000198967	ENST00000361284	T	0.46451	0.87	5.36	-1.87	0.07737	GPCR, rhodopsin-like superfamily (1);	0.887851	0.09141	N	0.843040	T	0.10337	0.0253	L	0.31752	0.955	0.09310	N	1	B	0.10296	0.003	B	0.20577	0.03	T	0.35699	-0.9778	10	0.33940	T	0.23	.	4.9305	0.13914	0.2362:0.287:0.0:0.4769	.	154	Q8NGY1	O10Z1_HUMAN	F	154	ENSP00000354707:L154F	ENSP00000354707:L154F	L	+	1	0	OR10Z1	156843312	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.264000	0.02847	-0.522000	0.06417	-0.982000	0.02568	CTC	.	.		0.498	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
SPTA1	6708	hgsc.bcm.edu	37	1	158605719	158605719	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158605719C>G	ENST00000368147.4	-	38	5596	c.5416G>C	c.(5416-5418)Gag>Cag	p.E1806Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1806					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGGCCAACTCTTTGAGCTTC	0.537																																					p.E1806Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5416C						.						90.0	93.0	92.0					1																	158605719		1942	4139	6081	SO:0001583	missense	6708	exon38			CCAACTCTTTGAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5416G>C	chr1.hg19:g.158605719C>G	ENSP00000357129:p.Glu1806Gln	48.0	0.0		72.0	55.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536202	0.27475	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51574	0.7;0.7	5.65	3.8	0.43715	.	0.266274	0.19779	N	0.106267	T	0.19765	0.0475	L	0.59967	1.855	0.32110	N	0.589433	B	0.30973	0.302	B	0.30401	0.115	T	0.09228	-1.0684	10	0.12766	T	0.61	.	7.8794	0.29614	0.0:0.7181:0.1338:0.1481	.	1806	P02549	SPTA1_HUMAN	Q	1806	ENSP00000357130:E1806Q;ENSP00000357129:E1806Q	ENSP00000357129:E1806Q	E	-	1	0	SPTA1	156872343	0.998000	0.40836	0.998000	0.56505	0.993000	0.82548	3.002000	0.49496	0.944000	0.37579	0.655000	0.94253	GAG	.	.		0.537	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
OR6K2	81448	hgsc.bcm.edu	37	1	158670099	158670099	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158670099G>C	ENST00000359610.2	-	1	387	c.344C>G	c.(343-345)aCa>aGa	p.T115R		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	115						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GGCCATAACTGTCAAGAGACA	0.478																																					p.T115R		Atlas-SNP	.											.	OR6K2	104	.	0			c.C344G						.						112.0	102.0	105.0					1																	158670099		2203	4300	6503	SO:0001583	missense	81448	exon1			ATAACTGTCAAGA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.344C>G	chr1.hg19:g.158670099G>C	ENSP00000352626:p.Thr115Arg	90.0	0.0		103.0	56.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484518	0.63962	.	.	ENSG00000196171	ENST00000359610	T	0.01359	4.98	4.7	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39341	N	0.001389	T	0.05914	0.0154	H	0.95224	3.64	0.31333	N	0.684559	D	0.60575	0.988	P	0.59825	0.864	T	0.00918	-1.1515	10	0.87932	D	0	-4.7894	12.2266	0.54463	0.0863:0.0:0.9137:0.0	.	115	Q8NGY2	OR6K2_HUMAN	R	115	ENSP00000352626:T115R	ENSP00000352626:T115R	T	-	2	0	OR6K2	156936723	0.009000	0.17119	1.000000	0.80357	0.973000	0.67179	1.689000	0.37700	2.413000	0.81919	0.650000	0.86243	ACA	.	.		0.478	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
DCAF6	55827	hgsc.bcm.edu	37	1	167971772	167971772	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:167971772C>T	ENST00000312263.6	+	8	1160	c.956C>T	c.(955-957)aCt>aTt	p.T319I	DCAF6_ENST00000432587.2_Missense_Mutation_p.T288I|DCAF6_ENST00000367843.3_Missense_Mutation_p.T319I|DCAF6_ENST00000367840.3_Missense_Mutation_p.T319I	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	319					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TGGTCAGATACTGGACCCAGA	0.373																																					p.T319I		Atlas-SNP	.											.	DCAF6	99	.	0			c.C956T						.						153.0	154.0	154.0					1																	167971772		2203	4300	6503	SO:0001583	missense	55827	exon8			CAGATACTGGACC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.956C>T	chr1.hg19:g.167971772C>T	ENSP00000311949:p.Thr319Ile	234.0	0.0		237.0	64.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183393	0.94885	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	D;T;D;D	0.84660	-1.8;-0.17;-1.79;-1.88	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.048107	0.85682	D	0.000000	D	0.91640	0.7358	M	0.74647	2.275	0.45076	D	0.998099	D;D;D;D	0.76494	0.999;0.999;0.994;0.997	D;D;P;D	0.78314	0.991;0.972;0.836;0.914	D	0.91405	0.5146	9	0.66056	D	0.02	.	19.8925	0.96935	0.0:1.0:0.0:0.0	.	288;319;319;319	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	I	319;288;319;319	ENSP00000356817:T319I;ENSP00000396238:T288I;ENSP00000311949:T319I;ENSP00000356814:T319I	ENSP00000311949:T319I	T	+	2	0	DCAF6	166238396	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.890000	0.75633	2.787000	0.95880	0.650000	0.86243	ACT	.	.		0.373	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
SHCBP1L	81626	hgsc.bcm.edu	37	1	182873386	182873386	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:182873386C>T	ENST00000367547.3	-	8	1752	c.1516G>A	c.(1516-1518)Gaa>Aaa	p.E506K	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Missense_Mutation_p.E387K	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	578										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CCTGTTCCTTCACATTTTAAT	0.413																																					p.E506K		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.G1516A						.						157.0	153.0	154.0					1																	182873386		2203	4300	6503	SO:0001583	missense	81626	exon8			TTCCTTCACATTT	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1516G>A	chr1.hg19:g.182873386C>T	ENSP00000356518:p.Glu506Lys	75.0	0.0		111.0	24.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664124	0.88251	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.41065	1.01;1.01	5.55	5.55	0.83447	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);Pectin lyase fold (1);	0.000000	0.64402	D	0.000014	T	0.57770	0.2076	L	0.47190	1.495	0.39150	D	0.962202	D;D;D	0.71674	0.998;0.991;0.998	D;P;D	0.79108	0.992;0.86;0.986	T	0.55786	-0.8086	10	0.38643	T	0.18	-27.4096	16.4312	0.83844	0.0:1.0:0.0:0.0	.	578;387;506	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	K	506;575;387	ENSP00000356518:E506K;ENSP00000397308:E387K	ENSP00000287709:E575K	E	-	1	0	SHCBP1L	181140009	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.085000	0.64468	2.618000	0.88619	0.655000	0.94253	GAA	.	.		0.413	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933	
HMCN1	83872	hgsc.bcm.edu	37	1	186097385	186097385	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:186097385C>T	ENST00000271588.4	+	83	13095	c.12866C>T	c.(12865-12867)cCc>cTc	p.P4289L	HMCN1_ENST00000367492.2_Missense_Mutation_p.P4289L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4289	Ig-like C2-type 42.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATTCCATTGCCCAAATTAACA	0.378																																					p.P4289L		Atlas-SNP	.											.	HMCN1	797	.	0			c.C12866T						.						89.0	84.0	86.0					1																	186097385		2203	4300	6503	SO:0001583	missense	83872	exon83			CATTGCCCAAATT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12866C>T	chr1.hg19:g.186097385C>T	ENSP00000271588:p.Pro4289Leu	37.0	0.0		57.0	23.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000600	0.93227	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.71461	-0.57;-0.57	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89548	0.3797	10	0.27785	T	0.31	.	19.0722	0.93143	0.0:1.0:0.0:0.0	.	4289	Q96RW7	HMCN1_HUMAN	L	4289	ENSP00000271588:P4289L;ENSP00000356462:P4289L	ENSP00000271588:P4289L	P	+	2	0	HMCN1	184364008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.469000	0.80959	2.502000	0.84385	0.585000	0.79938	CCC	.	.		0.378	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
IFT172	26160	hgsc.bcm.edu	37	2	27688641	27688641	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:27688641T>G	ENST00000260570.3	-	17	1904	c.1801A>C	c.(1801-1803)Aca>Cca	p.T601P		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	601					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TCAATGGCTGTTCCAAACTCG	0.567																																					p.T601P		Atlas-SNP	.											.	IFT172	119	.	0			c.A1801C						.						389.0	367.0	375.0					2																	27688641		2203	4300	6503	SO:0001583	missense	26160	exon17			TGGCTGTTCCAAA	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.1801A>C	chr2.hg19:g.27688641T>G	ENSP00000260570:p.Thr601Pro	75.0	0.0		67.0	33.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	T	31	5.065895	0.93898	.	.	ENSG00000138002	ENST00000260570	T	0.63580	-0.05	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.79215	0.4408	M	0.85373	2.75	0.80722	D	1	D	0.64830	0.994	P	0.61800	0.894	T	0.82916	-0.0220	10	0.72032	D	0.01	-10.8715	14.679	0.69004	0.0:0.0:0.0:1.0	.	601	Q9UG01	IF172_HUMAN	P	601	ENSP00000260570:T601P	ENSP00000260570:T601P	T	-	1	0	IFT172	27542145	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.281000	0.78621	2.157000	0.67596	0.533000	0.62120	ACA	.	.		0.567	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
ABCG8	64241	hgsc.bcm.edu	37	2	44099245	44099245	+	Silent	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:44099245G>T	ENST00000272286.2	+	7	1185	c.1095G>T	c.(1093-1095)acG>acT	p.T365T		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	365					ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	AAGCAGAGACGAAGGATCTTG	0.552																																					p.T365T		Atlas-SNP	.											.	ABCG8	98	.	0			c.G1095T						.						119.0	116.0	117.0					2																	44099245		2203	4300	6503	SO:0001819	synonymous_variant	64241	exon7			AGAGACGAAGGAT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1095G>T	chr2.hg19:g.44099245G>T		61.0	0.0		75.0	31.0	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	hg19	CCDS1815.1																																																																																			.	.		0.552	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
XIRP2	129446	hgsc.bcm.edu	37	2	168100450	168100450	+	Silent	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:168100450T>C	ENST00000409195.1	+	9	2637	c.2548T>C	c.(2548-2550)Tta>Cta	p.L850L	XIRP2_ENST00000409273.1_Silent_p.L628L|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.L850L|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	675					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACCCAGCCATTAGACATTCT	0.368																																					p.L850L		Atlas-SNP	.											.	XIRP2	914	.	0			c.T2548C						.						106.0	105.0	105.0					2																	168100450		1837	4093	5930	SO:0001819	synonymous_variant	129446	exon9			CAGCCATTAGACA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2548T>C	chr2.hg19:g.168100450T>C		173.0	0.0		135.0	55.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
XIRP2	129446	hgsc.bcm.edu	37	2	168104420	168104420	+	Missense_Mutation	SNP	G	G	T	rs375925351		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:168104420G>T	ENST00000409195.1	+	9	6607	c.6518G>T	c.(6517-6519)gGa>gTa	p.G2173V	XIRP2_ENST00000409273.1_Missense_Mutation_p.G1951V|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.G2173V|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1998	Pro-rich.				actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATGCCAGTTGGAGGAACTTAC	0.353																																					p.G2173V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G6518T						.						41.0	39.0	40.0					2																	168104420		1843	4084	5927	SO:0001583	missense	129446	exon9			CAGTTGGAGGAAC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6518G>T	chr2.hg19:g.168104420G>T	ENSP00000386840:p.Gly2173Val	124.0	0.0		116.0	55.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	13.51	2.259266	0.39995	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.21734	1.99;1.99;1.99	5.84	0.185	0.15096	.	1.178370	0.05809	N	0.613663	T	0.17534	0.0421	L	0.54323	1.7	0.09310	N	1	B;B;B	0.18610	0.017;0.029;0.029	B;B;B	0.21151	0.008;0.018;0.033	T	0.34030	-0.9845	10	0.21540	T	0.41	-2.0792	1.5813	0.02635	0.3283:0.1381:0.3935:0.1401	.	1998;1998;1951	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	2173;2173;1951	ENSP00000386840:G2173V;ENSP00000295237:G2173V;ENSP00000387255:G1951V	ENSP00000295237:G2173V	G	+	2	0	XIRP2	167812666	0.000000	0.05858	0.001000	0.08648	0.618000	0.37518	0.543000	0.23237	0.096000	0.17463	-0.142000	0.14014	GGA	.	.		0.353	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
TTN	7273	hgsc.bcm.edu	37	2	179560596	179560596	+	Silent	SNP	A	A	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:179560596A>G	ENST00000591111.1	-	112	30476	c.30252T>C	c.(30250-30252)taT>taC	p.Y10084Y	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.Y10401Y|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.Y9157Y			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATACCTTCATAGACCTCCT	0.373																																					p.Y10401Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T31203C						.						122.0	117.0	118.0					2																	179560596		1346	2805	4151	SO:0001819	synonymous_variant	7273	exon114			ACCTTCATAGACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30252T>C	chr2.hg19:g.179560596A>G		236.0	0.0		190.0	85.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SF3B1	23451	hgsc.bcm.edu	37	2	198267360	198267360	+	Missense_Mutation	SNP	T	T	G	rs374250186		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:198267360T>G	ENST00000335508.6	-	14	2088	c.1997A>C	c.(1996-1998)aAg>aCg	p.K666T	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	666					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K666R(7)|p.K666T(6)|p.K666M(6)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTGTACAATCTTAATACCAGT	0.413			Mis		myelodysplastic syndrome																																p.K666T		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,malignant_melanoma,0,27	SF3B1	1038	.	19	Substitution - Missense(19)	haematopoietic_and_lymphoid_tissue(18)|NS(1)	c.A1997C						.						116.0	116.0	116.0					2																	198267360		2203	4300	6503	SO:0001583	missense	23451	exon14			ACAATCTTAATAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1997A>C	chr2.hg19:g.198267360T>G	ENSP00000335321:p.Lys666Thr	120.0	0.0		128.0	58.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736206	0.89482	.	.	ENSG00000115524	ENST00000335508	T	0.65549	-0.16	5.68	5.68	0.88126	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85208	0.5644	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89754	0.3942	10	0.87932	D	0	.	15.938	0.79729	0.0:0.0:0.0:1.0	.	666	O75533	SF3B1_HUMAN	T	666	ENSP00000335321:K666T	ENSP00000335321:K666T	K	-	2	0	SF3B1	197975605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.877000	0.87225	2.167000	0.68274	0.459000	0.35465	AAG	.	.		0.413	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
TRAK2	66008	hgsc.bcm.edu	37	2	202245316	202245316	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:202245316C>G	ENST00000332624.3	-	16	3123	c.2695G>C	c.(2695-2697)Gcc>Ccc	p.A899P		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	899					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CAAACTGGGGCAGCAAAGCTA	0.423																																					p.A899P		Atlas-SNP	.											.	TRAK2	62	.	0			c.G2695C						.						66.0	59.0	61.0					2																	202245316		2203	4300	6503	SO:0001583	missense	66008	exon16			CTGGGGCAGCAAA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2695G>C	chr2.hg19:g.202245316C>G	ENSP00000328875:p.Ala899Pro	118.0	0.0		99.0	42.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	hg19	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802824	0.31869	.	.	ENSG00000115993	ENST00000332624	T	0.09723	2.95	6.03	-2.93	0.05598	.	0.524458	0.19144	N	0.121611	T	0.05227	0.0139	N	0.17082	0.46	0.28565	N	0.910905	B	0.06786	0.001	B	0.04013	0.001	T	0.21245	-1.0251	10	0.46703	T	0.11	.	6.8752	0.24143	0.0:0.4932:0.2116:0.2952	.	899	O60296	TRAK2_HUMAN	P	899	ENSP00000328875:A899P	ENSP00000328875:A899P	A	-	1	0	TRAK2	201953561	0.632000	0.27172	0.013000	0.15412	0.864000	0.49448	0.786000	0.26844	-0.451000	0.07097	-0.768000	0.03414	GCC	.	.		0.423	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
HACL1	26061	hgsc.bcm.edu	37	3	15604875	15604875	+	Missense_Mutation	SNP	C	C	G	rs149555880	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:15604875C>G	ENST00000321169.5	-	16	2061	c.1694G>C	c.(1693-1695)cGg>cCg	p.R565P	HACL1_ENST00000435217.2_Missense_Mutation_p.R324P|HACL1_ENST00000457447.2_Missense_Mutation_p.R505P|HACL1_ENST00000456194.2_Missense_Mutation_p.R538P|HACL1_ENST00000451445.2_Missense_Mutation_p.R483P	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	565					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CTGGGCCTTCCGTGTGGCTTG	0.453																																					p.R565P		Atlas-SNP	.											.	HACL1	33	.	0			c.G1694C						.						187.0	171.0	176.0					3																	15604875		2203	4300	6503	SO:0001583	missense	26061	exon16			GCCTTCCGTGTGG	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"""2-hydroxyphytanoyl-CoA lyase"""	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.1694G>C	chr3.hg19:g.15604875C>G	ENSP00000323811:p.Arg565Pro	327.0	0.0		259.0	132.0	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	hg19	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.886169	0.91814	.	.	ENSG00000131373	ENST00000321169;ENST00000435217;ENST00000451445;ENST00000456194;ENST00000457447	T;T;T;T;T	0.47528	1.44;0.84;1.43;1.44;0.89	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.72045	0.3412	M	0.78916	2.43	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.998;0.996;1.0;0.998	T	0.73347	-0.4011	10	0.66056	D	0.02	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	483;505;538;324;565	B4DXI5;E9PEN4;B4DWI1;B3KPX4;Q9UJ83	.;.;.;.;HACL1_HUMAN	P	565;324;483;538;505	ENSP00000323811:R565P;ENSP00000395278:R324P;ENSP00000403656:R483P;ENSP00000390699:R538P;ENSP00000404883:R505P	ENSP00000323811:R565P	R	-	2	0	HACL1	15579879	0.994000	0.37717	0.568000	0.28447	0.925000	0.55904	4.108000	0.57817	2.756000	0.94617	0.561000	0.74099	CGG	.	C|1.000;T|0.000		0.453	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260	
KCNH8	131096	hgsc.bcm.edu	37	3	19554731	19554731	+	Silent	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:19554731C>T	ENST00000328405.2	+	13	2615	c.2349C>T	c.(2347-2349)ccC>ccT	p.P783P		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	783					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAATTGACCCCCCCAACCATA	0.458																																					p.P783P	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.C2349T						.						80.0	87.0	85.0					3																	19554731		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon13			TGACCCCCCCAAC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2349C>T	chr3.hg19:g.19554731C>T		130.0	0.0		99.0	31.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266125	41266125	+	Missense_Mutation	SNP	C	C	T	rs121913413		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:41266125C>T	ENST00000349496.5	+	3	402	c.122C>T	c.(121-123)aCc>aTc	p.T41I	CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41I(74)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41N(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A39_T42del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGTGCCACTACCACAGCTCCT	0.507		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.T41I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,+1,98	CTNNB1	4904	.	204	Deletion - In frame(95)|Substitution - Missense(83)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	liver(105)|large_intestine(24)|pituitary(20)|endometrium(14)|stomach(8)|skin(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|pancreas(3)|thyroid(2)|small_intestine(2)|prostate(2)|ovary(2)|bone(2)|adrenal_gland(1)|cervix(1)	c.C122T						.						90.0	77.0	81.0					3																	41266125		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CCACTACCACAGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.122C>T	chr3.hg19:g.41266125C>T	ENSP00000344456:p.Thr41Ile	121.0	0.0		111.0	53.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568904	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.79258	2.445	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	T	0.72893	-0.4154	10	0.87932	D	0	-8.9189	20.2983	0.98569	0.0:1.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	I	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34I;ENSP00000385604:T41I;ENSP00000412219:T41I;ENSP00000379486:T41I;ENSP00000344456:T41I;ENSP00000411226:T34I;ENSP00000379488:T41I;ENSP00000409302:T41I;ENSP00000401599:T41I	ENSP00000344456:T41I	T	+	2	0	CTNNB1	41241129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
TRAIP	10293	hgsc.bcm.edu	37	3	49867199	49867199	+	Splice_Site	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:49867199C>T	ENST00000331456.2	-	13	1200	c.1087G>A	c.(1087-1089)Gag>Aag	p.E363K	TRAIP_ENST00000469027.1_Splice_Site_p.E208K	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	363	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGCTGGGACTCCTGCAGGGAA	0.567																																					p.E363K		Atlas-SNP	.											.	TRAIP	47	.	0			c.G1087A						.						31.0	31.0	31.0					3																	49867199		2203	4300	6503	SO:0001630	splice_region_variant	10293	exon13			GGGACTCCTGCAG	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1087-1G>A	chr3.hg19:g.49867199C>T		31.0	0.0		19.0	11.0	NM_005879	B5BU84|B5BUL3|O00467	Missense_Mutation	SNP	ENST00000331456.2	hg19	CCDS2806.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.844797	0.32606	.	.	ENSG00000183763	ENST00000331456;ENST00000469027	T	0.44881	0.91	5.08	4.21	0.49690	.	0.512387	0.20570	N	0.089742	T	0.31071	0.0785	L	0.51422	1.61	0.35350	D	0.787276	B;B	0.18610	0.001;0.029	B;B	0.14023	0.002;0.01	T	0.24835	-1.0149	10	0.06236	T	0.91	-14.4236	9.2917	0.37791	0.0:0.9033:0.0:0.0967	.	363;363	A8K807;Q9BWF2	.;TRAIP_HUMAN	K	363;208	ENSP00000420085:E208K	ENSP00000328203:E363K	E	-	1	0	TRAIP	49842203	0.998000	0.40836	0.993000	0.49108	0.134000	0.20937	1.262000	0.32992	1.376000	0.46267	0.561000	0.74099	GAG	.	.		0.567	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	Missense_Mutation
ADAMTS9	56999	hgsc.bcm.edu	37	3	64582656	64582656	+	Silent	SNP	G	G	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:64582656G>C	ENST00000498707.1	-	27	4371	c.4029C>G	c.(4027-4029)acC>acG	p.T1343T	ADAMTS9_ENST00000295903.4_Silent_p.T1315T	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1343	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CGCCAGCACAGGTACTGGAAC	0.468																																					p.T1343T		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.C4029G						.						95.0	92.0	93.0					3																	64582656		2203	4300	6503	SO:0001819	synonymous_variant	56999	exon27			AGCACAGGTACTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4029C>G	chr3.hg19:g.64582656G>C		72.0	0.0		60.0	33.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	G	9.122	1.009253	0.19277	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.4	1.43	0.22495	.	.	.	.	.	T	0.46658	0.1404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33266	-0.9875	4	.	.	.	.	4.4167	0.11459	0.0737:0.1726:0.4512:0.3025	.	.	.	.	R	399	.	.	P	-	2	0	ADAMTS9	64557696	0.743000	0.28239	1.000000	0.80357	0.994000	0.84299	-0.209000	0.09358	0.820000	0.34516	0.591000	0.81541	CCT	.	.		0.468	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
CADM2	253559	hgsc.bcm.edu	37	3	85984981	85984981	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:85984981G>T	ENST00000407528.2	+	6	800	c.738G>T	c.(736-738)ttG>ttT	p.L246F	CADM2_ENST00000405615.2_Missense_Mutation_p.L248F|CADM2_ENST00000383699.3_Missense_Mutation_p.L255F	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	246	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTTTAATTTTGACTTGTGAAT	0.308																																					p.L255F		Atlas-SNP	.											.	CADM2	195	.	0			c.G765T						.						96.0	102.0	100.0					3																	85984981		2203	4297	6500	SO:0001583	missense	253559	exon7			AATTTTGACTTGT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.738G>T	chr3.hg19:g.85984981G>T	ENSP00000384575:p.Leu246Phe	218.0	0.0		213.0	93.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155619	0.78114	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	D;T;T	0.89415	-2.51;-1.48;-1.48	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92280	0.7551	L	0.43554	1.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.89344	0.3656	10	0.23302	T	0.38	.	19.9785	0.97317	0.0:0.0:1.0:0.0	.	248;255;246	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	F	255;246;248	ENSP00000373200:L255F;ENSP00000384575:L246F;ENSP00000384193:L248F	ENSP00000373200:L255F	L	+	3	2	CADM2	86067671	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	2.724000	0.93272	0.650000	0.86243	TTG	.	.		0.308	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
PCDH7	5099	hgsc.bcm.edu	37	4	30726038	30726038	+	Silent	SNP	T	T	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:30726038T>A	ENST00000361762.2	+	1	4002	c.2994T>A	c.(2992-2994)tcT>tcA	p.S998S	PCDH7_ENST00000543491.1_Silent_p.S998S	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	998					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ATTACAAATCTAGTTCCCCAT	0.517																																					p.S998S		Atlas-SNP	.											.	PCDH7	215	.	0			c.T2994A						.						95.0	95.0	95.0					4																	30726038		2203	4300	6503	SO:0001819	synonymous_variant	5099	exon1			CAAATCTAGTTCC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2994T>A	chr4.hg19:g.30726038T>A		42.0	0.0		64.0	22.0	NM_032457	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	T	5.757	0.324047	0.10900	.	.	ENSG00000169851	ENST00000511884	.	.	.	5.08	-7.67	0.01272	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8975	0.86104	0.0:0.7091:0.1904:0.1005	.	.	.	.	K	688	.	.	X	+	1	0	PCDH7	30335136	0.000000	0.05858	0.860000	0.33809	0.989000	0.77384	-1.924000	0.01565	-1.434000	0.01975	-0.379000	0.06801	TAG	.	.		0.517	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	
SMIM14	201895	hgsc.bcm.edu	37	4	39553765	39553765	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:39553765G>A	ENST00000295958.5	-	5	667	c.281C>T	c.(280-282)cCa>cTa	p.P94L	SMIM14_ENST00000510628.1_5'UTR|SMIM14_ENST00000511809.1_Silent_p.T46T|UGDH-AS1_ENST00000504032.1_RNA	NM_174921.1	NP_777581.1	Q96QK8	SIM14_HUMAN	small integral membrane protein 14	94						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AGGAGGAGCTGGTGGATCTTG	0.318																																					p.P94L		Atlas-SNP	.											.	.	.	.	0			c.C281T						.						95.0	84.0	88.0					4																	39553765		2203	4300	6503	SO:0001583	missense	201895	exon5			GGAGCTGGTGGAT	BC008502	CCDS3456.1	4p14	2014-02-10	2012-12-03	2012-12-03	ENSG00000163683	ENSG00000163683			27321	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 34"""	C4orf34		15231747, 24499674, 23759569	Standard	NM_174921		Approved	FLJ13289	uc003guo.3	Q96QK8	OTTHUMG00000128581	ENST00000295958.5:c.281C>T	chr4.hg19:g.39553765G>A	ENSP00000295958:p.Pro94Leu	251.0	1.0		205.0	88.0	NM_174921		Missense_Mutation	SNP	ENST00000295958.5	hg19	CCDS3456.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133107	0.77662	.	.	ENSG00000163683	ENST00000295958	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.64735	0.2625	.	.	.	0.80722	D	1	P	0.47604	0.898	P	0.48089	0.566	T	0.68093	-0.5500	8	0.72032	D	0.01	-6.657	17.1564	0.86792	0.0:0.0:1.0:0.0	.	94	Q96QK8	CD034_HUMAN	L	94	.	ENSP00000295958:P94L	P	-	2	0	C4orf34	39230160	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.293000	0.72731	2.802000	0.96397	0.655000	0.94253	CCA	.	.		0.318	SMIM14-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250434.4	NM_174921	
GABRA2	2555	hgsc.bcm.edu	37	4	46390684	46390684	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:46390684G>T	ENST00000510861.1	-	2	213	c.40C>A	c.(40-42)Ctt>Att	p.L14I	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507460.1_Missense_Mutation_p.L14I|GABRA2_ENST00000507069.1_Missense_Mutation_p.L14I|GABRA2_ENST00000515082.1_Missense_Mutation_p.L14I|GABRA2_ENST00000381620.4_Missense_Mutation_p.L14I|GABRA2_ENST00000514090.1_Missense_Mutation_p.L14I|GABRA2_ENST00000356504.1_Missense_Mutation_p.L14I|GABRA2_ENST00000509716.1_5'UTR			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	14					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAAACAAAAAGCAGGAACTGC	0.378																																					p.L14I		Atlas-SNP	.											.	GABRA2	134	.	0			c.C40A						.						159.0	157.0	158.0					4																	46390684		2203	4300	6503	SO:0001583	missense	2555	exon2			CAAAAAGCAGGAA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.40C>A	chr4.hg19:g.46390684G>T	ENSP00000421828:p.Leu14Ile	302.0	1.0		309.0	139.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315639	0.60524	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000507069;ENST00000515082;ENST00000503806;ENST00000506961;ENST00000507460	T;T;T;T;T;D;T;T	0.81908	-1.34;-1.34;-1.34;-1.34;-1.49;-1.55;-1.17;-1.17	5.0	5.0	0.66597	.	1.271310	0.05211	N	0.506821	D	0.87621	0.6223	N	0.24115	0.695	0.26319	N	0.9777	D;P;P	0.67145	0.996;0.927;0.458	D;D;P	0.80764	0.994;0.953;0.745	T	0.79650	-0.1715	10	0.72032	D	0.01	.	15.9563	0.79889	0.0:0.0:1.0:0.0	.	14;14;14	D6RAA9;G5E9Z6;P47869	.;.;GBRA2_HUMAN	I	14	ENSP00000421828:L14I;ENSP00000421300:L14I;ENSP00000371033:L14I;ENSP00000348897:L14I;ENSP00000427603:L14I;ENSP00000423840:L14I;ENSP00000424362:L14I;ENSP00000424093:L14I	ENSP00000348897:L14I	L	-	1	0	GABRA2	46085441	0.998000	0.40836	0.269000	0.24586	0.582000	0.36321	2.893000	0.48633	2.746000	0.94184	0.561000	0.74099	CTT	.	.		0.378	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
ANKRD17	26057	hgsc.bcm.edu	37	4	73990633	73990633	+	Silent	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:73990633C>T	ENST00000358602.4	-	18	3605	c.3489G>A	c.(3487-3489)caG>caA	p.Q1163Q	ANKRD17_ENST00000509867.2_Silent_p.Q1050Q|ANKRD17_ENST00000330838.6_Silent_p.Q912Q|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1163				Q -> P (in Ref. 1; AAG48253). {ECO:0000305}.	blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACATTACCTCCTGTCTTCCCC	0.408																																					p.Q1163Q		Atlas-SNP	.											.	ANKRD17	214	.	0			c.G3489A						.						119.0	110.0	113.0					4																	73990633		2203	4300	6503	SO:0001819	synonymous_variant	26057	exon18			TACCTCCTGTCTT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.3489G>A	chr4.hg19:g.73990633C>T		57.0	0.0		45.0	18.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.408	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
ALB	213	hgsc.bcm.edu	37	4	74279198	74279198	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:74279198G>T	ENST00000503124.1	+	6	662	c.455G>T	c.(454-456)tGc>tTc	p.C152F	ALB_ENST00000401494.3_Missense_Mutation_p.C187F|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Missense_Mutation_p.C302F|ALB_ENST00000295897.4_Missense_Mutation_p.C302F|ALB_ENST00000415165.2_Missense_Mutation_p.C110F			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGAAGGAATGCTGTGAAAAA	0.408																																					p.C302F		Atlas-SNP	.											.	ALB	132	.	0			c.G905T						.						120.0	115.0	117.0					4																	74279198		2203	4300	6503	SO:0001583	missense	213	exon8			AGGAATGCTGTGA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.455G>T	chr4.hg19:g.74279198G>T	ENSP00000421027:p.Cys152Phe	62.0	0.0		69.0	30.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	3.993248|3.993248	0.74703|0.74703	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	D;D;D;D;D|.	0.99637|.	-6.29;-6.29;-6.29;-6.29;-6.29|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87204|0.87204	0.6119|0.6119	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0|.	D|D	0.89545|0.89545	0.3795|0.3795	10|5	0.87932|.	D|.	0|.	-14.7984|-14.7984	19.0219|19.0219	0.92919|0.92919	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	187;110;152;302;302|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	F|I	302;110;152;302;187;311|146	ENSP00000295897:C302F;ENSP00000401820:C110F;ENSP00000421027:C152F;ENSP00000422784:C302F;ENSP00000384695:C187F|.	ENSP00000295897:C302F|.	C|M	+|+	2|3	0|0	ALB|ALB	74498062|74498062	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.775000|0.775000	0.43874|0.43874	6.394000|6.394000	0.73223|0.73223	2.835000|2.835000	0.97688|0.97688	0.650000|0.650000	0.86243|0.86243	TGC|ATG	.	.		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
ANXA3	306	hgsc.bcm.edu	37	4	79494388	79494388	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:79494388G>T	ENST00000264908.6	+	3	449	c.70G>T	c.(70-72)Gct>Tct	p.A24S	ANXA3_ENST00000503570.2_5'UTR|ANXA3_ENST00000512884.1_Intron	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	24					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						ATCAGTGGATGCTGAAGCTAT	0.373																																					p.A24S	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.G70T						.						117.0	110.0	112.0					4																	79494388		2203	4300	6503	SO:0001583	missense	306	exon3			GTGGATGCTGAAG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"""Annexins"""	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.70G>T	chr4.hg19:g.79494388G>T	ENSP00000264908:p.Ala24Ser	43.0	0.0		27.0	13.0	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572749	0.65765	.	.	ENSG00000138772	ENST00000264908;ENST00000512373;ENST00000514171;ENST00000508214	T;T;T;T	0.09073	3.02;3.02;3.02;3.02	4.89	4.89	0.63831	.	0.057085	0.64402	D	0.000002	T	0.33789	0.0875	M	0.85859	2.78	0.80722	D	1	D	0.60575	0.988	D	0.75020	0.985	T	0.13683	-1.0500	10	0.72032	D	0.01	.	17.3412	0.87297	0.0:0.0:1.0:0.0	.	24	P12429	ANXA3_HUMAN	S	24	ENSP00000264908:A24S;ENSP00000424584:A24S;ENSP00000421512:A24S;ENSP00000422281:A24S	ENSP00000264908:A24S	A	+	1	0	ANXA3	79713412	1.000000	0.71417	1.000000	0.80357	0.392000	0.30506	5.386000	0.66238	2.689000	0.91719	0.591000	0.81541	GCT	.	.		0.373	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139	
TENM3	55714	hgsc.bcm.edu	37	4	183267884	183267884	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:183267884C>T	ENST00000511685.1	+	3	436	c.313C>T	c.(313-315)Ctc>Ttc	p.L105F	TENM3_ENST00000406950.2_Missense_Mutation_p.L105F			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	105	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGAAATGGGGCTCCCTCACAG	0.488																																					p.L105F		Atlas-SNP	.											.	.	.	.	0			c.C313T						.						53.0	53.0	53.0					4																	183267884		1908	4123	6031	SO:0001583	missense	55714	exon2			ATGGGGCTCCCTC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.313C>T	chr4.hg19:g.183267884C>T	ENSP00000424226:p.Leu105Phe	92.0	0.0		71.0	31.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.632750	0.87660	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.39787	1.06;1.06;1.06	5.15	5.15	0.70609	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.63248	0.2495	M	0.65975	2.015	0.47374	D	0.999401	D;D	0.63046	0.991;0.992	D;P	0.65987	0.94;0.898	T	0.64968	-0.6282	9	0.62326	D	0.03	.	18.8123	0.92063	0.0:1.0:0.0:0.0	.	105;105	D6RGC5;Q9P273	.;TEN3_HUMAN	F	105	ENSP00000421320:L105F;ENSP00000424226:L105F;ENSP00000385276:L105F	ENSP00000385276:L105F	L	+	1	0	ODZ3	183504878	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.589000	0.61006	2.681000	0.91329	0.563000	0.77884	CTC	.	.		0.488	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
MYO10	4651	hgsc.bcm.edu	37	5	16701447	16701447	+	Silent	SNP	T	T	C	rs372673284		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:16701447T>C	ENST00000513610.1	-	25	3511	c.3057A>G	c.(3055-3057)cgA>cgG	p.R1019R	MYO10_ENST00000274203.9_Silent_p.R376R|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000505695.1_Silent_p.R358R|MYO10_ENST00000515803.1_Silent_p.R358R|MYO10_ENST00000427430.2_Silent_p.R376R	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1019					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TGCCACTTGTTCGCTGGTCTG	0.637																																					p.R1019R		Atlas-SNP	.											.	MYO10	198	.	0			c.A3057G						.						46.0	52.0	50.0					5																	16701447		2173	4267	6440	SO:0001819	synonymous_variant	4651	exon25			ACTTGTTCGCTGG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3057A>G	chr5.hg19:g.16701447T>C		57.0	0.0		61.0	28.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
GDNF	2668	hgsc.bcm.edu	37	5	37815756	37815756	+	Silent	SNP	G	G	A	rs121918536		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:37815756G>A	ENST00000326524.2	-	3	832	c.633C>T	c.(631-633)atC>atT	p.I211I	GDNF_ENST00000515058.1_Silent_p.I185I|GDNF_ENST00000381826.4_Silent_p.I202I|GDNF_ENST00000427982.1_Silent_p.I228I|GDNF_ENST00000344622.4_Silent_p.I185I	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	211			I -> M (in HSCR3). {ECO:0000269|PubMed:10917288}.		adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					GCCGGAGTCAGATACATCCAC	0.458																																					p.I228I		Atlas-SNP	.											.	GDNF	56	.	0			c.C684T						.						104.0	93.0	96.0					5																	37815756		2203	4300	6503	SO:0001819	synonymous_variant	2668	exon3			GAGTCAGATACAT		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"""Endogenous ligands"""	4232	protein-coding gene	gene with protein product	"""astrocyte-derived trophic factor"", ""glial cell line derived neurotrophic factor"", ""glial derived neurotrophic factor"""	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.633C>T	chr5.hg19:g.37815756G>A		112.0	0.0		93.0	25.0	NM_001190468	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Silent	SNP	ENST00000326524.2	hg19	CCDS3922.1																																																																																			.	.		0.458	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54637586	54637586	+	Silent	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:54637586T>C	ENST00000230640.5	+	7	1022	c.768T>C	c.(766-768)taT>taC	p.Y256Y	SKIV2L2_ENST00000545714.1_Silent_p.Y155Y	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	256	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				AAATTCATTATATGAGAGATT	0.299																																					p.Y256Y	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T768C						.						88.0	92.0	91.0					5																	54637586		2202	4297	6499	SO:0001819	synonymous_variant	23517	exon7			TCATTATATGAGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.768T>C	chr5.hg19:g.54637586T>C		99.0	0.0		102.0	42.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.299	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
GRAMD3	65983	hgsc.bcm.edu	37	5	125819257	125819257	+	Missense_Mutation	SNP	A	A	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:125819257A>C	ENST00000285689.3	+	9	1299	c.838A>C	c.(838-840)Aac>Cac	p.N280H	RP11-517I3.1_ENST00000512500.1_RNA|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000542322.1_Missense_Mutation_p.N288H|GRAMD3_ENST00000515200.1_Missense_Mutation_p.N257H|GRAMD3_ENST00000511134.1_Missense_Mutation_p.N264H|GRAMD3_ENST00000543198.1_Missense_Mutation_p.N257H|GRAMD3_ENST00000544396.1_Missense_Mutation_p.N176H|GRAMD3_ENST00000502348.1_Missense_Mutation_p.N171H|GRAMD3_ENST00000513040.1_Missense_Mutation_p.N295H	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	280						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TGAATCTGAGAACTCTCGAGG	0.373																																					p.N295H		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A883C						.						77.0	74.0	75.0					5																	125819257		2203	4300	6503	SO:0001583	missense	65983	exon9			TCTGAGAACTCTC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.838A>C	chr5.hg19:g.125819257A>C	ENSP00000285689:p.Asn280His	39.0	0.0		43.0	18.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414771	0.42817	.	.	ENSG00000155324	ENST00000513040;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.37;1.34;1.38;1.39;1.38;1.36	6.07	4.92	0.64577	.	0.465860	0.26099	N	0.026350	T	0.37598	0.1009	M	0.66939	2.045	0.36831	D	0.886889	B;B;B;B;B	0.16166	0.005;0.003;0.004;0.016;0.005	B;B;B;B;B	0.11329	0.006;0.004;0.006;0.004;0.004	T	0.33137	-0.9880	10	0.37606	T	0.19	.	12.7036	0.57046	0.6522:0.3478:0.0:0.0	.	264;176;288;295;280	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	H	295;264;280;257;288;176;257;171;264	ENSP00000426120:N295H;ENSP00000285689:N280H;ENSP00000426143:N257H;ENSP00000441876:N288H;ENSP00000444049:N176H;ENSP00000442902:N257H;ENSP00000427596:N171H;ENSP00000426088:N264H	ENSP00000285689:N280H	N	+	1	0	GRAMD3	125847156	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.939000	0.48995	1.111000	0.41721	0.533000	0.62120	AAC	.	.		0.373	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
NSD1	64324	hgsc.bcm.edu	37	5	176562164	176562164	+	Silent	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:176562164G>A	ENST00000439151.2	+	2	105	c.60G>A	c.(58-60)gtG>gtA	p.V20V	NSD1_ENST00000347982.4_5'UTR|NSD1_ENST00000354179.4_5'UTR|NSD1_ENST00000361032.4_Silent_p.V20V|NSD1_ENST00000511258.1_5'UTR	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	20					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CCAATCCAGTGAATTTAGATG	0.463			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.V20V		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G60A						.						122.0	120.0	121.0					5																	176562164		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TCCAGTGAATTTA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.60G>A	chr5.hg19:g.176562164G>A		63.0	0.0		56.0	18.0	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.463	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
COL11A2	1302	hgsc.bcm.edu	37	6	33144048	33144048	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:33144048A>T	ENST00000374708.4	-	26	2202	c.1944T>A	c.(1942-1944)caT>caA	p.H648Q	COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374712.1_Missense_Mutation_p.H653Q|COL11A2_ENST00000361917.1_Missense_Mutation_p.H627Q|COL11A2_ENST00000357486.1_Missense_Mutation_p.H713Q|COL11A2_ENST00000374713.1_Missense_Mutation_p.H687Q|COL11A2_ENST00000395197.1_Missense_Mutation_p.H674Q|COL11A2_ENST00000341947.2_Missense_Mutation_p.H734Q|COL11A2_ENST00000374714.1_Missense_Mutation_p.H708Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	734	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TCTCACCCTTATGACCCTTCA	0.587																																					p.H734Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.T2202A						.						75.0	43.0	54.0					6																	33144048		1511	2709	4220	SO:0001583	missense	1302	exon28			ACCCTTATGACCC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1944T>A	chr6.hg19:g.33144048A>T	ENSP00000363840:p.His648Gln	81.0	0.0		82.0	36.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.747069	0.30955	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.95069	-3.35;-3.35;-3.35;-3.6;-3.35;-3.35;-3.35;-3.35	4.88	-0.479	0.12089	.	0.000000	0.85682	D	0.000000	T	0.81555	0.4847	N	0.03281	-0.365	0.47905	D	0.999546	P;P;D	0.57257	0.756;0.748;0.979	P;P;P	0.55055	0.583;0.583;0.767	T	0.78393	-0.2221	10	0.20519	T	0.43	.	8.0482	0.30562	0.4656:0.0:0.5344:0.0	.	627;648;734	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	Q	648;734;713;708;687;674;653;627	ENSP00000363840:H648Q;ENSP00000339915:H734Q;ENSP00000350079:H713Q;ENSP00000363846:H708Q;ENSP00000363845:H687Q;ENSP00000378623:H674Q;ENSP00000363844:H653Q;ENSP00000355123:H627Q	ENSP00000339915:H734Q	H	-	3	2	COL11A2	33252026	0.998000	0.40836	0.994000	0.49952	0.997000	0.91878	0.360000	0.20250	-0.219000	0.10003	0.448000	0.29417	CAT	.	.		0.587	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
SLC35B2	347734	hgsc.bcm.edu	37	6	44223037	44223037	+	Silent	SNP	G	G	A	rs538318523	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:44223037G>A	ENST00000393812.3	-	4	848	c.705C>T	c.(703-705)taC>taT	p.Y235Y	SLC35B2_ENST00000538577.1_Silent_p.Y142Y|SLC35B2_ENST00000537814.1_Silent_p.Y102Y|SLC35B2_ENST00000393810.1_3'UTR|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000495706.1_5'UTR	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	235					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCCAGTGTTCGTAGCTGCGCC	0.587													g|||	2	0.000399361	0.0015	0.0	5008	,	,		19503	0.0		0.0	False		,,,				2504	0.0				p.Y235Y		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C705T						.						82.0	80.0	81.0					6																	44223037		2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			GTGTTCGTAGCTG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"""Solute carriers"""	16872	protein-coding gene	gene with protein product		610788	"""solute carrier family 35, member B2"""				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.705C>T	chr6.hg19:g.44223037G>A		77.0	0.0		63.0	28.0	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	hg19	CCDS34462.1																																																																																			.	.		0.587	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2		
FBXL4	26235	hgsc.bcm.edu	37	6	99322272	99322272	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:99322272G>T	ENST00000369244.2	-	10	2176	c.1748C>A	c.(1747-1749)tCt>tAt	p.S583Y	FBXL4_ENST00000229971.1_Missense_Mutation_p.S583Y	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	583					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		ATCTTTACAAGATTCCAGGAG	0.343																																					p.S583Y		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1748A						.						119.0	123.0	122.0					6																	99322272		2203	4300	6503	SO:0001583	missense	26235	exon9			TTACAAGATTCCA	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1748C>A	chr6.hg19:g.99322272G>T	ENSP00000358247:p.Ser583Tyr	116.0	0.0		108.0	49.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783913	0.49891	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.19105	2.17;2.17	5.95	5.08	0.68730	.	0.166936	0.53938	D	0.000042	T	0.11707	0.0285	L	0.40543	1.245	0.45867	D	0.998725	P	0.36789	0.57	B	0.40101	0.319	T	0.04796	-1.0926	10	0.30854	T	0.27	.	15.774	0.78193	0.0:0.3814:0.6186:0.0	.	583	Q9UKA2	FBXL4_HUMAN	Y	583	ENSP00000358247:S583Y;ENSP00000229971:S583Y	ENSP00000229971:S583Y	S	-	2	0	FBXL4	99428993	1.000000	0.71417	0.990000	0.47175	0.999000	0.98932	4.331000	0.59273	1.504000	0.48704	0.655000	0.94253	TCT	.	.		0.343	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
RPF2	84154	hgsc.bcm.edu	37	6	111318428	111318428	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:111318428G>A	ENST00000441448.2	+	5	369	c.277G>A	c.(277-279)Ggc>Agc	p.G93S		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	93	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						ATTCATGTTTGGCTCCCATAA	0.299																																					p.G93S		Atlas-SNP	.											.	RPF2	26	.	0			c.G277A						.						71.0	66.0	68.0					6																	111318428		2202	4298	6500	SO:0001583	missense	84154	exon5			ATGTTTGGCTCCC	AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"""ribosomal processing factor 2 homolog (S. cerevisiae)"""		"""brix domain containing 1"""	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.277G>A	chr6.hg19:g.111318428G>A	ENSP00000402338:p.Gly93Ser	122.0	0.0		95.0	36.0	NM_032194	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	hg19	CCDS5088.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.467411	0.84533	.	.	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.41400	1.0;1.0;1.0	5.12	5.12	0.69794	Brix domain (3);	0.000000	0.85682	D	0.000000	T	0.52805	0.1757	L	0.60957	1.885	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65573	0.936;0.936	T	0.53308	-0.8457	10	0.54805	T	0.06	-32.9184	17.7258	0.88365	0.0:0.0:1.0:0.0	.	93;93	A8K800;Q9H7B2	.;RPF2_HUMAN	S	93;54;60	ENSP00000402338:G93S;ENSP00000357857:G54S;ENSP00000414026:G60S	ENSP00000357857:G54S	G	+	1	0	RPF2	111425121	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.901000	0.75693	2.542000	0.85734	0.655000	0.94253	GGC	.	.		0.299	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151161944	151161944	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:151161944T>G	ENST00000358517.2	+	16	4281	c.4070T>G	c.(4069-4071)cTt>cGt	p.L1357R	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.L1357R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1357							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AATGACTATCTTTGGAGGGGG	0.408																																					p.L1357R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T4070G						.						86.0	87.0	86.0					6																	151161944		2203	4300	6503	SO:0001583	missense	57480	exon17			ACTATCTTTGGAG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.4070T>G	chr6.hg19:g.151161944T>G	ENSP00000351318:p.Leu1357Arg	94.0	0.0		65.0	26.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.366450	0.82463	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	T;T	0.71934	-0.61;-0.61	5.7	5.7	0.88788	.	0.175401	0.51477	D	0.000093	T	0.79516	0.4459	M	0.66939	2.045	0.48571	D	0.99967	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.915	T	0.82540	-0.0406	10	0.87932	D	0	.	15.9568	0.79893	0.0:0.0:0.0:1.0	.	1164;1357	Q5EBL9;Q9ULL1	.;PKHG1_HUMAN	R	1357	ENSP00000356297:L1357R;ENSP00000351318:L1357R	ENSP00000351318:L1357R	L	+	2	0	PLEKHG1	151203637	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	7.170000	0.77587	2.160000	0.67779	0.533000	0.62120	CTT	.	.		0.408	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
RSPH10B	222967	hgsc.bcm.edu	37	7	5967916	5967916	+	Silent	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:5967916T>C	ENST00000405415.1	-	19	2729	c.2343A>G	c.(2341-2343)gaA>gaG	p.E781E	RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000404406.1_Silent_p.E781E|RSPH10B_ENST00000539903.1_3'UTR|RSPH10B_ENST00000337579.3_Silent_p.E781E|RSPH10B_ENST00000441023.2_Silent_p.E781E			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	781										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		CCTTGATAGCTTCTTCACGTT	0.463																																					p.E781E		Atlas-SNP	.											.	RSPH10B	28	.	0			c.A2343G						.						187.0	173.0	177.0					7																	5967916		2202	4298	6500	SO:0001819	synonymous_variant	222967	exon20			GATAGCTTCTTCA		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.2343A>G	chr7.hg19:g.5967916T>C		667.0	0.0		465.0	135.0	NM_173565	A6NMW7|Q86ST9|Q8NE68	Silent	SNP	ENST00000405415.1	hg19	CCDS34598.1																																																																																			.	.		0.463	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
MPP6	51678	hgsc.bcm.edu	37	7	24705683	24705683	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:24705683G>C	ENST00000222644.5	+	8	1177	c.927G>C	c.(925-927)atG>atC	p.M309I	MPP6_ENST00000396475.2_Missense_Mutation_p.M309I|MPP6_ENST00000409761.1_Missense_Mutation_p.M197I			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.M309I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						AGAAAAAGATGATGTATCTCA	0.303																																					p.M309I		Atlas-SNP	.											.	MPP6	62	.	1	Substitution - Missense(1)	lung(1)	c.G927C						.						92.0	107.0	102.0					7																	24705683		2197	4293	6490	SO:0001583	missense	51678	exon9			AAAGATGATGTAT	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.927G>C	chr7.hg19:g.24705683G>C	ENSP00000222644:p.Met309Ile	76.0	0.0		87.0	40.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.624452	0.46840	.	.	ENSG00000105926	ENST00000222644;ENST00000409761;ENST00000396475	D;D;D	0.82167	-1.58;-1.58;-1.58	5.32	5.32	0.75619	Src homology-3 domain (1);	0.000000	0.64402	D	0.000002	T	0.73877	0.3643	N	0.16743	0.435	0.80722	D	1	B	0.17268	0.021	B	0.12156	0.007	T	0.67707	-0.5601	10	0.36615	T	0.2	.	18.9769	0.92740	0.0:0.0:1.0:0.0	.	309	Q9NZW5	MPP6_HUMAN	I	309;197;309	ENSP00000222644:M309I;ENSP00000386262:M197I;ENSP00000379737:M309I	ENSP00000222644:M309I	M	+	3	0	MPP6	24672208	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.794000	0.85869	2.477000	0.83638	0.591000	0.81541	ATG	.	.		0.303	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		
ABCB4	5244	hgsc.bcm.edu	37	7	87051459	87051459	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:87051459G>A	ENST00000265723.4	-	18	2405	c.2294C>T	c.(2293-2295)tCt>tTt	p.S765F	ABCB4_ENST00000358400.3_Missense_Mutation_p.S765F|ABCB4_ENST00000359206.3_Missense_Mutation_p.S765F|ABCB4_ENST00000545634.1_Missense_Mutation_p.S765F|ABCB4_ENST00000453593.1_Missense_Mutation_p.S765F	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	765	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGTAAAAAAAGAAATAATTCC	0.318																																					p.S765F		Atlas-SNP	.											.	ABCB4	177	.	0			c.C2294T						.						43.0	45.0	45.0					7																	87051459		2203	4300	6503	SO:0001583	missense	5244	exon18			AAAAAAGAAATAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2294C>T	chr7.hg19:g.87051459G>A	ENSP00000265723:p.Ser765Phe	195.0	0.0		273.0	76.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529316	0.85706	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43	5.99	5.99	0.97316	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.053448	0.85682	D	0.000000	D	0.94843	0.8334	M	0.82517	2.595	0.80722	D	1	B;D;D	0.61697	0.357;0.987;0.99	B;D;D	0.70935	0.301;0.952;0.971	D	0.94818	0.7984	10	0.72032	D	0.01	-16.5265	18.2507	0.90002	0.0:0.0:1.0:0.0	.	765;765;765	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	F	765	ENSP00000352135:S765F;ENSP00000351172:S765F;ENSP00000265723:S765F;ENSP00000392983:S765F;ENSP00000437465:S765F	ENSP00000265723:S765F	S	-	2	0	ABCB4	86889395	1.000000	0.71417	0.972000	0.41901	0.987000	0.75469	6.605000	0.74155	2.840000	0.97914	0.655000	0.94253	TCT	.	.		0.318	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
PVRIG	79037	hgsc.bcm.edu	37	7	99818613	99818613	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:99818613C>A	ENST00000317271.2	+	6	1083	c.720C>A	c.(718-720)tgC>tgA	p.C240*	GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|AC005071.1_ENST00000410550.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	240						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACACCAGCTGCCGCCCAGCTA	0.677																																					p.C240X		Atlas-SNP	.											.	PVRIG	20	.	0			c.C720A						.						65.0	70.0	68.0					7																	99818613		2203	4300	6503	SO:0001587	stop_gained	79037	exon6			CAGCTGCCGCCCA	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.720C>A	chr7.hg19:g.99818613C>A	ENSP00000316675:p.Cys240*	100.0	0.0		102.0	30.0	NM_024070	D6W5U9|Q9BVK3	Nonsense_Mutation	SNP	ENST00000317271.2	hg19	CCDS5690.1	.	.	.	.	.	.	.	.	.	.	c	26.9	4.780649	0.90195	.	.	ENSG00000213413	ENST00000317271	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.35377	D	0.789556	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	9.7879	0.40688	0.0:1.0:0.0:0.0	.	.	.	.	X	240	.	ENSP00000316675:C240X	C	+	3	2	PVRIG	99656549	0.001000	0.12720	0.004000	0.12327	0.149000	0.21700	0.819000	0.27308	2.010000	0.58986	0.505000	0.49811	TGC	.	.		0.677	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070	
PNPLA8	50640	hgsc.bcm.edu	37	7	108131857	108131857	+	Silent	SNP	A	A	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:108131857A>T	ENST00000422087.1	-	9	2086	c.1680T>A	c.(1678-1680)ccT>ccA	p.P560P	PNPLA8_ENST00000453144.1_Silent_p.P460P|PNPLA8_ENST00000388728.5_Silent_p.P560P|PNPLA8_ENST00000257694.8_Silent_p.P560P|PNPLA8_ENST00000436062.1_Silent_p.P560P|PNPLA8_ENST00000426128.2_Silent_p.P560P	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	560	Patatin.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						AGCTTACCTTAGGACATGTGG	0.343																																					p.P560P		Atlas-SNP	.											.	PNPLA8	82	.	0			c.T1680A						.						139.0	134.0	136.0					7																	108131857		2203	4300	6503	SO:0001819	synonymous_variant	50640	exon7			TACCTTAGGACAT	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"""Patatin-like phospholipase domain containing"""	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.1680T>A	chr7.hg19:g.108131857A>T		115.0	0.0		147.0	56.0	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Silent	SNP	ENST00000422087.1	hg19	CCDS34733.1																																																																																			.	.		0.343	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723	
C9orf170	401535	hgsc.bcm.edu	37	9	89763702	89763702	+	Silent	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr9:89763702G>T	ENST00000375941.2	+	1	144	c.57G>T	c.(55-57)ggG>ggT	p.G19G		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	19										large_intestine(3)|lung(2)|prostate(1)	6						TCCTCCTGGGGGTGTGGGGGC	0.711																																					p.G19G		Atlas-SNP	.											.	C9orf170	17	.	0			c.G57T						.						16.0	19.0	18.0					9																	89763702		2202	4296	6498	SO:0001819	synonymous_variant	401535	exon1			CCTGGGGGTGTGG	AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.57G>T	chr9.hg19:g.89763702G>T		34.0	0.0		27.0	14.0	NM_001001709		Silent	SNP	ENST00000375941.2	hg19	CCDS35058.1																																																																																			.	.		0.711	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709	
PSAP	5660	hgsc.bcm.edu	37	10	73610968	73610968	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr10:73610968A>T	ENST00000394936.3	-	1	158	c.11T>A	c.(10-12)cTc>cAc	p.L4H	PSAP_ENST00000394934.1_Missense_Mutation_p.L4H			P07602	SAP_HUMAN	prosaposin	4					blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						CAGGAGGAAGAGGGCGTACAT	0.652																																					p.L4H		Atlas-SNP	.											.	PSAP	43	.	0			c.T11A						.						26.0	22.0	23.0					10																	73610968		1904	3576	5480	SO:0001583	missense	5660	exon1			AGGAAGAGGGCGT	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.11T>A	chr10.hg19:g.73610968A>T	ENSP00000378394:p.Leu4His	54.0	0.0		56.0	32.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399257	0.42512	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	T;T	0.76578	-1.02;-1.03	4.97	4.97	0.65823	.	0.992181	0.08197	N	0.982913	D	0.82637	0.5080	M	0.69358	2.11	0.09310	N	1	D	0.59767	0.986	P	0.51453	0.67	T	0.71517	-0.4569	10	0.87932	D	0	-15.3803	11.3155	0.49390	1.0:0.0:0.0:0.0	.	4	P07602	SAP_HUMAN	H	4;4;4;4;4;7	ENSP00000378394:L4H;ENSP00000378392:L4H	ENSP00000350063:L4H	L	-	2	0	PSAP	73280974	0.029000	0.19370	0.003000	0.11579	0.484000	0.33280	3.955000	0.56715	1.980000	0.57719	0.397000	0.26171	CTC	.	.		0.652	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778	
PLEKHA1	59338	hgsc.bcm.edu	37	10	124166157	124166157	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr10:124166157G>T	ENST00000368990.3	+	5	441	c.310G>T	c.(310-312)Gta>Tta	p.V104L	PLEKHA1_ENST00000538022.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000433307.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000368988.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000494222.1_Intron|PLEKHA1_ENST00000368989.2_Missense_Mutation_p.V104L	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	104	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AGTGGAATGGGTAAATGTGTT	0.313																																					p.V104L		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.G310T						.						133.0	134.0	133.0					10																	124166157		2203	4300	6503	SO:0001583	missense	59338	exon5			GAATGGGTAAATG	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"""Pleckstrin homology (PH) domain containing"""	14335	protein-coding gene	gene with protein product	"""tandem PH domain containing protein-1"""	607772	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"""			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.310G>T	chr10.hg19:g.124166157G>T	ENSP00000357986:p.Val104Leu	149.0	0.0		139.0	62.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	hg19	CCDS7629.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082336	0.76528	.	.	ENSG00000107679	ENST00000368990;ENST00000368989;ENST00000409427;ENST00000368988;ENST00000538022;ENST00000392799;ENST00000433307	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	6.17	5.25	0.73442	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.112241	0.64402	D	0.000010	D	0.84534	0.5493	M	0.65498	2.005	0.54753	D	0.999983	B;D	0.53619	0.012;0.961	B;D	0.63597	0.096;0.916	D	0.84930	0.0859	10	0.52906	T	0.07	-12.7731	10.9078	0.47090	0.1466:0.0:0.8534:0.0	.	104;104	B3KQ55;Q9HB21	.;PKHA1_HUMAN	L	104	ENSP00000357986:V104L;ENSP00000357985:V104L;ENSP00000357984:V104L;ENSP00000438608:V104L;ENSP00000376547:V104L;ENSP00000394416:V104L	ENSP00000357984:V104L	V	+	1	0	PLEKHA1	124156147	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.489000	0.60309	1.561000	0.49584	0.655000	0.94253	GTA	.	.		0.313	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974	
MOB2	81532	hgsc.bcm.edu	37	11	1491556	1491556	+	Missense_Mutation	SNP	C	C	T	rs565130082	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:1491556C>T	ENST00000329957.6	-	5	842	c.653G>A	c.(652-654)cGg>cAg	p.R218Q	MOB2_ENST00000526462.1_5'UTR	NM_001172223.1	NP_001165694.1	Q70IA6	MOB2_HUMAN	MOB kinase activator 2	187					actin cytoskeleton organization (GO:0030036)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cytoplasm (GO:0005737)|neuron projection terminus (GO:0044306)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)	4						GTTGAACTCCCGAGCAAAGAG	0.627													C|||	2	0.000399361	0.0	0.0	5008	,	,		14614	0.002		0.0	False		,,,				2504	0.0				p.R218Q		Atlas-SNP	.											.	MOB2	23	.	0			c.G653A						.						124.0	134.0	131.0					11																	1491556		2107	4223	6330	SO:0001583	missense	81532	exon5			AACTCCCGAGCAA		CCDS53591.1	11p15.5	2011-09-28			ENSG00000182208	ENSG00000182208		"""MOB kinase activators"""	24904	protein-coding gene	gene with protein product	"""MOB2 Mps One Binder homolog (yeast)"""	611969				11223154, 15067004	Standard	NM_053005		Approved	HCCA2	uc010qwz.2	Q70IA6	OTTHUMG00000165545	ENST00000329957.6:c.653G>A	chr11.hg19:g.1491556C>T	ENSP00000328694:p.Arg218Gln	86.0	0.0		61.0	24.0	NM_001172223	B4DKP3|Q96M67	Missense_Mutation	SNP	ENST00000329957.6	hg19	CCDS53591.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.877643	0.51801	.	.	ENSG00000182208	ENST00000329957	.	.	.	4.18	4.18	0.49190	.	0.055833	0.64402	D	0.000005	T	0.60945	0.2308	L	0.28400	0.85	0.80722	D	1	P;D	0.89917	0.784;1.0	B;D	0.72982	0.364;0.979	T	0.54057	-0.8350	9	0.06757	T	0.87	-38.8627	16.7007	0.85349	0.0:1.0:0.0:0.0	.	218;187	E9PDA5;Q70IA6	.;MOB2_HUMAN	Q	218	.	ENSP00000328694:R218Q	R	-	2	0	AC091196.1	1448132	1.000000	0.71417	0.791000	0.31998	0.346000	0.29079	7.154000	0.77437	2.176000	0.68965	0.563000	0.77884	CGG	.	.		0.627	MOB2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000384770.1	NM_053005	
HNRNPUL2	221092	hgsc.bcm.edu	37	11	62491884	62491884	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:62491884T>G	ENST00000301785.5	-	2	745	c.553A>C	c.(553-555)Agt>Cgt	p.S185R	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.S185R	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	185	Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GACTTTTCACTATCCTGGTCA	0.458																																					p.S185R		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A553C						.						105.0	103.0	104.0					11																	62491884		1875	4120	5995	SO:0001583	missense	221092	exon2			TTTCACTATCCTG		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.553A>C	chr11.hg19:g.62491884T>G	ENSP00000301785:p.Ser185Arg	122.0	0.0		88.0	42.0	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091707	0.36952	.	.	ENSG00000214753	ENST00000301785	T	0.43294	0.95	5.08	5.08	0.68730	.	0.541134	0.20885	N	0.083924	T	0.22975	0.0555	N	0.14661	0.345	0.36983	D	0.894393	P	0.39551	0.678	B	0.33799	0.17	T	0.18681	-1.0329	10	0.15499	T	0.54	-9.8168	12.8404	0.57800	0.0:0.0:0.0:1.0	.	185	Q1KMD3	HNRL2_HUMAN	R	185	ENSP00000301785:S185R	ENSP00000301785:S185R	S	-	1	0	HNRNPUL2	62248460	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.933000	0.40153	2.140000	0.66376	0.533000	0.62120	AGT	.	.		0.458	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877	
MRPL21	219927	hgsc.bcm.edu	37	11	68664055	68664055	+	Silent	SNP	C	C	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:68664055C>G	ENST00000362034.2	-	4	333	c.324G>C	c.(322-324)gtG>gtC	p.V108V	MRPL21_ENST00000450904.2_Silent_p.V23V|MRPL21_ENST00000567045.1_Silent_p.V23V	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21	108					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTTCAGAGGTCACCTTCCACT	0.527																																					p.V108V		Atlas-SNP	.											.	MRPL21	13	.	0			c.G324C						.						163.0	152.0	156.0					11																	68664055		2200	4294	6494	SO:0001819	synonymous_variant	219927	exon4			AGAGGTCACCTTC	AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"""Mitochondrial ribosomal proteins / large subunits"""	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.324G>C	chr11.hg19:g.68664055C>G		77.0	0.0		69.0	30.0	NM_181514	A6NKU0|C9JPR2	Silent	SNP	ENST00000362034.2	hg19	CCDS8186.1																																																																																			.	.		0.527	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396856.1	NM_181512	
NOX4	50507	hgsc.bcm.edu	37	11	89069054	89069054	+	Silent	SNP	C	C	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:89069054C>G	ENST00000263317.4	-	17	1813	c.1575G>C	c.(1573-1575)cgG>cgC	p.R525R	NOX4_ENST00000413594.2_Silent_p.R546R|NOX4_ENST00000343727.5_Silent_p.R501R|NOX4_ENST00000528341.1_Silent_p.R500R|NOX4_ENST00000534731.1_Silent_p.R485R|NOX4_ENST00000542487.1_Silent_p.R501R|NOX4_ENST00000531342.1_Silent_p.R178R|NOX4_ENST00000375979.3_Silent_p.R218R|NOX4_ENST00000527956.1_Silent_p.R501R|NOX4_ENST00000535633.1_Silent_p.R501R|NOX4_ENST00000527626.1_Silent_p.R338R|NOX4_ENST00000424319.1_Silent_p.R501R|NOX4_ENST00000525196.1_Silent_p.R289R|NOX4_ENST00000532825.1_Silent_p.R461R			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	525	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AAAGTTTCCACCGAGGACGTC	0.289																																					p.R525R		Atlas-SNP	.											.	NOX4	101	.	0			c.G1575C						.						70.0	72.0	72.0					11																	89069054		2201	4296	6497	SO:0001819	synonymous_variant	50507	exon17			TTTCCACCGAGGA	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1575G>C	chr11.hg19:g.89069054C>G		455.0	0.0		418.0	181.0	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	hg19	CCDS8285.1																																																																																			.	.		0.289	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
TMTC1	83857	hgsc.bcm.edu	37	12	29659790	29659790	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:29659790C>T	ENST00000539277.1	-	18	2696	c.2638G>A	c.(2638-2640)Gat>Aat	p.D880N	TMTC1_ENST00000552618.1_Missense_Mutation_p.D904N|TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Missense_Mutation_p.D772N|TMTC1_ENST00000551659.1_Missense_Mutation_p.D942N	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	880						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TATGTTTGATCCTTTTCTCGA	0.473																																					p.D880N		Atlas-SNP	.											.	TMTC1	147	.	0			c.G2638A						.						291.0	275.0	281.0					12																	29659790		2203	4300	6503	SO:0001583	missense	83857	exon18			TTTGATCCTTTTC		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2638G>A	chr12.hg19:g.29659790C>T	ENSP00000442046:p.Asp880Asn	149.0	0.0		119.0	47.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.115963	0.56505	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.69435	-0.39;-0.27;-0.4;-0.28	5.13	4.24	0.50183	.	0.315023	0.29876	N	0.010975	T	0.50905	0.1643	L	0.36672	1.1	0.80722	D	1	B;B;B	0.14438	0.001;0.001;0.01	B;B;B	0.14023	0.003;0.002;0.01	T	0.43212	-0.9405	10	0.02654	T	1	-11.0509	12.379	0.55295	0.0:0.9176:0.0:0.0824	.	880;942;225	Q8IUR5;F8VTQ9;Q8IUR5-4	TMTC1_HUMAN;.;.	N	643;772;942;904;880	ENSP00000256062:D772N;ENSP00000448112:D942N;ENSP00000449043:D904N;ENSP00000442046:D880N	ENSP00000256062:D772N	D	-	1	0	TMTC1	29551057	1.000000	0.71417	0.974000	0.42286	0.969000	0.65631	2.244000	0.43124	1.164000	0.42652	0.650000	0.86243	GAT	.	.		0.473	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
KRT1	3848	hgsc.bcm.edu	37	12	53071186	53071186	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:53071186C>A	ENST00000252244.3	-	5	1100	c.1042G>T	c.(1042-1044)Gac>Tac	p.D348Y		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	348	Linker 12.|Rod.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ATGATGCTGTCCAGGTCGAGA	0.493																																					p.D348Y		Atlas-SNP	.											.	KRT1	110	.	0			c.G1042T						.						130.0	121.0	124.0					12																	53071186		2203	4300	6503	SO:0001583	missense	3848	exon5			TGCTGTCCAGGTC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1042G>T	chr12.hg19:g.53071186C>A	ENSP00000252244:p.Asp348Tyr	64.0	0.0		57.0	26.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951589	0.53186	.	.	ENSG00000167768	ENST00000252244	D	0.83673	-1.75	5.22	0.0563	0.14319	Filament (1);	.	.	.	.	D	0.92835	0.7721	H	0.98466	4.24	0.38381	D	0.945122	D	0.89917	1.0	D	0.91635	0.999	D	0.89538	0.3790	9	0.87932	D	0	.	5.7045	0.17901	0.1216:0.537:0.0:0.3414	.	348	P04264	K2C1_HUMAN	Y	348	ENSP00000252244:D348Y	ENSP00000252244:D348Y	D	-	1	0	KRT1	51357453	0.929000	0.31497	0.887000	0.34795	0.800000	0.45204	0.456000	0.21859	0.037000	0.15575	-1.202000	0.01658	GAC	.	.		0.493	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
RAB3IP	117177	hgsc.bcm.edu	37	12	70149324	70149324	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:70149324T>G	ENST00000247833.7	+	2	512	c.136T>G	c.(136-138)Tca>Gca	p.S46A	RAB3IP_ENST00000362025.5_Missense_Mutation_p.S62A|RAB3IP_ENST00000550536.1_Missense_Mutation_p.S62A|RAB3IP_ENST00000325555.9_5'UTR|RAB3IP_ENST00000378815.6_Missense_Mutation_p.S46A|RAB3IP_ENST00000483530.2_Missense_Mutation_p.S46A					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			GCCACACCCTTCAGCTTTATC	0.468																																					p.S62A		Atlas-SNP	.											.	RAB3IP	48	.	0			c.T184G						.						175.0	156.0	162.0					12																	70149324		2203	4300	6503	SO:0001583	missense	117177	exon2			CACCCTTCAGCTT		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"""rabin3"""	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.136T>G	chr12.hg19:g.70149324T>G	ENSP00000247833:p.Ser46Ala	84.0	0.0		106.0	37.0	NM_175623		Missense_Mutation	SNP	ENST00000247833.7	hg19	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326084	0.41197	.	.	ENSG00000127328	ENST00000247833;ENST00000378815;ENST00000483530;ENST00000549760;ENST00000550536;ENST00000362025	T;T	0.44482	0.92;0.92	5.2	4.03	0.46877	.	0.321368	0.34067	N	0.004296	T	0.27134	0.0665	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.10296	0.003;0.0;0.002;0.0	B;B;B;B	0.11329	0.005;0.001;0.006;0.001	T	0.05582	-1.0876	10	0.38643	T	0.18	-5.4128	8.1652	0.31222	0.0:0.0714:0.136:0.7926	.	62;62;46;46	Q96QF0-4;Q96QF0;Q96QF0-3;Q96QF0-7	.;RAB3I_HUMAN;.;.	A	46;46;46;46;62;62	ENSP00000247833:S46A;ENSP00000447300:S62A	ENSP00000247833:S46A	S	+	1	0	RAB3IP	68435591	1.000000	0.71417	0.953000	0.39169	0.933000	0.57130	1.874000	0.39568	1.033000	0.39918	0.533000	0.62120	TCA	.	.		0.468	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456	
PTPRQ	374462	hgsc.bcm.edu	37	12	80933705	80933705	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:80933705G>A	ENST00000266688.5	+	25	3124	c.3124G>A	c.(3124-3126)Gta>Ata	p.V1042I				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1088	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CATCATTGAAGTATACACAGA	0.259																																					p.V874I		Atlas-SNP	.											.	PTPRQ	119	.	0			c.G2620A						.						106.0	86.0	92.0					12																	80933705		692	1585	2277	SO:0001583	missense	374462	exon17			ATTGAAGTATACA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.3124G>A	chr12.hg19:g.80933705G>A	ENSP00000266688:p.Val1042Ile	80.0	0.0		62.0	26.0	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	hg19		.	.	.	.	.	.	.	.	.	.	G	15.90	2.970769	0.53614	.	.	ENSG00000139304	ENST00000266688	T	0.55234	0.53	5.22	5.22	0.72569	Fibronectin, type III (2);Immunoglobulin-like fold (1);	.	.	.	.	T	0.37999	0.1024	.	.	.	0.41296	D	0.987019	P	0.36647	0.563	B	0.35931	0.214	T	0.19910	-1.0291	8	0.11794	T	0.64	.	14.4923	0.67660	0.0:0.0:0.8525:0.1475	.	1088	Q9UMZ3	PTPRQ_HUMAN	I	1042	ENSP00000266688:V1042I	ENSP00000266688:V1042I	V	+	1	0	PTPRQ	79457836	1.000000	0.71417	0.996000	0.52242	0.938000	0.57974	4.127000	0.57944	2.428000	0.82296	0.585000	0.79938	GTA	.	.		0.259	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
TMPO	7112	hgsc.bcm.edu	37	12	98938066	98938066	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:98938066G>A	ENST00000556029.1	+	5	1078	c.722G>A	c.(721-723)gGa>gAa	p.G241E	TMPO_ENST00000393053.2_Intron|TMPO_ENST00000548223.1_3'UTR|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	241	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TCAAAAGGCGGACCTCTGCAG	0.408																																					p.G241E		Atlas-SNP	.											.	TMPO	111	.	0			c.G722A						.						86.0	87.0	87.0					12																	98938066		2203	4300	6503	SO:0001583	missense	7112	exon5			AAGGCGGACCTCT		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"""LEM domain containing 4"""	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.722G>A	chr12.hg19:g.98938066G>A	ENSP00000450627:p.Gly241Glu	117.0	0.0		112.0	57.0	NM_001032283	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	hg19	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187716	0.78789	.	.	ENSG00000120802	ENST00000556029	T	0.71579	-0.58	5.75	5.75	0.90469	.	.	.	.	.	T	0.81735	0.4885	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77167	-0.2687	9	0.28530	T	0.3	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	241	P42167	LAP2B_HUMAN	E	241	ENSP00000450627:G241E	ENSP00000340251:G241E	G	+	2	0	TMPO	97462197	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.473000	0.73572	2.712000	0.92718	0.591000	0.81541	GGA	.	.		0.408	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	
KIAA1033	23325	hgsc.bcm.edu	37	12	105557965	105557965	+	Silent	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:105557965G>A	ENST00000332180.5	+	31	3321	c.3234G>A	c.(3232-3234)gaG>gaA	p.E1078E	KIAA1033_ENST00000547171.1_3'UTR	NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTGTTAGAGAGAAATACCTGA	0.418																																					p.E1078E		Atlas-SNP	.											.	KIAA1033	83	.	0			c.G3234A						.						130.0	119.0	122.0					12																	105557965		1876	4110	5986	SO:0001819	synonymous_variant	23325	exon31			TAGAGAGAAATAC	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.3234G>A	chr12.hg19:g.105557965G>A		106.0	0.0		77.0	31.0	NM_015275		Silent	SNP	ENST00000332180.5	hg19	CCDS41826.1																																																																																			.	.		0.418	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
DNAH10	196385	hgsc.bcm.edu	37	12	124377824	124377824	+	Silent	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:124377824C>T	ENST00000409039.3	+	52	8711	c.8686C>T	c.(8686-8688)Ctg>Ttg	p.L2896L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2896	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGAGTCTATCCTGAGTCAGAT	0.498																																					p.L2896L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C8686T						.						64.0	67.0	66.0					12																	124377824		2006	4194	6200	SO:0001819	synonymous_variant	196385	exon52			TCTATCCTGAGTC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.8686C>T	chr12.hg19:g.124377824C>T		90.0	0.0		67.0	28.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.498	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ZMYM2	7750	hgsc.bcm.edu	37	13	20567272	20567272	+	Silent	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr13:20567272G>A	ENST00000382874.2	+	4	250	c.60G>A	c.(58-60)ggG>ggA	p.G20G	ZMYM2_ENST00000382871.2_Silent_p.G20G|ZMYM2_ENST00000382881.3_Silent_p.G20G|ZMYM2_ENST00000382869.3_Silent_p.G20G	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TTTTATTAGGGAGTACGGCCA	0.393																																					p.G20G		Atlas-SNP	.											.	ZMYM2	191	.	0			c.G60A						.						141.0	140.0	140.0					13																	20567272		2062	4244	6306	SO:0001819	synonymous_variant	7750	exon4			ATTAGGGAGTACG	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.60G>A	chr13.hg19:g.20567272G>A		99.0	0.0		123.0	54.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	hg19	CCDS45016.1																																																																																			.	.		0.393	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
FARP1	10160	hgsc.bcm.edu	37	13	98896898	98896898	+	Intron	SNP	A	A	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr13:98896898A>G	ENST00000319562.6	+	2	436				FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Missense_Mutation_p.T109A	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TATTTCTTACACAAACTGGGC	0.418																																					p.T109A		Atlas-SNP	.											.	FARP1	207	.	0			c.A325G						.						117.0	116.0	116.0					13																	98896898		2203	4300	6503	SO:0001627	intron_variant	10160	exon3			TCTTACACAAACT	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.171+31231A>G	chr13.hg19:g.98896898A>G		57.0	0.0		57.0	32.0	NM_001001715	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	A	4.838	0.155825	0.09236	.	.	ENSG00000152767	ENST00000376581	T	0.49432	0.78	3.2	-4.09	0.03951	.	.	.	.	.	T	0.21590	0.0520	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.15549	-1.0433	9	0.87932	D	0	.	3.4211	0.07393	0.2581:0.0:0.394:0.3479	.	109	Q5JVI9	.	A	109	ENSP00000365765:T109A	ENSP00000365765:T109A	T	+	1	0	FARP1	97694899	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.013000	0.03645	-0.871000	0.04042	-0.403000	0.06358	ACA	.	.		0.418	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
NOVA1	4857	hgsc.bcm.edu	37	14	26917704	26917704	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:26917704G>T	ENST00000539517.2	-	5	1302	c.985C>A	c.(985-987)Ctc>Atc	p.L329I	NOVA1_ENST00000465357.2_Missense_Mutation_p.L305I|NOVA1_ENST00000267422.7_Missense_Mutation_p.L207I	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	332	Ala-rich.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		AAAGTGTTGAGATTATATCCA	0.502																																					p.L329I		Atlas-SNP	.											.	NOVA1	146	.	0			c.C985A						.						52.0	48.0	50.0					14																	26917704		2203	4300	6503	SO:0001583	missense	4857	exon5			TGTTGAGATTATA	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.985C>A	chr14.hg19:g.26917704G>T	ENSP00000438875:p.Leu329Ile	26.0	0.0		20.0	11.0	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	hg19	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	G	4.892	0.165831	0.09339	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422	T;T;T	0.34472	1.37;1.36;1.37	5.93	5.93	0.95920	.	0.168630	0.41712	D	0.000828	T	0.20251	0.0487	N	0.08118	0	0.53005	D	0.999967	B;B;P	0.35872	0.092;0.256;0.525	B;B;B	0.30572	0.018;0.055;0.117	T	0.09530	-1.0670	10	0.10902	T	0.67	-5.7973	20.3363	0.98740	0.0:0.0:1.0:0.0	.	332;305;329	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	I	305;329;207	ENSP00000447391:L305I;ENSP00000438875:L329I;ENSP00000267422:L207I	ENSP00000267422:L207I	L	-	1	0	NOVA1	25987544	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.392000	0.79840	2.814000	0.96858	0.563000	0.77884	CTC	.	.		0.502	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491	
TMEM260	54916	hgsc.bcm.edu	37	14	57070549	57070549	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:57070549G>A	ENST00000261556.6	+	4	483	c.361G>A	c.(361-363)Gct>Act	p.A121T	TMEM260_ENST00000536419.1_Intron|TMEM260_ENST00000538838.1_Missense_Mutation_p.A121T	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	121						integral component of membrane (GO:0016021)											TGGCTCATCTGCTGGAGGAAT	0.413																																					p.A121T		Atlas-SNP	.											.	.	.	.	0			c.G361A						.						104.0	107.0	106.0					14																	57070549		2203	4300	6503	SO:0001583	missense	0	exon4			TCATCTGCTGGAG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 101"""	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.361G>A	chr14.hg19:g.57070549G>A	ENSP00000261556:p.Ala121Thr	223.0	0.0		174.0	67.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	hg19	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273708	0.80580	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.49432	1.37;0.78	5.88	5.88	0.94601	.	0.054747	0.64402	D	0.000001	T	0.46927	0.1418	L	0.45051	1.395	0.80722	D	1	P	0.43477	0.808	B	0.43082	0.407	T	0.19745	-1.0296	10	0.20046	T	0.44	-11.5948	20.2381	0.98363	0.0:0.0:1.0:0.0	.	121	Q9NX78	CN101_HUMAN	T	121	ENSP00000261556:A121T;ENSP00000441934:A121T	ENSP00000261556:A121T	A	+	1	0	C14orf101	56140302	1.000000	0.71417	0.980000	0.43619	0.994000	0.84299	6.781000	0.75068	2.779000	0.95612	0.650000	0.86243	GCT	.	.		0.413	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
SYT16	83851	hgsc.bcm.edu	37	14	62550920	62550920	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:62550920G>T	ENST00000430451.2	+	5	1638	c.1441G>T	c.(1441-1443)Ggg>Tgg	p.G481W		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	481					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CCAGAGTGGAGGGTCTCCGCT	0.527																																					p.G481W		Atlas-SNP	.											.	SYT16	144	.	0			c.G1441T						.						99.0	96.0	97.0					14																	62550920		1973	4154	6127	SO:0001583	missense	83851	exon5			AGTGGAGGGTCTC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1441G>T	chr14.hg19:g.62550920G>T	ENSP00000394700:p.Gly481Trp	81.0	0.0		71.0	26.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137384	0.77775	.	.	ENSG00000139973	ENST00000430451	T	0.04406	3.63	5.44	5.44	0.79542	.	0.294878	0.36234	N	0.002719	T	0.10809	0.0264	L	0.29908	0.895	0.80722	D	1	P	0.49783	0.928	P	0.54060	0.741	T	0.01951	-1.1241	10	0.62326	D	0.03	-6.1342	19.4718	0.94966	0.0:0.0:1.0:0.0	.	481	Q17RD7	SYT16_HUMAN	W	481	ENSP00000394700:G481W	ENSP00000394700:G481W	G	+	1	0	SYT16	61620673	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.333000	0.79214	2.831000	0.97527	0.643000	0.83706	GGG	.	.		0.527	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
PPP2R5E	5529	hgsc.bcm.edu	37	14	63858560	63858560	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:63858560C>T	ENST00000337537.3	-	10	1531	c.929G>A	c.(928-930)tGg>tAg	p.W310*	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000555899.1_Nonsense_Mutation_p.W310*|PPP2R5E_ENST00000422769.2_Nonsense_Mutation_p.W234*	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	310					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TGTTTTAGGCCAAAATTTCAT	0.338																																					p.W310X		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.G929A						.						81.0	81.0	81.0					14																	63858560		2203	4300	6503	SO:0001587	stop_gained	5529	exon10			TTAGGCCAAAATT	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9313	protein-coding gene	gene with protein product		601647	"""protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"""			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.929G>A	chr14.hg19:g.63858560C>T	ENSP00000337641:p.Trp310*	121.0	0.0		88.0	34.0	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Nonsense_Mutation	SNP	ENST00000337537.3	hg19	CCDS9758.1	.	.	.	.	.	.	.	.	.	.	C	43	9.954419	0.99304	.	.	ENSG00000154001	ENST00000337537;ENST00000555899;ENST00000422769	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5188	19.5064	0.95118	0.0:1.0:0.0:0.0	.	.	.	.	X	310;310;234	.	ENSP00000337641:W310X	W	-	2	0	PPP2R5E	62928313	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.716000	0.84723	2.672000	0.90937	0.655000	0.94253	TGG	.	.		0.338	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246	
STON2	85439	hgsc.bcm.edu	37	14	81737182	81737182	+	Silent	SNP	A	A	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:81737182A>C	ENST00000267540.2	-	5	2645	c.2445T>G	c.(2443-2445)ctT>ctG	p.L815L	STON2_ENST00000555447.1_Silent_p.L815L	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	815	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		AGCCGAGTTCAAGGTGGCAAA	0.498																																					p.L815L		Atlas-SNP	.											.	STON2	94	.	0			c.T2445G						.						87.0	75.0	79.0					14																	81737182		2203	4300	6503	SO:0001819	synonymous_variant	85439	exon7			GAGTTCAAGGTGG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2445T>G	chr14.hg19:g.81737182A>C		46.0	0.0		34.0	11.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Silent	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.259519	0.23051	.	.	ENSG00000140022	ENST00000553821	T	0.26957	1.7	5.79	3.26	0.37387	.	0.000000	0.64402	D	0.000003	T	0.29423	0.0733	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02617	-1.1133	6	.	.	.	-21.4275	7.9458	0.29985	0.4081:0.4586:0.0:0.1332	.	.	.	.	W	23	ENSP00000450577:L23W	.	L	-	2	0	STON2	80806935	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.141000	0.31528	0.984000	0.38629	0.533000	0.62120	TTG	.	.		0.498	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
RPS6KA5	9252	hgsc.bcm.edu	37	14	91338575	91338575	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:91338575G>C	ENST00000261991.3	-	17	2425	c.2252C>G	c.(2251-2253)aCc>aGc	p.T751S	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.T672S	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	751					axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CTCGGTACTGGTGCTAGTCTT	0.483																																					p.T751S		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.C2252G						.						129.0	114.0	119.0					14																	91338575		2203	4300	6503	SO:0001583	missense	9252	exon17			GTACTGGTGCTAG	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"""ribosomal protein S6 kinase, 90kD, polypeptide 5"""			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.2252C>G	chr14.hg19:g.91338575G>C	ENSP00000261991:p.Thr751Ser	215.0	0.0		224.0	108.0	NM_004755	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354677	0.24512	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	T;T	0.66815	-0.23;-0.23	5.25	5.25	0.73442	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70290	0.3207	L	0.33485	1.01	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.61959	-0.6955	10	0.05959	T	0.93	.	19.2225	0.93803	0.0:0.0:1.0:0.0	.	751	O75582	KS6A5_HUMAN	S	751;672	ENSP00000261991:T751S;ENSP00000442803:T672S	ENSP00000261991:T751S	T	-	2	0	RPS6KA5	90408328	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.813000	0.99286	2.611000	0.88343	0.655000	0.94253	ACC	.	.		0.483	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755	
DUOXA2	405753	hgsc.bcm.edu	37	15	45408389	45408389	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr15:45408389C>A	ENST00000323030.5	+	3	558	c.273C>A	c.(271-273)agC>agA	p.S91R	DUOX2_ENST00000603300.1_5'Flank|DUOX2_ENST00000389039.6_5'Flank	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	91					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		AAGCCTTCAGCGCAGCGCGCG	0.572																																					p.S91R		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C273A						.						139.0	132.0	134.0					15																	45408389		2002	4151	6153	SO:0001583	missense	405753	exon3			CTTCAGCGCAGCG	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.273C>A	chr15.hg19:g.45408389C>A	ENSP00000319705:p.Ser91Arg	41.0	0.0		43.0	26.0	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	14.81	2.646005	0.47258	.	.	ENSG00000140274	ENST00000323030	T	0.67865	-0.29	5.41	-9.39	0.00619	.	0.117307	0.85682	D	0.000000	T	0.78742	0.4331	M	0.79123	2.44	0.31474	N	0.668055	D	0.76494	0.999	D	0.71870	0.975	T	0.82678	-0.0338	10	0.72032	D	0.01	-18.1639	23.4889	0.99983	0.0:0.8007:0.0:0.1993	.	91	Q1HG44	DOXA2_HUMAN	R	91	ENSP00000319705:S91R	ENSP00000319705:S91R	S	+	3	2	DUOXA2	43195681	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.207000	0.09384	-2.250000	0.00701	-1.267000	0.01435	AGC	.	.		0.572	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581	
SETD1A	9739	hgsc.bcm.edu	37	16	30977205	30977205	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr16:30977205G>T	ENST00000262519.8	+	8	2689	c.2003G>T	c.(2002-2004)cGa>cTa	p.R668L		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	668					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CTCATGGACCGACTTGGGGCT	0.617																																					p.R668L		Atlas-SNP	.											.	SETD1A	143	.	0			c.G2003T						.						76.0	73.0	74.0					16																	30977205		2197	4300	6497	SO:0001583	missense	9739	exon8			TGGACCGACTTGG	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2003G>T	chr16.hg19:g.30977205G>T	ENSP00000262519:p.Arg668Leu	113.0	0.0		113.0	48.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.694952	0.30052	.	.	ENSG00000099381	ENST00000262519	D	0.94000	-3.33	4.67	4.67	0.58626	.	0.084306	0.49916	D	0.000124	D	0.92093	0.7494	N	0.19112	0.55	0.46356	D	0.999007	D	0.63880	0.993	D	0.74023	0.982	D	0.87573	0.2479	10	0.02654	T	1	.	16.5112	0.84286	0.0:0.0:1.0:0.0	.	668	O15047	SET1A_HUMAN	L	668	ENSP00000262519:R668L	ENSP00000262519:R668L	R	+	2	0	SETD1A	30884706	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.187000	0.42602	2.434000	0.82447	0.655000	0.94253	CGA	.	.		0.617	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
DNAH2	146754	hgsc.bcm.edu	37	17	7734001	7734001	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:7734001A>G	ENST00000572933.1	+	79	13531	c.12071A>G	c.(12070-12072)tAt>tGt	p.Y4024C	DNAH2_ENST00000389173.2_Missense_Mutation_p.Y4024C			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4024					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(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGAGCCTCTATCTCGATGAG	0.542																																					p.Y4024C		Atlas-SNP	.											.	DNAH2	498	.	0			c.A12071G						.						75.0	73.0	74.0					17																	7734001		2203	4300	6503	SO:0001583	missense	146754	exon78			GCCTCTATCTCGA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.12071A>G	chr17.hg19:g.7734001A>G	ENSP00000458355:p.Tyr4024Cys	99.0	0.0		62.0	24.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777868	0.70107	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.13657	2.57	5.84	5.84	0.93424	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	H	0.96547	3.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.67937	-0.5541	10	0.87932	D	0	.	15.1984	0.73116	1.0:0.0:0.0:0.0	.	3985;4024	Q9P225-2;Q9P225	.;DYH2_HUMAN	C	3985;4024	ENSP00000373825:Y4024C	ENSP00000353818:Y3985C	Y	+	2	0	DNAH2	7674726	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.509000	0.67012	2.243000	0.73865	0.533000	0.62120	TAT	.	.		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
DLX4	1748	hgsc.bcm.edu	37	17	48046980	48046980	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:48046980C>T	ENST00000240306.3	+	1	443	c.148C>T	c.(148-150)Ccg>Tcg	p.P50S	DLX4_ENST00000505318.2_Missense_Mutation_p.P50S|DLX4_ENST00000503410.1_3'UTR	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	50				MTSLPCPLPGRDASKAVFPDLAPVPSVAAAYPLGLSPTTAA SPNLSYSRPYGHLLSYPYTEPANPGDSYLSCQQPAALSQPL CGPAEHPQELEA -> GGSLSLPPEPLCARCPTKEGAAPRR PGFWGSLETQAATVWRGRHGHFSCRVRLSRGAARYSRRGQG KPGVTISAARLVFKVLSAGPLTHPAGRSRRLPRGHRLKPLS IALSLCLQCPSSVISRPRLSPGPSLSAPPYPKLAPPPVAEL RPPTAGAAVPWLWPSARFLPRVTGPIRVGAPLGAELRLVSP GAVNVGVETLHAE (in Ref. 9). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CTACTCCAGGCCGTATGGCCA	0.652																																					p.P50S		Atlas-SNP	.											DLX4,caecum,carcinoma,0,1	DLX4	25	.	0			c.C148T						.						99.0	100.0	100.0					17																	48046980		2203	4300	6503	SO:0001583	missense	1748	exon1			TCCAGGCCGTATG		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"""Homeoboxes / ANTP class : NKL subclass"""	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.148C>T	chr17.hg19:g.48046980C>T	ENSP00000240306:p.Pro50Ser	33.0	0.0		26.0	12.0	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	hg19	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660455	0.29515	.	.	ENSG00000108813	ENST00000240306	D	0.91351	-2.83	3.88	0.596	0.17496	.	.	.	.	.	T	0.75027	0.3794	N	0.14661	0.345	0.09310	N	0.999997	B	0.09022	0.002	B	0.04013	0.001	T	0.61098	-0.7131	9	0.02654	T	1	-0.3069	3.3909	0.07289	0.2023:0.5656:0.0:0.2321	.	50	Q92988	DLX4_HUMAN	S	50	ENSP00000240306:P50S	ENSP00000240306:P50S	P	+	1	0	DLX4	45401979	0.007000	0.16637	0.006000	0.13384	0.898000	0.52572	1.018000	0.30002	0.304000	0.22809	0.313000	0.20887	CCG	.	.		0.652	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1		
VEZF1	7716	hgsc.bcm.edu	37	17	56056601	56056601	+	Silent	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:56056601T>C	ENST00000581208.1	-	5	1090	c.1050A>G	c.(1048-1050)caA>caG	p.Q350Q	VEZF1_ENST00000584396.1_Silent_p.Q341Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	350	Poly-Gln.			Missing (in Ref. 1; BAA05663). {ECO:0000305}.	angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgttgttgctgct	0.473																																					p.Q350Q		Atlas-SNP	.											.	VEZF1	50	.	0			c.A1050G						.						173.0	159.0	164.0					17																	56056601		2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGTTGTTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1050A>G	chr17.hg19:g.56056601T>C		84.0	0.0		112.0	10.0	NM_007146		Silent	SNP	ENST00000581208.1	hg19	CCDS32687.1																																																																																			.	.		0.473	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
CD300LF	146722	hgsc.bcm.edu	37	17	72700898	72700898	+	Missense_Mutation	SNP	C	C	A	rs146550147		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:72700898C>A	ENST00000326165.6	-	2	212	c.101G>T	c.(100-102)gGc>gTc	p.G34V	CD300LF_ENST00000301573.9_Missense_Mutation_p.G34V|CD300LF_ENST00000469092.1_Missense_Mutation_p.G37V|CD300LF_ENST00000361254.4_Missense_Mutation_p.G37V|RAB37_ENST00000340415.3_Intron|CD300LF_ENST00000343125.4_Missense_Mutation_p.G37V|CD300LF_ENST00000583937.1_Missense_Mutation_p.G34V|CD300LF_ENST00000464910.1_Missense_Mutation_p.G37V|RAB37_ENST00000402449.4_Intron|CD300LF_ENST00000581500.1_Missense_Mutation_p.G37V	NM_139018.3	NP_620587.2	Q8TDQ1	CLM1_HUMAN	CD300 molecule-like family member f	34	Ig-like V-type.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GGTCAAGGAGCCCCGCTCCAA	0.512																																					p.G34V		Atlas-SNP	.											.	CD300LF	55	.	0			c.G101T						.	C	VAL/GLY,	1,4405	2.1+/-5.4	0,1,2202	85.0	79.0	81.0		101,	4.4	0.1	17	dbSNP_134	81	0,8600		0,0,4300	no	missense,intron	CD300LF,RAB37	NM_139018.3,NM_175738.4	109,	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging,	34/291,	72700898	1,13005	2203	4300	6503	SO:0001583	missense	146722	exon2			AAGGAGCCCCGCT	BC028199	CCDS11704.1, CCDS74148.1, CCDS74149.1, CCDS74150.1, CCDS74151.1, CCDS74152.1	17q25.2	2013-01-11	2006-03-29		ENSG00000186074	ENSG00000186074		"""Immunoglobulin superfamily / V-set domain containing"""	29883	protein-coding gene	gene with protein product		609807	"""CD300 antigen like family member F"""			12975309	Standard	NM_139018		Approved	IREM1, NKIR, IGSF13, CD300f, CLM1	uc002jlg.3	Q8TDQ1	OTTHUMG00000067609	ENST00000326165.6:c.101G>T	chr17.hg19:g.72700898C>A	ENSP00000327075:p.Gly34Val	90.0	0.0		84.0	35.0	NM_139018	B2RCL2|C9JDN3|Q3Y6P0|Q6UX24|Q7Z6A6|Q7Z7I4|Q7Z7I5|Q8N6D0|Q8NAF5	Missense_Mutation	SNP	ENST00000326165.6	hg19	CCDS11704.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795488	0.50208	2.27E-4	0.0	ENSG00000186074	ENST00000301573;ENST00000361254;ENST00000343125;ENST00000326165	T;T;T;T	0.05081	3.5;3.5;3.5;3.5	5.35	4.38	0.52667	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.374624	0.23091	N	0.052033	T	0.31702	0.0805	H	0.94264	3.515	0.22851	N	0.998652	D;D;D;D;D;D	0.89917	0.994;1.0;0.967;1.0;1.0;1.0	D;D;P;D;D;D	0.87578	0.951;0.996;0.853;0.997;0.998;0.993	T	0.33266	-0.9875	10	0.87932	D	0	.	8.4986	0.33144	0.0:0.8221:0.0:0.1779	.	34;37;37;34;34;37	E7EME0;Q8TDQ1-2;Q8TDQ1-4;Q8TDQ1-5;Q8TDQ1;Q8TDQ1-6	.;.;.;.;CLM1_HUMAN;.	V	34;37;37;34	ENSP00000301573:G34V;ENSP00000355294:G37V;ENSP00000343751:G37V;ENSP00000327075:G34V	ENSP00000301573:G34V	G	-	2	0	CD300LF	70212493	0.000000	0.05858	0.078000	0.20375	0.024000	0.10985	-0.163000	0.09997	1.381000	0.46364	0.561000	0.74099	GGC	.	C|1.000;A|0.000		0.512	CD300LF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000145085.1	NM_139018	
SLC25A52	147407	hgsc.bcm.edu	37	18	29339767	29339767	+	Silent	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:29339767G>A	ENST00000579441.2	-	1	857	c.858C>T	c.(856-858)atC>atT	p.I286I	SLC25A52_ENST00000269205.5_Silent_p.I296I			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	286					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											AAGTTGCATTGATTATGCCCC	0.363																																					p.I296I		Atlas-SNP	.											.	.	.	.	0			c.C888T						.						44.0	47.0	46.0					18																	29339767		2198	4296	6494	SO:0001819	synonymous_variant	147407	exon1			TGCATTGATTATG		CCDS32812.1, CCDS32812.2	18q12.1	2013-07-15	2012-03-29	2012-03-29	ENSG00000141437	ENSG00000141437		"""Solute carriers"""	23324	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 2"""	MCART2			Standard	NM_001034172		Approved		uc002kxa.3	Q3SY17	OTTHUMG00000179617	ENST00000579441.2:c.858C>T	chr18.hg19:g.29339767G>A		132.0	0.0		131.0	46.0	NM_001034172		Silent	SNP	ENST00000579441.2	hg19																																																																																				.	.		0.363	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000	
SERPINB13	5275	hgsc.bcm.edu	37	18	61255920	61255920	+	Missense_Mutation	SNP	G	G	A	rs139825462		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:61255920G>A	ENST00000344731.5	+	2	121	c.19G>A	c.(19-21)Gtc>Atc	p.V7I	SERPINB13_ENST00000269489.5_Missense_Mutation_p.V7I	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	7					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V7I(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						ACTTGGCGCCGTCAGCACTCG	0.418																																					p.V7I		Atlas-SNP	.											SERPINB13,NS,carcinoma,0,3	SERPINB13	51	.	3	Substitution - Missense(3)	prostate(2)|kidney(1)	c.G19A						.	G	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	94.0	90.0	91.0		19	2.1	0.0	18	dbSNP_134	91	0,8600		0,0,4300	no	missense	SERPINB13	NM_012397.3	29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	7/392	61255920	3,13003	2203	4300	6503	SO:0001583	missense	5275	exon2			GGCGCCGTCAGCA	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"""Serine (or cysteine) peptidase inhibitors"""	8944	protein-coding gene	gene with protein product		604445	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"""	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.19G>A	chr18.hg19:g.61255920G>A	ENSP00000341584:p.Val7Ile	156.0	1.0		128.0	68.0	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	hg19	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.380737	0.24944	6.81E-4	0.0	ENSG00000197641	ENST00000431153;ENST00000269489;ENST00000539341;ENST00000344731	T;T;D	0.82081	-0.79;2.82;-1.57	4.89	2.12	0.27331	Serpin domain (1);	0.365172	0.23587	N	0.046598	T	0.69178	0.3082	N	0.20881	0.62	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.003	T	0.59547	-0.7434	10	0.59425	D	0.04	.	6.7555	0.23512	0.0764:0.1282:0.6636:0.1318	.	7;7	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	I	37;7;7;7	ENSP00000388300:V37I;ENSP00000269489:V7I;ENSP00000341584:V7I	ENSP00000269489:V7I	V	+	1	0	SERPINB13	59406900	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.742000	0.26216	0.261000	0.21753	-1.149000	0.01842	GTC	.	G|1.000;A|0.000		0.418	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397	
SALL3	27164	hgsc.bcm.edu	37	18	76754127	76754127	+	Silent	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:76754127C>T	ENST00000537592.2	+	2	2136	c.2136C>T	c.(2134-2136)tgC>tgT	p.C712C	SALL3_ENST00000536229.3_Silent_p.C579C|SALL3_ENST00000575389.2_Silent_p.C712C	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	712					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GCAAGATCTGCGGCCGCGCCT	0.662																																					p.C712C		Atlas-SNP	.											.	SALL3	162	.	0			c.C2136T						.						36.0	33.0	34.0					18																	76754127		2203	4299	6502	SO:0001819	synonymous_variant	27164	exon2			GATCTGCGGCCGC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2136C>T	chr18.hg19:g.76754127C>T		33.0	0.0		21.0	9.0	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	hg19	CCDS12013.1																																																																																			.	.		0.662	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
CLEC17A	388512	hgsc.bcm.edu	37	19	14705334	14705334	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:14705334A>T	ENST00000417570.1	+	5	321	c.283A>T	c.(283-285)Agt>Tgt	p.S95C	CLEC17A_ENST00000397439.2_Missense_Mutation_p.S78C|CLEC17A_ENST00000547437.1_Missense_Mutation_p.S95C	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	95						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										TCCAGGTTCAAGTGCTCCACC	0.582																																					p.S95C		Atlas-SNP	.											.	CLEC17A	27	.	0			c.A283T						.						40.0	41.0	40.0					19																	14705334		1957	4146	6103	SO:0001583	missense	388512	exon5			GGTTCAAGTGCTC	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.283A>T	chr19.hg19:g.14705334A>T	ENSP00000393719:p.Ser95Cys	57.0	0.0		66.0	31.0	NM_207390	A8MX68|B2RTX0|B7ZMM4	Missense_Mutation	SNP	ENST00000417570.1	hg19	CCDS56087.1	.	.	.	.	.	.	.	.	.	.	a	7.414	0.635337	0.14322	.	.	ENSG00000187912	ENST00000547437;ENST00000397439;ENST00000417570	T;T;T	0.64618	-0.11;2.22;-0.11	3.18	-6.36	0.01969	.	.	.	.	.	T	0.30603	0.0770	N	0.08118	0	0.09310	N	1	P;P;P;P	0.46327	0.876;0.768;0.804;0.768	B;B;B;B	0.40982	0.345;0.26;0.187;0.26	T	0.34004	-0.9846	9	0.41790	T	0.15	-36.3205	0.4882	0.00559	0.2203:0.2181:0.2921:0.2695	.	95;95;95;95	Q6ZS10-2;Q6ZS10-3;Q6ZS10;F8W1T8	.;.;CL17A_HUMAN;.	C	95;78;95	ENSP00000450065:S95C;ENSP00000380581:S78C;ENSP00000393719:S95C	ENSP00000341620:S95C	S	+	1	0	CLEC17A	14566334	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.707000	0.05041	-3.115000	0.00240	-1.668000	0.00747	AGT	.	.		0.582	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390	
JAK3	3718	hgsc.bcm.edu	37	19	17950393	17950393	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:17950393C>T	ENST00000527670.1	-	9	1363	c.1334G>A	c.(1333-1335)cGa>cAa	p.R445Q	JAK3_ENST00000534444.1_Missense_Mutation_p.R445Q|JAK3_ENST00000458235.1_Missense_Mutation_p.R445Q|JAK3_ENST00000526008.1_5'UTR			P52333	JAK3_HUMAN	Janus kinase 3	445	SH2; atypical.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GCTGTGGGGTCGGCTGAGGCC	0.612		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.R445Q		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.G1334A						.						36.0	31.0	33.0					19																	17950393		2203	4300	6503	SO:0001583	missense	3718	exon10			TGGGGTCGGCTGA	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1334G>A	chr19.hg19:g.17950393C>T	ENSP00000432511:p.Arg445Gln	15.0	0.0		20.0	8.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	C	4.419	0.077400	0.08485	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.26518	1.73;1.73;1.73	3.7	-1.12	0.09808	SH2 motif (2);	0.386456	0.26297	N	0.025183	T	0.12390	0.0301	N	0.19112	0.55	0.09310	N	1	B;B;B	0.23891	0.093;0.085;0.023	B;B;B	0.15870	0.011;0.014;0.003	T	0.14811	-1.0459	10	0.42905	T	0.14	-4.1589	6.6306	0.22855	0.0:0.511:0.0:0.489	.	445;445;445	B4DK43;P52333-2;P52333	.;.;JAK3_HUMAN	Q	445	ENSP00000391676:R445Q;ENSP00000432511:R445Q;ENSP00000436421:R445Q	ENSP00000413248:R445Q	R	-	2	0	JAK3	17811393	0.000000	0.05858	0.098000	0.21074	0.002000	0.02628	-0.150000	0.10189	-0.030000	0.13804	-0.463000	0.05309	CGA	.	.		0.612	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
ZNF676	163223	hgsc.bcm.edu	37	19	22363944	22363944	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:22363944G>T	ENST00000397121.2	-	3	892	c.575C>A	c.(574-576)aCt>aAt	p.T192N		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTTCTCTCCAGTATGAATACT	0.348																																					p.T192N		Atlas-SNP	.											.	ZNF676	146	.	0			c.C575A						.						52.0	56.0	55.0					19																	22363944		2031	4219	6250	SO:0001583	missense	163223	exon3			TCTCCAGTATGAA	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.575C>A	chr19.hg19:g.22363944G>T	ENSP00000380310:p.Thr192Asn	46.0	0.0		55.0	29.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	7.323	0.617441	0.14129	.	.	ENSG00000196109	ENST00000397121	T	0.26067	1.76	1.03	-2.06	0.07298	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33644	0.0870	M	0.71036	2.16	0.21933	N	0.999468	P	0.46987	0.888	P	0.52386	0.697	T	0.23332	-1.0191	9	0.72032	D	0.01	.	3.9636	0.09421	0.1909:0.0:0.5787:0.2305	.	192	Q8N7Q3	ZN676_HUMAN	N	192	ENSP00000380310:T192N	ENSP00000380310:T192N	T	-	2	0	ZNF676	22155784	0.799000	0.28903	0.005000	0.12908	0.031000	0.12232	1.222000	0.32515	-0.631000	0.05560	0.195000	0.17529	ACT	.	.		0.348	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
HIPK4	147746	hgsc.bcm.edu	37	19	40895613	40895613	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:40895613T>C	ENST00000291823.2	-	1	481	c.197A>G	c.(196-198)gAc>gGc	p.D66G		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	66	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			CTCTTCAGGGTCTAGGCCTCG	0.547																																					p.D66G		Atlas-SNP	.											.	HIPK4	100	.	0			c.A197G						.						160.0	141.0	147.0					19																	40895613		2203	4300	6503	SO:0001583	missense	147746	exon1			TCAGGGTCTAGGC	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.197A>G	chr19.hg19:g.40895613T>C	ENSP00000291823:p.Asp66Gly	118.0	0.0		70.0	33.0	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	hg19	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.633943	0.67130	.	.	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.20738	2.05	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000060	T	0.40119	0.1104	M	0.79343	2.45	0.40835	D	0.983623	D	0.56746	0.977	P	0.60012	0.867	T	0.40194	-0.9576	10	0.87932	D	0	.	8.1293	0.31018	0.0:0.0917:0.0:0.9083	.	66	Q8NE63	HIPK4_HUMAN	G	66;31	ENSP00000291823:D66G	ENSP00000291823:D66G	D	-	2	0	HIPK4	45587453	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.587000	0.60991	1.987000	0.57996	0.460000	0.39030	GAC	.	.		0.547	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
TBC1D17	79735	hgsc.bcm.edu	37	19	50387721	50387721	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:50387721G>A	ENST00000221543.5	+	12	1548	c.1249G>A	c.(1249-1251)Gtc>Atc	p.V417I	TBC1D17_ENST00000535102.2_Missense_Mutation_p.V384I	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	417	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		CCCAGGCTACGTCCAGGGCAT	0.642																																					p.V417I		Atlas-SNP	.											TBC1D17,NS,carcinoma,0,1	TBC1D17	39	.	0			c.G1249A						.						171.0	160.0	164.0					19																	50387721		2203	4300	6503	SO:0001583	missense	79735	exon12			GGCTACGTCCAGG	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1249G>A	chr19.hg19:g.50387721G>A	ENSP00000221543:p.Val417Ile	87.0	0.0		80.0	39.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	hg19	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068829	0.93950	.	.	ENSG00000104946	ENST00000221543;ENST00000535102	T;T	0.12984	2.63;2.63	5.22	5.22	0.72569	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000001	T	0.45256	0.1333	M	0.91768	3.24	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.67900	0.88;0.954	T	0.54931	-0.8219	10	0.52906	T	0.07	-43.7203	16.2481	0.82460	0.0:0.0:1.0:0.0	.	384;417	F5H1W7;Q9HA65	.;TBC17_HUMAN	I	417;384	ENSP00000221543:V417I;ENSP00000446323:V384I	ENSP00000221543:V417I	V	+	1	0	TBC1D17	55079533	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	9.097000	0.94193	2.424000	0.82194	0.561000	0.74099	GTC	.	.		0.642	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56735066	56735066	+	Silent	SNP	T	T	C	rs199886337		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:56735066T>C	ENST00000587340.1	-	5	1217	c.522A>G	c.(520-522)ccA>ccG	p.P174P	ZSCAN5A_ENST00000254165.3_Silent_p.P57P|ZSCAN5A_ENST00000587492.1_Silent_p.P28P|ZSCAN5A_ENST00000391713.1_Silent_p.P174P|ZSCAN5A_ENST00000592355.1_Silent_p.P174P			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	174					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGCCTTCCCCTGGACGCATCT	0.612																																					p.P174P		Atlas-SNP	.											.	ZSCAN5A	118	.	0			c.A522G						.						67.0	60.0	62.0					19																	56735066		2203	4300	6503	SO:0001819	synonymous_variant	79149	exon3			TTCCCCTGGACGC	AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"""-"", ""Zinc fingers, C2H2-type"""	23710	protein-coding gene	gene with protein product			"""zinc finger protein 495"", ""zinc finger and SCAN domain containing 5"""	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.522A>G	chr19.hg19:g.56735066T>C		44.0	0.0		32.0	16.0	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Silent	SNP	ENST00000587340.1	hg19	CCDS12941.1																																																																																			.	T|0.999;C|0.001		0.612	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
ZNF71	58491	hgsc.bcm.edu	37	19	57133787	57133787	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:57133787G>T	ENST00000328070.6	+	3	1366	c.1132G>T	c.(1132-1134)Ggc>Tgc	p.G378C		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CATCCACACCGGCGAGAAGCC	0.627																																					p.G378C		Atlas-SNP	.											.	ZNF71	69	.	0			c.G1132T						.						94.0	79.0	84.0					19																	57133787		2203	4300	6503	SO:0001583	missense	58491	exon3			CACACCGGCGAGA	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.1132G>T	chr19.hg19:g.57133787G>T	ENSP00000328245:p.Gly378Cys	118.0	0.0		78.0	30.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670820	0.47781	.	.	ENSG00000197951	ENST00000328070	T	0.26660	1.72	3.58	3.58	0.41010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47875	0.1469	M	0.79258	2.445	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.27262	-1.0079	9	0.87932	D	0	.	6.744	0.23451	0.1285:0.0:0.8715:0.0	.	378	Q9NQZ8	ZNF71_HUMAN	C	378	ENSP00000328245:G378C	ENSP00000328245:G378C	G	+	1	0	ZNF71	61825599	0.994000	0.37717	0.049000	0.19019	0.895000	0.52256	4.080000	0.57620	1.815000	0.52974	0.561000	0.74099	GGC	.	.		0.627	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
SCARF2	91179	hgsc.bcm.edu	37	22	20784723	20784723	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:20784723C>T	ENST00000266214.5	-	6	1299	c.1195G>A	c.(1195-1197)Ggg>Agg	p.G399R	SCARF2_ENST00000405555.3_Missense_Mutation_p.G399R	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	399	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			CACTGGGGCCCGTGGACGCCA	0.716																																					p.G399R		Atlas-SNP	.											.	SCARF2	23	.	0			c.G1195A						.						6.0	7.0	7.0					22																	20784723		2139	4207	6346	SO:0001583	missense	91179	exon6			GGGGCCCGTGGAC	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.1195G>A	chr22.hg19:g.20784723C>T	ENSP00000266214:p.Gly399Arg	19.0	0.0		22.0	14.0	NM_182895	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	hg19	CCDS13779.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556727	0.86231	.	.	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.72394	-0.65;-0.65	4.45	4.45	0.53987	EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85718	0.1323	10	0.87932	D	0	-21.5452	14.9433	0.71012	0.0:1.0:0.0:0.0	.	399;399	E5RFB8;Q96GP6	.;SREC2_HUMAN	R	399	ENSP00000385589:G399R;ENSP00000266214:G399R	ENSP00000266214:G399R	G	-	1	0	SCARF2	19114723	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	6.737000	0.74816	2.188000	0.69820	0.561000	0.74099	GGG	.	.		0.716	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1		
TRIOBP	11078	hgsc.bcm.edu	37	22	38120914	38120914	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:38120914A>G	ENST00000406386.3	+	7	2606	c.2351A>G	c.(2350-2352)aAt>aGt	p.N784S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	784					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCTCTCCCAATAGAGCCACA	0.562																																					p.N784S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A2351G						.						136.0	147.0	143.0					22																	38120914		1980	4156	6136	SO:0001583	missense	11078	exon7			CTCCCAATAGAGC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2351A>G	chr22.hg19:g.38120914A>G	ENSP00000384312:p.Asn784Ser	148.0	0.0		138.0	69.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	7.619	0.676520	0.14841	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19394	2.15	3.65	-1.7	0.08159	.	.	.	.	.	T	0.11750	0.0286	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32587	-0.9901	9	0.33940	T	0.23	.	1.5067	0.02488	0.3434:0.3775:0.1108:0.1683	.	784	Q9H2D6	TARA_HUMAN	S	784	ENSP00000384312:N784S	ENSP00000384312:N784S	N	+	2	0	TRIOBP	36450860	0.075000	0.21258	0.003000	0.11579	0.028000	0.11728	-0.418000	0.07080	-0.145000	0.11294	-0.560000	0.04181	AAT	.	.		0.562	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
EP300	2033	hgsc.bcm.edu	37	22	41560092	41560092	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:41560092A>T	ENST00000263253.7	+	22	4983	c.3764A>T	c.(3763-3765)cAt>cTt	p.H1255L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1255					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGAAAGATGCATCAGATCTGT	0.388			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.H1255L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A3764T						.						229.0	201.0	211.0					22																	41560092		2203	4300	6503	SO:0001583	missense	2033	exon22	Familial Cancer Database	Broad Thumb-Hallux syndrome	AGATGCATCAGAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3764A>T	chr22.hg19:g.41560092A>T	ENSP00000263253:p.His1255Leu	232.0	0.0		217.0	98.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.457081	0.84317	.	.	ENSG00000100393	ENST00000263253	D	0.97941	-4.62	5.59	5.59	0.84812	.	0.000000	0.47852	D	0.000207	D	0.99026	0.9667	M	0.93328	3.405	0.54753	D	0.999986	D	0.76494	0.999	D	0.78314	0.991	D	0.99533	1.0961	10	0.87932	D	0	-13.0515	15.7693	0.78152	1.0:0.0:0.0:0.0	.	1255	Q09472	EP300_HUMAN	L	1255	ENSP00000263253:H1255L	ENSP00000263253:H1255L	H	+	2	0	EP300	39890038	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	2.125000	0.65367	0.459000	0.35465	CAT	.	.		0.388	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
CPT1B	1375	hgsc.bcm.edu	37	22	51010728	51010728	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:51010728G>C	ENST00000360719.2	-	12	1499	c.1362C>G	c.(1360-1362)gaC>gaG	p.D454E	CPT1B_ENST00000440709.1_Missense_Mutation_p.D373E|CPT1B_ENST00000395650.2_Missense_Mutation_p.D454E|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Missense_Mutation_p.D251E|CPT1B_ENST00000312108.7_Missense_Mutation_p.D454E|CPT1B_ENST00000405237.3_Missense_Mutation_p.D454E|CPT1B_ENST00000457250.1_Missense_Mutation_p.D420E	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	454					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		TGAAGGATTTGTCAAACCACC	0.498																																					p.D454E	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1362G						.						66.0	59.0	61.0					22																	51010728		2203	4298	6501	SO:0001583	missense	1375	exon12			GGATTTGTCAAAC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1362C>G	chr22.hg19:g.51010728G>C	ENSP00000353945:p.Asp454Glu	54.0	0.0		34.0	16.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255430	0.59321	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.97598	-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45	5.51	3.42	0.39159	.	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	H	0.96748	3.875	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;D	0.91635	0.998;0.999;0.971;0.971	D	0.97931	1.0320	10	0.87932	D	0	-39.6839	7.2184	0.25973	0.2329:0.0:0.7671:0.0	.	373;420;251;454	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	E	454;454;454;420;373;251;454	ENSP00000385486:D454E;ENSP00000312189:D454E;ENSP00000353945:D454E;ENSP00000409342:D420E;ENSP00000414713:D373E;ENSP00000410966:D251E;ENSP00000379011:D454E	ENSP00000312189:D454E	D	-	3	2	CPT1B	49357594	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	1.093000	0.30939	2.586000	0.87340	0.561000	0.74099	GAC	.	.		0.498	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
GDPD2	54857	hgsc.bcm.edu	37	X	69644840	69644840	+	Silent	SNP	C	C	T			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chrX:69644840C>T	ENST00000374382.3	+	2	257	c.6C>T	c.(4-6)gcC>gcT	p.A2A	GDPD2_ENST00000453994.2_Silent_p.A2A|GDPD2_ENST00000536730.1_Intron|GDPD2_ENST00000538649.1_Intron	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	2					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					TCACCATGGCCGAGTCCCCCG	0.647																																					p.A2A		Atlas-SNP	.											.	GDPD2	80	.	0			c.C6T						.						17.0	13.0	14.0					X																	69644840		2197	4287	6484	SO:0001819	synonymous_variant	54857	exon2			CATGGCCGAGTCC	AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"""osteoblast differentiation promoting factor"""					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.6C>T	chrX.hg19:g.69644840C>T		46.0	0.0		46.0	43.0	NM_017711	B4DRH4|B4DVC9|Q9NXJ6	Silent	SNP	ENST00000374382.3	hg19	CCDS14402.1																																																																																			.	.		0.647	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711	
MT-ND3	4537	hgsc.bcm.edu	37	M	10390	10390	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chrM:10390T>C	ENST00000361227.2	+	1	332	c.332T>C	c.(331-333)tTa>tCa	p.L111S	MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	111					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)										ACAAAAAGGATTAGACTGAGC	0.348																																					p.L111S		Atlas-SNP	.											.	.	.	.	0			c.T332C						.																																			SO:0001583	missense	0	exon1			AAGGATTAGACTG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.332T>C	chrM.hg19:g.10390T>C	ENSP00000355206:p.Leu111Ser	147.0	0.0		401.0	53.0	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	hg19																																																																																				.	.		0.348	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
EIF3C	8663	hgsc.bcm.edu	37	16	28734840	28734840	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr16:28734840delC	ENST00000331666.6	+	10	1194	c.1008delC	c.(1006-1008)atcfs	p.I336fs	EIF3C_ENST00000566866.1_Frame_Shift_Del_p.I336fs|EIF3C_ENST00000564243.1_Frame_Shift_Del_p.I326fs|EIF3C_ENST00000395587.1_Frame_Shift_Del_p.I336fs|EIF3C_ENST00000566501.1_Frame_Shift_Del_p.I336fs					eukaryotic translation initiation factor 3, subunit C											lung(5)|skin(1)	6						TGAATGAGATCCTACAGGCAC	0.512																																					p.E336fs		Atlas-INDEL	.											.	EIF3C	8	.	0			c.1007delA						.						162.0	182.0	175.0					16																	28734840		2190	4278	6468	SO:0001589	frameshift_variant	8663	exon10			.	U46025	CCDS10638.1, CCDS66993.1	16p11.2	2008-02-05	2007-07-27	2007-07-27		ENSG00000184110			3279	protein-coding gene	gene with protein product		603916	"""eukaryotic translation initiation factor 3, subunit 8, 110kDa"""	EIF3S8		8995409	Standard	NM_001199142		Approved	eIF3-p110, eIF3c	uc002dph.4	Q99613		ENST00000331666.6:c.1008delC	chr16.hg19:g.28734840delC	ENSP00000332604:p.Ile336fs	801.0	0.0		729.0	112.0	NM_001199142		Frame_Shift_Del	DEL	ENST00000331666.6	hg19	CCDS10638.1																																																																																			.	.		0.512	EIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216908.3	NM_003752	
EIF3CL	728689	hgsc.bcm.edu	37	16	28403104	28403104	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr16:28403104delG	ENST00000398943.3	-	10	1148	c.1012delC	c.(1012-1014)ctafs	p.L338fs	EIF3CL_ENST00000380876.4_Frame_Shift_Del_p.L338fs|EIF3CL_ENST00000398944.3_Frame_Shift_Del_p.L338fs			B5ME19	EIFCL_HUMAN	eukaryotic translation initiation factor 3, subunit C-like	338					formation of translation preinitiation complex (GO:0001731)|regulation of translational initiation (GO:0006446)	eukaryotic 43S preinitiation complex (GO:0016282)|eukaryotic 48S preinitiation complex (GO:0033290)|eukaryotic translation initiation factor 3 complex (GO:0005852)	translation initiation factor activity (GO:0003743)										CGTGCCTGTAGGATCTCATTC	0.507																																					p.L338fs		Atlas-INDEL	.											.	EIF3C	8	.	0			c.1013delT						.						18.0	22.0	21.0					16																	28403104		2005	3655	5660	SO:0001589	frameshift_variant	8663	exon9			.		CCDS42136.1	16p11.2	2008-10-28			ENSG00000205609	ENSG00000205609			26347	protein-coding gene	gene with protein product							Standard	NM_001099661		Approved			B5ME19	OTTHUMG00000097025	ENST00000398943.3:c.1012delC	chr16.hg19:g.28403104delG	ENSP00000381916:p.Leu338fs	799.0	0.0		644.0	67.0	NM_001267574		Frame_Shift_Del	DEL	ENST00000398943.3	hg19	CCDS42136.1																																																																																			.	.		0.507	EIF3CL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214116.1		
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206902164	206902166	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:206902164_206902166delGGA	ENST00000367103.3	+	2	582_584	c.389_391delGGA	c.(388-393)gggagg>ggg	p.R131del	MAPKAPK2_ENST00000294981.4_In_Frame_Del_p.R131del	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			CTGTACGCAGGGAGGAAGTGCCT	0.611																																					p.130_130del		Atlas-Indel,Pindel	.											.	MAPKAPK2	45	.	0			c.388_390del						.																																			SO:0001651	inframe_deletion	9261	exon2			.	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.389_391delGGA	chr1.hg19:g.206902167_206902169delGGA	ENSP00000356070:p.Arg131del	73.0	0.0		62.0	15.0	NM_004759	Q5SY30|Q5SY41|Q8IYD6	In_Frame_Del	DEL	ENST00000367103.3	hg19	CCDS31001.1																																																																																			.	.		0.611	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
HMBS	3145	hgsc.bcm.edu	37	11	118963906	118963907	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:118963906_118963907delCT	ENST00000278715.3	+	14	1150_1151	c.999_1000delCT	c.(997-1002)aacttgfs	p.L334fs	HMBS_ENST00000537841.1_Frame_Shift_Del_p.L317fs|HMBS_ENST00000543090.1_Frame_Shift_Del_p.L303fs|HMBS_ENST00000442944.2_Frame_Shift_Del_p.L317fs|HMBS_ENST00000544387.1_Frame_Shift_Del_p.L294fs|HMBS_ENST00000542729.1_Frame_Shift_Del_p.L277fs|HMBS_ENST00000392841.1_Frame_Shift_Del_p.L317fs	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	334					heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CTGCCCAGAACTTGGGCATCAG	0.545																																					p.333_333del		Atlas-INDEL	.											.	HMBS	27	.	0			c.998_999del	GRCh37	CD085816	HMBS	D		.																																			SO:0001589	frameshift_variant	3145	exon14			.	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"""uroporphyrinogen I synthase"", ""porphobilinogen deaminase"", ""porphyria, acute; Chester type"""	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.999_1000delCT	chr11.hg19:g.118963906_118963907delCT	ENSP00000278715:p.Leu334fs	26.0	0.0		31.0	14.0	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Frame_Shift_Del	DEL	ENST00000278715.3	hg19	CCDS8409.1																																																																																			.	.		0.545	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190	
DCN	1634	hgsc.bcm.edu	37	12	91558424	91558424	+	Frame_Shift_Del	DEL	G	G	-	rs3138221	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:91558424delG	ENST00000052754.5	-	3	783	c.282delC	c.(280-282)accfs	p.T94fs	DCN_ENST00000547568.2_Intron|DCN_ENST00000420120.2_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000393155.1_Frame_Shift_Del_p.T94fs|DCN_ENST00000441303.2_Frame_Shift_Del_p.T94fs|DCN_ENST00000303320.3_Frame_Shift_Del_p.T94fs|DCN_ENST00000456569.2_Intron|DCN_ENST00000425043.1_Intron|DCN_ENST00000552962.1_Frame_Shift_Del_p.T94fs	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	94					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						CTTTGATTTCGGTTATTTTGT	0.378																																					p.E95fs		Atlas-Indel,Pindel	.											DCN,NS,carcinoma,0,3	DCN	61	.	0			c.283delG						.						153.0	137.0	142.0					12																	91558424		2203	4300	6503	SO:0001589	frameshift_variant	1634	exon2			.	AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	2705	protein-coding gene	gene with protein product	"""decorin proteoglycan"""	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.282delC	chr12.hg19:g.91558424delG	ENSP00000052754:p.Thr94fs	203.0	0.0		145.0	60.0	NM_133506	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Frame_Shift_Del	DEL	ENST00000052754.5	hg19	CCDS9039.1																																																																																			.	.		0.378	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507	
GABRA2	2555	hgsc.bcm.edu	37	4	46390679	46390679	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:46390679delA	ENST00000510861.1	-	2	218	c.45delT	c.(43-45)tttfs	p.F15fs	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507460.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000507069.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000515082.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000381620.4_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000514090.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000356504.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000509716.1_5'UTR			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	15					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CCAAGAAAACAAAAAGCAGGA	0.373																																					p.V16fs		Atlas-Indel,Pindel	.											.	GABRA2	134	.	0			c.46delG						.						157.0	155.0	156.0					4																	46390679		2203	4300	6503	SO:0001589	frameshift_variant	2555	exon1			.		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.45delT	chr4.hg19:g.46390679delA	ENSP00000421828:p.Phe15fs	306.0	0.0		311.0	137.0	NM_001114175	A8K0U7|B7Z1H8|Q59G14	Frame_Shift_Del	DEL	ENST00000510861.1	hg19	CCDS3471.1																																																																																			.	.		0.373	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
MED13L	23389	hgsc.bcm.edu	37	12	116586417	116586420	+	Intron	DEL	TATA	TATA	-	rs113328518|rs375659860|rs140957424		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	TATA	TATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:116586417_116586420delTATA	ENST00000281928.3	-	3	517				MED13L_ENST00000551197.1_Intron|MIR620_ENST00000385232.1_RNA	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		gagatatctatatatatatatata	0.255																																					.		Pindel	.											.	.	.	.	0			.						.																																			SO:0001627	intron_variant	693205	.			.	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.311-37100TATA>-	chr12.hg19:g.116586425_116586428delTATA		55.0	0.0		70.0	11.0	.	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	RNA	DEL	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.		0.255	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
