#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PBX1	5087	hgsc.bcm.edu	37	1	164761953	164761953	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:164761953C>T	ENST00000420696.2	+	3	676	c.488C>T	c.(487-489)aCg>aTg	p.T163M	PBX1_ENST00000540236.1_Missense_Mutation_p.T163M|PBX1_ENST00000559240.1_Missense_Mutation_p.T163M|PBX1_ENST00000540246.1_Missense_Mutation_p.T58M|PBX1_ENST00000367897.1_Missense_Mutation_p.T163M|PBX1_ENST00000560641.1_Missense_Mutation_p.T58M|PBX1_ENST00000401534.1_Missense_Mutation_p.T163M	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	163					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						ATCTACCATACGGAGCTGGAG	0.577			T	"""TCF3, EWSR1"""	"""pre B-ALL, myoepithelioma"""																																p.T163M		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"""L, M"""	.	PBX1	60	.	0			c.C488T						PASS	.						27.0	31.0	30.0					1																	164761953		2202	4300	6502	SO:0001583	missense	5087	exon3			ACCATACGGAGCT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"""Homeoboxes / TALE class"""	8632	protein-coding gene	gene with protein product		176310	"""pre-B-cell leukemia transcription factor 1"""				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.488C>T	chr1.hg19:g.164761953C>T	ENSP00000405890:p.Thr163Met	72.0	0.0	.		60.0	30.0	.	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709033	0.89018	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.23	5.23	0.72850	PBX (1);	0.000000	0.85682	D	0.000000	T	0.43144	0.1234	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.65815	0.995;0.994;0.993;0.994;0.994	P;P;P;D;P	0.64877	0.738;0.806;0.852;0.93;0.82	T	0.39643	-0.9604	10	0.72032	D	0.01	-9.5716	18.3959	0.90497	0.0:1.0:0.0:0.0	.	58;163;163;163;163	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	M	163;163;163;163;163;58	ENSP00000341455:T163M;ENSP00000405890:T163M;ENSP00000356872:T163M;ENSP00000439943:T163M;ENSP00000384856:T163M;ENSP00000440869:T58M	ENSP00000341455:T163M	T	+	2	0	PBX1	163028577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.376000	0.79658	2.405000	0.81733	0.563000	0.77884	ACG	.	.	.	none		0.577	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585	
SUSD4	55061	hgsc.bcm.edu	37	1	223438095	223438095	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:223438095G>A	ENST00000343846.3	-	4	1234	c.601C>T	c.(601-603)Ccg>Tcg	p.P201S	SUSD4_ENST00000478605.1_Intron|SUSD4_ENST00000454695.2_Missense_Mutation_p.P41S|SUSD4_ENST00000484758.2_Missense_Mutation_p.P130S|SUSD4_ENST00000344029.6_Missense_Mutation_p.P201S|SUSD4_ENST00000494793.2_Missense_Mutation_p.P201S|SUSD4_ENST00000366878.4_Missense_Mutation_p.P201S			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	201	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GTCCCCACCGGGAAGGAGGTC	0.498																																					p.P201S		Atlas-SNP	.											.	SUSD4	82	.	0			c.C601T						PASS	.						85.0	91.0	89.0					1																	223438095		2203	4300	6503	SO:0001583	missense	55061	exon5			CCACCGGGAAGGA	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.601C>T	chr1.hg19:g.223438095G>A	ENSP00000344219:p.Pro201Ser	102.0	0.0	.		88.0	18.0	.	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	hg19	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775431	0.49786	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000454695;ENST00000344029	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.32	4.38	0.52667	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.47093	D	0.000255	T	0.58764	0.2145	N	0.20685	0.6	0.80722	D	1	B;D;P	0.71674	0.426;0.998;0.626	B;D;B	0.80764	0.329;0.994;0.432	T	0.56890	-0.7904	10	0.05721	T	0.95	-16.3711	10.3108	0.43708	0.0756:0.1375:0.7869:0.0	.	130;201;201	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	S	201;201;130;41;201	ENSP00000344219:P201S;ENSP00000355843:P201S;ENSP00000399288:P41S;ENSP00000339926:P201S	ENSP00000344219:P201S	P	-	1	0	SUSD4	221504718	1.000000	0.71417	0.997000	0.53966	0.827000	0.46813	4.506000	0.60428	1.415000	0.47037	0.491000	0.48974	CCG	.	.	.	none		0.498	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982	
GIGYF2	26058	hgsc.bcm.edu	37	2	233651899	233651899	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:233651899G>C	ENST00000409547.1	+	11	883	c.572G>C	c.(571-573)gGg>gCg	p.G191A	GIGYF2_ENST00000409451.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000373566.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000452341.2_Missense_Mutation_p.G22A|GIGYF2_ENST00000409196.3_Missense_Mutation_p.G191A|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G213A|GIGYF2_ENST00000373563.4_Missense_Mutation_p.G191A	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	191	Arg-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		ACATCAGTAGGGAGAAAGCAT	0.403																																					p.G213A		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G638C						PASS	.						104.0	106.0	106.0					2																	233651899		2203	4300	6503	SO:0001583	missense	26058	exon11			CAGTAGGGAGAAA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.572G>C	chr2.hg19:g.233651899G>C	ENSP00000386537:p.Gly191Ala	78.0	0.0	.		92.0	16.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498686	0.64298	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000445650;ENST00000452341;ENST00000421778	T;T;T;T;T;T;T;T;T;T	0.78364	-0.69;-0.69;-0.69;-0.69;-1.02;-0.7;-0.69;-0.82;-1.17;-0.89	5.63	5.63	0.86233	.	0.192608	0.46442	D	0.000288	D	0.86247	0.5887	L	0.57536	1.79	0.36437	D	0.865276	D;D;P;D	0.76494	0.999;0.982;0.953;0.989	D;P;B;P	0.75484	0.986;0.898;0.371;0.874	D	0.84937	0.0863	10	0.29301	T	0.29	-24.5013	20.0345	0.97552	0.0:0.0:1.0:0.0	.	22;213;191;191	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	A	213;140;191;213;191;191;140;191;213;191;22;22;18	ENSP00000362667:G213A;ENSP00000362664:G191A;ENSP00000386765:G213A;ENSP00000386537:G191A;ENSP00000404195:G140A;ENSP00000387070:G191A;ENSP00000387170:G213A;ENSP00000410297:G191A;ENSP00000392218:G22A;ENSP00000411505:G22A	ENSP00000362664:G191A	G	+	2	0	GIGYF2	233360143	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.552000	0.67281	2.797000	0.96272	0.655000	0.94253	GGG	.	.	.	none		0.403	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
NUP210	23225	hgsc.bcm.edu	37	3	13438880	13438880	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:13438880T>C	ENST00000254508.5	-	3	495	c.413A>G	c.(412-414)aAg>aGg	p.K138R		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	138					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GGCCTGGATCTTCAGCTCCAG	0.602																																					p.K138R		Atlas-SNP	.											.	NUP210	182	.	0			c.A413G						PASS	.						67.0	63.0	64.0					3																	13438880		2203	4300	6503	SO:0001583	missense	23225	exon3			TGGATCTTCAGCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.413A>G	chr3.hg19:g.13438880T>C	ENSP00000254508:p.Lys138Arg	78.0	0.0	.		85.0	25.0	.	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	5.986	0.365927	0.11352	.	.	ENSG00000132182	ENST00000254508	T	0.04758	3.56	3.96	2.77	0.32553	.	0.049223	0.85682	D	0.000000	T	0.03608	0.0103	L	0.33137	0.985	0.43203	D	0.995057	B	0.31817	0.341	B	0.31245	0.126	T	0.39099	-0.9630	10	0.07325	T	0.83	-12.7074	9.9009	0.41346	0.0:0.0:0.172:0.8279	.	138	Q8TEM1	PO210_HUMAN	R	138	ENSP00000254508:K138R	ENSP00000254508:K138R	K	-	2	0	NUP210	13413880	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	2.196000	0.42686	0.680000	0.31366	0.454000	0.30748	AAG	.	.	.	none		0.602	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
RBM5	10181	hgsc.bcm.edu	37	3	50147868	50147868	+	Silent	SNP	T	T	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:50147868T>C	ENST00000347869.3	+	16	1510	c.1335T>C	c.(1333-1335)ccT>ccC	p.P445P	RBM5_ENST00000441812.2_Intron	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	445	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCGCTTCCCCTACTGGTGTAG	0.458																																					p.P445P		Atlas-SNP	.											.	RBM5	76	.	0			c.T1335C						PASS	.						54.0	58.0	56.0					3																	50147868		2203	4300	6503	SO:0001819	synonymous_variant	10181	exon16			TTCCCCTACTGGT	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1335T>C	chr3.hg19:g.50147868T>C		180.0	0.0	.		149.0	36.0	.	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	hg19	CCDS2810.1																																																																																			.	.	.	none		0.458	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
GOLIM4	27333	hgsc.bcm.edu	37	3	167747034	167747034	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:167747034T>C	ENST00000470487.1	-	11	2179	c.1490A>G	c.(1489-1491)cAg>cGg	p.Q497R	GOLIM4_ENST00000309027.4_Missense_Mutation_p.Q469R	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	497	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TTGGATTCCCTGGTCCTCTGC	0.383																																					p.Q497R		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1490G						PASS	.						133.0	116.0	122.0					3																	167747034		2203	4300	6503	SO:0001583	missense	27333	exon11			ATTCCCTGGTCCT	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"""golgi phosphoprotein 4"""	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1490A>G	chr3.hg19:g.167747034T>C	ENSP00000417354:p.Gln497Arg	105.0	0.0	.		90.0	6.0	.	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305022	0.60305	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	4.97	4.97	0.65823	.	0.242984	0.44097	D	0.000487	T	0.69575	0.3126	M	0.74881	2.28	0.43029	D	0.994599	D;D	0.64830	0.994;0.989	D;P	0.67103	0.949;0.814	T	0.68405	-0.5417	9	0.09590	T	0.72	-18.1647	11.9183	0.52778	0.0:0.0:0.1451:0.8549	.	469;497	F8W785;O00461	.;GOLI4_HUMAN	R	497;469	.	ENSP00000309893:Q469R	Q	-	2	0	GOLIM4	169229728	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	4.279000	0.58953	1.884000	0.54569	0.449000	0.29647	CAG	.	.	.	none		0.383	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
APBB2	323	hgsc.bcm.edu	37	4	40818110	40818110	+	Nonstop_Mutation	SNP	T	T	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:40818110T>A	ENST00000295974.8	-	18	2905	c.2276A>T	c.(2275-2277)tAg>tTg	p.*759L	APBB2_ENST00000506352.1_Nonstop_Mutation_p.*738L|APBB2_ENST00000508593.1_Nonstop_Mutation_p.*760L|APBB2_ENST00000513140.1_Nonstop_Mutation_p.*737L|APBB2_ENST00000502841.1_Nonstop_Mutation_p.*211L|APBB2_ENST00000543538.1_Nonstop_Mutation_p.*211L|APBB2_ENST00000504305.1_Nonstop_Mutation_p.*211L|RP11-632F7.3_ENST00000513127.1_RNA	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	0					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CATGTGCAGCTATGGCATTTC	0.458																																					p.X760L	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A2279T						PASS	.						255.0	249.0	251.0					4																	40818110		1979	4157	6136	SO:0001578	stop_lost	323	exon18			TGCAGCTATGGCA	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.2276A>T	chr4.hg19:g.40818110T>A		98.0	0.0	.		99.0	22.0	.	NM_004307	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614383	0.46631	.	.	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000543538;ENST00000513140;ENST00000508593;ENST00000502841;ENST00000506352;ENST00000504305	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	.	.	.	L	759;758;211;737;760;211;738;211	.	.	X	-	2	0	APBB2	40512867	1.000000	0.71417	0.936000	0.37596	0.073000	0.16967	8.000000	0.88501	2.040000	0.60383	0.477000	0.44152	TAG	.	.	.	none		0.458	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
FRYL	285527	hgsc.bcm.edu	37	4	48536646	48536646	+	Silent	SNP	A	A	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:48536646A>G	ENST00000503238.1	-	46	6620	c.6621T>C	c.(6619-6621)agT>agC	p.S2207S	FRYL_ENST00000537810.1_Silent_p.S2207S|FRYL_ENST00000358350.4_Silent_p.S2207S|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	2207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GACTCAATAGACTATAAATAA	0.333																																					p.S2207S		Atlas-SNP	.											.	FRYL	242	.	0			c.T6621C						PASS	.						76.0	72.0	73.0					4																	48536646		1829	4086	5915	SO:0001819	synonymous_variant	285527	exon49			CAATAGACTATAA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.6621T>C	chr4.hg19:g.48536646A>G		66.0	0.0	.		67.0	10.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	0.350	-0.945182	0.02304	.	.	ENSG00000075539	ENST00000514617	T	0.12879	2.64	5.57	-1.09	0.09904	.	0.000000	0.85682	D	0.000000	T	0.18882	0.0453	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02844	-1.1103	7	0.35671	T	0.21	.	10.974	0.47454	0.529:0.0:0.471:0.0	.	.	.	.	P	1077	ENSP00000425344:S1077P	ENSP00000425344:S1077P	S	-	1	0	FRYL	48231403	1.000000	0.71417	0.766000	0.31476	0.006000	0.05464	1.028000	0.30128	0.032000	0.15435	-0.256000	0.11100	TCT	.	.	.	none		0.333	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
PDLIM4	8572	hgsc.bcm.edu	37	5	131602211	131602211	+	Silent	SNP	C	C	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131602211C>T	ENST00000253754.3	+	3	364	c.300C>T	c.(298-300)caC>caT	p.H100H	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_Silent_p.H100H	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	100							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCAGGCACACAGGATCCACA	0.592																																					p.H100H		Atlas-SNP	.											.	PDLIM4	22	.	0			c.C300T						PASS	.						93.0	69.0	77.0					5																	131602211		2203	4300	6503	SO:0001819	synonymous_variant	8572	exon3			GGCACACAGGATC	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.300C>T	chr5.hg19:g.131602211C>T		251.0	0.0	.		235.0	70.0	.	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Silent	SNP	ENST00000253754.3	hg19	CCDS4152.1																																																																																			.	.	.	none		0.592	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
SLC22A4	6583	hgsc.bcm.edu	37	5	131647952	131647952	+	Silent	SNP	A	A	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131647952A>C	ENST00000200652.3	+	2	666	c.492A>C	c.(490-492)tcA>tcC	p.S164S	SLC22A4_ENST00000491257.1_3'UTR|AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	164					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	GGCAGCTGTCAGACAGGTAAG	0.572																																					p.S164S		Atlas-SNP	.											.	SLC22A4	45	.	0			c.A492C						PASS	.						132.0	107.0	116.0					5																	131647952		2203	4300	6503	SO:0001819	synonymous_variant	6583	exon2			GCTGTCAGACAGG	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.492A>C	chr5.hg19:g.131647952A>C		75.0	0.0	.		56.0	18.0	.	NM_003059	O14546	Silent	SNP	ENST00000200652.3	hg19	CCDS4153.1																																																																																			.	.	.	none		0.572	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
DCANP1	140947	hgsc.bcm.edu	37	5	134785315	134785315	+	5'Flank	SNP	G	G	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:134785315G>C	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Silent_p.V105V|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGAGAAGGAGACCCTGTTGA	0.577																																					p.V105V		Atlas-SNP	.											TIFAB,NS,carcinoma,0,1	TIFAB	23	.	0			c.C315G						PASS	.						101.0	104.0	103.0					5																	134785315		2082	4221	6303	SO:0001631	upstream_gene_variant	497189	exon2			GAAGGAGACCCTG																													chr5.hg19:g.134785315G>C	Exception_encountered	148.0	0.0	.		133.0	24.0	.	NM_001099221		Silent	SNP	ENST00000503143.2	hg19	CCDS4186.1																																																																																			.	.	.	none		0.577	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
GABRA6	2559	hgsc.bcm.edu	37	5	161116041	161116041	+	Silent	SNP	T	T	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:161116041T>C	ENST00000274545.5	+	4	745	c.312T>C	c.(310-312)aaT>aaC	p.N104N	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Silent_p.N94N			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	104					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|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)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TGAGTCTGAATAATTTGATGG	0.403										TCGA Ovarian(5;0.080)																											p.N104N		Atlas-SNP	.											.	GABRA6	139	.	0			c.T312C						PASS	.						76.0	77.0	77.0					5																	161116041		2203	4299	6502	SO:0001819	synonymous_variant	2559	exon4			TCTGAATAATTTG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.312T>C	chr5.hg19:g.161116041T>C		65.0	0.0	.		85.0	17.0	.	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	T	8.919	0.960604	0.18583	.	.	ENSG00000145863	ENST00000520000	.	.	.	5.65	2.01	0.26516	.	.	.	.	.	T	0.54581	0.1867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.8819	0.24179	0.0:0.4395:0.0:0.5605	.	.	.	.	T	44	.	.	I	+	2	0	GABRA6	161048619	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.646000	0.46630	0.507000	0.28148	-0.274000	0.10170	ATA	.	.	.	none		0.403	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
DTNBP1	84062	hgsc.bcm.edu	37	6	15523339	15523339	+	Missense_Mutation	SNP	C	C	G	rs374085686		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:15523339C>G	ENST00000344537.5	-	10	1095	c.923G>C	c.(922-924)cGg>cCg	p.R308P	DTNBP1_ENST00000462989.2_Missense_Mutation_p.R152P|DTNBP1_ENST00000355917.3_Missense_Mutation_p.R309P	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	308	Dysbindin.				actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			ACTGATGTCCCGGGTGGCCGA	0.567									Hermansky-Pudlak syndrome																												p.R308P		Atlas-SNP	.											.	DTNBP1	56	.	0			c.G923C						PASS	.						137.0	142.0	141.0					6																	15523339		2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	ATGTCCCGGGTGG	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.923G>C	chr6.hg19:g.15523339C>G	ENSP00000341680:p.Arg308Pro	163.0	0.0	.		197.0	32.0	.	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	hg19	CCDS4534.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.710179	0.30322	.	.	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.62	-7.93	0.01156	.	1.163890	0.06365	N	0.712440	T	0.01558	0.0050	N	0.01297	-0.9	0.19300	N	0.999978	B	0.02656	0.0	B	0.08055	0.003	T	0.27331	-1.0077	10	0.08179	T	0.78	-9.2314	4.2873	0.10862	0.0902:0.1668:0.4361:0.307	.	308	Q96EV8	DTBP1_HUMAN	P	308;152;309;227;125	ENSP00000341680:R308P;ENSP00000427239:R152P;ENSP00000348183:R309P;ENSP00000421797:R125P	ENSP00000341680:R308P	R	-	2	0	DTNBP1	15631318	0.501000	0.26099	0.000000	0.03702	0.022000	0.10575	0.142000	0.16096	-2.293000	0.00664	-0.254000	0.11334	CGG	.	.	.	alt		0.567	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858516	27858516	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27858516T>G	ENST00000359303.2	-	1	54	c.55A>C	c.(55-57)Aag>Cag	p.K19Q	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	19					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GCCAGCTGCTTCCGCGGTGCC	0.617																																					p.K19Q		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.A55C						PASS	.						29.0	33.0	31.0					6																	27858516		2203	4299	6502	SO:0001583	missense	8356	exon1			GCTGCTTCCGCGG	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.55A>C	chr6.hg19:g.27858516T>G	ENSP00000352252:p.Lys19Gln	111.0	0.0	.		89.0	25.0	.	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000359303.2	hg19	CCDS4638.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572970	0.45798	.	.	ENSG00000197153	ENST00000359303	T	0.48522	0.81	4.06	4.06	0.47325	.	.	.	.	.	T	0.52224	0.1721	.	.	.	0.42070	D	0.991202	.	.	.	.	.	.	T	0.59316	-0.7477	6	0.87932	D	0	.	12.8321	0.57752	0.0:0.0:0.0:1.0	.	.	.	.	Q	19	ENSP00000352252:K19Q	ENSP00000352252:K19Q	K	-	1	0	HIST1H3J	27966495	1.000000	0.71417	0.997000	0.53966	0.747000	0.42532	7.496000	0.81526	2.071000	0.62044	0.533000	0.62120	AAG	.	.	.	none		0.617	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
DNAJB9	4189	hgsc.bcm.edu	37	7	108212287	108212287	+	Silent	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:108212287G>A	ENST00000249356.3	+	2	663	c.117G>A	c.(115-117)gaG>gaA	p.E39E	THAP5_ENST00000493722.1_5'Flank|THAP5_ENST00000438865.1_5'Flank|THAP5_ENST00000415914.3_5'Flank|DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000313516.5_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	39	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						CGGCATCAGAGCGCCAAATCA	0.403																																					p.E39E		Atlas-SNP	.											.	DNAJB9	25	.	0			c.G117A						PASS	.						107.0	116.0	113.0					7																	108212287		2203	4300	6503	SO:0001819	synonymous_variant	4189	exon2			ATCAGAGCGCCAA	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"""Heat shock proteins / DNAJ (HSP40)"""	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.117G>A	chr7.hg19:g.108212287G>A		131.0	0.0	.		137.0	43.0	.	NM_012328		Silent	SNP	ENST00000249356.3	hg19	CCDS5752.1																																																																																			.	.	.	none		0.403	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1		
FAM83H	286077	hgsc.bcm.edu	37	8	144809730	144809730	+	Missense_Mutation	SNP	G	G	C	rs367877690	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:144809730G>C	ENST00000388913.3	-	5	2026	c.1901C>G	c.(1900-1902)gCa>gGa	p.A634G		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	634					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GGGGAAGGCTGCTGGGACGCG	0.751													G|||	5	0.000998403	0.0038	0.0	5008	,	,		9374	0.0		0.0	False		,,,				2504	0.0				p.A634G		Atlas-SNP	.											.	FAM83H	68	.	0			c.C1901G						PASS	.	G	GLY/ALA	5,3093		0,5,1544	6.0	8.0	7.0		1901	0.6	0.0	8		7	0,7130		0,0,3565	no	missense	FAM83H	NM_198488.3	60	0,5,5109	CC,CG,GG		0.0,0.1614,0.0489	benign	634/1180	144809730	5,10223	1549	3565	5114	SO:0001583	missense	286077	exon5			AAGGCTGCTGGGA	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1901C>G	chr8.hg19:g.144809730G>C	ENSP00000373565:p.Ala634Gly	3.0	0.0	.		12.0	6.0	.	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	0.018	-1.474564	0.01044	0.001614	0.0	ENSG00000180921	ENST00000388913	T	0.14516	2.5	3.85	0.608	0.17569	.	16.316900	0.01476	U	0.016496	T	0.08980	0.0222	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27054	-1.0085	10	0.20519	T	0.43	.	5.3436	0.15996	0.2787:0.3057:0.4156:0.0	.	634	Q6ZRV2	FA83H_HUMAN	G	634	ENSP00000373565:A634G	ENSP00000373565:A634G	A	-	2	0	FAM83H	144881718	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	0.100000	0.15231	0.258000	0.21686	0.561000	0.74099	GCA	.	.	.	weak		0.751	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
PLEC	5339	hgsc.bcm.edu	37	8	145001217	145001217	+	Silent	SNP	C	C	T	rs374669316		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:145001217C>T	ENST00000322810.4	-	29	4453	c.4284G>A	c.(4282-4284)gcG>gcA	p.A1428A	PLEC_ENST00000398774.2_Silent_p.A1259A|PLEC_ENST00000436759.2_Silent_p.A1318A|PLEC_ENST00000356346.3_Silent_p.A1277A|PLEC_ENST00000357649.2_Silent_p.A1295A|PLEC_ENST00000345136.3_Silent_p.A1291A|PLEC_ENST00000354958.2_Silent_p.A1269A|PLEC_ENST00000354589.3_Silent_p.A1291A|PLEC_ENST00000527096.1_Silent_p.A1314A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1428	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTCAAGCTGCGCCTTGTACG	0.637																																					p.A1428A		Atlas-SNP	.											.	PLEC	1144	.	0			c.G4284A						PASS	.	C	,,,,,,,	1,4183		0,1,2091	58.0	63.0	62.0		3954,3831,3807,4284,3777,3873,3885,3873	-9.9	0.3	8		62	0,8434		0,0,4217	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	0,1,6308	TT,TC,CC		0.0,0.0239,0.0079	,,,,,,,	1318/4575,1277/4534,1269/4526,1428/4685,1259/4516,1291/4548,1295/4552,1291/4548	145001217	1,12617	2092	4217	6309	SO:0001819	synonymous_variant	5339	exon29			AAGCTGCGCCTTG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4284G>A	chr8.hg19:g.145001217C>T		64.0	0.0	.		69.0	4.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	weak		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CDKN2A	1029	hgsc.bcm.edu	37	9	21971184	21971184	+	Silent	SNP	T	T	G	rs201208890	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:21971184T>G	ENST00000304494.5	-	2	444	c.174A>C	c.(172-174)cgA>cgC	p.R58R	CDKN2A_ENST00000579122.1_Silent_p.R58R|CDKN2A_ENST00000579755.1_Missense_Mutation_p.S73R|CDKN2A_ENST00000479692.2_Silent_p.R7R|CDKN2A_ENST00000494262.1_Silent_p.R7R|CDKN2A_ENST00000530628.2_Missense_Mutation_p.S73R|CDKN2A_ENST00000578845.2_Silent_p.R7R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000497750.1_Silent_p.R7R|CDKN2A_ENST00000361570.3_Missense_Mutation_p.S114R|CDKN2A_ENST00000498628.2_Silent_p.R7R|CDKN2A_ENST00000446177.1_Silent_p.R58R|CDKN2A_ENST00000498124.1_Silent_p.R58R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	58			R -> Q (in dbSNP:rs36204273).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(45)|p.M53_R58del(3)|p.R58fs*59(2)|p.V59fs*82(2)|p.0(1)|p.V28_V51del(1)|p.V59fs*63(1)|p.V59fs*61(1)|p.V59fs*60(1)|p.G55fs*86(1)|p.A57fs*85(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCTCCGCCACTCGGGCGCTGC	0.682		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			G|||	15	0.00299521	0.0113	0.0	5008	,	,		11788	0.0		0.0	False		,,,				2504	0.0				p.S73R		Atlas-SNP	.											CDKN2A_ENST00000498124,mucosal,malignant_melanoma,-2,3	CDKN2A	4810	.	1374	Whole gene deletion(1316)|Unknown(45)|Deletion - Frameshift(7)|Deletion - In frame(4)|Insertion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(285)|skin(176)|central_nervous_system(167)|lung(145)|urinary_tract(92)|bone(74)|soft_tissue(57)|upper_aerodigestive_tract(55)|oesophagus(52)|pleura(51)|ovary(37)|kidney(32)|breast(32)|pancreas(30)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.A217C						PASS	.	G	,,,ARG/SER	25,4025		0,25,2000	7.0	9.0	8.0		174,174,,217	-4.5	0.0	9		8	0,8162		0,0,4081	no	coding-synonymous,coding-synonymous,utr-3,missense	CDKN2A	NM_000077.4,NM_001195132.1,NM_058197.4,NM_058195.3	,,,110	0,25,6081	GG,GT,TT		0.0,0.6173,0.2047	,,,benign	58/157,58/168,,73/133	21971184	25,12187	2025	4081	6106	SO:0001819	synonymous_variant	1029	exon2			CGCCACTCGGGCG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.174A>C	chr9.hg19:g.21971184T>G		4.0	2.0	.		34.0	18.0	.	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	G	6.483	0.457206	0.12342	0.006173	0.0	ENSG00000147889	ENST00000361570;ENST00000530628	T;T	0.76186	-1.0;-0.95	5.79	-4.48	0.03515	.	0.576553	0.14595	N	0.309984	T	0.41789	0.1174	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22941	-1.0202	8	.	.	.	-3.0019	5.0452	0.14480	0.1174:0.1641:0.1404:0.5781	.	114	Q8N726	CD2A2_HUMAN	R	114;73	ENSP00000355153:S114R;ENSP00000432664:S73R	.	S	-	1	0	CDKN2A	21961184	0.000000	0.05858	0.001000	0.08648	0.194000	0.23727	-2.443000	0.01013	-1.206000	0.02641	-2.190000	0.00312	AGT	.	.	.	weak		0.682	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
GLYATL2	219970	hgsc.bcm.edu	37	11	58601915	58601915	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:58601915T>C	ENST00000287275.1	-	6	1262	c.872A>G	c.(871-873)aAg>aGg	p.K291R	GLYATL2_ENST00000532258.1_Missense_Mutation_p.K291R|GLYATL2_ENST00000533636.1_5'Flank	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	291						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	ACAATATTTCTTGGGGGTGCA	0.363																																					p.K291R		Atlas-SNP	.											.	GLYATL2	40	.	0			c.A872G						PASS	.						53.0	49.0	50.0					11																	58601915		1831	4083	5914	SO:0001583	missense	219970	exon6			TATTTCTTGGGGG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.872A>G	chr11.hg19:g.58601915T>C	ENSP00000287275:p.Lys291Arg	41.0	0.0	.		37.0	11.0	.	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	hg19	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	T	7.457	0.643799	0.14451	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.14640	2.49;2.49	2.81	-1.38	0.09027	.	0.816947	0.10184	U	0.705518	T	0.08133	0.0203	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.39921	-0.9590	10	0.25106	T	0.35	.	3.0975	0.06314	0.0:0.2741:0.2254:0.5005	.	291	Q8WU03	GLYL2_HUMAN	R	291	ENSP00000287275:K291R;ENSP00000434277:K291R	ENSP00000287275:K291R	K	-	2	0	GLYATL2	58358491	0.008000	0.16893	0.022000	0.16811	0.453000	0.32348	0.974000	0.29436	-0.398000	0.07679	-1.222000	0.01597	AAG	.	.	.	none		0.363	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016	
MAML2	84441	hgsc.bcm.edu	37	11	95825395	95825395	+	Silent	SNP	C	C	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825395C>T	ENST00000524717.1	-	2	3084	c.1800G>A	c.(1798-1800)caG>caA	p.Q600Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	600					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgct	0.537			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q600Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1800A						PASS	.						21.0	29.0	26.0					11																	95825395		1989	3928	5917	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1800G>A	chr11.hg19:g.95825395C>T		159.0	0.0	.		137.0	16.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.537	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
CD163L1	283316	hgsc.bcm.edu	37	12	7526001	7526001	+	Silent	SNP	C	C	T	rs368002565		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:7526001C>T	ENST00000313599.3	-	14	3702	c.3645G>A	c.(3643-3645)acG>acA	p.T1215T	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000396630.1_Silent_p.T1215T|CD163L1_ENST00000416109.2_Silent_p.T1225T			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1215	SRCR 11. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TGGAGATATGCGTTTTAGGAC	0.527																																					p.T1215T		Atlas-SNP	.											.	CD163L1	238	.	0			c.G3645A						PASS	.	T		0,4406		0,0,2203	148.0	120.0	129.0		3645	-4.5	0.0	12		129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CD163L1	NM_174941.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1215/1454	7526001	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon14			GATATGCGTTTTA	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3645G>A	chr12.hg19:g.7526001C>T		332.0	0.0	.		280.0	46.0	.	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.	.	weak		0.527	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
SLC38A4	55089	hgsc.bcm.edu	37	12	47170779	47170779	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:47170779C>T	ENST00000447411.1	-	12	1288	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	SLC38A4_ENST00000266579.4_Missense_Mutation_p.R361Q	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	361					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					CATTTTTCTCCGGGACCGACT	0.358																																					p.R361Q		Atlas-SNP	.											.	SLC38A4	58	.	0			c.G1082A						PASS	.						87.0	88.0	88.0					12																	47170779		2203	4299	6502	SO:0001583	missense	55089	exon12			TTTCTCCGGGACC	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"""Solute carriers"""	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.1082G>A	chr12.hg19:g.47170779C>T	ENSP00000389843:p.Arg361Gln	87.0	0.0	.		64.0	16.0	.	NM_001143824	A8K553	Missense_Mutation	SNP	ENST00000447411.1	hg19	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.479698	0.26511	.	.	ENSG00000139209	ENST00000447411;ENST00000266579	T;T	0.02158	4.42;4.42	5.96	3.18	0.36537	.	0.116259	0.64402	N	0.000017	T	0.03871	0.0109	L	0.49640	1.575	0.45607	D	0.998544	B	0.24258	0.1	B	0.33890	0.172	T	0.41288	-0.9517	10	0.17369	T	0.5	-4.6085	15.3035	0.73972	0.0:0.872:0.0:0.128	.	361	Q969I6	S38A4_HUMAN	Q	361	ENSP00000389843:R361Q;ENSP00000266579:R361Q	ENSP00000266579:R361Q	R	-	2	0	SLC38A4	45457046	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	1.399000	0.34566	0.425000	0.26087	-0.940000	0.02684	CGG	.	.	.	none		0.358	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1		
XPOT	11260	hgsc.bcm.edu	37	12	64808728	64808728	+	Silent	SNP	C	C	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:64808728C>A	ENST00000332707.5	+	3	631	c.102C>A	c.(100-102)gcC>gcA	p.A34A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	34	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		CCCCAGATGCCTGGCAGGTGT	0.388																																					p.A34A		Atlas-SNP	.											.	XPOT	105	.	0			c.C102A						PASS	.						91.0	97.0	95.0					12																	64808728		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon3			AGATGCCTGGCAG	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.102C>A	chr12.hg19:g.64808728C>A		31.0	0.0	.		37.0	5.0	.	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	hg19	CCDS31852.1																																																																																			.	.	.	none		0.388	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235	
USP44	84101	hgsc.bcm.edu	37	12	95907438	95907438	+	IGR	SNP	A	A	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:95907438A>G	ENST00000258499.3	-	0	4022				METAP2_ENST00000261220.9_Missense_Mutation_p.T376A|METAP2_ENST00000546753.1_Missense_Mutation_p.T376A|METAP2_ENST00000323666.5_Missense_Mutation_p.T399A|METAP2_ENST00000551840.1_Missense_Mutation_p.T398A|METAP2_ENST00000550777.1_Missense_Mutation_p.T363A	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44						mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						GCTTCCAAGAACAAAACACTT	0.418																																					p.T399A		Atlas-SNP	.											.	METAP2	28	.	0			c.A1195G						PASS	.						84.0	82.0	83.0					12																	95907438		2203	4300	6503	SO:0001628	intergenic_variant	10988	exon11			CCAAGAACAAAAC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7			chr12.hg19:g.95907438A>G		69.0	0.0	.		88.0	21.0	.	NM_006838	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	A	2.554	-0.303387	0.05495	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000550777;ENST00000551840	.	.	.	5.83	2.17	0.27698	Winged helix-turn-helix transcription repressor DNA-binding (1);Peptidase M24, structural domain (2);	0.135470	0.64402	N	0.000002	T	0.03220	0.0094	N	0.00003	-3.5	0.39326	D	0.96532	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.02654	T	1	-9.0542	6.8846	0.24193	0.3929:0.0:0.6071:0.0	.	376;363;376;398;399	B4DUX5;F8VRR3;G3XA91;F8VQZ7;P50579	.;.;.;.;AMPM2_HUMAN	A	399;376;376;363;398	.	ENSP00000261220:T376A	T	+	1	0	METAP2	94431569	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.393000	0.59665	0.466000	0.27193	0.533000	0.62120	ACA	.	.	.	none		0.418	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
KBTBD13	390594	hgsc.bcm.edu	37	15	65369367	65369367	+	Silent	SNP	C	C	T	rs550537101	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:65369367C>T	ENST00000432196.2	+	1	214	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	72	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CCGGCCGGCGCTGGCGGCGGA	0.736													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		9554	0.0		0.0	False		,,,				2504	0.0				p.L72L		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C214T						PASS	.						2.0	2.0	2.0					15																	65369367		1202	2816	4018	SO:0001819	synonymous_variant	390594	exon1			CCGGCGCTGGCGG		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"""BTB/POZ domain containing"""	37227	protein-coding gene	gene with protein product	"""nemaline myopathy type 6"""	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.214C>T	chr15.hg19:g.65369367C>T		0.0	0.0	.		7.0	5.0	.	NM_001101362		Silent	SNP	ENST00000432196.2	hg19	CCDS45281.1																																																																																			.	.	.	none		0.736	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362	
CDR2	1039	hgsc.bcm.edu	37	16	22358803	22358803	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:22358803A>G	ENST00000268383.2	-	5	1155	c.848T>C	c.(847-849)tTc>tCc	p.F283S		NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	283						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GGGCTCTTTGAAAGGAACATA	0.532																																					p.F283S		Atlas-SNP	.											.	CDR2	34	.	0			c.T848C						PASS	.						38.0	39.0	39.0					16																	22358803		2197	4300	6497	SO:0001583	missense	1039	exon5			TCTTTGAAAGGAA	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"""Yo paraneoplastic antigen"""	117340	"""cerebellar degeneration-related protein (62kD)"""			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.848T>C	chr16.hg19:g.22358803A>G	ENSP00000268383:p.Phe283Ser	43.0	0.0	.		64.0	15.0	.	NM_001802	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	hg19	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	A	3.865	-0.029069	0.07589	.	.	ENSG00000140743	ENST00000268383	T	0.41065	1.01	5.79	4.68	0.58851	.	0.159588	0.56097	D	0.000023	T	0.29093	0.0723	L	0.27053	0.805	0.38438	D	0.946635	B	0.23185	0.081	B	0.20577	0.03	T	0.09100	-1.0690	10	0.15952	T	0.53	-9.0507	13.0653	0.59030	0.8657:0.1343:0.0:0.0	.	283	Q01850	CDR2_HUMAN	S	283	ENSP00000268383:F283S	ENSP00000268383:F283S	F	-	2	0	CDR2	22266304	0.890000	0.30428	0.599000	0.28851	0.617000	0.37484	3.322000	0.52007	0.991000	0.38814	0.533000	0.62120	TTC	.	.	.	none		0.532	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1		
ZNF629	23361	hgsc.bcm.edu	37	16	30794425	30794425	+	Silent	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:30794425G>A	ENST00000262525.4	-	3	1431	c.1224C>T	c.(1222-1224)ggC>ggT	p.G408G	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	408					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			TGAAGCTCTTGCCGCACTCTG	0.652																																					p.G408G		Atlas-SNP	.											.	ZNF629	44	.	0			c.C1224T						PASS	.						47.0	51.0	49.0					16																	30794425		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			GCTCTTGCCGCAC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.1224C>T	chr16.hg19:g.30794425G>A		184.0	0.0	.		179.0	51.0	.	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.	.	none		0.652	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
OSGIN1	29948	hgsc.bcm.edu	37	16	83994295	83994295	+	Nonsense_Mutation	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:83994295G>A	ENST00000343939.2	+	5	958	c.575G>A	c.(574-576)tGg>tAg	p.W192*	OSGIN1_ENST00000393306.1_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000565123.1_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000361711.3_Nonsense_Mutation_p.W109*			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	192					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GTCCTCACCTGGAAGCACCGG	0.652																																					p.W109X		Atlas-SNP	.											.	OSGIN1	33	.	0			c.G326A						PASS	.						61.0	60.0	60.0					16																	83994295		2200	4300	6500	SO:0001587	stop_gained	29948	exon4			TCACCTGGAAGCA	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.575G>A	chr16.hg19:g.83994295G>A	ENSP00000343376:p.Trp192*	189.0	0.0	.		185.0	62.0	.	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Nonsense_Mutation	SNP	ENST00000343939.2	hg19		.	.	.	.	.	.	.	.	.	.	G	38	7.081125	0.98051	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.1195	16.9387	0.86210	0.0:0.0:1.0:0.0	.	.	.	.	X	192;109;109	.	ENSP00000343376:W192X	W	+	2	0	OSGIN1	82551796	1.000000	0.71417	0.998000	0.56505	0.495000	0.33615	5.463000	0.66712	2.228000	0.72767	0.491000	0.48974	TGG	.	.	.	none		0.652	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
MTHFSD	64779	hgsc.bcm.edu	37	16	86565821	86565821	+	Silent	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:86565821G>A	ENST00000360900.6	-	8	973	c.948C>T	c.(946-948)gaC>gaT	p.D316D	MTHFSD_ENST00000381214.5_Silent_p.D316D|MTHFSD_ENST00000546093.1_Silent_p.D153D|MTHFSD_ENST00000543303.2_Silent_p.D315D|MTHFSD_ENST00000322911.6_Silent_p.D315D	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	316	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TCACACGGGCGTCCCCGGGGA	0.682																																					p.D316D		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C948T						PASS	.						11.0	14.0	13.0					16																	86565821		1876	4097	5973	SO:0001819	synonymous_variant	64779	exon8			ACGGGCGTCCCCG	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.948C>T	chr16.hg19:g.86565821G>A		131.0	0.0	.		143.0	25.0	.	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Silent	SNP	ENST00000360900.6	hg19	CCDS54047.1																																																																																			.	.	.	none		0.682	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
ACSF2	80221	hgsc.bcm.edu	37	17	48541577	48541577	+	Splice_Site	SNP	A	A	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:48541577A>G	ENST00000300441.4	+	10	1242		c.e10-1		ACSF2_ENST00000502667.1_Splice_Site|ACSF2_ENST00000427954.2_Splice_Site|ACSF2_ENST00000541920.1_Splice_Site|ACSF2_ENST00000504392.1_Splice_Site	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2						fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCTCTGATTCAGGTGTCATTG	0.547																																					.		Atlas-SNP	.											.	ACSF2	46	.	0			c.1139-2A>G						PASS	.						130.0	117.0	121.0					17																	48541577		2203	4300	6503	SO:0001630	splice_region_variant	80221	exon10			TGATTCAGGTGTC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1139-1A>G	chr17.hg19:g.48541577A>G		150.0	0.0	.		129.0	44.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Splice_Site	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562393	0.65538	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	.	.	.	4.48	4.48	0.54585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.256	0.66053	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACSF2	45896576	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.372000	0.79612	2.016000	0.59253	0.533000	0.62120	.	.	.	.	none		0.547	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	Intron
SMARCA4	6597	hgsc.bcm.edu	37	19	11134286	11134286	+	Silent	SNP	C	C	G	rs371276213		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:11134286C>G	ENST00000429416.3	+	21	3233	c.2952C>G	c.(2950-2952)gtC>gtG	p.V984V	SMARCA4_ENST00000344626.4_Silent_p.V984V|SMARCA4_ENST00000589677.1_Silent_p.V984V|SMARCA4_ENST00000413806.3_Silent_p.V984V|SMARCA4_ENST00000590574.1_Silent_p.V984V|SMARCA4_ENST00000444061.3_Silent_p.V984V|SMARCA4_ENST00000358026.2_Silent_p.V984V|SMARCA4_ENST00000541122.2_Silent_p.V984V|SMARCA4_ENST00000450717.3_Silent_p.V984V	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	984					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|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 transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AGAAGGAAGTCGAGGCCCAGT	0.597			"""F, N, Mis"""		NSCLC																																p.V984V		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.C2952G						PASS	.						46.0	42.0	44.0					19																	11134286		2202	4300	6502	SO:0001819	synonymous_variant	6597	exon20			GGAAGTCGAGGCC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2952C>G	chr19.hg19:g.11134286C>G		141.0	0.0	.		142.0	26.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	hg19	CCDS12253.1																																																																																			.	.	.	alt		0.597	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
NCCRP1	342897	hgsc.bcm.edu	37	19	39687743	39687743	+	Silent	SNP	C	C	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:39687743C>T	ENST00000339852.4	+	1	143	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	41	Pro-rich.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						gccgccaccactgccctcgcc	0.776																																					p.L41L	Melanoma(107;1207 1556 14956 29427 52130)	Atlas-SNP	.											.	NCCRP1	25	.	0			c.C121T						PASS	.						2.0	3.0	3.0					19																	39687743		1158	2257	3415	SO:0001819	synonymous_variant	342897	exon1			CCACCACTGCCCT	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.121C>T	chr19.hg19:g.39687743C>T		0.0	0.0	.		9.0	5.0	.	NM_001001414	Q6NVV5	Silent	SNP	ENST00000339852.4	hg19	CCDS12529.1																																																																																			.	.	.	none		0.776	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414	
LILRB1	10859	hgsc.bcm.edu	37	19	55143956	55143956	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:55143956A>G	ENST00000396331.1	+	7	1060	c.703A>G	c.(703-705)Atc>Gtc	p.I235V	LILRB1_ENST00000448689.1_Missense_Mutation_p.I235V|LILRB1_ENST00000434867.2_Missense_Mutation_p.I235V|LILRB1_ENST00000418536.2_Missense_Mutation_p.I235V|LILRB1_ENST00000396327.3_Missense_Mutation_p.I235V|LILRB1_ENST00000396321.2_Missense_Mutation_p.I235V|LILRB1_ENST00000324602.7_Missense_Mutation_p.I235V|LILRB1_ENST00000396315.1_Missense_Mutation_p.I235V|LILRB1_ENST00000396332.4_Missense_Mutation_p.I235V|LILRB1_ENST00000396317.1_Missense_Mutation_p.I235V|LILRB1_ENST00000427581.2_Missense_Mutation_p.I271V	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	235	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GCCAGGTCCTATCGTGGCCCC	0.537										HNSCC(37;0.09)																											p.I235V		Atlas-SNP	.											.	LILRB1	140	.	0			c.A703G						PASS	.						98.0	102.0	101.0					19																	55143956		2203	4300	6503	SO:0001583	missense	10859	exon6			GGTCCTATCGTGG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.703A>G	chr19.hg19:g.55143956A>G	ENSP00000379622:p.Ile235Val	333.0	0.0	.		264.0	83.0	.	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	hg19	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.218786	0.00286	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87	1.49	-1.31	0.09230	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.873016	0.09637	N	0.775542	T	0.01592	0.0051	N	0.00219	-1.825	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.001;0.001;0.006;0.001;0.002	T	0.39014	-0.9634	10	0.02654	T	1	.	2.0446	0.03557	0.3776:0.0:0.3682:0.2542	.	235;235;235;235;235	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	V	235;235;235;235;235;235;235;235;271;235;235	ENSP00000379614:I235V;ENSP00000391514:I235V;ENSP00000409968:I235V;ENSP00000379622:I235V;ENSP00000379618:I235V;ENSP00000315997:I235V;ENSP00000405243:I235V;ENSP00000379623:I235V;ENSP00000395004:I271V;ENSP00000379610:I235V;ENSP00000379608:I235V	ENSP00000315997:I235V	I	+	1	0	LILRB1	59835768	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.930000	0.03972	-0.750000	0.04740	-1.160000	0.01791	ATC	.	.	.	none		0.537	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
HNF4A	3172	hgsc.bcm.edu	37	20	42984469	42984469	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr20:42984469G>T	ENST00000316673.4	+	1	130	c.25G>T	c.(25-27)Ggg>Tgg	p.G9W	HNF4A_ENST00000609795.1_Missense_Mutation_p.G9W|RP5-881L22.5_ENST00000438702.1_RNA|HNF4A_ENST00000457232.1_Missense_Mutation_p.G9W			P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	157					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G9W(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CGCGCCCCTCGGGGCTCCAGT	0.682																																					p.G9W	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	1	Substitution - Missense(1)	lung(1)	c.G25T						PASS	.						24.0	28.0	26.0					20																	42984469		2037	4184	6221	SO:0001583	missense	3172	exon1			CCCCTCGGGGCTC	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"""Nuclear hormone receptors"""	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316673.4:c.25G>T	chr20.hg19:g.42984469G>T	ENSP00000315180:p.Gly9Trp	66.0	0.0	.		75.0	16.0	.	NM_001030003	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316673.4	hg19	CCDS42876.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213853	0.39102	.	.	ENSG00000101076	ENST00000316673;ENST00000457232	D;D	0.92595	-3.07;-3.06	4.98	3.04	0.35103	.	.	.	.	.	D	0.91099	0.7198	N	0.24115	0.695	0.80722	D	1	D;D;P	0.71674	0.998;0.998;0.948	D;D;P	0.70227	0.93;0.968;0.759	D	0.89491	0.3757	9	0.72032	D	0.01	.	7.9382	0.29941	0.1907:0.0:0.8093:0.0	.	9;9;9	F1D8T0;P41235-6;P41235-7	.;.;.	W	9	ENSP00000315180:G9W;ENSP00000396216:G9W	ENSP00000315180:G9W	G	+	1	0	HNF4A	42417883	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.571000	0.45990	0.635000	0.30488	-0.136000	0.14681	GGG	.	.	.	none		0.682	HNF4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079362.2		
GGT5	2687	hgsc.bcm.edu	37	22	24628898	24628898	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:24628898G>C	ENST00000327365.4	-	4	905	c.489C>G	c.(487-489)ttC>ttG	p.F163L	GGT5_ENST00000398292.3_Missense_Mutation_p.F163L|GGT5_ENST00000418439.2_Missense_Mutation_p.P88A|GGT5_ENST00000263112.7_Missense_Mutation_p.F131L	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	163					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						TGGTGGGCTGGAACAGCTGCG	0.701																																					p.F163L		Atlas-SNP	.											.	GGT5	61	.	0			c.C489G						PASS	.						23.0	25.0	24.0					22																	24628898		2184	4285	6469	SO:0001583	missense	2687	exon4			GGGCTGGAACAGC	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.489C>G	chr22.hg19:g.24628898G>C	ENSP00000330080:p.Phe163Leu	122.0	0.0	.		193.0	36.0	.	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.533985|4.533985	0.85812|0.85812	.|.	.|.	ENSG00000099998|ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292|ENST00000418439	T;T;T|T	0.03717|0.66638	3.83;3.83;3.83|-0.22	4.32|4.32	3.3|3.3	0.37823|0.37823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58264|0.58264	0.2110|0.2110	M|M	0.64997|0.64997	1.995|1.995	0.25198|0.25198	N|N	0.990074|0.990074	D;D;B;D|B	0.69078|0.25667	0.967;0.997;0.095;0.997|0.131	P;D;B;D|B	0.67900|0.25140	0.775;0.954;0.129;0.954|0.058	T|T	0.45469|0.45469	-0.9259|-0.9259	10|9	0.72032|0.17369	D|T	0.01|0.5	-37.4629|-37.4629	6.7667|6.7667	0.23571|0.23571	0.2119:0.0:0.7881:0.0|0.2119:0.0:0.7881:0.0	.|.	131;163;163;163|88	P36269-2;Q53XM9;Q6GMP0;P36269|E7EUG3	.;.;.;GGT5_HUMAN|.	L|A	163;131;78;163|88	ENSP00000330080:F163L;ENSP00000263112:F131L;ENSP00000381340:F163L|ENSP00000392146:P88A	ENSP00000263112:F131L|ENSP00000392146:P88A	F|P	-|-	3|1	2|0	GGT5|GGT5	22958898|22958898	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	1.180000|1.180000	0.32005|0.32005	1.170000|1.170000	0.42753|0.42753	0.585000|0.585000	0.79938|0.79938	TTC|CCA	.	.	.	none		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
SH3KBP1	30011	hgsc.bcm.edu	37	X	19560045	19560045	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560045C>A	ENST00000397821.3	-	16	2180	c.1890G>T	c.(1888-1890)caG>caT	p.Q630H	SH3KBP1_ENST00000541422.1_Missense_Mutation_p.Q369H|SH3KBP1_ENST00000379698.4_Missense_Mutation_p.Q593H|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.Q392H	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	630					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						GCACTCACTTCTGCTGGTCCT	0.627																																					p.Q630H		Atlas-SNP	.											.	SH3KBP1	96	.	0			c.G1890T						PASS	.						106.0	96.0	100.0					X																	19560045		2203	4300	6503	SO:0001583	missense	30011	exon16			TCACTTCTGCTGG	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1890G>T	chrX.hg19:g.19560045C>A	ENSP00000380921:p.Gln630His	84.0	0.0	.		81.0	40.0	.	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Missense_Mutation	SNP	ENST00000397821.3	hg19	CCDS14193.1	.	.	.	.	.	.	.	.	.	.	C	3.308	-0.141521	0.06669	.	.	ENSG00000147010	ENST00000379702;ENST00000397821;ENST00000379716;ENST00000379698;ENST00000541422;ENST00000379726	T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4	5.39	4.41	0.53225	.	0.000000	0.64402	D	0.000010	T	0.30541	0.0768	N	0.12887	0.27	0.37413	D	0.9133	D;B;D	0.89917	1.0;0.156;0.997	D;B;D	0.85130	0.997;0.031;0.99	T	0.44050	-0.9353	10	0.02654	T	1	-14.024	6.2238	0.20695	0.0:0.7735:0.0:0.2265	.	392;630;593	Q5JPT4;Q96B97;Q5JPT5	.;SH3K1_HUMAN;.	H	615;630;392;593;369;610	ENSP00000380921:Q630H;ENSP00000369039:Q392H;ENSP00000369020:Q593H;ENSP00000442499:Q369H;ENSP00000369049:Q610H	ENSP00000369020:Q593H	Q	-	3	2	SH3KBP1	19469966	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.388000	0.34442	2.265000	0.75225	0.529000	0.55759	CAG	.	.	.	none		0.627	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	
TAF1	6872	hgsc.bcm.edu	37	X	70618524	70618524	+	Silent	SNP	G	G	A			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:70618524G>A	ENST00000373790.4	+	24	3771	c.3720G>A	c.(3718-3720)aaG>aaA	p.K1240K	TAF1_ENST00000449580.1_Silent_p.K1240K|TAF1_ENST00000276072.3_Silent_p.K1261K|TAF1_ENST00000423759.1_Silent_p.K1261K	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1240					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ACCAGGAAAAGGAGAAGCTTA	0.458																																					p.K1261K		Atlas-SNP	.											.	TAF1	439	.	0			c.G3783A						PASS	.						93.0	79.0	84.0					X																	70618524		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon24			GGAAAAGGAGAAG		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3720G>A	chrX.hg19:g.70618524G>A		157.0	0.0	.		129.0	74.0	.	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	9.733	1.162842	0.21538	.	.	ENSG00000147133	ENST00000483985	.	.	.	5.54	3.77	0.43336	.	.	.	.	.	T	0.59074	0.2167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53129	-0.8482	4	.	.	.	.	9.3163	0.37937	0.2564:0.0:0.7436:0.0	.	.	.	.	K	151	.	.	R	+	2	0	TAF1	70535249	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.737000	0.26144	0.520000	0.28426	0.468000	0.43344	AGG	.	.	.	none		0.458	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833355	27833357	+	In_Frame_Del	DEL	AAG	AAG	-	rs376667817		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27833355_27833357delAAG	ENST00000357320.2	+	1	322_324	c.223_225delAAG	c.(223-225)aagdel	p.K76del		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	76						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CCGCGACAACAAGAAGACCCGCA	0.665																																					p.74_75del		Atlas-Indel,Pindel	.											HIST1H2AL,lower_third,carcinoma,0,1	HIST1H2AL	14	.	0			c.222_224del						PASS	.																																			SO:0001651	inframe_deletion	8332	exon1			.	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.223_225delAAG	chr6.hg19:g.27833358_27833360delAAG	ENSP00000349873:p.Lys76del	216.0	0.0	0		217.0	47.0	0.21659	NM_003511	P02261|Q2M1R2|Q76PA6	In_Frame_Del	DEL	ENST00000357320.2	hg19	CCDS4634.1																																																																																			.	.	.	none		0.665	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
RFC5	5985	hgsc.bcm.edu	37	12	118462664	118462664	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:118462664delA	ENST00000454402.2	+	6	548	c.430delA	c.(430-432)aaafs	p.K144fs	RFC5_ENST00000229043.3_Frame_Shift_Del_p.K59fs|RFC5_ENST00000392542.2_Frame_Shift_Del_p.K123fs	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	144					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGTAATTGAGAAATTCACAGA	0.428																																					p.E143fs		Atlas-INDEL	.											RFC5,NS,carcinoma,0,1	RFC5	35	.	0			c.429delG						PASS	.						75.0	81.0	79.0					12																	118462664		2203	4300	6503	SO:0001589	frameshift_variant	5985	exon6			.		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.430delA	chr12.hg19:g.118462664delA	ENSP00000408295:p.Lys144fs	48.0	0.0	0		53.0	15.0	0.283019	NM_001206801	A8MZ62|B3KSX8	Frame_Shift_Del	DEL	ENST00000454402.2	hg19	CCDS9185.1																																																																																			.	.	.	none		0.428	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370	
LRRC16B	90668	hgsc.bcm.edu	37	14	24528535	24528547	+	Frame_Shift_Del	DEL	CATCAATGCCCTG	CATCAATGCCCTG	-			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CATCAATGCCCTG	CATCAATGCCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr14:24528535_24528547delCATCAATGCCCTG	ENST00000342740.5	+	21	1837_1849	c.1683_1695delCATCAATGCCCTG	c.(1681-1695)ctcatcaatgccctgfs	p.LINAL561fs	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	561						cytoplasm (GO:0005737)		p.N563D(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CCAGCATCCTCATCAATGCCCTGGGCAGCAACA	0.62																																					p.561_565del		Atlas-Indel,Pindel	.											.	LRRC16B	120	.	1	Substitution - Missense(1)	large_intestine(1)	c.1682_1694del						PASS	.																																			SO:0001589	frameshift_variant	90668	exon21			.	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1683_1695delCATCAATGCCCTG	chr14.hg19:g.24528535_24528547delCATCAATGCCCTG	ENSP00000340467:p.Leu561fs	288.0	0.0	0		154.0	40.0	0.25974	NM_138360	Q8TEF7|Q96HS9	Frame_Shift_Del	DEL	ENST00000342740.5	hg19	CCDS32054.1																																																																																			.	.	.	none		0.620	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
TCEANC	170082	hgsc.bcm.edu	37	X	13680806	13680808	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:13680806_13680808delCCT	ENST00000380600.1	+	2	266_268	c.179_181delCCT	c.(178-183)ccctct>cct	p.S61del	TCEANC_ENST00000490617.1_3'UTR|TCEANC_ENST00000545566.1_In_Frame_Del_p.S61del|TCEANC_ENST00000314720.4_In_Frame_Del_p.S91del|TCEANC_ENST00000544987.1_In_Frame_Del_p.S61del			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	61	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						AAAAACTGCCCCTCTGTGGCTTT	0.443																																					p.90_90del		Atlas-Indel,Pindel	.											.	TCEANC	29	.	0			c.268_270del						PASS	.																																			SO:0001651	inframe_deletion	170082	exon4			.		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.179_181delCCT	chrX.hg19:g.13680806_13680808delCCT	ENSP00000369974:p.Ser61del	64.0	0.0	0		58.0	33.0	0.568965	NM_152634	A6NI06|B2RDM3	In_Frame_Del	DEL	ENST00000380600.1	hg19																																																																																				.	.	.	none		0.443	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634	
NEFH	4744	hgsc.bcm.edu	37	22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	chr22.hg19:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	173.0	0.0	0		223.0	71.0	0.318386	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
TMCC3	57458	hgsc.bcm.edu	37	12	94975986	94975987	+	Frame_Shift_Ins	INS	-	-	A	rs530422400		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:94975986_94975987insA	ENST00000261226.4	-	2	537_538	c.406_407insT	c.(406-408)tatfs	p.Y136fs	TMCC3_ENST00000551457.1_Frame_Shift_Ins_p.Y105fs	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	136						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						CTTTCGATGATACTGCTCTAAC	0.475																																					p.Y136fs		Atlas-INDEL	.											.	TMCC3	63	.	0			c.407_408insT						PASS	.																																			SO:0001589	frameshift_variant	57458	exon2			.	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.407dupT	chr12.hg19:g.94975987_94975987dupA	ENSP00000261226:p.Tyr136fs	100.0	0.0	0		73.0	12.0	0.164384	NM_020698	Q8IWB2	Frame_Shift_Ins	INS	ENST00000261226.4	hg19	CCDS31877.1																																																																																			.	.	.	none		0.475	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
SH3KBP1	30011	hgsc.bcm.edu	37	X	19560042	19560043	+	Splice_Site	INS	-	-	T			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560042_19560043insT	ENST00000397821.3	-	16	2182_2183		c.e16+1		SH3KBP1_ENST00000541422.1_Splice_Site|SH3KBP1_ENST00000379698.4_Splice_Site|SH3KBP1_ENST00000379716.1_Splice_Site	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1						apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CAGGCACTCACTTCTGCTGGTC	0.634																																					.		Atlas-INDEL	.											.	SH3KBP1	96	.	0			c.1178+1->A						PASS	.																																			SO:0001630	splice_region_variant	30011	exon12			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1892+1->A	chrX.hg19:g.19560044_19560044dupT		81.0	0.0	0		81.0	41.0	0.506173	NM_001184960	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Splice_Site	INS	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.	.	none		0.634	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	Intron
KMT2C	58508	hgsc.bcm.edu	37	7	151859497	151859497	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:151859497delT	ENST00000262189.6	-	43	11383	c.11165delA	c.(11164-11166)aagfs	p.K3722fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K3722fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3722					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGTCTCAGCCTTTTCCAGTTT	0.468																																					p.K3722fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.11166delG						PASS	.						178.0	182.0	181.0					7																	151859497		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon43			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11165delA	chr7.hg19:g.151859497delT	ENSP00000262189:p.Lys3722fs	75.0	0.0	0		80.0	23.0	0.2875	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
NEUROD1	4760	hgsc.bcm.edu	37	2	182543048	182543051	+	Frame_Shift_Del	DEL	GGTG	GGTG	-	rs565522208		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGTG	GGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:182543048_182543051delGGTG	ENST00000295108.3	-	2	994_997	c.537_540delCACC	c.(535-540)cccaccfs	p.PT179fs	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	179					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|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 transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CCAGGTTGGTGGTGGGTTGGGATA	0.598																																					p.180_181del		Atlas-Indel,Pindel	.											.	NEUROD1	67	.	0			c.538_541del						PASS	.																																			SO:0001589	frameshift_variant	4760	exon2			.	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"""Basic helix-loop-helix proteins"""	7762	protein-coding gene	gene with protein product	"""beta-cell E-box transactivator 2"", ""neurogenic helix-loop-helix protein NEUROD"""	601724	"""neurogenic differentiation 1"""	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.537_540delCACC	chr2.hg19:g.182543048_182543051delGGTG	ENSP00000295108:p.Pro179fs	75.0	0.0	0		80.0	22.0	0.275	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Frame_Shift_Del	DEL	ENST00000295108.3	hg19	CCDS2283.1																																																																																			.	.	.	none		0.598	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500	
ZNF225	7768	hgsc.bcm.edu	37	19	44636876	44636889	+	Stop_Codon_Del	DEL	AAATGACACATAAC	AAATGACACATAAC	-	rs143348426	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAATGACACATAAC	AAATGACACATAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:44636876_44636889delAAATGACACATAAC	ENST00000262894.6	+	0	2389_2402				ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Stop_Codon_Del	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				CAttatttttaaatgacacataactgttgtactc	0.355																																					p.703_707del		Pindel	.											.	ZNF225	41	.	0			c.2108_2121del						PASS	.																																			SO:0001567	stop_retained_variant	7768	exon5			.	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"""Zinc fingers, C2H2-type"", ""-"""	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		Exception_encountered	chr19.hg19:g.44636876_44636889delAAATGACACATAAC	ENSP00000262894:p.*707Pheext*8	117.0	0.0	.		91.0	16.0	0.176	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Frame_Shift_Del	DEL	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.	.	none		0.355	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1		
METTL7A	25840	hgsc.bcm.edu	37	12	51319010	51319030	+	In_Frame_Del	DEL	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	-	rs142438796		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENST00000548553.1	+	2	1170_1190	c.189_209delGGAGTTTGCGGGCCCCTCCGG	c.(187-210)caggagtttgcgggcccctccggg>cag	p.EFAGPSG64del	METTL7A_ENST00000332160.4_In_Frame_Del_p.EFAGPSG64del			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	64						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)	p.A66V(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GTAACCTGCAGGAGTTTGCGGGCCCCTCCGGGAAACTCTCC	0.543																																					p.63_70del		Pindel	.											.	METTL7A	19	.	1	Substitution - Missense(1)	lung(1)	c.188_208del						PASS	.																																			SO:0001651	inframe_deletion	25840	exon1			.		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.189_209delGGAGTTTGCGGGCCCCTCCGG	chr12.hg19:g.51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENSP00000448785:p.Glu64_Gly70del	71.0	0.0	.		80.0	12.0	0.150	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	In_Frame_Del	DEL	ENST00000548553.1	hg19	CCDS8804.1																																																																																			.	.	.	none		0.543	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033	
