#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_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
VWA3A	146177	hgsc.bcm.edu	37	16	22144375	22144375	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144375delC	ENST00000389398.5	+	20	2123	c.2027delC	c.(2026-2028)accfs	p.T676fs	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	676	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		AAGGAGGTCACCCGGGCTGCA	0.577																																					p.T676fs		Atlas-Indel	.											.	VWA3A	115	.	0			c.2026delA						PASS	.						38.0	42.0	41.0					16																	22144375		2053	4186	6239	SO:0001589	frameshift_variant	146177	exon20			.	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2027delC	16.37:g.22144375delC	ENSP00000374049:p.Thr676fs	91.0	0.0	0		69.0	27.0	0.391304	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Frame_Shift_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
DAAM2	23500	hgsc.bcm.edu	37	6	39869657	39869659	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39869657_39869659delGGA	ENST00000398904.2	+	25	3233_3235	c.3051_3053delGGA	c.(3049-3054)ctggag>ctg	p.E1019del	DAAM2_ENST00000274867.4_In_Frame_Del_p.E1019del|DAAM2_ENST00000538976.1_In_Frame_Del_p.E1018del|RP11-61I13.3_ENST00000437947.1_RNA			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1019	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCAGCTCGCTGGAGGAGGGAGGA	0.65																																					p.1017_1018del		Pindel,Atlas-Indel	.											.	DAAM2	101	.	0			c.3050_3052del						PASS	.																																			SO:0001651	inframe_deletion	23500	exon25			.	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.3051_3053delGGA	6.37:g.39869660_39869662delGGA	ENSP00000381876:p.Glu1019del	57.0	0.0	.		45.0	22.0	0.489	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	In_Frame_Del	DEL	ENST00000398904.2	37	CCDS56426.1																																																																																			.	.	none		0.650	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38840427	38840428	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38840427_38840428delAT	ENST00000359357.3	+	48	6709_6710	c.6455_6456delAT	c.(6454-6456)catfs	p.H2152fs	DNAH8_ENST00000449981.2_Frame_Shift_Del_p.H2369fs|DNAH8_ENST00000441566.1_Frame_Shift_Del_p.H2116fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2152	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GGAAGGCCTCATAGAGAAATGC	0.47																																					p.2369_2369del		Pindel,Atlas-Indel	.											.	DNAH8	1239	.	0			c.7105_7106del						PASS	.																																			SO:0001589	frameshift_variant	1769	exon50			.	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6455_6456delAT	6.37:g.38840427_38840428delAT	ENSP00000352312:p.His2152fs	117.0	0.0	.		128.0	43.0	0.336	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37																																																																																				.	.	none		0.470	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
AOC1	26	hgsc.bcm.edu	37	7	150558156	150558156	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150558156delC	ENST00000493429.1	+	7	2699	c.2115delC	c.(2113-2115)gacfs	p.D705fs	AOC1_ENST00000416793.2_Frame_Shift_Del_p.D724fs|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000467291.1_Frame_Shift_Del_p.D705fs|AOC1_ENST00000360937.4_Frame_Shift_Del_p.D705fs			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	705					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	TCCCAGAGGACCCCTCCCTGG	0.617																																					p.D724fs		Pindel,Atlas-Indel	.											.	ABP1	92	.	0			c.2171delA						PASS	.						63.0	74.0	70.0					7																	150558156		2045	4197	6242	SO:0001589	frameshift_variant	26	exon5			.	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.2115delC	7.37:g.150558156delC	ENSP00000418614:p.Asp705fs	95.0	0.0	.		81.0	17.0	0.210	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Frame_Shift_Del	DEL	ENST00000493429.1	37	CCDS43679.1																																																																																			.	.	none		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
L1TD1	54596	hgsc.bcm.edu	37	1	62672389	62672390	+	In_Frame_Ins	INS	-	-	AACAGA	rs374688773|rs150799576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62672389_62672390insAACAGA	ENST00000498273.1	+	3	384_385	c.89_90insAACAGA	c.(88-93)ttaaca>ttAACAGAaaca	p.33_34insET		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	33										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						agagagcagttaacagaaactg	0.327														173	0.0345447	0.084	0.0159	5008	,	,		18275	0.001		0.0258	False		,,,				2504	0.0245				p.L30delinsLTE		Pindel,Atlas-Indel	.											.	L1TD1	114	.	0			c.89_90insAACAGA						PASS	.		,	271,3517		14,243,1637					,	1.0	0.0		dbSNP_134	24	117,7287		5,107,3590	no	coding,coding	L1TD1	NM_019079.4,NM_001164835.1	,	19,350,5227	A1A1,A1R,RR		1.5802,7.1542,3.4668	,	,		388,10804				SO:0001652	inframe_insertion	54596	exon4			.	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.90_95dupAACAGA	1.37:g.62672390_62672395dupAACAGA	ENSP00000419901:p.Glu32_Thr33dup	215.0	0.0	.		127.0	38.0	0.299	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	In_Frame_Ins	INS	ENST00000498273.1	37	CCDS619.1																																																																																			-|0.971;AACAGA|0.029	0.029	strong		0.327	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
DOC2A	8448	hgsc.bcm.edu	37	16	30018351	30018353	+	Splice_Site	DEL	CCT	CCT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30018351_30018353delCCT	ENST00000350119.4	-	7	903_905	c.713_715delAGG	c.(712-717)gaggtg>gtg	p.E238del	DOC2A_ENST00000564944.1_Splice_Site_p.E238del|DOC2A_ENST00000564979.1_Splice_Site_p.E238del	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	238	Interaction with UNC13D.			E -> D (in Ref. 1; BAA06695). {ECO:0000305}.	nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGGTGCCTCACCTCCTTCAGATA	0.65																																					p.238_238del		Pindel,Atlas-Indel	.											.	DOC2A	40	.	0			c.714_714del						PASS	.																																			SO:0001630	splice_region_variant	8448	exon7			.	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.714+1AGG>-	16.37:g.30018354_30018356delCCT		139.0	0.0	.		184.0	32.0	0.174	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Frame_Shift_Del	DEL	ENST00000350119.4	37	CCDS10666.1																																																																																			.	.	none		0.650	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	In_Frame_Del
GRAMD1A	57655	hgsc.bcm.edu	37	19	35505282	35505282	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35505282delG	ENST00000317991.5	+	10	1252	c.1060delG	c.(1060-1062)gggfs	p.G354fs	GRAMD1A_ENST00000411896.2_Frame_Shift_Del_p.G347fs|GRAMD1A_ENST00000504615.2_Frame_Shift_Del_p.G120fs|GRAMD1A_ENST00000599564.1_Frame_Shift_Del_p.G441fs|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	354						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TTCATCCACTGGGGAGGAAGG	0.607																																					p.T353fs		Pindel,Atlas-Indel	.											.	GRAMD1A	39	.	0			c.1059delT						PASS	.						38.0	43.0	41.0					19																	35505282		1972	4145	6117	SO:0001589	frameshift_variant	57655	exon10			.	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1060delG	19.37:g.35505282delG	ENSP00000441032:p.Gly354fs	158.0	0.0	.		143.0	43.0	0.301	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Frame_Shift_Del	DEL	ENST00000317991.5	37	CCDS42546.1																																																																																			.	.	none		0.607	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	
FBXW10	10517	hgsc.bcm.edu	37	17	18682351	18682352	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18682351_18682352delAA	ENST00000395665.4	+	14	3120_3121	c.2899_2900delAA	c.(2899-2901)aaafs	p.K967fs	FBXW10_ENST00000301938.4_Frame_Shift_Del_p.K914fs|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000308799.4_Frame_Shift_Del_p.K976fs|TVP23B_ENST00000476139.1_5'Flank|FBXW10_ENST00000395667.1_Frame_Shift_Del_p.K966fs|TVP23B_ENST00000574226.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	967								p.K966fs*10(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GTCTCTTAAGAAAGAACGGCCT	0.53																																					p.966_967del		Atlas-Indel	.											.	FBXW10	82	.	1	Deletion - Frameshift(1)	skin(1)	c.2898_2899del						PASS	.			6,4034		2,2,2016						1.3	0.5			20	27,7731		6,15,3858	no	frameshift	FBXW10	NM_031456.3		8,17,5874	A1A1,A1R,RR		0.348,0.1485,0.2797				33,11765				SO:0001589	frameshift_variant	10517	exon14			.	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2899_2900delAA	17.37:g.18682351_18682352delAA	ENSP00000379025:p.Lys967fs	343.0	0.0	0		153.0	43.0	0.281046	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Frame_Shift_Del	DEL	ENST00000395665.4	37	CCDS11199.3																																																																																			.	.	none		0.530	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
MSI2	124540	hgsc.bcm.edu	37	17	55693404	55693405	+	Frame_Shift_Ins	INS	-	-	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:55693404_55693405insT	ENST00000284073.2	+	9	820_821	c.611_612insT	c.(610-615)ccttacfs	p.Y205fs	MSI2_ENST00000579505.1_3'UTR|MSI2_ENST00000579180.1_Frame_Shift_Ins_p.Y101fs|RN7SL449P_ENST00000464937.2_RNA|MSI2_ENST00000442934.2_Frame_Shift_Ins_p.Y144fs|MSI2_ENST00000322684.3_Frame_Shift_Ins_p.Y201fs|MSI2_ENST00000416426.2_Frame_Shift_Ins_p.Y183fs	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	205						cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		CGGGGACTGCCTTACACCATGG	0.559			T	HOXA9	CML																																p.P204fs		Pindel,Atlas-Indel	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.611_612insT						PASS	.																																			SO:0001589	frameshift_variant	124540	exon9			.	BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	18585	protein-coding gene	gene with protein product		607897	"""musashi homolog 2 (Drosophila)"""			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.613dupT	17.37:g.55693406_55693406dupT	ENSP00000284073:p.Tyr205fs	52.0	0.0	.		51.0	11.0	0.216	NM_138962	Q7Z6M7|Q8N9T4	Frame_Shift_Ins	INS	ENST00000284073.2	37	CCDS11596.1																																																																																			.	.	none		0.559	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1		
RPGR	6103	hgsc.bcm.edu	37	X	38145805	38145805	+	Intron	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145805delC	ENST00000339363.3	-	14	2688				RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_Frame_Shift_Del_p.G817fs|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tacttcccctccctctacttc	0.597																																					p.G816fs		Atlas-Indel	.											.	RPGR	175	.	0			c.2448delA						PASS	.						159.0	119.0	133.0					X																	38145805		1802	3474	5276	SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+541G>-	X.37:g.38145805delC		209.0	0.0	0		38.0	17.0	0.447368	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Frame_Shift_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.597	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68.0	74.0	72.0			2.8	1.0	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	79.0	0.0	.		50.0	20.0	0.400	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
CCDC71	64925	hgsc.bcm.edu	37	3	49200611	49200616	+	In_Frame_Del	DEL	GCCTTG	GCCTTG	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCCTTG	GCCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49200611_49200616delGCCTTG	ENST00000321895.6	-	2	1132_1137	c.1026_1031delCAAGGC	c.(1024-1032)gccaaggct>gct	p.342_344AKA>A		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	342										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		cttggctttagccttggccttggccc	0.617																																					p.343_344del		Pindel,Atlas-Indel	.											.	CCDC71	33	.	0			c.1027_1032del						PASS	.																																			SO:0001651	inframe_deletion	64925	exon2			.	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.1026_1031delCAAGGC	3.37:g.49200617_49200622delGCCTTG	ENSP00000319006:p.Ala346_Lys347del	69.0	0.0	.		86.0	21.0	0.244	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	In_Frame_Del	DEL	ENST00000321895.6	37	CCDS2790.1																																																																																			.	.	none		0.617	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
DNAH5	1767	hgsc.bcm.edu	37	5	13883045	13883045	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13883045delC	ENST00000265104.4	-	20	3246	c.3142delG	c.(3142-3144)gtcfs	p.V1048fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1048	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACTGTCTGACCCCCTTAGGG	0.507									Kartagener syndrome																												p.V1048fs		Atlas-Indel	.											.	DNAH5	868	.	0			c.3143delT						PASS	.						167.0	149.0	155.0					5																	13883045		2203	4300	6503	SO:0001589	frameshift_variant	1767	exon20	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3142delG	5.37:g.13883045delC	ENSP00000265104:p.Val1048fs	142.0	0.0	0		164.0	26.0	0.158537	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Del	DEL	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	none		0.507	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CCR8	1237	hgsc.bcm.edu	37	3	39374514	39374516	+	In_Frame_Del	DEL	ACA	ACA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374514_39374516delACA	ENST00000326306.4	+	2	830_832	c.692_694delACA	c.(691-696)cacaac>cac	p.N232del	CCR8_ENST00000545843.1_In_Frame_Del_p.N149del|CCR8_ENST00000414803.1_3'UTR	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	232					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		TGTCAAAACCACAACAAGACCAA	0.429																																					p.231_231del		Pindel,Atlas-Indel	.											.	CCR8	34	.	0			c.691_693del						PASS	.			1,4265		0,1,2132						3.9	1.0			109	0,8248		0,0,4124	no	coding	CCR8	NM_005201.3		0,1,6256	A1A1,A1R,RR		0.0,0.0234,0.0080				1,12513				SO:0001651	inframe_deletion	1237	exon2			.	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.692_694delACA	3.37:g.39374517_39374519delACA	ENSP00000326432:p.Asn232del	372.0	0.0	.		296.0	57.0	0.193	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	In_Frame_Del	DEL	ENST00000326306.4	37	CCDS2684.1																																																																																			.	.	none		0.429	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
GTF3C1	2975	hgsc.bcm.edu	37	16	27499956	27499956	+	Splice_Site	DEL	C	C	-	rs560536443		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:27499956delC	ENST00000356183.4	-	22	3445	c.3430delG	c.(3430-3432)gag>ag	p.E1144fs	GTF3C1_ENST00000561623.1_Splice_Site_p.E1144fs	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1144					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GCAGTGTTCTCCTGTGAGACA	0.557																																					p.E1144fs		Pindel,Atlas-Indel	.											.	GTF3C1	210	.	0			c.3431delA						PASS	.						97.0	90.0	92.0					16																	27499956		2197	4300	6497	SO:0001630	splice_region_variant	2975	exon22			.	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3430-1G>-	16.37:g.27499956delC		44.0	0.0	.		46.0	13.0	0.283	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Frame_Shift_Del	DEL	ENST00000356183.4	37	CCDS32414.1																																																																																			.	.	none		0.557	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Frame_Shift_Del
CFTR	1080	hgsc.bcm.edu	37	7	117199645	117199647	+	In_Frame_Del	DEL	TCT	TCT	-	rs121909001|rs199826652|rs113993960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:117199645_117199647delTCT	ENST00000003084.6	+	11	1652_1654	c.1520_1522delTCT	c.(1519-1524)atcttt>att	p.F508del	CFTR_ENST00000454343.1_In_Frame_Del_p.F447del|AC000111.3_ENST00000441019.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	508	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		F -> C (in dbSNP:rs1800093).|Missing (in CF and CBAVD; most common mutation; 72% of the population; CFTR fails to be properly delivered to plasma membrane).		cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GAAAATATCATCTTTGGTGTTTC	0.365									Cystic Fibrosis					20	0.00399361	0.0	0.0101	5008	,	,		18625	0.0		0.0089	False		,,,				2504	0.0041				p.507_507del		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.1519_1521del	GRCh37	CD890142|CI075604	CFTR	D|I	rs1800093	PASS	.			13,4251		0,13,2119				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		1.9	1.0		dbSNP_133	89	809,7445		317,175,3635	no	coding	CFTR	NM_000492.3		317,188,5754	A1A1,A1R,RR		9.8013,0.3049,6.5665				822,11696				SO:0001651	inframe_deletion	1080	exon11	Familial Cancer Database	CF	.	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1520_1522delTCT	7.37:g.117199645_117199647delTCT	ENSP00000003084:p.Phe508del	81.0	0.0	.		49.0	17.0	0.347	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	In_Frame_Del	DEL	ENST00000003084.6	37	CCDS5773.1																																																																																			TCT|0.994;-|0.006	0.006	strong		0.365	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
ZNF568	374900	hgsc.bcm.edu	37	19	37440852	37440852	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37440852delT	ENST00000333987.7	+	7	1303	c.797delT	c.(796-798)attfs	p.I266fs	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Frame_Shift_Del_p.I202fs	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	266					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(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAAAATCTTATTACACATCAG	0.353																																					p.I266fs		Atlas-Indel	.											.	ZNF568	106	.	0			c.796delA						PASS	.						39.0	43.0	41.0					19																	37440852		2118	4251	6369	SO:0001589	frameshift_variant	374900	exon7			.	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.797delT	19.37:g.37440852delT	ENSP00000334685:p.Ile266fs	30.0	0.0	0		45.0	11.0	0.244444	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Frame_Shift_Del	DEL	ENST00000333987.7	37	CCDS42558.1																																																																																			.	.	none		0.353	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
NFKBIE	4794	hgsc.bcm.edu	37	6	44232739	44232742	+	Frame_Shift_Del	DEL	GTAA	GTAA	-	rs375669043		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44232739_44232742delGTAA	ENST00000275015.5	-	1	758_761	c.759_762delTTAC	c.(757-762)acttacfs	p.TY253fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	253					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCTCGGAGATGTAAGTGAGTGCTT	0.676																																					p.254_255del		Atlas-Indel	.											.	NFKBIE	31	.	0			c.760_763del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.759_762delTTAC	6.37:g.44232739_44232742delGTAA	ENSP00000275015:p.Thr253fs	44.0	0.0	0		35.0	11.0	0.314286	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.676	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	rs148187838|rs566862006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170387132_170387133insT	ENST00000453153.2	-	14	2752_2753	c.2406_2407insA	c.(2404-2409)aaacgafs	p.R803fs	FASTKD1_ENST00000495505.1_5'UTR|FASTKD1_ENST00000453929.2_Frame_Shift_Ins_p.R760fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	803	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						TCCAAATGTCGTTTTTTCATAG	0.342													TTTTTT|TTTTTT|TTTTTTT|insertion	18	0.00359425	0.0008	0.0029	5008	,	,		15503	0.0		0.007	False		,,,				2504	0.0082				p.R803fs		Pindel,Atlas-Indel	.											.	FASTKD1	86	.	0			c.2407_2408insA						PASS	.			8,4258		0,8,2125						3.3	1.0			159	99,8155		1,97,4029	no	frameshift	FASTKD1	NM_024622.3		1,105,6154	A1A1,A1R,RR		1.1994,0.1875,0.8546				107,12413				SO:0001589	frameshift_variant	79675	exon14			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.2407dupA	2.37:g.170387138_170387138dupT	ENSP00000400513:p.Arg803fs	213.0	0.0	.		206.0	69.0	0.335	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Ins	INS	ENST00000453153.2	37	CCDS33318.1																																																																																			.	.	none		0.342	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
COL12A1	1303	hgsc.bcm.edu	37	6	75887427	75887436	+	Frame_Shift_Del	DEL	AATATTCAGG	AATATTCAGG	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AATATTCAGG	AATATTCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:75887427_75887436delAATATTCAGG	ENST00000322507.8	-	12	2689_2698	c.2380_2389delCCTGAATATT	c.(2380-2391)cctgaatatttcfs	p.PEYF794fs	COL12A1_ENST00000483888.2_Frame_Shift_Del_p.PEYF794fs|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Frame_Shift_Del_p.PEYF794fs	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	794	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GGTCCTGAGAAATATTCAGGAATTACAGAT	0.438																																					p.794_797del		Atlas-Indel	.											.	COL12A1	385	.	0			c.2381_2390del						PASS	.																																			SO:0001589	frameshift_variant	1303	exon12			.	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2380_2389delCCTGAATATT	6.37:g.75887427_75887436delAATATTCAGG	ENSP00000325146:p.Pro794fs	155.0	0.0	0		155.0	16.0	0.103226	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	37	CCDS43482.1																																																																																			.	.	none		0.438	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
TAF1	6872	hgsc.bcm.edu	37	X	70612454	70612455	+	In_Frame_Ins	INS	-	-	ATT			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:70612454_70612455insATT	ENST00000373790.4	+	19	2865_2866	c.2814_2815insATT	c.(2815-2817)att>ATTatt	p.939_939I>II	TAF1_ENST00000449580.1_In_Frame_Ins_p.939_939I>II|TAF1_ENST00000423759.1_In_Frame_Ins_p.960_960I>II|TAF1_ENST00000276072.3_In_Frame_Ins_p.960_960I>II	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	939	Histone acetyltransferase (HAT).				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)				CAAGGGCCTTCATTGCTGCCAT	0.49																																					p.F959delinsFI		Pindel,Atlas-Indel	.											.	TAF1	439	.	0			c.2877_2878insATT						PASS	.																																			SO:0001652	inframe_insertion	6872	exon19			.		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.2815_2817dupATT	X.37:g.70612455_70612457dupATT	ENSP00000362895:p.Ile939dup	127.0	0.0	.		118.0	27.0	0.229	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	In_Frame_Ins	INS	ENST00000373790.4	37	CCDS35325.1																																																																																			.	.	none		0.490	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
DUSP18	150290	hgsc.bcm.edu	37	22	31059499	31059500	+	Frame_Shift_Del	DEL	CA	CA	-	rs538206035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31059499_31059500delCA	ENST00000334679.3	-	2	996_997	c.491_492delTG	c.(490-492)gtgfs	p.V164fs	DUSP18_ENST00000404885.1_Frame_Shift_Del_p.V164fs|DUSP18_ENST00000403268.1_3'UTR|DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000407308.1_Frame_Shift_Del_p.V164fs	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	164					peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						TGACCATGTGCACAGTGTTCTT	0.535														9	0.00179712	0.0	0.0	5008	,	,		20452	0.0		0.0089	False		,,,				2504	0.0				p.164_165del		Pindel,Atlas-Indel	.											.	DUSP18	10	.	0			c.492_493del						PASS	.			3,4261		0,3,2129						5.3	0.9		dbSNP_130	115	32,8222		0,32,4095	no	frameshift	DUSP18	NM_152511.3		0,35,6224	A1A1,A1R,RR		0.3877,0.0704,0.2796				35,12483				SO:0001589	frameshift_variant	150290	exon2			.	AF461689	CCDS13883.1	22q12.1	2011-06-09				ENSG00000167065		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18484	protein-coding gene	gene with protein product		611446				12408986	Standard	NM_152511		Approved	DUSP20	uc003aiw.1	Q8NEJ0		ENST00000334679.3:c.491_492delTG	22.37:g.31059501_31059502delCA	ENSP00000333917:p.Val164fs	128.0	0.0	.		119.0	32.0	0.269	NM_152511	B3KPA4	Frame_Shift_Del	DEL	ENST00000334679.3	37	CCDS13883.1																																																																																			.	.	weak		0.535	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1		
SCN9A	6335	hgsc.bcm.edu	37	2	167144980	167144980	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:167144980delT	ENST00000409435.1	-	9	1280	c.1281delA	c.(1279-1281)ttafs	p.L427fs	SCN9A_ENST00000375387.4_Frame_Shift_Del_p.L428fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.L428fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.L427fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	427					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAAGACGGTCTAACATCTGTT	0.383																																					p.D428fs		Atlas-Indel	.											.	SCN9A	296	.	0			c.1282delG						PASS	.						146.0	154.0	151.0					2																	167144980		1841	4092	5933	SO:0001589	frameshift_variant	6335	exon10			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1281delA	2.37:g.167144980delT	ENSP00000386330:p.Leu427fs	78.0	0.0	0		79.0	12.0	0.151899	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
CCDC87	55231	hgsc.bcm.edu	37	11	66358631	66358633	+	In_Frame_Del	DEL	TCT	TCT	-	rs535066162		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66358631_66358633delTCT	ENST00000333861.3	-	1	1921_1923	c.1854_1856delAGA	c.(1852-1857)gaagag>gag	p.618_619EE>E	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	618					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CACAGGAACCTCTTCTTCATGCA	0.473																																					p.619_619del		Pindel,Atlas-Indel	.											.	CCDC87	83	.	0			c.1855_1857del						PASS	.			3,4259		0,3,2128						-1.9	0.2			112	18,8232		0,18,4107	no	coding	CCDC87	NM_018219.2		0,21,6235	A1A1,A1R,RR		0.2182,0.0704,0.1678				21,12491				SO:0001651	inframe_deletion	55231	exon1			.	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1854_1856delAGA	11.37:g.66358634_66358636delTCT	ENSP00000328487:p.Glu619del	229.0	0.0	.		180.0	78.0	0.433	NM_018219	Q8NE76	In_Frame_Del	DEL	ENST00000333861.3	37	CCDS8145.1																																																																																			.	.	none		0.473	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
NLGN4Y	22829	hgsc.bcm.edu	37	Y	16952663	16952663	+	3'UTR	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrY:16952663delC	ENST00000476359.1	+	0	2517							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						CAAAACAGGGCCCGAGGACAC	0.532																																					p.G657fs		Pindel,Atlas-Indel	.											.	NLGN4Y	44	.	0			c.1971delG						PASS	.																																			SO:0001624	3_prime_UTR_variant	22829	exon6			.		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"""neuroligin 4, Y linked"""			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2514C>-	Y.37:g.16952663delC		3.0	0.0	.		79.0	41.0	0.519	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Frame_Shift_Del	DEL	ENST00000476359.1	37																																																																																				.	.	none		0.532	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893	
HLA-C	3107	hgsc.bcm.edu	37	6	31238973	31238986	+	Frame_Shift_Del	DEL	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	-	rs45578735|rs2308584|rs200155513|rs45622747|rs2308585|rs200892438|rs41541313|rs281860498|rs45505091|rs281860496|rs281860497|rs281860495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31238973_31238986delTCTGAGCCGCGGTG	ENST00000376228.5	-	3	497_510	c.483_496delCACCGCGGCTCAGA	c.(481-498)gacaccgcggctcagatcfs	p.TAAQI162fs	HLA-C_ENST00000383329.3_Frame_Shift_Del_p.TAAQI162fs	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	162	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CGCTGGGTGATCTGAGCCGCGGTGTCCGCGGCGG	0.692																																					p.162_166del		Atlas-Indel	.											.	HLA-C	92	.	0			c.484_497del						PASS	.																																			SO:0001589	frameshift_variant	3107	exon3			.	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.483_496delCACCGCGGCTCAGA	6.37:g.31238973_31238986delTCTGAGCCGCGGTG	ENSP00000365402:p.Thr162fs	123.0	0.0	0		151.0	29.0	0.192053	NM_002117	O02864|O02958|Q29643|Q9MY30	Frame_Shift_Del	DEL	ENST00000376228.5	37	CCDS34393.1																																																																																			.	.	none		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SRSF2	6427	hgsc.bcm.edu	37	17	74732390	74732395	+	In_Frame_Del	DEL	GGACTT	GGACTT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGACTT	GGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:74732390_74732395delGGACTT	ENST00000392485.2	-	2	686_691	c.514_519delAAGTCC	c.(514-519)aagtccdel	p.KS172del	MFSD11_ENST00000355954.3_5'Flank|MFSD11_ENST00000586622.1_5'UTR|MFSD11_ENST00000336509.4_5'Flank|MIR636_ENST00000384825.1_RNA|SRSF2_ENST00000359995.5_In_Frame_Del_p.KS172del|MFSD11_ENST00000591864.1_5'Flank|SRSF2_ENST00000508921.3_In_Frame_Del_p.KS160del|MFSD11_ENST00000590514.1_5'Flank|MFSD11_ENST00000593181.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000590393.1_5'Flank|MFSD11_ENST00000588460.1_5'UTR	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	172	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						AGACCGACGAGGACTTGGACTTGGAC	0.617			Mis		"""MDS, CLL"""																																p.172_174del		Pindel,Atlas-Indel	.		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	.	SRSF2	544	.	0			c.515_520del						PASS	.																																			SO:0001651	inframe_deletion	6427	exon2			.	M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10783	protein-coding gene	gene with protein product	"""SR splicing factor 2"""	600813	"""splicing factor, arginine/serine-rich 2"""	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.514_519delAAGTCC	17.37:g.74732396_74732401delGGACTT	ENSP00000376276:p.Lys172_Ser173del	72.0	0.0	.		67.0	14.0	0.209	NM_001195427	B3KWD5|B4DN89|H0YG49	In_Frame_Del	DEL	ENST00000392485.2	37	CCDS11749.1																																																																																			.	.	none		0.617	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016	
HK3	3101	hgsc.bcm.edu	37	5	176314086	176314086	+	Frame_Shift_Del	DEL	G	G	-	rs534008020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176314086delG	ENST00000292432.5	-	13	1865	c.1774delC	c.(1774-1776)cagfs	p.Q593fs		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	593	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCTTCTGCTGGAAGTCCACG	0.602																																					p.Q592fs		Pindel,Atlas-Indel	.											.	HK3	210	.	0			c.1775delA						PASS	.						84.0	76.0	79.0					5																	176314086		2203	4300	6503	SO:0001589	frameshift_variant	3101	exon13			.		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1774delC	5.37:g.176314086delG	ENSP00000292432:p.Gln593fs	86.0	0.0	.		121.0	41.0	0.339	NM_002115	Q8N1E7	Frame_Shift_Del	DEL	ENST00000292432.5	37	CCDS4407.1																																																																																			.	.	none		0.602	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
HIST1H4J	8363	hgsc.bcm.edu	37	6	27792127	27792128	+	Frame_Shift_Ins	INS	-	-	CACGC			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27792127_27792128insCACGC	ENST00000355057.1	+	1	244_245	c.225_226insCACGC	c.(226-228)cacfs	p.-77fs		NM_021968.3	NP_068803.1	P62805	H4_HUMAN	histone cluster 1, H4j						CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	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)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(1)|pancreas(1)	4						CCTATACAGAGCACGCCAAGCG	0.624																																					p.E75fs		Atlas-Indel	.											HIST1H4J,NS,carcinoma,+2,1	HIST1H4J	11	1	0			c.225_226insCACGC						PASS	.																																			SO:0001589	frameshift_variant	8363	exon1			.	J00188	CCDS4630.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197238	ENSG00000197238		"""Histones / Replication-dependent"""	4785	protein-coding gene	gene with protein product		602826	"""H4 histone family, member E"", ""histone 1, H4j"""	H4FE		6265100, 9439656, 12408966	Standard	NM_021968		Approved	H4/e, H4F2iv	uc003njp.3	P62805	OTTHUMG00000014487	ENST00000355057.1:c.226_230dupCACGC	6.37:g.27792128_27792132dupCACGC	ENSP00000347168:p.Ala77fs	242.0	0.0	0		199.0	13.0	0.0653266	NM_021968	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Frame_Shift_Ins	INS	ENST00000355057.1	37	CCDS4630.1																																																																																			.	.	none		0.624	HIST1H4J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040155.1	NM_021968	
VWA3A	146177	hgsc.bcm.edu	37	16	22144376	22144378	+	In_Frame_Del	DEL	CCG	CCG	-	rs200086497|rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144376_22144378delCCG	ENST00000389398.5	+	20	2124_2126	c.2028_2030delCCG	c.(2026-2031)acccgg>acg	p.R677del	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		AGGAGGTCACCCGGGCTGCAGGT	0.576																																					p.676_677del		Pindel	.											.	VWA3A	115	.	0			c.2027_2029del						PASS	.																																			SO:0001651	inframe_deletion	146177	exon20			.	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2028_2030delCCG	16.37:g.22144376_22144378delCCG	ENSP00000374049:p.Arg677del	90.0	0.0	.		71.0	21.0	0.296	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	In_Frame_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.576	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
RPGR	6103	hgsc.bcm.edu	37	X	38145791	38145805	+	Intron	DEL	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145791_38145805delCCTCTACTTCCCCTC	ENST00000339363.3	-	14	2688				RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.GGEVE816del|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cctttcccctcctctacttcccctccctctacttc	0.595														2	0.000529801	0.0	0.0	3775	,	,		7341	0.0		0.002	False		,,,				2504	0.0				p.816_821del		Pindel	.											.	RPGR	175	.	0			c.2448_2462del	GRCh37	CD020354	orf15	D		PASS	.		,	16,2991		1,13,1,1344,290					,	1.2	0.0			113	16,4996		3,7,3,1902,1185	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	4,20,4,3246,1475	A1A1,A1R,A1,RR,R		0.3192,0.5321,0.3991	,	,		32,7987				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+541GAGGGGAAGTAGAGG>-	X.37:g.38145791_38145805delCCTCTACTTCCCCTC		197.0	0.0	.		33.0	18.0	0.545	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.595	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004942	153005013	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	rs2339500|rs145337134|rs201925274|rs367847286|rs12195|rs368848590|rs200829544|rs551505658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENST00000307098.4	+	2	186_257	c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	c.(121-192)tgccaccccaaggtgcctgagccctgccaccccaaagtgcccgagccctgccagcccaaggttccagagccadel	p.CHPKVPEPCHPKVPEPCQPKVPEP41del	SPRR1B_ENST00000392661.3_Splice_Site_p.CHPKVPEPCHPK41del	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	41	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)|p.P43A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAAGGAGCCCTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCATGCCACCCCA	0.621																																					p.40_64del		Pindel	.											.	SPRR1B	18	.	2	Substitution - Missense(1)|Deletion - In frame(1)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	c.120_191del						PASS	.																																			SO:0001651	inframe_deletion	6699	exon2			.	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	1.37:g.153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENSP00000306461:p.Cys41_Pro64del	104.0	0.0	.		78.0	23.0	0.295	NM_003125	B2R5H7|P22529|P22530|Q5T524	In_Frame_Del	DEL	ENST00000307098.4	37	CCDS30863.1																																																																																			.	.	none		0.621	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
MUC16	94025	hgsc.bcm.edu	37	19	8999044	8999044	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8999044G>A	ENST00000397910.4	-	57	41003	c.40800C>T	c.(40798-40800)agC>agT	p.S13600S	MUC16_ENST00000380951.5_Silent_p.S241S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13602				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGGCACAGAGCTCCGCTGTG	0.547																																					p.S13600S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40800T						PASS	.						71.0	71.0	71.0					19																	8999044		1988	4149	6137	SO:0001819	synonymous_variant	94025	exon57			CACAGAGCTCCGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40800C>T	19.37:g.8999044G>A		107.0	0.0	0		100.0	22.0	0.22	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	1.631	-0.518888	0.04171	.	.	ENSG00000181143	ENST00000542240	.	.	.	1.04	1.04	0.20106	.	.	.	.	.	T	0.37348	0.1000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.43523	-0.9386	3	.	.	.	.	5.4159	0.16374	0.0:0.0:1.0:0.0	.	.	.	.	V	440	.	.	A	-	2	0	MUC16	8860044	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.186000	0.03070	0.865000	0.35603	0.455000	0.32223	GCT	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TTC39B	158219	hgsc.bcm.edu	37	9	15189791	15189791	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:15189791C>T	ENST00000512701.2	-	12	1142		c.e12-1		TTC39B_ENST00000507993.1_Splice_Site|TTC39B_ENST00000380850.4_Splice_Site|TTC39B_ENST00000355694.2_Splice_Site|TTC39B_ENST00000297615.5_Splice_Site|TTC39B_ENST00000507285.1_Splice_Site			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B											NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						TCTCCTGTACCTAGAAATTTA	0.408																																					.		Atlas-SNP	.											.	TTC39B	83	.	0			c.1100-1G>A						PASS	.						52.0	48.0	49.0					9																	15189791		2203	4300	6503	SO:0001630	splice_region_variant	158219	exon13			CTGTACCTAGAAA	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1106-1G>A	9.37:g.15189791C>T		59.0	0.0	0		57.0	11.0	0.192982	NM_001168339	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Splice_Site	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.859434	0.91433	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8823	0.96903	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTC39B	15179791	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.261000	0.78400	2.693000	0.91896	0.585000	0.79938	.	.	.	none		0.408	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	Intron
DSC1	1823	hgsc.bcm.edu	37	18	28710619	28710619	+	Missense_Mutation	SNP	C	C	A	rs985861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710619C>A	ENST00000257198.5	-	16	2804	c.2543G>T	c.(2542-2544)tGt>tTt	p.C848F	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	848			C -> F (in dbSNP:rs985861). {ECO:0000269|PubMed:8507556}.		homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			GTTATACGAACAAACGTAGTC	0.413													C|||	467	0.0932508	0.2549	0.0533	5008	,	,		17746	0.0		0.0477	False		,,,				2504	0.046				p.C848F		Atlas-SNP	.											.	DSC1	240	.	0			c.G2543T						PASS	.	C	,PHE/CYS	885,3521	340.5+/-306.2	88,709,1406	132.0	133.0	132.0		,2543	2.0	0.2	18	dbSNP_86	132	344,8256	117.4+/-177.0	6,332,3962	yes	utr-3,missense	DSC1	NM_004948.3,NM_024421.2	,205	94,1041,5368	AA,AC,CC		4.0,20.0862,9.4495	,benign	,848/895	28710619	1229,11777	2203	4300	6503	SO:0001583	missense	1823	exon16			TACGAACAAACGT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2543G>T	18.37:g.28710619C>A	ENSP00000257198:p.Cys848Phe	240.0	0.0	0		198.0	85.0	0.429293	NM_024421	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	180	0.08241758241758242	125	0.2540650406504065	21	0.058011049723756904	0	0.0	34	0.044854881266490766	C	10.91	1.485333	0.26598	0.200862	0.04	ENSG00000134765	ENST00000257198	T	0.76060	-0.99	6.17	2.05	0.26809	Cadherin, cytoplasmic domain (1);	0.127555	0.35615	N	0.003081	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.05937	-1.0855	9	0.72032	D	0.01	.	6.2715	0.20956	0.4608:0.3859:0.0:0.1532	rs985861;rs52820787;rs985861	848	Q08554	DSC1_HUMAN	F	848	ENSP00000257198:C848F	ENSP00000257198:C848F	C	-	2	0	DSC1	26964617	0.682000	0.27624	0.197000	0.23402	0.663000	0.39108	1.525000	0.35953	0.485000	0.27652	0.655000	0.94253	TGT	C|0.914;A|0.086	0.086	strong		0.413	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
PPP1R32	220004	hgsc.bcm.edu	37	11	61253841	61253841	+	Missense_Mutation	SNP	C	C	A	rs11230707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61253841C>A	ENST00000338608.2	+	8	838	c.713C>A	c.(712-714)aCc>aAc	p.T238N	PPP1R32_ENST00000432063.2_Intron|PPP1R32_ENST00000366212.4_5'Flank|PPP1R32_ENST00000538185.1_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	238			T -> N (in dbSNP:rs11230707).				phosphatase binding (GO:0019902)										CAGAGTGTCACCAAGTCAGAC	0.637													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19286	0.001		0.008	False		,,,				2504	0.0092				p.T238N		Atlas-SNP	.											.	.	.	.	0			c.C713A						PASS	.	C	,ASN/THR	512,3892	233.3+/-246.5	36,440,1726	48.0	47.0	47.0		,713	3.4	1.0	11	dbSNP_120	47	62,8536	38.3+/-94.2	0,62,4237	yes	intron,missense	C11orf66	NM_001170753.1,NM_145017.2	,65	36,502,5963	AA,AC,CC		0.7211,11.6258,4.4147	,possibly-damaging	,238/426	61253841	574,12428	2202	4299	6501	SO:0001583	missense	220004	exon8			GTGTCACCAAGTC	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.713C>A	11.37:g.61253841C>A	ENSP00000344140:p.Thr238Asn	194.0	0.0	0		143.0	107.0	0.748252	NM_145017	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	89	0.04075091575091575	79	0.16056910569105692	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	17.86	3.492963	0.64074	0.116258	0.007211	ENSG00000162148	ENST00000338608;ENST00000542951;ENST00000535545	T;T;T	0.44881	1.39;0.91;1.3	4.37	3.39	0.38822	.	0.338132	0.23748	N	0.044945	T	0.00384	0.0012	M	0.73598	2.24	0.09310	P	0.9999999999999436	D	0.67145	0.996	D	0.66847	0.947	T	0.13899	-1.0492	9	0.56958	D	0.05	-0.1502	12.184	0.54227	0.0:0.8279:0.1721:0.0	rs11230707;rs11230707	238	Q7Z5V6	PPR32_HUMAN	N	238;18;5	ENSP00000344140:T238N;ENSP00000441053:T18N;ENSP00000437511:T5N	ENSP00000344140:T238N	T	+	2	0	C11orf66	61010417	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.646000	0.37249	2.153000	0.67306	0.650000	0.86243	ACC	C|0.955;A|0.045	0.045	strong		0.637	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
KRT73	319101	hgsc.bcm.edu	37	12	53012053	53012053	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53012053A>C	ENST00000305748.3	-	1	290	c.256T>G	c.(256-258)Ttt>Gtt	p.F86V	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	86	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		ACACTGCCAAACATGCTGCCA	0.637																																					p.F86V		Atlas-SNP	.											.	KRT73	101	.	0			c.T256G						PASS	.						107.0	119.0	115.0					12																	53012053		2203	4300	6503	SO:0001583	missense	319101	exon1			TGCCAAACATGCT	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.256T>G	12.37:g.53012053A>C	ENSP00000307014:p.Phe86Val	108.0	0.0	0		118.0	69.0	0.584746	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.025490	0.35701	.	.	ENSG00000186049	ENST00000305748	D	0.91351	-2.83	4.64	3.5	0.40072	.	0.114168	0.38959	N	0.001513	D	0.91372	0.7278	M	0.89534	3.04	0.28878	N	0.894598	P	0.38455	0.632	B	0.43155	0.41	D	0.84270	0.0488	10	0.23302	T	0.38	.	6.9916	0.24758	0.7232:0.1908:0.086:0.0	.	86	Q86Y46	K2C73_HUMAN	V	86	ENSP00000307014:F86V	ENSP00000307014:F86V	F	-	1	0	KRT73	51298320	0.193000	0.23313	1.000000	0.80357	0.888000	0.51559	3.442000	0.52900	0.887000	0.36136	0.533000	0.62120	TTT	.	.	none		0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
CD101	9398	hgsc.bcm.edu	37	1	117554247	117554247	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117554247C>T	ENST00000256652.4	+	3	558	c.500C>T	c.(499-501)aCc>aTc	p.T167I	CD101_ENST00000369470.1_Missense_Mutation_p.T167I	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	167	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TTAGCCCTCACCTGTGAGGCA	0.483																																					p.T167I		Atlas-SNP	.											.	CD101	95	.	0			c.C500T						PASS	.						107.0	93.0	98.0					1																	117554247		2203	4300	6503	SO:0001583	missense	9398	exon3			CCCTCACCTGTGA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.500C>T	1.37:g.117554247C>T	ENSP00000256652:p.Thr167Ile	168.0	0.0	0		141.0	60.0	0.425532	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999464	0.35320	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.67171	-0.25;-0.25	5.33	4.41	0.53225	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.565464	0.18042	N	0.153594	T	0.73729	0.3624	M	0.82823	2.61	0.33375	D	0.574133	D	0.89917	1.0	D	0.80764	0.994	T	0.76672	-0.2873	10	0.72032	D	0.01	-9.8961	7.5864	0.27995	0.0:0.7445:0.1664:0.0891	.	167	Q93033	IGSF2_HUMAN	I	167	ENSP00000256652:T167I;ENSP00000358482:T167I	ENSP00000256652:T167I	T	+	2	0	CD101	117355770	0.104000	0.21937	0.653000	0.29593	0.026000	0.11368	0.930000	0.28858	1.254000	0.44035	0.650000	0.86243	ACC	.	.	none		0.483	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
CCDC168	643677	hgsc.bcm.edu	37	13	103388015	103388015	+	Missense_Mutation	SNP	C	C	G	rs17507841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103388015C>G	ENST00000322527.2	-	1	1144	c.1145G>C	c.(1144-1146)gGa>gCa	p.G382A		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	382			G -> A (in dbSNP:rs17507841).														TTTCTCTTCTCCCTGTGCTGT	0.408													C|||	98	0.0195687	0.0023	0.0202	5008	,	,		22051	0.001		0.0328	False		,,,				2504	0.0481				p.G5011A		Atlas-SNP	.											.	.	.	.	0			c.G15032C						PASS	.	C	ALA/GLY	4,1380		0,4,688	205.0	161.0	174.0		15032	1.3	0.1	13	dbSNP_123	174	91,3091		3,85,1503	yes	missense	CCDC168	NM_001146197.1	60	3,89,2191	GG,GC,CC		2.8598,0.289,2.0806	benign	5011/7082	103388015	95,4471	692	1591	2283	SO:0001583	missense	643677	exon4			TCTTCTCCCTGTG		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.1145G>C	13.37:g.103388015C>G	ENSP00000320232:p.Gly382Ala	183.0	0.0	0		180.0	93.0	0.516667	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		36	0.016483516483516484	3	0.006097560975609756	8	0.022099447513812154	0	0.0	25	0.032981530343007916	C	3.488	-0.104389	0.06967	0.00289	0.028598	ENSG00000175820	ENST00000322527	T	0.03635	3.86	2.53	1.28	0.21552	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.09377	0.004	T	0.49560	-0.8927	9	0.19147	T	0.46	.	4.3333	0.11075	0.0:0.1678:0.0:0.8322	rs17507841;rs52799978;rs17507841	382	Q8NDH2	CC168_HUMAN	A	382	ENSP00000320232:G382A	ENSP00000320232:G382A	G	-	2	0	CCDC168	102186016	0.000000	0.05858	0.065000	0.19835	0.080000	0.17528	-0.038000	0.12144	0.384000	0.24942	-0.624000	0.04008	GGA	C|0.984;G|0.016	0.016	strong		0.408	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	200.0	2.0	0.01		198.0	13.0	0.0656566	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70.0	72.0	72.0		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1323C>T	2.37:g.170403106G>A		225.0	0.0	0		220.0	92.0	0.418182	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703286	56703286	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56703286G>A	ENST00000586855.2	-	3	834	c.521C>T	c.(520-522)cCg>cTg	p.P174L	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.P174L			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	174					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GCCTGTCCCCGGATGCATCTG	0.632																																					p.P174L		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C521T						PASS	.						33.0	35.0	34.0					19																	56703286		2203	4300	6503	SO:0001583	missense	342933	exon2			GTCCCCGGATGCA		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.521C>T	19.37:g.56703286G>A	ENSP00000466072:p.Pro174Leu	90.0	0.0	0		87.0	33.0	0.37931	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	G	6.658	0.489887	0.12702	.	.	ENSG00000197213	ENST00000358992	T	0.05580	3.42	1.9	0.827	0.18835	.	.	.	.	.	T	0.08358	0.0208	M	0.78049	2.395	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33085	-0.9882	9	0.34782	T	0.22	.	3.7907	0.08719	0.2493:0.0:0.7507:0.0	.	174	A6NJL1	ZSA5B_HUMAN	L	174	ENSP00000351883:P174L	ENSP00000351883:P174L	P	-	2	0	ZSCAN5B	61395098	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.329000	0.19698	0.345000	0.23873	0.306000	0.20318	CCG	.	.	none		0.632	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
LIMD2	80774	hgsc.bcm.edu	37	17	61775992	61775992	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61775992A>T	ENST00000259006.3	-	5	462	c.304T>A	c.(304-306)Tac>Aac	p.Y102N	LIMD2_ENST00000578061.1_Missense_Mutation_p.Y102N|LIMD2_ENST00000583211.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000578402.1_Missense_Mutation_p.Y102N|LIMD2_ENST00000582055.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000578993.1_Missense_Mutation_p.Y62N	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	102							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						CCCTCGTCGTAGTTGCCTTTG	0.617																																					p.Y102N		Atlas-SNP	.											.	LIMD2	6	.	0			c.T304A						PASS	.						73.0	58.0	63.0					17																	61775992		2203	4300	6503	SO:0001583	missense	80774	exon5			CGTCGTAGTTGCC	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.304T>A	17.37:g.61775992A>T	ENSP00000259006:p.Tyr102Asn	94.0	0.0	0		102.0	27.0	0.264706	NM_030576	D3DU16|Q96S91	Missense_Mutation	SNP	ENST00000259006.3	37	CCDS11641.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358147	0.82243	.	.	ENSG00000136490	ENST00000259006	T	0.79845	-1.31	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.90212	0.6940	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91871	0.5507	10	0.87932	D	0	-26.4471	14.5766	0.68252	1.0:0.0:0.0:0.0	.	102	Q9BT23	LIMD2_HUMAN	N	102	ENSP00000259006:Y102N	ENSP00000259006:Y102N	Y	-	1	0	LIMD2	59129724	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	9.313000	0.96297	2.100000	0.63781	0.533000	0.62120	TAC	.	.	none		0.617	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576	
SYNE1	23345	hgsc.bcm.edu	37	6	152746593	152746593	+	Missense_Mutation	SNP	A	A	T	rs111250109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152746593A>T	ENST00000367255.5	-	39	5791	c.5190T>A	c.(5188-5190)gaT>gaA	p.D1730E	SYNE1_ENST00000265368.4_Missense_Mutation_p.D1730E|SYNE1_ENST00000423061.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000448038.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000341594.5_Missense_Mutation_p.D1767E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1730					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTTCACATCATCTTTGGAGG	0.363										HNSCC(10;0.0054)			A|||	164	0.0327476	0.0287	0.0288	5008	,	,		18407	0.005		0.0577	False		,,,				2504	0.044				p.D1737E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T5211A						PASS	.	A	GLU/ASP,GLU/ASP	183,4223	118.8+/-156.5	5,173,2025	153.0	143.0	147.0		5211,5190	-6.3	0.8	6	dbSNP_132	147	444,8156	134.3+/-191.7	18,408,3874	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	45,45	23,581,5899	TT,TA,AA		5.1628,4.1534,4.8209	benign,benign	1737/8750,1730/8798	152746593	627,12379	2203	4300	6503	SO:0001583	missense	23345	exon39			CACATCATCTTTG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5190T>A	6.37:g.152746593A>T	ENSP00000356224:p.Asp1730Glu	230.0	0.0	0		142.0	95.0	0.669014	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	68	0.031135531135531136	14	0.028455284552845527	10	0.027624309392265192	2	0.0034965034965034965	42	0.055408970976253295	A	12.76	2.033458	0.35893	0.041534	0.051628	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.71	-6.32	0.01995	.	0.397222	0.23999	N	0.042496	T	0.02230	0.0069	N	0.04959	-0.14	0.80722	D	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.36744	-0.9735	10	0.02654	T	1	.	5.6049	0.17374	0.1571:0.5244:0.1775:0.141	.	1713;1730;1730;1737	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	E	1730;1737;1730;1737;1767	ENSP00000356224:D1730E;ENSP00000396024:D1737E;ENSP00000265368:D1730E;ENSP00000390975:D1737E;ENSP00000341887:D1767E	ENSP00000265368:D1730E	D	-	3	2	SYNE1	152788286	0.003000	0.15002	0.784000	0.31847	0.973000	0.67179	-2.103000	0.01341	-1.475000	0.01876	-0.314000	0.08810	GAT	A|0.951;T|0.049	0.049	strong		0.363	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ERCC2	2068	hgsc.bcm.edu	37	19	45855478	45855478	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45855478G>A	ENST00000391945.4	-	22	2256	c.2179C>T	c.(2179-2181)Ccc>Tcc	p.P727S	ERCC2_ENST00000391944.3_Missense_Mutation_p.P649S	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	727			Missing (in XP-D and TTDP). {ECO:0000269|PubMed:9195225}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CGGTGGAAGGGCTGTGCCATC	0.652			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.P727S		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.C2179T						PASS	.						73.0	55.0	61.0					19																	45855478		2203	4300	6503	SO:0001583	missense	2068	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAAGGGCTGTGC		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2179C>T	19.37:g.45855478G>A	ENSP00000375809:p.Pro727Ser	91.0	0.0	0		114.0	30.0	0.263158	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159589	0.78226	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82984	-1.41;-1.67	5.27	5.27	0.74061	.	0.126130	0.52532	D	0.000065	D	0.87815	0.6272	M	0.91663	3.23	0.80722	D	1	P;P;P	0.46987	0.762;0.756;0.888	B;B;B	0.43194	0.411;0.391;0.343	D	0.90746	0.4653	10	0.66056	D	0.02	-31.7778	16.3902	0.83532	0.0:0.0:1.0:0.0	.	649;727;420	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	S	677;703;727;649	ENSP00000375809:P727S;ENSP00000375808:P649S	ENSP00000375805:P677S	P	-	1	0	ERCC2	50547318	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	8.735000	0.91549	2.461000	0.83175	0.561000	0.74099	CCC	.	.	none		0.652	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
NOL6	65083	hgsc.bcm.edu	37	9	33464897	33464897	+	Missense_Mutation	SNP	T	T	C	rs142747625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33464897T>C	ENST00000379471.2	-	21	2846	c.2759A>G	c.(2758-2760)aAc>aGc	p.N920S	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Missense_Mutation_p.N868S			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	920					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		ATTATTGAGGTTGACAAAGAG	0.478													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19701	0.0		0.005	False		,,,				2504	0.0				p.N920S		Atlas-SNP	.											.	NOL6	85	.	0			c.A2759G						PASS	.	T	SER/ASN,	1,4405	2.1+/-5.4	0,1,2202	95.0	100.0	99.0		2759,	5.4	1.0	9	dbSNP_134	99	20,8580	14.6+/-50.1	0,20,4280	yes	missense,intron	NOL6	NM_022917.4,NM_139235.3	46,	0,21,6482	CC,CT,TT		0.2326,0.0227,0.1615	probably-damaging,	920/1147,	33464897	21,12985	2203	4300	6503	SO:0001583	missense	65083	exon21			TTGAGGTTGACAA	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2759A>G	9.37:g.33464897T>C	ENSP00000368784:p.Asn920Ser	79.0	0.0	0		77.0	34.0	0.441558	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	16.69	3.193496	0.58017	2.27E-4	0.002326	ENSG00000165271	ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T	0.47869	0.83;0.83;0.83	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.58807	0.2148	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.62365	0.984;0.991;0.981;0.985	P;P;P;P	0.59546	0.794;0.833;0.59;0.859	T	0.68765	-0.5322	10	0.66056	D	0.02	.	15.5171	0.75833	0.0:0.0:0.0:1.0	.	868;917;920;920	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4	.;.;.;NOL6_HUMAN	S	920;920;476;920;868	ENSP00000297990:N920S;ENSP00000368784:N920S;ENSP00000395915:N868S	ENSP00000297990:N920S	N	-	2	0	NOL6	33454897	1.000000	0.71417	0.993000	0.49108	0.024000	0.10985	7.579000	0.82511	2.059000	0.61396	0.533000	0.62120	AAC	T|0.998;C|0.002	0.002	strong		0.478	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657894	46657894	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:46657894C>T	ENST00000253255.5	-	1	1325	c.1326G>A	c.(1324-1326)gcG>gcA	p.A442A		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	442	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TATCAGAAAACGCTGTCCTAG	0.468																																					p.A442A		Atlas-SNP	.											.	PKDREJ	195	.	0			c.G1326A						PASS	.						110.0	103.0	105.0					22																	46657894		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AGAAAACGCTGTC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1326G>A	22.37:g.46657894C>T		199.0	0.0	0		183.0	47.0	0.256831	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			.	.	none		0.468	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CAMK2G	818	hgsc.bcm.edu	37	10	75574956	75574956	+	Silent	SNP	G	G	A	rs55640406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75574956G>A	ENST00000351293.3	-	18	1362	c.1305C>T	c.(1303-1305)caC>caT	p.H435H	CAMK2G_ENST00000372765.1_Silent_p.H456H|CAMK2G_ENST00000322635.3_Silent_p.H467H|CAMK2G_ENST00000423381.1_Silent_p.H528H|CAMK2G_ENST00000322680.3_Silent_p.H496H|CAMK2G_ENST00000394762.2_Silent_p.H473H|RP11-574K11.5_ENST00000434147.1_RNA|CAMK2G_ENST00000305762.7_Silent_p.H469H|CAMK2G_ENST00000472912.1_5'UTR	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	498					calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	TCACGTGGACGTGTGGGTTTA	0.607													G|||	37	0.00738818	0.0	0.0144	5008	,	,		14899	0.0		0.0169	False		,,,				2504	0.0102				p.H496H		Atlas-SNP	.											.	CAMK2G	79	.	0			c.C1488T						PASS	.	G	,,,,,	25,4381	32.6+/-62.9	0,25,2178	151.0	123.0	133.0		1437,1305,1401,1374,1488,1332	-0.9	0.9	10	dbSNP_129	133	172,8428	79.2+/-141.9	3,166,4131	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2G	NM_001204492.1,NM_001222.3,NM_172169.2,NM_172170.4,NM_172171.2,NM_172173.2	,,,,,	3,191,6309	AA,AG,GG		2.0,0.5674,1.5147	,,,,,	479/540,435/496,467/528,458/519,496/557,444/505	75574956	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	818	exon20			GTGGACGTGTGGG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.1305C>T	10.37:g.75574956G>A		195.0	0.0	0		143.0	142.0	0.993007	NM_172171	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Silent	SNP	ENST00000351293.3	37	CCDS7336.1	18	0.008241758241758242	0	0.0	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	9.245	1.039308	0.19669	0.005674	0.02	ENSG00000148660	ENST00000441192	.	.	.	5.51	-0.849	0.10723	.	.	.	.	.	T	0.41766	0.1173	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45716	-0.9242	4	.	.	.	.	11.3382	0.49516	0.5165:0.0:0.4835:0.0	rs55640406	.	.	.	C	275	.	.	R	-	1	0	CAMK2G	75244962	0.853000	0.29707	0.880000	0.34516	0.996000	0.88848	-0.037000	0.12164	-0.477000	0.06832	-0.137000	0.14449	CGT	G|0.988;A|0.012	0.012	strong		0.607	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
IL10RA	3587	hgsc.bcm.edu	37	11	117869642	117869642	+	Missense_Mutation	SNP	C	C	A	rs369418818		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117869642C>A	ENST00000227752.3	+	7	1143	c.1023C>A	c.(1021-1023)caC>caA	p.H341Q	IL10RA_ENST00000541785.1_Missense_Mutation_p.H321Q|IL10RA_ENST00000545409.1_Missense_Mutation_p.H192Q|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	341					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CTGACCCTCACCCCCAGGCTG	0.617																																					p.H341Q		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1023A						PASS	.	C	GLN/HIS	0,4400		0,0,2200	59.0	54.0	56.0		1023	-2.5	0.0	11		56	4,8588	3.0+/-9.4	0,4,4292	no	missense	IL10RA	NM_001558.3	24	0,4,6492	AA,AC,CC		0.0466,0.0,0.0308	benign	341/579	117869642	4,12988	2200	4296	6496	SO:0001583	missense	3587	exon7			CCCTCACCCCCAG	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1023C>A	11.37:g.117869642C>A	ENSP00000227752:p.His341Gln	47.0	0.0	0		53.0	43.0	0.811321	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350897	0.24512	0.0	4.66E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.21031	2.03;2.03;2.03	5.66	-2.55	0.06288	.	1.951570	0.01920	N	0.040455	T	0.17195	0.0413	L	0.56769	1.78	0.09310	N	1	B;B	0.16802	0.019;0.011	B;B	0.15484	0.013;0.006	T	0.13926	-1.0491	10	0.12430	T	0.62	-2.9137	1.8617	0.03190	0.1108:0.3559:0.2405:0.2928	.	321;341	F5GYV8;Q13651	.;I10R1_HUMAN	Q	341;321;192;321	ENSP00000227752:H341Q;ENSP00000441397:H321Q;ENSP00000443019:H192Q	ENSP00000227752:H341Q	H	+	3	2	IL10RA	117374852	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.122000	0.10627	0.058000	0.16222	0.563000	0.77884	CAC	.	.	weak		0.617	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
PCNT	5116	hgsc.bcm.edu	37	21	47817316	47817316	+	Missense_Mutation	SNP	G	G	A	rs143796569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47817316G>A	ENST00000359568.5	+	22	4461	c.4354G>A	c.(4354-4356)Ggg>Agg	p.G1452R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1452			G -> R (found in a patient with mental retardation, no speech, facial and limbs dysmorphisms). {ECO:0000269|PubMed:23033978}.		brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TCAGCATCGCGGGTGTGCCAA	0.562													G|||	18	0.00359425	0.0	0.0	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0174				p.G1452R		Atlas-SNP	.											PCNT,NS,carcinoma,-2,1	PCNT	283	1	0			c.G4354A						PASS	.	G	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	70.0	68.0	69.0		4354	5.5	0.0	21	dbSNP_134	69	17,8583	12.6+/-44.7	0,17,4283	yes	missense	PCNT	NM_006031.5	125	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	1452/3337	47817316	19,12987	2203	4300	6503	SO:0001583	missense	5116	exon22			CATCGCGGGTGTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4354G>A	21.37:g.47817316G>A	ENSP00000352572:p.Gly1452Arg	93.0	0.0	0		100.0	27.0	0.27	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.43	2.830357	0.50845	4.54E-4	0.001977	ENSG00000160299	ENST00000359568	T	0.58506	0.33	5.46	5.46	0.80206	.	0.511594	0.14699	N	0.303674	T	0.66056	0.2751	L	0.44542	1.39	0.09310	N	0.999996	D;D	0.76494	0.999;0.998	P;P	0.57152	0.814;0.807	T	0.60182	-0.7313	10	0.51188	T	0.08	.	16.8006	0.85613	0.0:0.0:1.0:0.0	.	1334;1452	O95613-2;O95613	.;PCNT_HUMAN	R	1452	ENSP00000352572:G1452R	ENSP00000352572:G1452R	G	+	1	0	PCNT	46641744	0.968000	0.33430	0.009000	0.14445	0.009000	0.06853	4.647000	0.61418	2.560000	0.86352	0.561000	0.74099	GGG	G|0.999;A|0.001	0.001	strong		0.562	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
OSBPL10	114884	hgsc.bcm.edu	37	3	32022622	32022622	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:32022622C>T	ENST00000396556.2	-	1	172	c.50G>A	c.(49-51)aGc>aAc	p.S17N	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S17N|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	17					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		gctgcggctgctgctgttgct	0.791																																					p.S17N		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G50A						PASS	.						2.0	3.0	2.0					3																	32022622		662	1473	2135	SO:0001583	missense	114884	exon1			CGGCTGCTGCTGT	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.50G>A	3.37:g.32022622C>T	ENSP00000379804:p.Ser17Asn	8.0	0.0	0		21.0	12.0	0.571429	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141933	0.37825	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.26518	1.73;2.07	3.91	3.91	0.45181	.	2.901820	0.03061	N	0.155841	T	0.22898	0.0553	N	0.19112	0.55	0.26378	N	0.976786	B;B	0.27498	0.18;0.18	B;B	0.23716	0.048;0.048	T	0.23119	-1.0197	10	0.51188	T	0.08	.	13.8256	0.63348	0.0:1.0:0.0:0.0	.	17;17	B4E212;Q9BXB5	.;OSB10_HUMAN	N	17	ENSP00000379804:S17N;ENSP00000406124:S17N	ENSP00000379804:S17N	S	-	2	0	OSBPL10	31997626	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.460000	0.45031	2.196000	0.70406	0.298000	0.19748	AGC	.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
ZNF248	57209	hgsc.bcm.edu	37	10	38121631	38121631	+	Missense_Mutation	SNP	T	T	C	rs11011379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:38121631T>C	ENST00000395867.3	-	6	1202	c.652A>G	c.(652-654)Aaa>Gaa	p.K218E	ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000357328.4_Missense_Mutation_p.K218E|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	218			K -> E (in dbSNP:rs11011379).		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)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TGTCCATTTTTACTATACTCA	0.353													T|||	38	0.00758786	0.0023	0.0202	5008	,	,		18155	0.0		0.0149	False		,,,				2504	0.0061				p.K218E		Atlas-SNP	.											.	ZNF248	61	.	0			c.A652G						PASS	.	T	GLU/LYS	17,4385	20.2+/-43.8	0,17,2184	53.0	53.0	53.0		652	1.3	0.8	10	dbSNP_120	53	185,8411	78.4+/-141.0	0,185,4113	yes	missense	ZNF248	NM_021045.1	56	0,202,6297	CC,CT,TT		2.1522,0.3862,1.5541	benign	218/580	38121631	202,12796	2201	4298	6499	SO:0001583	missense	57209	exon6			CATTTTTACTATA	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.652A>G	10.37:g.38121631T>C	ENSP00000379208:p.Lys218Glu	90.0	0.0	0		56.0	29.0	0.517857	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	19	0.0086996336996337	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	11	0.014511873350923483	T	0.003	-2.502296	0.00157	0.003862	0.021522	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.04194	3.68;3.68	4.3	1.32	0.21799	.	0.331549	0.22037	N	0.065510	T	0.00496	0.0016	N	0.00347	-1.61	0.21719	N	0.999574	B	0.02656	0.0	B	0.01281	0.0	T	0.44937	-0.9295	10	0.02654	T	1	.	4.193	0.10430	0.0:0.5858:0.1909:0.2233	rs11011379;rs17662331;rs11011379	218	Q8NDW4	ZN248_HUMAN	E	218	ENSP00000379208:K218E;ENSP00000349882:K218E	ENSP00000349882:K218E	K	-	1	0	ZNF248	38161637	0.935000	0.31712	0.812000	0.32479	0.150000	0.21749	-0.179000	0.09768	0.165000	0.19558	-0.468000	0.05107	AAA	T|0.986;C|0.014	0.014	strong		0.353	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
TAF1L	138474	hgsc.bcm.edu	37	9	32631518	32631518	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32631518C>G	ENST00000242310.4	-	1	4149	c.4060G>C	c.(4060-4062)Gag>Cag	p.E1354Q	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1354					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTGCGAACCTCATGCACATTC	0.403																																					p.E1354Q		Atlas-SNP	.											.	TAF1L	382	.	0			c.G4060C						PASS	.						238.0	236.0	236.0					9																	32631518		2203	4300	6503	SO:0001583	missense	138474	exon1			GAACCTCATGCAC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4060G>C	9.37:g.32631518C>G	ENSP00000418379:p.Glu1354Gln	433.0	1.0	0.00230947		338.0	86.0	0.254438	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465042	0.43839	.	.	ENSG00000122728	ENST00000242310	T	0.09163	3.01	0.479	0.479	0.16796	.	0.097387	0.64402	D	0.000001	T	0.13415	0.0325	L	0.47190	1.495	0.51233	D	0.999915	D	0.55605	0.972	P	0.52343	0.696	T	0.05716	-1.0868	10	0.40728	T	0.16	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1354	Q8IZX4	TAF1L_HUMAN	Q	1354	ENSP00000418379:E1354Q	ENSP00000418379:E1354Q	E	-	1	0	TAF1L	32621518	1.000000	0.71417	0.942000	0.38095	0.559000	0.35586	4.785000	0.62418	0.507000	0.28148	0.195000	0.17529	GAG	.	.	none		0.403	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
ARID4B	51742	hgsc.bcm.edu	37	1	235416122	235416122	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235416122A>G	ENST00000264183.3	-	6	774	c.277T>C	c.(277-279)Ttt>Ctt	p.F93L	ARID4B_ENST00000349213.3_Missense_Mutation_p.F93L|ARID4B_ENST00000366603.2_Missense_Mutation_p.F93L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	93					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CCGTCATCAAAAACTATGAGA	0.373																																					p.F93L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T277C						PASS	.						63.0	63.0	63.0					1																	235416122		2203	4300	6503	SO:0001583	missense	51742	exon6			CATCAAAAACTAT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.277T>C	1.37:g.235416122A>G	ENSP00000264183:p.Phe93Leu	168.0	0.0	0		172.0	36.0	0.209302	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	A	32	5.147074	0.94603	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.73	5.73	0.89815	Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.80773	0.4687	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.71674	0.974;0.99;0.998;0.982	D;D;D;D	0.76071	0.953;0.979;0.987;0.952	D	0.83844	0.0259	10	0.87932	D	0	-14.2235	15.7063	0.77583	1.0:0.0:0.0:0.0	.	93;93;93;93	F8WB31;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	93	ENSP00000264184:F93L;ENSP00000355562:F93L;ENSP00000264183:F93L;ENSP00000391497:F93L	ENSP00000264183:F93L	F	-	1	0	ARID4B	233482745	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	8.951000	0.93025	2.197000	0.70478	0.533000	0.62120	TTT	.	.	none		0.373	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
ZNF623	9831	hgsc.bcm.edu	37	8	144733176	144733176	+	Silent	SNP	C	C	T	rs141224385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144733176C>T	ENST00000501748.2	+	1	1223	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	ZNF623_ENST00000458270.2_Silent_p.N338N|ZNF623_ENST00000526926.1_Silent_p.N338N	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	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;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ATGAATGTAACGAGTGTGGGA	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21487	0.0		0.0	False		,,,				2504	0.002				p.N378N		Atlas-SNP	.											ZNF623,NS,carcinoma,0,1	ZNF623	63	1	0			c.C1134T						scavenged	.	C	,	1,4405	2.1+/-5.4	0,1,2202	71.0	67.0	69.0		1014,1134	-8.1	0.0	8	dbSNP_134	69	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	ZNF623	NM_001082480.1,NM_014789.3	,	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	,	338/497,378/537	144733176	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9831	exon1			ATGTAACGAGTGT	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.1134C>T	8.37:g.144733176C>T		32.0	0.0	0		35.0	5.0	0.142857	NM_014789	A4FU80|B4DGP3|E7ENV5	Silent	SNP	ENST00000501748.2	37	CCDS34957.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
ABCB8	11194	hgsc.bcm.edu	37	7	150739054	150739054	+	Missense_Mutation	SNP	G	G	A	rs56198402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150739054G>A	ENST00000297504.6	+	15	1741	c.1675G>A	c.(1675-1677)Gtc>Atc	p.V559I	ABCB8_ENST00000498578.1_Missense_Mutation_p.V542I|ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000542328.1_Missense_Mutation_p.V454I|ABCB8_ENST00000358849.4_Missense_Mutation_p.V542I			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	559	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	ACAGGAGCCCGTCCTGTTTGG	0.542													G|||	133	0.0265575	0.0008	0.0476	5008	,	,		19339	0.0208		0.0447	False		,,,				2504	0.0337				p.V542I		Atlas-SNP	.											.	ABCB8	65	.	0			c.G1624A						PASS	.	G	ILE/VAL	34,4372	37.6+/-69.7	0,34,2169	57.0	59.0	58.0		1624	3.8	1.0	7	dbSNP_129	58	348,8252	118.1+/-177.6	7,334,3959	yes	missense	ABCB8	NM_007188.3	29	7,368,6128	AA,AG,GG		4.0465,0.7717,2.9371	benign	542/719	150739054	382,12624	2203	4300	6503	SO:0001583	missense	11194	exon14			GAGCCCGTCCTGT	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1675G>A	7.37:g.150739054G>A	ENSP00000297504:p.Val559Ile	31.0	0.0	0		42.0	26.0	0.619048	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		67	0.030677655677655676	0	0.0	17	0.04696132596685083	14	0.024475524475524476	36	0.047493403693931395	G	10.61	1.399063	0.25291	0.007717	0.040465	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	4.73	3.83	0.44106	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.066008	0.64402	D	0.000013	T	0.45756	0.1358	N	0.10916	0.065	0.80722	D	1	B;B;B;B	0.24963	0.08;0.115;0.099;0.094	B;B;B;B	0.29716	0.047;0.106;0.079;0.079	T	0.65524	-0.6147	10	0.28530	T	0.3	-6.061	11.0243	0.47736	0.093:0.0:0.907:0.0	rs56198402;rs61274547;rs61734191	454;542;559;542	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2	.;.;ABCB8_HUMAN;.	I	542;525;559;454;542	ENSP00000351717:V542I;ENSP00000297504:V559I;ENSP00000438776:V454I;ENSP00000418271:V542I	ENSP00000297504:V559I	V	+	1	0	ABCB8	150369987	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	5.412000	0.66392	2.456000	0.83038	0.462000	0.41574	GTC	G|0.969;A|0.031	0.031	strong		0.542	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
FRAS1	80144	hgsc.bcm.edu	37	4	79353587	79353587	+	Missense_Mutation	SNP	C	C	G	rs35219594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79353587C>G	ENST00000325942.6	+	38	5486	c.5046C>G	c.(5044-5046)gaC>gaG	p.D1682E	FRAS1_ENST00000264895.6_Missense_Mutation_p.D1682E	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1682					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CCCGGGAAGACAGCATGGAGA	0.483													C|||	10	0.00199681	0.0008	0.0086	5008	,	,		21025	0.0		0.003	False		,,,				2504	0.0				p.D1682E		Atlas-SNP	.											FRAS1_ENST00000325942,NS,carcinoma,+2,3	FRAS1	779	3	0			c.C5046G						PASS	.	C	GLU/ASP,GLU/ASP	5,3945		0,5,1970	64.0	65.0	65.0		5046,5046	4.5	1.0	4	dbSNP_126	65	38,8276		0,38,4119	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	45,45	0,43,6089	GG,GC,CC		0.4571,0.1266,0.3506	probably-damaging,probably-damaging	1682/1977,1682/4013	79353587	43,12221	1975	4157	6132	SO:0001583	missense	80144	exon38			GGAAGACAGCATG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5046C>G	4.37:g.79353587C>G	ENSP00000326330:p.Asp1682Glu	174.0	0.0	0		120.0	59.0	0.491667	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.55|13.55	2.270864|2.270864	0.40194|0.40194	0.001266|0.001266	0.004571|0.004571	ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316|ENST00000510944	T;T|.	0.50001|.	0.76;0.76|.	6.17|6.17	4.47|4.47	0.54385|0.54385	.|.	0.048301|.	0.85682|.	D|.	0.000000|.	T|T	0.64450|0.64450	0.2599|0.2599	M|M	0.67517|0.67517	2.055|2.055	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.982;0.998|.	T|T	0.62167|0.62167	-0.6911|-0.6911	10|5	0.52906|.	T|.	0.07|.	.|.	9.988|9.988	0.41854|0.41854	0.0:0.7975:0.0:0.2025|0.0:0.7975:0.0:0.2025	rs35219594|rs35219594	1682;1682|.	E9PHH6;A2RRR8|.	.;.|.	E|E	1682;1682;102|132	ENSP00000326330:D1682E;ENSP00000264895:D1682E|.	ENSP00000264895:D1682E|.	D|Q	+|+	3|1	2|0	FRAS1|FRAS1	79572611|79572611	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.004000|0.004000	0.04260|0.04260	2.301000|2.301000	0.43628|0.43628	0.954000|0.954000	0.37851|0.37851	-0.136000|-0.136000	0.14681|0.14681	GAC|CAG	C|0.998;G|0.002	0.002	strong		0.483	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
AK9	221264	hgsc.bcm.edu	37	6	109827528	109827528	+	Splice_Site	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109827528A>G	ENST00000424296.2	-	35	4926		c.e35+1		RP5-919F19.5_ENST00000423747.2_RNA|AL109947.2_ENST00000517228.1_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9						ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										GTGCTATCTTACCTGCTTTTA	0.338																																					.		Atlas-SNP	.											C6orf224,NS,carcinoma,-2,2	AKD1	223	2	0			c.4849+2T>C						PASS	.						108.0	105.0	106.0					6																	109827528		2202	4298	6500	SO:0001630	splice_region_variant	221264	exon36			TATCTTACCTGCT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.4849+1T>C	6.37:g.109827528A>G		131.0	0.0	0		78.0	24.0	0.307692	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Splice_Site	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943658	0.53079	.	.	ENSG00000155085	ENST00000424296;ENST00000470564;ENST00000490722	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0182	0.71605	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AKD1	109934221	1.000000	0.71417	0.997000	0.53966	0.685000	0.39939	8.305000	0.89960	1.995000	0.58328	0.533000	0.62120	.	.	.	none		0.338	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	Intron
OR5H14	403273	hgsc.bcm.edu	37	3	97868959	97868959	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97868959C>A	ENST00000437310.1	+	1	790	c.730C>A	c.(730-732)Cat>Aat	p.H244N	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CTGTGGAGCTCATCTCTTATC	0.418																																					p.H244N		Atlas-SNP	.											.	OR5H14	56	.	0			c.C730A						PASS	.						57.0	55.0	56.0					3																	97868959		2203	4298	6501	SO:0001583	missense	403273	exon1			GGAGCTCATCTCT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.730C>A	3.37:g.97868959C>A	ENSP00000401706:p.His244Asn	181.0	0.0	0		140.0	73.0	0.521429	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.424491	0.43020	.	.	ENSG00000236032	ENST00000437310	T	0.00314	8.14	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.01029	0.0034	H	0.97707	4.06	0.28760	N	0.900936	D	0.89917	1.0	D	0.97110	1.0	T	0.04178	-1.0971	10	0.87932	D	0	.	10.6214	0.45483	0.0:1.0:0.0:0.0	.	244	A6NHG9	O5H14_HUMAN	N	244	ENSP00000401706:H244N	ENSP00000401706:H244N	H	+	1	0	OR5H14	99351649	1.000000	0.71417	0.954000	0.39281	0.342000	0.28953	6.703000	0.74633	1.380000	0.46344	0.195000	0.17529	CAT	.	.	none		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000417302.1_Silent_p.H27H	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		124.0	0.0	0		139.0	104.0	0.748201	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
APOL6	80830	hgsc.bcm.edu	37	22	36054944	36054944	+	Silent	SNP	C	C	T	rs34527373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36054944C>T	ENST00000409652.4	+	3	609	c.333C>T	c.(331-333)acC>acT	p.T111T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	111					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TGCTCTCCACCGCTGGTCAAG	0.572													C|||	106	0.0211661	0.0424	0.013	5008	,	,		17602	0.0		0.0169	False		,,,				2504	0.0245				p.T111T		Atlas-SNP	.											.	APOL6	26	.	0			c.C333T						PASS	.	C		139,4267	98.0+/-136.7	1,137,2065	62.0	59.0	60.0		333	-8.3	0.0	22	dbSNP_126	60	165,8435	77.5+/-140.1	4,157,4139	no	coding-synonymous	APOL6	NM_030641.3		5,294,6204	TT,TC,CC		1.9186,3.1548,2.3374		111/344	36054944	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			CTCCACCGCTGGT	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.333C>T	22.37:g.36054944C>T		67.0	0.0	0		69.0	41.0	0.594203	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			C|0.975;T|0.025	0.025	strong		0.572	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
SIVA1	10572	hgsc.bcm.edu	37	14	105222988	105222988	+	Missense_Mutation	SNP	G	G	A	rs144031294	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105222988G>A	ENST00000329967.6	+	3	463	c.361G>A	c.(361-363)Gtg>Atg	p.V121M	SIVA1_ENST00000347067.5_Missense_Mutation_p.V56M	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	121	Interaction with coxsackievirus B3 VP2.				activation-induced cell death of T cells (GO:0006924)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	CD27 receptor binding (GO:0005175)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3		all_cancers(154;0.14)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.173)		CGTGCGAGCCGTGGATGGGAA	0.647																																					p.V121M		Atlas-SNP	.											.	SIVA1	12	.	0			c.G361A						PASS	.	G	MET/VAL,MET/VAL	0,4406		0,0,2203	117.0	104.0	108.0		361,166	2.9	0.0	14	dbSNP_134	108	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	SIVA1	NM_006427.3,NM_021709.2	21,21	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	possibly-damaging,possibly-damaging	121/176,56/111	105222988	15,12991	2203	4300	6503	SO:0001583	missense	10572	exon3			CGAGCCGTGGATG	U82938	CCDS9992.1, CCDS9993.1	14q32.33	2007-03-19							17712	protein-coding gene	gene with protein product		605567				9177220	Standard	NM_006427		Approved	SIVA, Siva-1, Siva-2, CD27BP	uc001yph.3	O15304		ENST00000329967.6:c.361G>A	14.37:g.105222988G>A	ENSP00000329213:p.Val121Met	134.0	0.0	0		135.0	73.0	0.540741	NM_006427	Q96P98|Q9UPD6	Missense_Mutation	SNP	ENST00000329967.6	37	CCDS9992.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860882	0.32884	0.0	0.001744	ENSG00000184990	ENST00000329967;ENST00000347067;ENST00000553810	.	.	.	4.77	2.9	0.33743	.	1.203960	0.05732	N	0.599742	T	0.56001	0.1956	L	0.56769	1.78	0.09310	N	1	D;D;D	0.67145	0.994;0.996;0.994	P;P;P	0.58130	0.779;0.759;0.833	T	0.38650	-0.9651	9	0.49607	T	0.09	-10.267	9.5779	0.39470	0.1695:0.0:0.8305:0.0	.	121;56;121	B4DTY2;O15304-2;O15304	.;.;SIVA_HUMAN	M	121;56;121	.	ENSP00000329213:V121M	V	+	1	0	SIVA1	104294033	0.011000	0.17503	0.004000	0.12327	0.026000	0.11368	1.844000	0.39269	1.227000	0.43598	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.647	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427	
THNSL1	79896	hgsc.bcm.edu	37	10	25314005	25314005	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:25314005G>A	ENST00000524413.1	+	3	2200	c.1853G>A	c.(1852-1854)tGg>tAg	p.W618*	THNSL1_ENST00000376356.4_Nonsense_Mutation_p.W618*			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	618						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	GTAGCTGACTGGTGCTCTGAG	0.408																																					p.W618X		Atlas-SNP	.											.	THNSL1	70	.	0			c.G1853A						PASS	.						85.0	91.0	89.0					10																	25314005		2203	4300	6503	SO:0001587	stop_gained	79896	exon3			CTGACTGGTGCTC	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1853G>A	10.37:g.25314005G>A	ENSP00000434887:p.Trp618*	149.0	0.0	0		139.0	30.0	0.215827	NM_024838	B3KWL1|D3DRV3|Q5VV21	Nonsense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	G	40	8.166791	0.98686	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	.	.	.	5.94	5.94	0.96194	.	0.062472	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9473	20.3632	0.98871	0.0:0.0:1.0:0.0	.	.	.	.	X	618	.	ENSP00000365534:W618X	W	+	2	0	THNSL1	25354011	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.861000	0.92277	2.826000	0.97356	0.561000	0.74099	TGG	.	.	none		0.408	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
LRRN3	54674	hgsc.bcm.edu	37	7	110764596	110764596	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:110764596A>G	ENST00000422987.3	+	2	2599	c.1768A>G	c.(1768-1770)Aaa>Gaa	p.K590E	IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.K590E|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.K590E|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000452895.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	590	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		AACTGAGTATAAAATTTGTAT	0.348																																					p.K590E		Atlas-SNP	.											.	LRRN3	132	.	0			c.A1768G						PASS	.						44.0	43.0	43.0					7																	110764596		2203	4300	6503	SO:0001583	missense	54674	exon2			GAGTATAAAATTT	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1768A>G	7.37:g.110764596A>G	ENSP00000412417:p.Lys590Glu	62.0	0.0	0		69.0	22.0	0.318841	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	A	0.129	-1.115378	0.01799	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.55052	0.54;0.54;0.54	5.59	4.41	0.53225	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.190873	0.36303	N	0.002673	T	0.25195	0.0612	N	0.10733	0.035	0.38993	D	0.959181	B	0.10296	0.003	B	0.13407	0.009	T	0.16689	-1.0394	10	0.02654	T	1	.	7.5231	0.27639	0.7855:0.1436:0.0709:0.0	.	590	Q9H3W5	LRRN3_HUMAN	E	590	ENSP00000312001:K590E;ENSP00000397312:K590E;ENSP00000412417:K590E	ENSP00000312001:K590E	K	+	1	0	LRRN3	110551832	0.995000	0.38212	0.997000	0.53966	0.964000	0.63967	2.962000	0.49176	1.033000	0.39918	0.529000	0.55759	AAA	.	.	none		0.348	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926522	88926522	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926522C>A	ENST00000303236.3	-	1	572	c.271G>T	c.(271-273)Gaa>Taa	p.E91*	AC062029.1_ENST00000606164.1_RNA|AC062029.1_ENST00000453008.2_RNA|EIF2AK3_ENST00000419748.1_5'Flank	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TCGTCTGGTTCCGGACCCCGA	0.731																																					p.E91X	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.G271T						PASS	.						15.0	18.0	17.0					2																	88926522		2023	4091	6114	SO:0001587	stop_gained	9451	exon1			CTGGTTCCGGACC	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.271G>T	2.37:g.88926522C>A	ENSP00000307235:p.Glu91*	59.0	0.0	0		71.0	24.0	0.338028	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Nonsense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692593	0.88735	.	.	ENSG00000172071	ENST00000303236	.	.	.	4.2	4.2	0.49525	.	0.382598	0.20874	N	0.084102	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-8.9866	12.3586	0.55190	0.0:1.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000307235:E91X	E	-	1	0	EIF2AK3	88707637	0.245000	0.23899	0.013000	0.15412	0.003000	0.03518	3.145000	0.50623	2.032000	0.59987	0.561000	0.74099	GAA	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
MOCS2	4338	hgsc.bcm.edu	37	5	52397199	52397199	+	Missense_Mutation	SNP	G	G	A	rs2233218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:52397199G>A	ENST00000396954.3	-	5	1044	c.367C>T	c.(367-369)Cat>Tat	p.H123Y	MOCS2_ENST00000361377.4_Intron|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000510818.2_3'UTR	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				CCAAGTCTATGGAACACTGCT	0.348													G|||	13	0.00259585	0.0	0.0029	5008	,	,		15837	0.0		0.0109	False		,,,				2504	0.0				p.H123Y		Atlas-SNP	.											.	MOCS2	28	.	0			c.C367T						PASS	.	G	TYR/HIS,	6,4400	11.4+/-27.6	0,6,2197	201.0	200.0	200.0		367,	5.8	1.0	5	dbSNP_98	200	47,8553	30.1+/-81.4	1,45,4254	yes	missense,utr-3	MOCS2	NM_004531.3,NM_176806.2	83,	1,51,6451	AA,AG,GG		0.5465,0.1362,0.4075	probably-damaging,	123/189,	52397199	53,12953	2203	4300	6503	SO:0001583	missense	4338	exon5			GTCTATGGAACAC	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.367C>T	5.37:g.52397199G>A	ENSP00000380157:p.His123Tyr	126.0	0.0	0		148.0	71.0	0.47973	NM_004531		Missense_Mutation	SNP	ENST00000396954.3	37	CCDS3958.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	26.2	4.718212	0.89205	0.001362	0.005465	ENSG00000164172	ENST00000396954;ENST00000527216	T	0.63744	-0.06	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.85496	0.5710	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91373	0.5121	10	0.87932	D	0	-10.3275	20.1184	0.97949	0.0:0.0:1.0:0.0	rs2233218;rs52802686;rs2233218	123	O96007	MOC2B_HUMAN	Y	123	ENSP00000380157:H123Y	ENSP00000380157:H123Y	H	-	1	0	MOCS2	52432956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.715000	0.84713	2.775000	0.95449	0.650000	0.86243	CAT	G|0.995;A|0.005	0.005	strong		0.348	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418	
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114289	27114289	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27114289T>C	ENST00000356950.1	-	1	288	c.289A>G	c.(289-291)Acg>Gcg	p.T97A	MIR3143_ENST00000584253.1_RNA|HIST1H2AH_ENST00000377459.1_5'Flank|HIST1H2BK_ENST00000396891.4_Missense_Mutation_p.T97A			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	97					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						CGCACGGCCGTCTGGATCTCC	0.622																																					p.T97A		Atlas-SNP	.											.	HIST1H2BK	68	.	0			c.A289G						PASS	.						56.0	62.0	60.0					6																	27114289		2203	4294	6497	SO:0001583	missense	85236	exon1			CGGCCGTCTGGAT	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"""Histones / Replication-dependent"""	13954	protein-coding gene	gene with protein product		615045	"""H2B histone family, member T"", ""histone 1, H2bk"""	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.289A>G	6.37:g.27114289T>C	ENSP00000349430:p.Thr97Ala	90.0	0.0	0		105.0	34.0	0.32381	NM_080593	A8K7P7|Q2VPI7	Missense_Mutation	SNP	ENST00000356950.1	37	CCDS4621.1	.	.	.	.	.	.	.	.	.	.	.	26.7	4.762466	0.89932	.	.	ENSG00000197903	ENST00000396891;ENST00000356950	T;T	0.41758	0.99;0.99	4.05	4.05	0.47172	Histone-fold (2);Histone core (1);	0.000000	0.38548	U	0.001653	T	0.61413	0.2345	M	0.92691	3.335	0.46396	D	0.999028	D	0.57899	0.981	D	0.64042	0.921	T	0.71745	-0.4500	10	0.87932	D	0	.	11.5972	0.50981	0.0:0.0:0.0:1.0	.	97	O60814	H2B1K_HUMAN	A	97	ENSP00000380100:T97A;ENSP00000349430:T97A	ENSP00000349430:T97A	T	-	1	0	HIST1H2BK	27222268	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.391000	0.66266	1.783000	0.52377	0.528000	0.53228	ACG	.	.	none		0.622	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593	
CYTH3	9265	hgsc.bcm.edu	37	7	6227341	6227341	+	Silent	SNP	A	A	G	rs41282682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6227341A>G	ENST00000350796.3	-	3	265	c.129T>C	c.(127-129)taT>taC	p.Y43Y		NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	43					establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						CTGCAATTTCATATTTCAGCC	0.408													A|||	48	0.00958466	0.0008	0.0173	5008	,	,		20705	0.0		0.0199	False		,,,				2504	0.0153				p.Y43Y		Atlas-SNP	.											.	CYTH3	44	.	0			c.T129C						PASS	.	A		14,4392	22.3+/-47.3	0,14,2189	157.0	143.0	148.0		129	-4.4	0.8	7	dbSNP_127	148	196,8404	85.8+/-148.2	2,192,4106	no	coding-synonymous	CYTH3	NM_004227.3		2,206,6295	GG,GA,AA		2.2791,0.3177,1.6146		43/400	6227341	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	9265	exon3			AATTTCATATTTC	AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"""Pleckstrin homology (PH) domain containing"""	9504	protein-coding gene	gene with protein product		605081	"""pleckstrin homology, Sec7 and coiled-coil domains 3"""	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.129T>C	7.37:g.6227341A>G		89.0	0.0	0		80.0	58.0	0.725	NM_004227	A4D2N8	Silent	SNP	ENST00000350796.3	37	CCDS5346.1																																																																																			A|0.986;G|0.014	0.014	strong		0.408	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227	
DOCK4	9732	hgsc.bcm.edu	37	7	111503547	111503547	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111503547T>C	ENST00000437633.1	-	23	2610	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	DOCK4_ENST00000428084.1_Missense_Mutation_p.N785S|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	785					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTGGACCAAGTTGGCTACTTC	0.498																																					p.N785S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A2354G						PASS	.						56.0	55.0	55.0					7																	111503547		1957	4132	6089	SO:0001583	missense	9732	exon23			ACCAAGTTGGCTA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2354A>G	7.37:g.111503547T>C	ENSP00000404179:p.Asn785Ser	75.0	0.0	0		81.0	27.0	0.333333	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.27|13.27	2.186733|2.186733	0.38609|0.38609	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250|ENST00000423057;ENST00000445943	T;T|.	0.02812|.	4.15;4.15|.	5.23|5.23	4.07|4.07	0.47477|0.47477	.|.	0.213000|.	0.49305|.	D|.	0.000152|.	T|T	0.60843|0.60843	0.2300|0.2300	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.17465|.	0.013;0.013;0.013;0.022|.	B;B;B;B|.	0.19666|.	0.017;0.017;0.011;0.026|.	T|T	0.57406|0.57406	-0.7817|-0.7817	10|5	0.09843|.	T|.	0.71|.	.|.	11.1557|11.1557	0.48486|0.48486	0.0:0.0722:0.0:0.9278|0.0:0.0722:0.0:0.9278	.|.	785;785;785;785|.	Q149N2;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;DOCK4_HUMAN;.|.	S|A	773;785;785;773;784|237;773	ENSP00000410746:N785S;ENSP00000404179:N785S|.	ENSP00000345432:N773S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111290783|111290783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.861000|0.861000	0.49209|0.49209	4.653000|4.653000	0.61462|0.61462	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	AAC|ACT	.	.	none		0.498	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
KIAA0319	9856	hgsc.bcm.edu	37	6	24576706	24576706	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24576706G>A	ENST00000378214.3	-	10	2148	c.1624C>T	c.(1624-1626)Ccc>Tcc	p.P542S	KIAA0319_ENST00000537886.1_Missense_Mutation_p.P542S|KIAA0319_ENST00000430948.2_Missense_Mutation_p.P497S|KIAA0319_ENST00000535378.1_Missense_Mutation_p.P533S|KIAA0319_ENST00000543707.1_Missense_Mutation_p.P542S	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	542	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						GAGTTTTGGGGCAAAGTTATG	0.498																																					p.P542S		Atlas-SNP	.											.	KIAA0319	117	.	0			c.C1624T						PASS	.						514.0	503.0	507.0					6																	24576706		2203	4300	6503	SO:0001583	missense	9856	exon10			TTTGGGGCAAAGT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1624C>T	6.37:g.24576706G>A	ENSP00000367459:p.Pro542Ser	490.0	0.0	0		359.0	65.0	0.181058	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333242	0.81801	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	3.9	3.9	0.45041	PKD/Chitinase domain (1);PKD/REJ-like protein (1);PKD domain (2);	0.000000	0.64402	D	0.000001	T	0.82268	0.5000	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.86674	0.1912	10	0.72032	D	0.01	-15.2462	16.4334	0.83861	0.0:0.0:1.0:0.0	.	542;533;542	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	S	542;533;497;542;542	ENSP00000439700:P542S;ENSP00000442403:P533S;ENSP00000401086:P497S;ENSP00000367459:P542S;ENSP00000437656:P542S	ENSP00000367459:P542S	P	-	1	0	KIAA0319	24684685	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	6.424000	0.73366	2.153000	0.67306	0.655000	0.94253	CCC	.	.	none		0.498	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279944	39279944	+	Missense_Mutation	SNP	C	C	G	rs536638484		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39279944C>G	ENST00000394014.1	-	1	475	c.431G>C	c.(430-432)aGc>aCc	p.S144T		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	144	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gatgcagcagctggggcggca	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		15496	0.001		0.0	False		,,,				2504	0.0				p.S144T		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.G431C						PASS	.						18.0	24.0	22.0					17																	39279944		2195	4276	6471	SO:0001583	missense	83755	exon1			CAGCAGCTGGGGC	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.431G>C	17.37:g.39279944C>G	ENSP00000377582:p.Ser144Thr	60.0	0.0	0		55.0	16.0	0.290909	NM_031854	A3KMC5|Q495I0	Missense_Mutation	SNP	ENST00000394014.1	37	CCDS32649.1	.	.	.	.	.	.	.	.	.	.	.	10.81	1.455027	0.26161	.	.	ENSG00000213416	ENST00000394014	T	0.01484	4.84	5.33	-2.99	0.05497	.	3.044690	0.01738	N	0.029234	T	0.02083	0.0065	L	0.39085	1.19	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.48758	-0.9007	10	0.21540	T	0.41	.	9.6148	0.39685	0.0998:0.2179:0.611:0.0713	.	144	Q9BQ66	KR412_HUMAN	T	144	ENSP00000377582:S144T	ENSP00000377582:S144T	S	-	2	0	KRTAP4-12	36533470	0.009000	0.17119	0.062000	0.19696	0.021000	0.10359	-0.260000	0.08708	-0.227000	0.09884	0.561000	0.74099	AGC	.	.	none		0.672	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
C6	729	hgsc.bcm.edu	37	5	41181578	41181578	+	Silent	SNP	T	T	A	rs61734263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41181578T>A	ENST00000263413.3	-	7	1074	c.810A>T	c.(808-810)tcA>tcT	p.S270S	C6_ENST00000337836.5_Silent_p.S270S|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	270	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GACTTGAGAATGAGCCTTGTT	0.378													T|||	23	0.00459265	0.0	0.0014	5008	,	,		15500	0.0		0.0129	False		,,,				2504	0.0092				p.S270S		Atlas-SNP	.											.	C6	197	.	0			c.A810T						PASS	.	T	,	11,4395	16.8+/-37.8	0,11,2192	81.0	80.0	80.0		810,810	-1.8	0.0	5	dbSNP_129	80	158,8442	75.7+/-138.4	2,154,4144	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	2,165,6336	AA,AT,TT		1.8372,0.2497,1.2994	,	270/935,270/935	41181578	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	729	exon7			TGAGAATGAGCCT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.810A>T	5.37:g.41181578T>A		146.0	0.0	0		154.0	94.0	0.61039	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			T|0.980;A|0.020	0.020	strong		0.378	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
CDCP2	200008	hgsc.bcm.edu	37	1	54605769	54605769	+	Silent	SNP	C	C	T	rs372034165		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:54605769C>T	ENST00000371330.1	-	4	1621	c.774G>A	c.(772-774)caG>caA	p.Q258Q	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_5'Flank	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	258	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						TGTATACCTCCTGGCATTCTC	0.612																																					p.Q258Q		Atlas-SNP	.											.	CDCP2	52	.	0			c.G774A						PASS	.	C		0,4218		0,0,2109	39.0	31.0	34.0		774	4.0	1.0	1		34	1,8315		0,1,4157	no	coding-synonymous	CDCP2	NM_201546.2		0,1,6266	TT,TC,CC		0.012,0.0,0.0080		258/450	54605769	1,12533	2109	4158	6267	SO:0001819	synonymous_variant	200008	exon4			TACCTCCTGGCAT		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.774G>A	1.37:g.54605769C>T		177.0	0.0	0		138.0	68.0	0.492754	NM_201546	Q6ZWJ3	Silent	SNP	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.612	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
LENG8	114823	hgsc.bcm.edu	37	19	54967408	54967408	+	Missense_Mutation	SNP	C	C	T	rs75472495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54967408C>T	ENST00000326764.5	+	9	1767	c.1288C>T	c.(1288-1290)Cgc>Tgc	p.R430C	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	393										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GTCCCCGACGCGCCACTTCCG	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		16004	0.0		0.003	False		,,,				2504	0.0				p.R430C		Atlas-SNP	.											LENG8,colon,carcinoma,-1,1	LENG8	73	1	0			c.C1288T						PASS	.	C	CYS/ARG	2,4404		0,2,2201	96.0	114.0	107.0		1288	3.7	0.6	19	dbSNP_131	107	26,8566		0,26,4270	yes	missense	LENG8	NM_052925.2	180	0,28,6471	TT,TC,CC		0.3026,0.0454,0.2154	probably-damaging	430/801	54967408	28,12970	2203	4296	6499	SO:0001583	missense	114823	exon9			CCGACGCGCCACT	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1288C>T	19.37:g.54967408C>T	ENSP00000318374:p.Arg430Cys	140.0	0.0	0		128.0	68.0	0.53125	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	C	17.47	3.397139	0.62177	4.54E-4	0.003026	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.37058	1.26;1.25;1.22	4.73	3.68	0.42216	.	0.063133	0.64402	D	0.000016	T	0.41558	0.1164	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.72338	0.855;0.977	T	0.18241	-1.0343	10	0.37606	T	0.19	-12.3824	10.6314	0.45538	0.3457:0.6543:0.0:0.0	.	430;393	Q96PV6-2;F8W9Q9	.;.	C	430;393;393;430	ENSP00000318374:R430C;ENSP00000365709:R393C;ENSP00000388053:R430C	ENSP00000301196:R393C	R	+	1	0	LENG8	59659220	0.987000	0.35691	0.550000	0.28217	0.537000	0.34900	2.804000	0.47931	1.111000	0.41721	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.617	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
MUC2	4583	hgsc.bcm.edu	37	11	1092843	1092843	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092843C>G	ENST00000441003.2	+	30	4689	c.4662C>G	c.(4660-4662)ggC>ggG	p.G1554G	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.G1555G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CACCCACCGGCACACAGACCC	0.632																																					p.G1554G		Atlas-SNP	.											MUC2_ENST00000441003,trunk,malignant_melanoma,+1,2	MUC2	614	2	0			c.C4662G						PASS	.						88.0	119.0	108.0					11																	1092843		1875	3464	5339	SO:0001819	synonymous_variant	4583	exon30			CACCGGCACACAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4662C>G	11.37:g.1092843C>G		48.0	0.0	0		67.0	5.0	0.0746269	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CFAP46	54777	hgsc.bcm.edu	37	10	134649709	134649709	+	Missense_Mutation	SNP	C	C	T	rs76581191	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134649709C>T	ENST00000368586.5	-	46	6650	c.6550G>A	c.(6550-6552)Ggc>Agc	p.G2184S	TTC40_ENST00000263170.5_Missense_Mutation_p.G345S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TAGGCAGCGCCGTACAGACGG	0.647													c|||	33	0.00658946	0.0015	0.0043	5008	,	,		11914	0.0		0.0129	False		,,,				2504	0.0153				p.G2184S		Atlas-SNP	.											TTC40,NS,carcinoma,0,2	TTC40	100	2	0			c.G6550A						PASS	.		SER/GLY	11,4391	16.8+/-37.8	0,11,2190	76.0	58.0	64.0		1486	0.1	0.0	10	dbSNP_131	64	145,8453	70.7+/-133.2	0,145,4154	yes	missense	C10orf92	NM_001200049.1	56	0,156,6344	TT,TC,CC		1.6864,0.2499,1.2	benign	496/1028	134649709	156,12844	2201	4299	6500	SO:0001583	missense	54777	exon46			CAGCGCCGTACAG																												ENST00000368586.5:c.6550G>A	10.37:g.134649709C>T	ENSP00000357575:p.Gly2184Ser	44.0	0.0	0		42.0	20.0	0.47619	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	4.026	0.002278	0.07819	0.002499	0.016864	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.25912	2.01;1.77	4.17	0.0804	0.14420	.	0.210433	0.27535	N	0.018933	T	0.06005	0.0156	N	0.25647	0.755	0.09310	N	0.999999	B	0.24132	0.098	B	0.15870	0.014	T	0.11966	-1.0566	10	0.40728	T	0.16	.	3.0641	0.06209	0.1917:0.4861:0.0:0.3222	.	345	Q8IYW2	CJ092_HUMAN	S	2184;345	ENSP00000357575:G2184S;ENSP00000263170:G345S	ENSP00000263170:G345S	G	-	1	0	C10orf93	134499699	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.167000	0.09940	0.040000	0.15660	-0.251000	0.11542	GGC	C|0.990;T|0.010	0.010	strong		0.647	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
MUC4	4585	hgsc.bcm.edu	37	3	195515422	195515422	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515422G>T	ENST00000463781.3	-	2	3488	c.3029C>A	c.(3028-3030)cCt>cAt	p.P1010H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1010H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	445	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGGTGACAGGAAGAGGGGT	0.577																																					p.P1010H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3029A						PASS	.						63.0	35.0	44.0					3																	195515422		692	1591	2283	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3029C>A	3.37:g.195515422G>T	ENSP00000417498:p.Pro1010His	65.0	0.0	0		74.0	23.0	0.310811	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.962	0.361410	0.11296	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.55588	0.51;0.53	1.24	-2.49	0.06403	.	.	.	.	.	T	0.29749	0.0743	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.12889	-1.0530	8	.	.	.	.	5.6108	0.17404	0.0:0.3425:0.467:0.1905	.	1010	E7ESK3	.	H	1010	ENSP00000417498:P1010H;ENSP00000420243:P1010H	.	P	-	2	0	MUC4	196999817	.	.	0.000000	0.03702	0.077000	0.17291	.	.	-1.667000	0.01473	0.064000	0.15345	CCT	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ARVCF	421	hgsc.bcm.edu	37	22	19965563	19965563	+	Missense_Mutation	SNP	C	C	T	rs16982871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:19965563C>T	ENST00000263207.3	-	8	1907	c.1616G>A	c.(1615-1617)cGa>cAa	p.R539Q	ARVCF_ENST00000406522.1_Missense_Mutation_p.R476Q|ARVCF_ENST00000344269.3_Missense_Mutation_p.R476Q|ARVCF_ENST00000401994.1_Missense_Mutation_p.R476Q|ARVCF_ENST00000406259.1_Missense_Mutation_p.R539Q	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	539			R -> Q (in dbSNP:rs16982871).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CTCCCGGAGTCGCCGCCGGGC	0.667													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18613	0.0		0.003	False		,,,				2504	0.0061				p.R539Q		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1616A						PASS	.	C	GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	49.0	45.0	47.0		1616	4.0	1.0	22	dbSNP_123	47	79,8517	46.7+/-105.8	0,79,4219	yes	missense	ARVCF	NM_001670.2	43	0,88,6413	TT,TC,CC		0.919,0.2043,0.6768	probably-damaging	539/963	19965563	88,12914	2203	4298	6501	SO:0001583	missense	421	exon8			CGGAGTCGCCGCC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1616G>A	22.37:g.19965563C>T	ENSP00000263207:p.Arg539Gln	104.0	0.0	0		95.0	36.0	0.378947	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	30	5.053953	0.93793	0.002043	0.00919	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	L	0.37507	1.11	0.58432	D	0.999999	D;D	0.89917	0.995;1.0	P;D	0.79108	0.877;0.992	T	0.73282	-0.4032	9	.	.	.	-9.945	17.0615	0.86548	0.0:1.0:0.0:0.0	rs16982871;rs16982871	539;61	O00192;E7EV58	ARVC_HUMAN;.	Q	539;476;476;476;539	ENSP00000263207:R539Q;ENSP00000342042:R476Q;ENSP00000384341:R476Q;ENSP00000384732:R476Q;ENSP00000385444:R539Q	.	R	-	2	0	ARVCF	18345563	0.394000	0.25246	0.973000	0.42090	0.993000	0.82548	1.722000	0.38042	2.541000	0.85698	0.655000	0.94253	CGA	C|0.995;T|0.005	0.005	strong		0.667	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
C14orf159	80017	hgsc.bcm.edu	37	14	91633706	91633706	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91633706G>A	ENST00000523771.1	+	4	844	c.241G>A	c.(241-243)Gct>Act	p.A81T	C14orf159_ENST00000518665.2_Missense_Mutation_p.A81T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A81T|C14orf159_ENST00000519019.1_Missense_Mutation_p.A81T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A81T|C14orf159_ENST00000298858.4_Missense_Mutation_p.A81T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A81T|C14orf159_ENST00000517877.1_Missense_Mutation_p.A81T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A81T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A81T|C14orf159_ENST00000256324.10_Missense_Mutation_p.A81T|C14orf159_ENST00000521077.2_Missense_Mutation_p.A81T|C14orf159_ENST00000428926.2_Missense_Mutation_p.A81T|C14orf159_ENST00000525393.2_Intron			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	81						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCCTCAAGGTGCTATCTCAGA	0.547																																					p.A81T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G241A						PASS	.						103.0	99.0	100.0					14																	91633706		2203	4300	6503	SO:0001583	missense	80017	exon6			CAAGGTGCTATCT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.241G>A	14.37:g.91633706G>A	ENSP00000429655:p.Ala81Thr	107.0	0.0	0		106.0	20.0	0.188679	NM_001102366	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773383	0.49786	.	.	ENSG00000133943	ENST00000521334;ENST00000522837;ENST00000518871;ENST00000298858;ENST00000520328;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000523879;ENST00000521077;ENST00000518665;ENST00000518868;ENST00000519019;ENST00000523816;ENST00000517518;ENST00000428926;ENST00000523894;ENST00000522322;ENST00000523771;ENST00000521064;ENST00000412671;ENST00000517877	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	1.52;0.43;1.52;0.77;1.52;1.52;1.52;1.52;0.36;1.52;0.77;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;0.78	5.09	2.29	0.28610	.	0.539348	0.18409	N	0.142104	T	0.39835	0.1093	L	0.52126	1.63	0.09310	N	1	P;B;B;B;B;B	0.42203	0.773;0.036;0.036;0.06;0.06;0.06	B;B;B;B;B;B	0.38428	0.273;0.012;0.012;0.028;0.028;0.028	T	0.18461	-1.0336	10	0.17832	T	0.49	.	7.2233	0.26002	0.3591:0.0:0.6409:0.0	.	81;81;81;81;81;81	Q7Z3D6-6;Q7Z3D6;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	.;CN159_HUMAN;.;.;.;.	T	81	ENSP00000430022:A81T;ENSP00000427971:A81T;ENSP00000429189:A81T;ENSP00000298858:A81T;ENSP00000429453:A81T;ENSP00000256324:A81T;ENSP00000430666:A81T;ENSP00000428296:A81T;ENSP00000428122:A81T;ENSP00000430137:A81T;ENSP00000429098:A81T;ENSP00000428263:A81T;ENSP00000430318:A81T;ENSP00000428974:A81T;ENSP00000428652:A81T;ENSP00000404343:A81T;ENSP00000429459:A81T;ENSP00000427953:A81T;ENSP00000429655:A81T;ENSP00000429392:A81T;ENSP00000404196:A81T;ENSP00000429949:A81T	ENSP00000256324:A81T	A	+	1	0	C14orf159	90703459	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.029000	0.12329	0.192000	0.20272	0.561000	0.74099	GCT	.	.	none		0.547	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
GCSAM	257144	hgsc.bcm.edu	37	3	111844089	111844089	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111844089G>T	ENST00000308910.4	-	5	387	c.203C>A	c.(202-204)tCa>tAa	p.S68*	GCSAM_ENST00000484193.1_Nonsense_Mutation_p.S70*|C3orf52_ENST00000467942.2_Intron	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	68					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										GGGAGTAGATGACATTCTTTC	0.388																																					p.S70X		Atlas-SNP	.											.	.	.	.	0			c.C209A						PASS	.						117.0	117.0	117.0					3																	111844089		2203	4300	6503	SO:0001587	stop_gained	257144	exon5			GTAGATGACATTC	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"""human germinal center-associated lymphoma"""	607792	"""germinal center expressed transcript 2"""	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.203C>A	3.37:g.111844089G>T	ENSP00000309487:p.Ser68*	60.0	0.0	0		41.0	8.0	0.195122	NM_001190259	C9JD17|C9JUG6	Nonsense_Mutation	SNP	ENST00000308910.4	37	CCDS2964.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.050229	0.55218	.	.	ENSG00000174500	ENST00000308910;ENST00000484193;ENST00000460387;ENST00000488580;ENST00000487901	.	.	.	4.23	4.23	0.50019	.	0.783537	0.10863	N	0.625847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.8044	12.4209	0.55520	0.0:0.0:1.0:0.0	.	.	.	.	X	68;70;53;51;51	.	ENSP00000309487:S68X	S	-	2	0	GCET2	113326779	0.073000	0.21202	0.007000	0.13788	0.040000	0.13550	3.817000	0.55668	2.656000	0.90262	0.561000	0.74099	TCA	.	.	none		0.388	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	
ZNF883	169834	hgsc.bcm.edu	37	9	115760345	115760345	+	lincRNA	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115760345T>C	ENST00000427548.1	-	0	1468							P0CG24	ZN883_HUMAN	zinc finger protein 883						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AAGGTTTCTCTCCAGTATGTA	0.353																																					p.G65G		Atlas-SNP	.											.	.	.	.	0			c.A195G						PASS	.						60.0	67.0	64.0					9																	115760345		2192	4295	6487			169834	exon5			TTTCTCTCCAGTA	AK095843		9q32	2010-07-23			ENSG00000228623	ENSG00000228623		"""Zinc fingers, C2H2-type"""	27271	protein-coding gene	gene with protein product							Standard	NM_001101338		Approved		uc011lwy.2	P0CG24	OTTHUMG00000020514		9.37:g.115760345T>C		80.0	0.0	0		53.0	9.0	0.169811	NM_001101338		Silent	SNP	ENST00000427548.1	37																																																																																				.	.	none		0.353	ZNF883-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000053704.1	NM_001101338	
WDR90	197335	hgsc.bcm.edu	37	16	708308	708308	+	Silent	SNP	G	G	A	rs369151964		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:708308G>A	ENST00000293879.4	+	22	2730	c.2730G>A	c.(2728-2730)gtG>gtA	p.V910V	WDR90_ENST00000549091.1_Silent_p.V910V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	910										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				ACAGAGTCGTGGTGCTGGATG	0.677																																					p.V910V		Atlas-SNP	.											.	WDR90	107	.	0			c.G2730A						PASS	.						57.0	63.0	61.0					16																	708308		2141	4248	6389	SO:0001819	synonymous_variant	197335	exon22			AGTCGTGGTGCTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2730G>A	16.37:g.708308G>A		121.0	0.0	0		70.0	27.0	0.385714	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	alt		0.677	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
LCT	3938	hgsc.bcm.edu	37	2	136547204	136547204	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136547204C>T	ENST00000264162.2	-	16	5510	c.5500G>A	c.(5500-5502)Gtg>Atg	p.V1834M		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1834	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCGGACCACAGAGGCGTAG	0.552																																					p.V1834M		Atlas-SNP	.											.	LCT	309	.	0			c.G5500A						PASS	.						102.0	96.0	98.0					2																	136547204		2203	4300	6503	SO:0001583	missense	3938	exon16			GGACCACAGAGGC	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.5500G>A	2.37:g.136547204C>T	ENSP00000264162:p.Val1834Met	156.0	0.0	0		101.0	32.0	0.316832	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469955	0.43839	.	.	ENSG00000115850	ENST00000264162	T	0.37752	1.18	5.74	-4.63	0.03359	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.267610	0.39687	N	0.001286	T	0.25344	0.0616	L	0.33792	1.035	0.09310	N	1	B	0.24092	0.097	B	0.32624	0.149	T	0.29366	-1.0014	10	0.87932	D	0	-3.5549	10.4645	0.44600	0.0:0.1835:0.0967:0.7198	.	1834	P09848	LPH_HUMAN	M	1834	ENSP00000264162:V1834M	ENSP00000264162:V1834M	V	-	1	0	LCT	136263674	0.000000	0.05858	0.001000	0.08648	0.814000	0.46013	-0.379000	0.07437	-0.868000	0.04058	0.563000	0.77884	GTG	.	.	none		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
HOXA11	3207	hgsc.bcm.edu	37	7	27222437	27222437	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:27222437T>C	ENST00000006015.3	-	2	991	c.920A>G	c.(919-921)tAc>tGc	p.Y307C	HOXA11-AS_ENST00000520395.1_RNA|HOXA10_ENST00000396344.4_5'Flank|RP1-170O19.20_ENST00000470747.4_5'Flank|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000522863.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	307					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						ATTTGCTGAGTAGTACTGTAA	0.443			T	NUP98	CML																																p.Y307C		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.A920G						PASS	.						70.0	70.0	70.0					7																	27222437		2203	4300	6503	SO:0001583	missense	3207	exon2			GCTGAGTAGTACT		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.920A>G	7.37:g.27222437T>C	ENSP00000006015:p.Tyr307Cys	68.0	0.0	0		63.0	27.0	0.428571	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	37	CCDS5411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.23|17.23	3.336101|3.336101	0.60963|0.60963	.|.	.|.	ENSG00000005073|ENSG00000005073	ENST00000517402|ENST00000006015	.|D	.|0.90844	.|-2.74	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.92303|0.92303	0.7558|0.7558	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.76071	.|0.987	D|D	0.93496|0.93496	0.6840|0.6840	5|10	.|0.87932	.|D	.|0	.|.	15.9527|15.9527	0.79855|0.79855	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|307	.|P31270	.|HXA11_HUMAN	A|C	277|307	.|ENSP00000006015:Y307C	.|ENSP00000006015:Y307C	T|Y	-|-	1|2	0|0	HOXA11|HOXA11	27188962|27188962	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.017000|5.017000	0.64047|0.64047	2.173000|2.173000	0.68751|0.68751	0.533000|0.533000	0.62120|0.62120	ACT|TAC	.	.	none		0.443	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1254064	1254064	+	Missense_Mutation	SNP	C	C	T	rs145376050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1254064C>T	ENST00000348261.5	+	10	2305	c.2057C>T	c.(2056-2058)cCc>cTc	p.P686L	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.P686L|CACNA1H_ENST00000565831.1_Missense_Mutation_p.P686L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	686					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGCCCCCTGCCCAGCCCCCCA	0.701													C|||	7	0.00139776	0.0	0.0014	5008	,	,		14466	0.0		0.006	False		,,,				2504	0.0				p.P686L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2057T						PASS	.	C	LEU/PRO,LEU/PRO	1,3833		0,1,1916	8.0	10.0	9.0		2057,2057	4.1	1.0	16	dbSNP_134	9	9,8195		0,9,4093	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	98,98	0,10,6009	TT,TC,CC		0.1097,0.0261,0.0831	probably-damaging,probably-damaging	686/2348,686/2354	1254064	10,12028	1917	4102	6019	SO:0001583	missense	8912	exon10			CCCTGCCCAGCCC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2057C>T	16.37:g.1254064C>T	ENSP00000334198:p.Pro686Leu	70.0	0.0	0		73.0	13.0	0.178082	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	15.89	2.965415	0.53507	2.61E-4	0.001097	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96396	-4.0;-3.95	4.05	4.05	0.47172	.	0.785431	0.10696	U	0.644627	D	0.95526	0.8546	L	0.48642	1.525	0.42385	D	0.992503	D;D	0.53462	0.96;0.958	P;P	0.49252	0.574;0.604	D	0.93067	0.6479	10	0.30854	T	0.27	.	15.3789	0.74637	0.0:1.0:0.0:0.0	.	686;686	O95180-2;O95180	.;CAC1H_HUMAN	L	686	ENSP00000334198:P686L;ENSP00000351401:P686L	ENSP00000334198:P686L	P	+	2	0	CACNA1H	1194065	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.108000	0.50337	2.114000	0.64651	0.561000	0.74099	CCC	C|0.998;T|0.002	0.002	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ZNF469	84627	hgsc.bcm.edu	37	16	88494604	88494604	+	Silent	SNP	C	C	T	rs555256402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88494604C>T	ENST00000437464.1	+	1	726	c.726C>T	c.(724-726)agC>agT	p.S242S	ZNF469_ENST00000565624.1_Silent_p.S242S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	242	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CTGAGAATAGCTTCCCAGGTG	0.677													C|||	4	0.000798722	0.0	0.0	5008	,	,		11142	0.0		0.002	False		,,,				2504	0.002				p.S242S		Atlas-SNP	.											.	ZNF469	121	.	0			c.C726T						PASS	.						8.0	11.0	10.0					16																	88494604		688	1589	2277	SO:0001819	synonymous_variant	84627	exon1			GAATAGCTTCCCA	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.726C>T	16.37:g.88494604C>T		113.0	0.0	0		100.0	64.0	0.64	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			.	.	none		0.677	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
RTN3	10313	hgsc.bcm.edu	37	11	63486204	63486204	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63486204C>T	ENST00000377819.5	+	3	384	c.230C>T	c.(229-231)cCa>cTa	p.P77L	RTN3_ENST00000354497.4_Intron|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.P58L|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000540798.1_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	77					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TCTGATGAGCCATCTTCAGAA	0.378																																					p.P77L		Atlas-SNP	.											.	RTN3	104	.	0			c.C230T						PASS	.						44.0	42.0	43.0					11																	63486204		2201	4298	6499	SO:0001583	missense	10313	exon3			ATGAGCCATCTTC	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.230C>T	11.37:g.63486204C>T	ENSP00000367050:p.Pro77Leu	67.0	0.0	0		42.0	12.0	0.285714	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231150	0.39399	.	.	ENSG00000133318	ENST00000377819;ENST00000339997	T;T	0.27104	1.82;1.69	5.84	3.81	0.43845	.	1.261160	0.05469	N	0.552739	T	0.22627	0.0546	L	0.27053	0.805	0.80722	D	1	B;P	0.36535	0.421;0.557	B;B	0.36418	0.04;0.224	T	0.03473	-1.1033	10	0.87932	D	0	-9.0E-4	10.0371	0.42135	0.1446:0.6966:0.1589:0.0	.	77;58	O95197;O95197-2	RTN3_HUMAN;.	L	77;58	ENSP00000367050:P77L;ENSP00000344106:P58L	ENSP00000344106:P58L	P	+	2	0	RTN3	63242780	0.997000	0.39634	1.000000	0.80357	0.466000	0.32739	1.436000	0.34980	1.412000	0.46977	0.591000	0.81541	CCA	.	.	none		0.378	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054	
DEFB110	245913	hgsc.bcm.edu	37	6	49986788	49986788	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49986788T>A	ENST00000371148.2	-	2	151	c.106A>T	c.(106-108)Aga>Tga	p.R36*	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	36					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					TTACCTATTCTGCACTCTCTC	0.393																																					p.R36X		Atlas-SNP	.											.	DEFB110	5	.	0			c.A106T						PASS	.						176.0	158.0	164.0					6																	49986788		2203	4300	6503	SO:0001587	stop_gained	245913	exon2			CTATTCTGCACTC	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.106A>T	6.37:g.49986788T>A	ENSP00000360190:p.Arg36*	181.0	0.0	0		168.0	40.0	0.238095	NM_001037497	Q30KR0	Nonsense_Mutation	SNP	ENST00000371148.2	37	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	9.497	1.102324	0.20632	.	.	ENSG00000203970	ENST00000371148	.	.	.	5.03	1.22	0.21188	.	1.271720	0.05234	N	0.510955	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.0123	3.4489	0.07491	0.167:0.1849:0.0:0.6482	.	.	.	.	X	36	.	.	R	-	1	2	DEFB110	50094747	0.848000	0.29623	0.483000	0.27378	0.035000	0.12851	1.146000	0.31589	0.390000	0.25115	-0.333000	0.08304	AGA	.	.	none		0.393	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
FSCB	84075	hgsc.bcm.edu	37	14	44975349	44975349	+	Missense_Mutation	SNP	G	G	A	rs139581441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44975349G>A	ENST00000340446.4	-	1	1133	c.842C>T	c.(841-843)gCg>gTg	p.A281V	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	281						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TCTGGGCTCCGCTTTAGCAGT	0.483													G|||	5	0.000998403	0.003	0.0	5008	,	,		16874	0.0		0.001	False		,,,				2504	0.0				p.A281V		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.C842T						PASS	.	G	VAL/ALA	11,4395	17.9+/-39.9	0,11,2192	55.0	57.0	56.0		842	-7.7	0.0	14	dbSNP_134	56	30,8570	20.4+/-63.3	1,28,4271	yes	missense	FSCB	NM_032135.3	64	1,39,6463	AA,AG,GG		0.3488,0.2497,0.3152	benign	281/826	44975349	41,12965	2203	4300	6503	SO:0001583	missense	84075	exon1			GGCTCCGCTTTAG	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.842C>T	14.37:g.44975349G>A	ENSP00000344579:p.Ala281Val	109.0	0.0	0		89.0	37.0	0.41573	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.452098	0.01080	0.002497	0.003488	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.25414	1.8	3.86	-7.73	0.01245	.	.	.	.	.	T	0.11623	0.0283	L	0.29908	0.895	0.09310	N	1	B	0.28971	0.229	B	0.15870	0.014	T	0.12066	-1.0562	9	0.18710	T	0.47	1.4119	6.3551	0.21397	0.1309:0.2257:0.5317:0.1117	.	281	Q5H9T9	FSCB_HUMAN	V	281	ENSP00000344579:A281V	ENSP00000344579:A281V	A	-	2	0	FSCB	44045099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.261000	0.02855	-2.588000	0.00458	-1.224000	0.01588	GCG	G|0.997;A|0.003	0.003	strong		0.483	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
ANO8	57719	hgsc.bcm.edu	37	19	17439450	17439450	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17439450C>T	ENST00000159087.4	-	13	1905	c.1747G>A	c.(1747-1749)Gag>Aag	p.E583K		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	583	Glu-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						tcctcgtcctcctcctTGCCC	0.741																																					p.E583K		Atlas-SNP	.											.	ANO8	67	.	0			c.G1747A						PASS	.						7.0	6.0	6.0					19																	17439450		2003	3931	5934	SO:0001583	missense	57719	exon13			CGTCCTCCTCCTT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.1747G>A	19.37:g.17439450C>T	ENSP00000159087:p.Glu583Lys	25.0	0.0	0		22.0	4.0	0.181818	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027094	0.54683	.	.	ENSG00000074855	ENST00000159087	T	0.61859	0.07	5.3	5.3	0.74995	.	0.247398	0.27836	N	0.017658	T	0.46112	0.1376	N	0.08118	0	0.38121	D	0.937857	P	0.37914	0.611	P	0.45998	0.5	T	0.52200	-0.8607	10	0.31617	T	0.26	.	14.4449	0.67342	0.0:1.0:0.0:0.0	.	583	Q9HCE9	ANO8_HUMAN	K	583	ENSP00000159087:E583K	ENSP00000159087:E583K	E	-	1	0	ANO8	17300450	0.150000	0.22732	0.996000	0.52242	0.352000	0.29268	0.878000	0.28126	2.489000	0.83994	0.484000	0.47621	GAG	.	.	none		0.741	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394421	103394421	+	RNA	SNP	T	T	C	rs111294175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103394421T>C	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		GTCCTGTCTTTTGGCTTGTCT	0.393													T|||	3	0.000599042	0.0	0.0	5008	,	,		21250	0.0		0.002	False		,,,				2504	0.001				p.K2876E		Atlas-SNP	.											.	.	.	.	0			c.A8626G						PASS	.	T	GLU/LYS	1,1383		0,1,691	142.0	101.0	113.0		8626	-4.6	0.0	13	dbSNP_132	113	12,3168		0,12,1578	yes	missense	CCDC168	NM_001146197.1	56	0,13,2269	CC,CT,TT		0.3774,0.0723,0.2848		2876/7082	103394421	13,4551	692	1590	2282			643677	exon4			TGTCTTTTGGCTT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394421T>C		202.0	0.0	0		191.0	96.0	0.502618	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.998;C|0.002	0.002	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
GUCY2D	3000	hgsc.bcm.edu	37	17	7909890	7909890	+	Silent	SNP	C	C	T	rs61749678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7909890C>T	ENST00000254854.4	+	4	1386	c.1236C>T	c.(1234-1236)gaC>gaT	p.D412D		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	412					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				CGGCGGGAGACCGGCTTTTTG	0.677													C|||	2	0.000399361	0.0	0.0	5008	,	,		13052	0.0		0.002	False		,,,				2504	0.0				p.D412D		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C1236T						PASS	.	C		0,4406		0,0,2203	30.0	29.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1236	2.0	0.2	17	dbSNP_129	29	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous	GUCY2D	NM_000180.3		0,9,6494	TT,TC,CC		0.1047,0.0,0.0692		412/1104	7909890	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon4			GGGAGACCGGCTT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1236C>T	17.37:g.7909890C>T		91.0	0.0	0		79.0	37.0	0.468354	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
PSG8	440533	hgsc.bcm.edu	37	19	43259169	43259169	+	Missense_Mutation	SNP	C	C	T	rs140722778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43259169C>T	ENST00000306511.4	-	4	1056	c.959G>A	c.(958-960)cGc>cAc	p.R320H	PSG8_ENST00000600709.1_Intron|PSG8_ENST00000406636.3_Missense_Mutation_p.R198H|PSG8_ENST00000404209.4_Missense_Mutation_p.R320H|PSG8_ENST00000401467.2_Missense_Mutation_p.R227H	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	320	Ig-like C2-type 2.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				TGGGTAACTGCGGATGCCACC	0.488													.|||	4	0.000798722	0.0015	0.0029	5008	,	,		21450	0.0		0.0	False		,,,				2504	0.0				p.R320H		Atlas-SNP	.											PSG8_ENST00000404209,NS,carcinoma,0,5	PSG8	101	5	0			c.G959A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	8,4398		0,8,2195	180.0	181.0	181.0		959,593,959	-2.8	0.0	19	dbSNP_134	181	0,8598		0,0,4299	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	29,29,29	0,8,6494	TT,TC,CC		0.0,0.1816,0.0615	benign,benign,benign	320/420,198/298,320/427	43259169	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon4			TAACTGCGGATGC	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.959G>A	19.37:g.43259169C>T	ENSP00000305005:p.Arg320His	55.0	0.0	0		28.0	15.0	0.535714	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	5	0.008741258741258742	1	0.0013192612137203166	N	0.102	-1.150122	0.01700	0.001816	0.0	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000426252;ENST00000407488;ENST00000306511	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	1.38	-2.76	0.05896	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08626	0.0214	L	0.59967	1.855	0.09310	N	1	B;B;B;B;B;B	0.21606	0.029;0.058;0.004;0.005;0.005;0.006	B;B;B;B;B;B	0.27887	0.021;0.084;0.005;0.042;0.005;0.009	T	0.24154	-1.0168	9	0.40728	T	0.16	.	3.1318	0.06425	0.1899:0.3611:0.0:0.4489	.	198;227;320;227;320;320	Q9UQ74-2;B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;.;PSG8_HUMAN;.;.;.	H	320;198;227;132;227;320	ENSP00000385869:R320H;ENSP00000385081:R198H;ENSP00000386090:R227H;ENSP00000305005:R320H	ENSP00000305005:R320H	R	-	2	0	PSG8	47951009	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.062000	0.00623	-3.472000	0.00157	-3.315000	0.00045	CGC	C|0.998;T|0.002	0.002	strong		0.488	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
ACAD8	27034	hgsc.bcm.edu	37	11	134128923	134128923	+	Missense_Mutation	SNP	C	C	G	rs113488591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:134128923C>G	ENST00000281182.4	+	5	618	c.512C>G	c.(511-513)tCt>tGt	p.S171C	ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Missense_Mutation_p.S94C|ACAD8_ENST00000374752.4_Missense_Mutation_p.S44C|ACAD8_ENST00000543332.1_Missense_Mutation_p.S73C	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	171					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GATGCTGCCTCTCTTCTGACC	0.522													C|||	34	0.00678914	0.0023	0.0144	5008	,	,		19971	0.0		0.0199	False		,,,				2504	0.001				p.S171C	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C512G	GRCh37	CM070644	ACAD8	M	rs113488591	PASS	.	C	CYS/SER	38,4364	43.1+/-76.7	0,38,2163	113.0	106.0	109.0		512	4.8	1.0	11	dbSNP_132	109	190,8404	85.6+/-148.0	0,190,4107	yes	missense	ACAD8	NM_014384.2	112	0,228,6270	GG,GC,CC		2.2108,0.8632,1.7544	probably-damaging	171/416	134128923	228,12768	2201	4297	6498	SO:0001583	missense	27034	exon5			CTGCCTCTCTTCT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.512C>G	11.37:g.134128923C>G	ENSP00000281182:p.Ser171Cys	121.0	0.0	0		138.0	26.0	0.188406	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	C	23.8	4.453578	0.84209	0.008632	0.022108	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99129	-5.46;-5.46;-5.46;-5.46	5.73	4.82	0.62117	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, conserved site (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.000000	0.85682	D	0.000000	D	0.98776	0.9588	M	0.92317	3.295	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.73708	0.964;0.968;0.98;0.974;0.981;0.98	D	0.93512	0.6854	10	0.72032	D	0.01	.	14.7653	0.69634	0.0:0.9304:0.0:0.0696	.	112;94;73;73;44;171	B7Z767;B7Z5W4;B7Z9L5;B7Z7F1;Q6ZWP6;Q9UKU7	.;.;.;.;.;ACAD8_HUMAN	C	171;94;73;44;133	ENSP00000281182:S171C;ENSP00000443763:S94C;ENSP00000438302:S73C;ENSP00000363884:S44C	ENSP00000281182:S171C	S	+	2	0	ACAD8	133634133	1.000000	0.71417	0.987000	0.45799	0.964000	0.63967	7.385000	0.79763	1.421000	0.47157	-0.140000	0.14226	TCT	C|0.985;G|0.015	0.015	strong		0.522	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
VCAN	1462	hgsc.bcm.edu	37	5	82816190	82816190	+	Missense_Mutation	SNP	A	A	G	rs61754531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:82816190A>G	ENST00000265077.3	+	7	2630	c.2065A>G	c.(2065-2067)Aca>Gca	p.T689A	VCAN_ENST00000342785.4_Missense_Mutation_p.T689A|VCAN_ENST00000512590.2_Missense_Mutation_p.T641A|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	689	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAGAACAGAAACACTAATACC	0.328													A|||	16	0.00319489	0.0008	0.0014	5008	,	,		20334	0.0		0.0139	False		,,,				2504	0.0				p.T689A		Atlas-SNP	.											.	VCAN	498	.	0			c.A2065G						PASS	.	A	,,ALA/THR,ALA/THR	8,4372		0,8,2182	51.0	53.0	52.0		,,2065,2065	1.6	0.2	5	dbSNP_129	52	90,8492		0,90,4201	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,58,58	0,98,6383	GG,GA,AA		1.0487,0.1826,0.7561	,,possibly-damaging,possibly-damaging	,,689/1643,689/3397	82816190	98,12864	2190	4291	6481	SO:0001583	missense	1462	exon7			ACAGAAACACTAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2065A>G	5.37:g.82816190A>G	ENSP00000265077:p.Thr689Ala	88.0	0.0	0		64.0	34.0	0.53125	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	0.784	-0.761296	0.02996	0.001826	0.010487	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.25579	1.79;1.79;1.79	4.03	1.58	0.23477	.	0.518499	0.17701	N	0.164934	T	0.10637	0.0260	M	0.65975	2.015	0.09310	N	1	B;B	0.33940	0.433;0.307	B;B	0.27887	0.084;0.038	T	0.10590	-1.0623	10	0.23302	T	0.38	.	7.4005	0.26960	0.7289:0.0:0.2711:0.0	rs61754531	689;689	P13611-3;P13611	.;CSPG2_HUMAN	A	689;689;641	ENSP00000265077:T689A;ENSP00000342768:T689A;ENSP00000425959:T641A	ENSP00000265077:T689A	T	+	1	0	VCAN	82851946	0.018000	0.18449	0.153000	0.22517	0.029000	0.11900	1.202000	0.32271	0.336000	0.23639	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.328	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ZNF217	7764	hgsc.bcm.edu	37	20	52193542	52193542	+	Silent	SNP	C	C	T	rs61748380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52193542C>T	ENST00000371471.2	-	4	2186	c.1761G>A	c.(1759-1761)ctG>ctA	p.L587L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Silent_p.L587L			O75362	ZN217_HUMAN	zinc finger protein 217	587					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CAGCGCTGCCCAGAACATTCT	0.428													C|||	9	0.00179712	0.0	0.0	5008	,	,		20409	0.0		0.0089	False		,,,				2504	0.0				p.L587L		Atlas-SNP	.											.	ZNF217	227	.	0			c.G1761A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	121.0	113.0	116.0		1761	1.9	1.0	20	dbSNP_129	116	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	ZNF217	NM_006526.2		0,27,6476	TT,TC,CC		0.2791,0.0681,0.2076		587/1049	52193542	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			GCTGCCCAGAACA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1761G>A	20.37:g.52193542C>T		126.0	0.0	0		122.0	68.0	0.557377	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
KIAA1217	56243	hgsc.bcm.edu	37	10	24813585	24813585	+	Silent	SNP	G	G	A	rs145162894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24813585G>A	ENST00000376454.3	+	13	2820	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	KIAA1217_ENST00000376452.3_Silent_p.S895S|KIAA1217_ENST00000307544.6_Silent_p.S613S|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000396446.1_Silent_p.S613S|KIAA1217_ENST00000376451.2_Silent_p.S613S|KIAA1217_ENST00000376462.1_Silent_p.S850S|KIAA1217_ENST00000396445.1_Silent_p.S613S|KIAA1217_ENST00000458595.1_Silent_p.S895S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	930					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TGCAGATGTCGCAGGCTCCGC	0.592													G|||	8	0.00159744	0.0	0.0	5008	,	,		18873	0.001		0.007	False		,,,				2504	0.0				p.S930S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G2790A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	49.0	46.0	47.0		2550,2685,2790	-8.3	0.0	10	dbSNP_134	47	49,8551	31.7+/-84.0	0,49,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	0,53,6450	AA,AG,GG		0.5698,0.0908,0.4075	,,	850/1265,895/1310,930/1944	24813585	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon13			GATGTCGCAGGCT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2790G>A	10.37:g.24813585G>A		63.0	0.0	0		61.0	32.0	0.52459	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			G|0.996;A|0.004	0.004	strong		0.592	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
FFAR4	338557	hgsc.bcm.edu	37	10	95347041	95347041	+	Missense_Mutation	SNP	G	G	A	rs116454156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95347041G>A	ENST00000371483.4	+	4	865	c.809G>A	c.(808-810)cGc>cAc	p.R270H	FFAR4_ENST00000604414.1_Intron|FFAR4_ENST00000371481.4_Missense_Mutation_p.R254H	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	270			R -> H (polymorphism associated with increased risk of obesity; dbSNP:rs116454156). {ECO:0000269|PubMed:22343897}.		hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										CACCAGATCCGCGTGTCCCAG	0.562													G|||	75	0.014976	0.0008	0.0072	5008	,	,		18560	0.001		0.0149	False		,,,				2504	0.0542				p.R270H		Atlas-SNP	.											.	.	.	.	0			c.G809A						PASS	.	G	HIS/ARG,HIS/ARG	21,4385	27.2+/-55.0	0,21,2182	110.0	103.0	105.0		761,809	5.0	1.0	10	dbSNP_132	105	150,8450	72.9+/-135.5	1,148,4151	yes	missense,missense	O3FAR1	NM_001195755.1,NM_181745.3	29,29	1,169,6333	AA,AG,GG		1.7442,0.4766,1.3148	benign,benign	254/362,270/378	95347041	171,12835	2203	4300	6503	SO:0001583	missense	338557	exon4			AGATCCGCGTGTC		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"""GPCR / Class A : Fatty acid receptors"""	19061	protein-coding gene	gene with protein product		609044	"""G protein-coupled receptor 129"", ""G protein-coupled receptor 120"", ""omega-3 fatty acid receptor 1"""	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.809G>A	10.37:g.95347041G>A	ENSP00000360538:p.Arg270His	112.0	0.0	0		97.0	59.0	0.608247	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	37	CCDS31248.1	16	0.007326007326007326	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	15.28	2.785286	0.49997	0.004766	0.017442	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.72725	-0.68;-0.68	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.096786	0.44097	D	0.000500	T	0.48390	0.1497	L	0.57536	1.79	0.29401	N	0.861934	B;B	0.26195	0.07;0.144	B;B	0.18561	0.019;0.022	T	0.60146	-0.7320	10	0.59425	D	0.04	-20.7853	10.4759	0.44665	0.1505:0.0:0.8495:0.0	.	254;270	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	H	254;270	ENSP00000360536:R254H;ENSP00000360538:R270H	ENSP00000360536:R254H	R	+	2	0	O3FAR1	95337031	0.617000	0.27043	0.998000	0.56505	0.924000	0.55760	1.721000	0.38032	2.741000	0.93983	0.555000	0.69702	CGC	G|0.987;A|0.013	0.013	strong		0.562	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	
FAT4	79633	hgsc.bcm.edu	37	4	126336201	126336201	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336201C>T	ENST00000394329.3	+	5	6096	c.6083C>T	c.(6082-6084)gCc>gTc	p.A2028V	FAT4_ENST00000335110.5_Missense_Mutation_p.A326V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2028	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CAGATTCCAGCCTCCAGATTC	0.423																																					p.A2028V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C6083T						PASS	.						162.0	167.0	165.0					4																	126336201		2203	4300	6503	SO:0001583	missense	79633	exon5			TTCCAGCCTCCAG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6083C>T	4.37:g.126336201C>T	ENSP00000377862:p.Ala2028Val	137.0	0.0	0		156.0	15.0	0.0961538	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837537	0.32513	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53206	0.63;0.63	5.1	4.24	0.50183	Cadherin (4);Cadherin-like (1);	0.239720	0.20285	U	0.095376	T	0.43523	0.1251	L	0.43923	1.385	0.30709	N	0.749492	B;B	0.24675	0.053;0.109	B;B	0.28916	0.096;0.047	T	0.43589	-0.9382	10	0.30854	T	0.27	.	15.7102	0.77620	0.0:0.8632:0.1368:0.0	.	326;2028	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	2028;326	ENSP00000377862:A2028V;ENSP00000335169:A326V	ENSP00000335169:A326V	A	+	2	0	FAT4	126555651	0.140000	0.22579	0.932000	0.37286	0.927000	0.56198	2.732000	0.47352	1.111000	0.41721	0.557000	0.71058	GCC	.	.	none		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
ROBO2	6092	hgsc.bcm.edu	37	3	77607099	77607099	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:77607099G>C	ENST00000461745.1	+	9	2136	c.1236G>C	c.(1234-1236)ttG>ttC	p.L412F	ROBO2_ENST00000487694.3_Missense_Mutation_p.L428F|ROBO2_ENST00000332191.8_Missense_Mutation_p.L412F	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	412					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CTTCAGTTTTGACAGATAGAC	0.413																																					p.L412F		Atlas-SNP	.											.	ROBO2	527	.	0			c.G1236C						PASS	.						67.0	70.0	69.0					3																	77607099		1853	4083	5936	SO:0001583	missense	6092	exon9			AGTTTTGACAGAT	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1236G>C	3.37:g.77607099G>C	ENSP00000417164:p.Leu412Phe	109.0	0.0	0		103.0	32.0	0.31068	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	G	2.000	-0.429551	0.04701	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.65364	-0.15;-0.13;-0.13	5.53	0.656	0.17844	.	0.203361	0.24178	N	0.040830	T	0.61813	0.2377	L	0.31526	0.94	0.43234	D	0.995137	D;D;D	0.69078	0.994;0.997;0.994	D;D;D	0.72075	0.947;0.976;0.921	T	0.63637	-0.6592	9	0.19147	T	0.46	.	9.9156	0.41432	0.4075:0.0:0.5925:0.0	.	428;412;412	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	F	428;428;432;412;412;133	ENSP00000417335:L428F;ENSP00000417164:L412F;ENSP00000327536:L412F	ENSP00000327536:L412F	L	+	3	2	ROBO2	77689789	1.000000	0.71417	0.998000	0.56505	0.232000	0.25224	1.789000	0.38724	0.111000	0.17947	0.585000	0.79938	TTG	.	.	none		0.413	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
RET	5979	hgsc.bcm.edu	37	10	43615633	43615633	+	Silent	SNP	C	C	G	rs1800863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43615633C>G	ENST00000355710.3	+	15	2944	c.2712C>G	c.(2710-2712)tcC>tcG	p.S904S	RET_ENST00000340058.5_Silent_p.S904S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	904	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			S -> P (in Ref. 6; AAA36786). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AAGAGGATTCCTACGTGAAGA	0.592		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				C|||	864	0.172524	0.1051	0.2536	5008	,	,		15815	0.121		0.1928	False		,,,				2504	0.2382				p.S904S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	RET	916	.	0			c.C2712G	GRCh37	CM023822	RET	M	rs1800863	PASS	.	C	,	489,3917	225.2+/-241.2	24,441,1738	64.0	57.0	59.0		2712,2712	3.7	1.0	10	dbSNP_89	59	1604,6994	293.1+/-301.2	159,1286,2854	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	183,1727,4592	GG,GC,CC		18.6555,11.0985,16.095	,	904/1073,904/1115	43615633	2093,10911	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon15	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	GGATTCCTACGTG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2712C>G	10.37:g.43615633C>G		102.0	0.0	0		90.0	40.0	0.444444	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.844;G|0.156	0.156	strong		0.592	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
CUL9	23113	hgsc.bcm.edu	37	6	43193877	43193877	+	IGR	SNP	G	G	A	rs7832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000393987.2_Silent_p.V90V|DNPH1_ENST00000230431.6_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30.0	24.0	26.0		270,270	-9.2	0.0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723		6.37:g.43193877G>A		40.0	0.0	0		27.0	6.0	0.222222	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
COL28A1	340267	hgsc.bcm.edu	37	7	7398423	7398423	+	Silent	SNP	C	C	T	rs373840985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7398423C>T	ENST00000399429.3	-	35	3359	c.3219G>A	c.(3217-3219)ttG>ttA	p.L1073L		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1073	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TCAAGGCTTCCAAACATCTAG	0.358													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18071	0.0		0.0	False		,,,				2504	0.0				p.L1073L		Atlas-SNP	.											.	COL28A1	113	.	0			c.G3219A						PASS	.	C		2,3712		0,2,1855	132.0	116.0	121.0		3219	-3.5	0.0	7		121	0,8186		0,0,4093	no	coding-synonymous	COL28A1	NM_001037763.2		0,2,5948	TT,TC,CC		0.0,0.0539,0.0168		1073/1126	7398423	2,11898	1857	4093	5950	SO:0001819	synonymous_variant	340267	exon35			GGCTTCCAAACAT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.3219G>A	7.37:g.7398423C>T		201.0	0.0	0		166.0	40.0	0.240964	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			.	.	weak		0.358	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859792	144859792	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859792T>C	ENST00000369354.3	-	38	6481	c.6292A>G	c.(6292-6294)Act>Gct	p.T2098A	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T2098A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T1992A|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2234A|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2183A|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2098					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CCAGGGTCAGTGCTGGCTGGG	0.572			T	PDGFRB	MPD																																p.T2098A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6292G						PASS	.						66.0	64.0	65.0					1																	144859792		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTCAGTGCTGGC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6292A>G	1.37:g.144859792T>C	ENSP00000358360:p.Thr2098Ala	143.0	0.0	0		151.0	10.0	0.0662252	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	6.344	0.431590	0.12045	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01647	4.71;4.8;4.8;4.8;4.8	4.91	-3.04	0.05412	.	.	.	.	.	T	0.00271	0.0008	N	0.16166	0.38	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43893	-0.9363	9	0.02654	T	1	.	7.2849	0.26333	0.0:0.2735:0.1194:0.6071	.	1992;2098	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	1992;2098;2098;2183;2234	ENSP00000327209:T1992A;ENSP00000358360:T2098A;ENSP00000358363:T2098A;ENSP00000435654:T2183A;ENSP00000358366:T2234A	ENSP00000327209:T1992A	T	-	1	0	PDE4DIP	143571149	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-1.197000	0.02673	-1.569000	0.00873	ACT	.	.	none		0.572	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
MUC4	4585	hgsc.bcm.edu	37	3	195515411	195515411	+	Missense_Mutation	SNP	G	G	C	rs55803325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515411G>C	ENST00000463781.3	-	2	3499	c.3040C>G	c.(3040-3042)Cct>Gct	p.P1014A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1014A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	449	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAGGGCTGGTGACA	0.572																																					p.P1014A		Atlas-SNP	.											.	MUC4	1505	.	4	Deletion - In frame(4)	stomach(4)	c.C3040G						PASS	.						51.0	28.0	35.0					3																	195515411		686	1591	2277	SO:0001583	missense	4585	exon2			AGGAAGGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3040C>G	3.37:g.195515411G>C	ENSP00000417498:p.Pro1014Ala	61.0	0.0	0		72.0	26.0	0.361111	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.439	0.081317	0.08533	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	0.814	-1.63	0.08345	.	.	.	.	.	T	0.13372	0.0324	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.21109	-1.0255	8	.	.	.	.	3.0122	0.06048	0.0:0.2389:0.4536:0.3075	.	1014	E7ESK3	.	A	1014	ENSP00000417498:P1014A;ENSP00000420243:P1014A	.	P	-	1	0	MUC4	196999806	.	.	0.000000	0.03702	0.011000	0.07611	.	.	-2.334000	0.00630	-2.366000	0.00237	CCT	G|0.993;T|0.007	.	alt		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748013	8748013	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748013G>C	ENST00000276282.6	-	1	3142	c.2556C>G	c.(2554-2556)tgC>tgG	p.C852W		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	852										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TCTGCACATAGCATGGGAACT	0.507																																					p.C852W	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.C2556G						PASS	.						80.0	76.0	77.0					8																	8748013		2203	4300	6503	SO:0001583	missense	9258	exon1			CACATAGCATGGG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2556C>G	8.37:g.8748013G>C	ENSP00000276282:p.Cys852Trp	61.0	0.0	0		53.0	30.0	0.566038	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.617809	0.28801	.	.	ENSG00000147324	ENST00000276282	T	0.30448	1.53	5.04	4.17	0.49024	.	0.117044	0.64402	D	0.000016	T	0.20210	0.0486	N	0.08118	0	0.58432	D	0.999999	D	0.57571	0.98	P	0.46975	0.533	T	0.04440	-1.0951	10	0.36615	T	0.2	.	12.5332	0.56128	0.0798:0.0:0.9202:0.0	.	852	Q9Y4C4	MFHA1_HUMAN	W	852	ENSP00000276282:C852W	ENSP00000276282:C852W	C	-	3	2	MFHAS1	8785423	1.000000	0.71417	0.973000	0.42090	0.980000	0.70556	5.899000	0.69846	1.359000	0.45940	0.655000	0.94253	TGC	.	.	none		0.507	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
OR56A4	120793	hgsc.bcm.edu	37	11	6024031	6024031	+	Silent	SNP	G	G	A	rs143488149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6024031G>A	ENST00000330728.4	-	1	393	c.348C>T	c.(346-348)taC>taT	p.Y116Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCTGAGCAGGTAGTACAGGG	0.607													.|||	3	0.000599042	0.0	0.0	5008	,	,		20915	0.0		0.003	False		,,,				2504	0.0				p.Y116Y		Atlas-SNP	.											.	OR56A4	66	.	0			c.C348T						PASS	.	G		0,4400		0,0,2200	69.0	69.0	69.0		348	1.7	1.0	11	dbSNP_134	69	14,8534	10.5+/-38.8	0,14,4260	no	coding-synonymous	OR56A4	NM_001005179.2		0,14,6460	AA,AG,GG		0.1638,0.0,0.1081		116/366	6024031	14,12934	2200	4274	6474	SO:0001819	synonymous_variant	120793	exon1			GAGCAGGTAGTAC	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.348C>T	11.37:g.6024031G>A		132.0	0.0	0		160.0	110.0	0.6875	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000356226.4_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		95.0	0.0	0		76.0	35.0	0.460526	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
PHKG2	5261	hgsc.bcm.edu	37	16	30762886	30762886	+	Silent	SNP	C	C	T	rs56029513		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30762886C>T	ENST00000563588.1	+	4	527	c.288C>T	c.(286-288)tcC>tcT	p.S96S	RP11-2C24.4_ENST00000483578.1_lincRNA|PHKG2_ENST00000424889.3_Silent_p.S96S|PHKG2_ENST00000328273.7_Silent_p.S96S	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			ovary(1)|skin(1)	2			Colorectal(24;0.198)			TCATCGATTCCTACGAGTCTT	0.547													c|||	1	0.000199681	0.0008	0.0	5008	,	,		22627	0.0		0.0	False		,,,				2504	0.0				p.S96S		Atlas-SNP	.											.	PHKG2	29	.	0			c.C288T						PASS	.	G	,	3,4391	6.2+/-15.9	0,3,2194	522.0	465.0	484.0		288,288	3.2	1.0	16	dbSNP_129	484	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	PHKG2	NM_000294.2,NM_001172432.1	,	0,24,6473	TT,TC,CC		0.2442,0.0683,0.1847	,	96/407,96/375	30762886	24,12970	2197	4300	6497	SO:0001819	synonymous_variant	5261	exon4			CGATTCCTACGAG	S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.288C>T	16.37:g.30762886C>T		533.0	1.0	0.00187617		672.0	239.0	0.355655	NM_001172432	A8K0C7|B4DEB7|E9PEU3|P11800	Silent	SNP	ENST00000563588.1	37	CCDS10690.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294	
SGK1	6446	hgsc.bcm.edu	37	6	134494619	134494619	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494619C>G	ENST00000237305.7	-	4	402	c.314G>C	c.(313-315)gGa>gCa	p.G105A	SGK1_ENST00000528577.1_Missense_Mutation_p.G133A|SGK1_ENST00000413996.3_Missense_Mutation_p.G119A|SGK1_ENST00000367857.5_Missense_Mutation_p.G95A|SGK1_ENST00000367858.5_Missense_Mutation_p.G200A|SGK1_ENST00000475719.2_Missense_Mutation_p.G105A|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		ACTGCCCTTTCCGATCACTTT	0.398																																					p.G200A		Atlas-SNP	.											.	SGK1	387	.	0			c.G599C						PASS	.						63.0	68.0	66.0					6																	134494619		2203	4300	6503	SO:0001583	missense	6446	exon6			CCCTTTCCGATCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.314G>C	6.37:g.134494619C>G	ENSP00000237305:p.Gly105Ala	105.0	0.0	0		89.0	19.0	0.213483	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000125	0.93227	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	D;D;D;D;D;T	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;0.61	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91965	0.7455	M	0.85041	2.73	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;1.0	D;D;D;D;D;D	0.97110	0.999;0.998;1.0;0.999;0.998;0.999	D	0.91872	0.5508	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	133;119;105;95;200;105	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	A	200;119;105;95;133;105	ENSP00000356832:G200A;ENSP00000396242:G119A;ENSP00000237305:G105A;ENSP00000356831:G95A;ENSP00000434450:G133A;ENSP00000434302:G105A	ENSP00000237305:G105A	G	-	2	0	SGK1	134536312	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	GGA	.	.	none		0.398	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
DFNB59	494513	hgsc.bcm.edu	37	2	179325714	179325714	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179325714A>G	ENST00000409117.3	+	7	1128	c.772A>G	c.(772-774)Aga>Gga	p.R258G	DFNB59_ENST00000375129.4_Missense_Mutation_p.R258G	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	258					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TTTAGATAGAAGAGTGATGGA	0.323																																					p.R258G		Atlas-SNP	.											.	DFNB59	37	.	0			c.A772G						PASS	.						186.0	164.0	171.0					2																	179325714		1845	4095	5940	SO:0001583	missense	494513	exon7			GATAGAAGAGTGA	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.772A>G	2.37:g.179325714A>G	ENSP00000386647:p.Arg258Gly	84.0	0.0	0		71.0	4.0	0.056338	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610445	0.46527	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.62788	0.0;0.0	6.04	6.04	0.98038	.	0.105144	0.33959	U	0.004397	T	0.54062	0.1835	L	0.47716	1.5	0.51012	D	0.999909	B	0.09022	0.002	B	0.12156	0.007	T	0.49283	-0.8956	10	0.22706	T	0.39	-25.5225	12.3569	0.55180	0.9331:0.0:0.0669:0.0	.	258	Q0ZLH3	PJVK_HUMAN	G	258	ENSP00000386647:R258G;ENSP00000364271:R258G	ENSP00000364271:R258G	R	+	1	2	DFNB59	179033960	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.839000	0.48207	2.317000	0.78254	0.460000	0.39030	AGA	.	.	none		0.323	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
PIM1	5292	hgsc.bcm.edu	37	6	37138345	37138345	+	5'UTR	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37138345G>A	ENST00000373509.5	+	0	367					NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase						apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	ACATCCTGGAGGTTGGGATGC	0.687			T	BCL6	NHL																																p.E89E		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G267A						PASS	.						28.0	27.0	27.0					6																	37138345		2200	4298	6498	SO:0001623	5_prime_UTR_variant	5292	exon1			CCTGGAGGTTGGG		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.-7G>A	6.37:g.37138345G>A		39.0	0.0	0		63.0	15.0	0.238095	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.687	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494661G>C	ENST00000237305.7	-	4	360	c.272C>G	c.(271-273)cCt>cGt	p.P91R	SGK1_ENST00000528577.1_Missense_Mutation_p.P119R|SGK1_ENST00000413996.3_Missense_Mutation_p.P105R|SGK1_ENST00000367857.5_Missense_Mutation_p.P81R|SGK1_ENST00000367858.5_Missense_Mutation_p.P186R|SGK1_ENST00000475719.2_Missense_Mutation_p.P91R|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	91					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.P186L(1)|p.P81L(1)|p.P91L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTTAGCATGAGGATTGGACGA	0.378																																					p.P186R		Atlas-SNP	.											SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C557G						PASS	.						73.0	77.0	76.0					6																	134494661		2203	4300	6503	SO:0001583	missense	6446	exon6			GCATGAGGATTGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.272C>G	6.37:g.134494661G>C	ENSP00000237305:p.Pro91Arg	90.0	0.0	0		70.0	14.0	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.388841	0.61956	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.73152	3.18;3.18;3.18;3.18;3.18;-0.72	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	M	0.62723	1.935	0.80722	D	1	B;D;B;B;P;B	0.67145	0.105;0.996;0.023;0.086;0.503;0.102	B;D;B;B;B;B	0.63703	0.093;0.917;0.046;0.082;0.248;0.059	T	0.75371	-0.3341	10	0.41790	T	0.15	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	119;105;91;81;186;91	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	R	186;105;91;81;119;91	ENSP00000356832:P186R;ENSP00000396242:P105R;ENSP00000237305:P91R;ENSP00000356831:P81R;ENSP00000434450:P119R;ENSP00000434302:P91R	ENSP00000237305:P91R	P	-	2	0	SGK1	134536354	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	CCT	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
KDR	3791	hgsc.bcm.edu	37	4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	rs34231037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81.0	85.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	187.0	0.0	0		176.0	89.0	0.505682	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
SLC8A3	6547	hgsc.bcm.edu	37	14	70633998	70633998	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70633998G>A	ENST00000381269.2	-	2	1895	c.1142C>T	c.(1141-1143)tCc>tTc	p.S381F	SLC8A3_ENST00000357887.3_Missense_Mutation_p.S381F|SLC8A3_ENST00000528359.1_Missense_Mutation_p.S381F|SLC8A3_ENST00000534137.1_Missense_Mutation_p.S381F|SLC8A3_ENST00000356921.2_Missense_Mutation_p.S381F	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	381					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GCTCATGCTGGAGGCCTTCTT	0.517																																					p.S381F		Atlas-SNP	.											.	SLC8A3	234	.	0			c.C1142T						PASS	.						126.0	115.0	119.0					14																	70633998		2203	4300	6503	SO:0001583	missense	6547	exon2			ATGCTGGAGGCCT	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1142C>T	14.37:g.70633998G>A	ENSP00000370669:p.Ser381Phe	139.0	0.0	0		148.0	40.0	0.27027	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	9.140	1.013566	0.19277	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.36699	1.32;1.24;1.38;1.32;1.38	5.83	5.83	0.93111	.	0.446831	0.24891	N	0.034769	T	0.43077	0.1231	L	0.50333	1.59	0.46396	D	0.999023	B;B;B;B	0.32543	0.135;0.083;0.375;0.242	B;B;B;B	0.39590	0.213;0.066;0.304;0.136	T	0.14671	-1.0464	10	0.35671	T	0.21	.	20.1242	0.97973	0.0:0.0:1.0:0.0	.	381;381;381;381	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	F	381	ENSP00000349392:S381F;ENSP00000370669:S381F;ENSP00000350560:S381F;ENSP00000436688:S381F;ENSP00000433531:S381F	ENSP00000349392:S381F	S	-	2	0	SLC8A3	69703751	1.000000	0.71417	0.991000	0.47740	0.909000	0.53808	4.043000	0.57354	2.744000	0.94065	0.643000	0.83706	TCC	.	.	none		0.517	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
LAMA5	3911	hgsc.bcm.edu	37	20	60889385	60889385	+	Missense_Mutation	SNP	G	G	T	rs117480847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60889385G>T	ENST00000252999.3	-	62	8545	c.8479C>A	c.(8479-8481)Cag>Aag	p.Q2827K		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2827	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCTGCGAACTGCTCCCCAATG	0.627													.|||	61	0.0121805	0.0	0.0115	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0348				p.Q2827K		Atlas-SNP	.											LAMA5,NS,haematopoietic_neoplasm,0,1	LAMA5	268	1	0			c.C8479A						scavenged	.	G	LYS/GLN	21,4383	28.1+/-56.4	0,21,2181	113.0	97.0	103.0		8479	2.6	1.0	20	dbSNP_132	103	174,8422	79.8+/-142.4	0,174,4124	yes	missense	LAMA5	NM_005560.3	53	0,195,6305	TT,TG,GG		2.0242,0.4768,1.5	benign	2827/3696	60889385	195,12805	2202	4298	6500	SO:0001583	missense	3911	exon62			CGAACTGCTCCCC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.8479C>A	20.37:g.60889385G>T	ENSP00000252999:p.Gln2827Lys	94.0	1.0	0.0106383		75.0	36.0	0.48	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	g	8.022	0.759813	0.15846	0.004768	0.020242	ENSG00000130702	ENST00000252999	T	0.78126	-1.15	3.61	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.621906	0.16406	U	0.215834	T	0.51517	0.1679	L	0.40543	1.245	0.80722	D	1	B	0.33345	0.409	B	0.34489	0.184	T	0.49808	-0.8900	10	0.15952	T	0.53	.	11.3438	0.49548	0.0:0.3552:0.6448:0.0	.	2827	O15230	LAMA5_HUMAN	K	2827	ENSP00000252999:Q2827K	ENSP00000252999:Q2827K	Q	-	1	0	LAMA5	60322780	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.300000	0.33436	0.469000	0.27268	0.457000	0.33378	CAG	G|0.986;T|0.014	0.014	strong		0.627	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SEMA6B	10501	hgsc.bcm.edu	37	19	4555084	4555084	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4555084C>A	ENST00000586582.1	-	8	896	c.586G>T	c.(586-588)Gtt>Ttt	p.V196F	SEMA6B_ENST00000301293.3_Missense_Mutation_p.V196F|SEMA6B_ENST00000586965.1_Missense_Mutation_p.V196F	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	196	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGTCGGTAACAGTAGCTGTG	0.587																																					p.V196F		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G586T						PASS	.						109.0	87.0	95.0					19																	4555084		2203	4300	6503	SO:0001583	missense	10501	exon8			CGGTAACAGTAGC	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.586G>T	19.37:g.4555084C>A	ENSP00000467290:p.Val196Phe	59.0	0.0	0		46.0	17.0	0.369565	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592476	0.66219	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.12147	2.71	2.8	2.8	0.32819	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.141549	0.46145	D	0.000304	T	0.39600	0.1084	M	0.85197	2.74	0.51012	D	0.999904	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	T	0.50285	-0.8846	10	0.87932	D	0	.	13.2603	0.60101	0.0:1.0:0.0:0.0	.	196;196	B4DT36;Q9H3T3	.;SEM6B_HUMAN	F	196	ENSP00000301293:V196F	ENSP00000301292:V196F	V	-	1	0	SEMA6B	4506084	1.000000	0.71417	0.087000	0.20705	0.468000	0.32798	5.648000	0.67930	1.882000	0.54519	0.455000	0.32223	GTT	.	.	none		0.587	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		85.0	0.0	0		73.0	37.0	0.506849	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
NAV2	89797	hgsc.bcm.edu	37	11	20124807	20124807	+	Missense_Mutation	SNP	C	C	T	rs34329467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20124807C>T	ENST00000396087.3	+	36	6700	c.6601C>T	c.(6601-6603)Cgc>Tgc	p.R2201C	NAV2_ENST00000527559.2_Missense_Mutation_p.R2130C|NAV2_ENST00000311043.8_Missense_Mutation_p.R1206C|NAV2_ENST00000533917.1_Missense_Mutation_p.R1206C|NAV2_ENST00000360655.4_Missense_Mutation_p.R2078C|NAV2_ENST00000349880.4_Missense_Mutation_p.R2142C|NAV2_ENST00000396085.1_Missense_Mutation_p.R2145C|NAV2_ENST00000540292.1_Missense_Mutation_p.R2132C	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2201					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ATAGGAATTGCGCCAGTACCT	0.567													C|||	3	0.000599042	0.0008	0.0	5008	,	,		23293	0.0		0.002	False		,,,				2504	0.0				p.R2201C		Atlas-SNP	.											.	NAV2	255	.	0			c.C6601T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	167.0	130.0	143.0		6232,3616,6424,6433	5.6	1.0	11	dbSNP_126	143	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	180,180,180,180	0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537	probably-damaging,probably-damaging,probably-damaging,probably-damaging	2078/2366,1206/1494,2142/2430,2145/2433	20124807	33,12973	2203	4300	6503	SO:0001583	missense	89797	exon35			GAATTGCGCCAGT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6601C>T	11.37:g.20124807C>T	ENSP00000379396:p.Arg2201Cys	114.0	0.0	0		75.0	20.0	0.266667	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	23.6	4.432361	0.83776	9.08E-4	0.003372	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	D;D;D;D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000003	D	0.94988	0.8378	M	0.83384	2.64	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.978;0.984;0.993;0.999	D	0.94611	0.7804	9	.	.	.	.	19.2099	0.93749	0.0:1.0:0.0:0.0	rs34329467	2145;1206;2142;2078	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	C	2078;2145;2142;2201;2130;2132;1206;1206	ENSP00000353871:R2078C;ENSP00000379394:R2145C;ENSP00000309577:R2142C;ENSP00000379396:R2201C;ENSP00000435395:R2130C;ENSP00000443489:R2132C;ENSP00000437316:R1206C;ENSP00000312169:R1206C	.	R	+	1	0	NAV2	20081383	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.954000	0.70298	2.631000	0.89168	0.655000	0.94253	CGC	C|0.997;T|0.003	0.003	strong		0.567	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
TRIM50	135892	hgsc.bcm.edu	37	7	72732848	72732848	+	Silent	SNP	G	G	T	rs201525569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:72732848G>T	ENST00000333149.2	-	4	899	c.699C>A	c.(697-699)ggC>ggA	p.G233G	TRIM50_ENST00000453152.1_Silent_p.G233G	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	233						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						GGTCCTCATTGCCGAACTGTT	0.657													G|||	5	0.000998403	0.0008	0.0043	5008	,	,		17310	0.0		0.001	False		,,,				2504	0.0				p.G233G		Atlas-SNP	.											.	TRIM50	78	.	0			c.C699A						PASS	.						153.0	138.0	143.0					7																	72732848		2203	4300	6503	SO:0001819	synonymous_variant	135892	exon4			CTCATTGCCGAAC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19017	protein-coding gene	gene with protein product		612548	"""tripartite motif-containing 50A"", ""tripartite motif-containing 50"""	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.699C>A	7.37:g.72732848G>T		463.0	0.0	0		457.0	32.0	0.0700219	NM_178125	Q86XT3	Silent	SNP	ENST00000333149.2	37	CCDS34654.1																																																																																			G|0.999;T|0.001	0.001	weak		0.657	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125	
SLC30A3	7781	hgsc.bcm.edu	37	2	27481661	27481661	+	Silent	SNP	G	G	A	rs41288821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27481661G>A	ENST00000233535.4	-	2	589	c.237C>T	c.(235-237)gcC>gcT	p.A79A	SLC30A3_ENST00000447008.2_Silent_p.A74A	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	79					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAACGGCACAGGCAGCATATA	0.602													G|||	13	0.00259585	0.0008	0.0072	5008	,	,		18488	0.0		0.006	False		,,,				2504	0.001				p.A79A		Atlas-SNP	.											.	SLC30A3	39	.	0			c.C237T						PASS	.	G		10,4396	11.4+/-27.6	0,10,2193	58.0	62.0	61.0		237	4.4	1.0	2	dbSNP_127	61	84,8516	47.2+/-106.3	0,84,4216	no	coding-synonymous	SLC30A3	NM_003459.4		0,94,6409	AA,AG,GG		0.9767,0.227,0.7227		79/389	27481661	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	7781	exon2			GGCACAGGCAGCA	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"""Solute carriers"""	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.237C>T	2.37:g.27481661G>A		84.0	0.0	0		91.0	62.0	0.681319	NM_003459	Q8TC03	Silent	SNP	ENST00000233535.4	37	CCDS1743.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2		
IWS1	55677	hgsc.bcm.edu	37	2	128244216	128244216	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128244216T>C	ENST00000295321.4	-	13	2500	c.2241A>G	c.(2239-2241)ggA>ggG	p.G747G	AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	747	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		GGGCACAGAATCCAGGATCTC	0.517																																					p.G747G		Atlas-SNP	.											.	IWS1	61	.	0			c.A2241G						PASS	.						96.0	89.0	91.0					2																	128244216		2203	4300	6503	SO:0001819	synonymous_variant	55677	exon13			ACAGAATCCAGGA	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2241A>G	2.37:g.128244216T>C		121.0	0.0	0		142.0	29.0	0.204225	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Silent	SNP	ENST00000295321.4	37	CCDS2146.1																																																																																			.	.	none		0.517	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
GLRB	2743	hgsc.bcm.edu	37	4	158060077	158060077	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158060077T>A	ENST00000264428.4	+	7	997	c.727T>A	c.(727-729)Tgt>Agt	p.C243S	GLRB_ENST00000509282.1_Missense_Mutation_p.C243S|GLRB_ENST00000512619.1_Intron|GLRB_ENST00000541722.1_Missense_Mutation_p.C243S	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	243					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)			central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	ATATGGTAACTGTACAAAATA	0.313																																					p.C243S		Atlas-SNP	.											GLRB,caecum,carcinoma,-2,1	GLRB	74	1	0			c.T727A						PASS	.						57.0	62.0	60.0					4																	158060077		2203	4295	6498	SO:0001583	missense	2743	exon7			GGTAACTGTACAA	U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.727T>A	4.37:g.158060077T>A	ENSP00000264428:p.Cys243Ser	139.0	0.0	0		124.0	20.0	0.16129	NM_000824	A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	37	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825550	0.90955	.	.	ENSG00000109738	ENST00000264428;ENST00000541722;ENST00000509282	T;T;T	0.77620	-1.11;-1.11;-1.11	5.5	5.5	0.81552	Neurotransmitter-gated ion-channel ligand-binding (3);	0.093422	0.85682	D	0.000000	D	0.84392	0.5462	L	0.49455	1.56	0.80722	D	1	D	0.54772	0.968	D	0.69824	0.966	D	0.83745	0.0206	10	0.39692	T	0.17	.	15.5984	0.76606	0.0:0.0:0.0:1.0	.	243	P48167	GLRB_HUMAN	S	243	ENSP00000264428:C243S;ENSP00000441873:C243S;ENSP00000427186:C243S	ENSP00000264428:C243S	C	+	1	0	GLRB	158279527	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.961000	0.87903	2.090000	0.63153	0.528000	0.53228	TGT	.	.	none		0.313	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824	
DHX33	56919	hgsc.bcm.edu	37	17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	rs75426953	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						scavenged	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74.0	69.0	70.0		1342,1861	4.6	1.0	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	119.0	1.0	0.00840336		96.0	54.0	0.5625	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
FCHSD1	89848	hgsc.bcm.edu	37	5	141026182	141026182	+	Missense_Mutation	SNP	G	G	T	rs3749760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141026182G>T	ENST00000435817.2	-	11	1082	c.1032C>A	c.(1030-1032)aaC>aaA	p.N344K	FCHSD1_ENST00000522126.1_Missense_Mutation_p.N268K|FCHSD1_ENST00000522783.1_Missense_Mutation_p.N342K|FCHSD1_ENST00000523856.1_5'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	344			N -> K (in dbSNP:rs3749760).						FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGCCCATGGTTCTGGATCT	0.592													G|||	65	0.0129792	0.0015	0.0259	5008	,	,		19308	0.0258		0.0119	False		,,,				2504	0.0072				p.N344K		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C1032A						PASS	.	G	LYS/ASN	8,3962		0,8,1977	33.0	37.0	36.0		1032	2.2	1.0	5	dbSNP_107	36	131,8141		2,127,4007	yes	missense	FCHSD1	NM_033449.2	94	2,135,5984	TT,TG,GG		1.5837,0.2015,1.1354	benign	344/691	141026182	139,12103	1985	4136	6121	SO:0001583	missense	89848	exon11			CCCATGGTTCTGG	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.1032C>A	5.37:g.141026182G>T	ENSP00000399259:p.Asn344Lys	88.0	0.0	0		63.0	32.0	0.507937	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	39	0.017857142857142856	3	0.006097560975609756	8	0.022099447513812154	18	0.03146853146853147	10	0.013192612137203167	G	15.12	2.738413	0.49045	0.002015	0.015837	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783	T;T;T	0.39997	1.84;1.05;1.44	5.47	2.22	0.28083	.	0.849984	0.10666	N	0.648098	T	0.09069	0.0224	N	0.22421	0.69	0.80722	D	1	B	0.16396	0.017	B	0.20184	0.028	T	0.08146	-1.0736	10	0.02654	T	1	-17.3402	9.4986	0.39004	0.2876:0.0:0.7124:0.0	rs3749760;rs52802373;rs3749760	344	Q86WN1	FCSD1_HUMAN	K	344;268;342	ENSP00000399259:N344K;ENSP00000427796:N268K;ENSP00000428677:N342K	ENSP00000399259:N344K	N	-	3	2	FCHSD1	141006366	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.933000	0.28897	0.673000	0.31224	0.462000	0.41574	AAC	G|0.981;T|0.019	0.019	strong		0.592	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717513	2717513	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2717513C>G	ENST00000323469.4	-	2	475	c.292G>C	c.(292-294)Ggg>Cgg	p.G98R	DIRAS1_ENST00000585334.1_Missense_Mutation_p.G98R	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	98					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAGATGGGCCCCAGCTCCTCC	0.627																																					p.G98R		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G292C						PASS	.						45.0	40.0	41.0					19																	2717513		2203	4297	6500	SO:0001583	missense	148252	exon2			TGGGCCCCAGCTC	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.292G>C	19.37:g.2717513C>G	ENSP00000325836:p.Gly98Arg	84.0	0.0	0		71.0	21.0	0.295775	NM_145173		Missense_Mutation	SNP	ENST00000323469.4	37	CCDS12092.1	.	.	.	.	.	.	.	.	.	.	C	9.401	1.078074	0.20227	.	.	ENSG00000176490	ENST00000323469	T	0.75477	-0.94	4.07	-0.695	0.11291	Small GTP-binding protein domain (1);	0.169303	0.49305	D	0.000145	T	0.42017	0.1184	N	0.04245	-0.25	0.26980	N	0.965374	B	0.02656	0.0	B	0.06405	0.002	T	0.17745	-1.0359	10	0.20519	T	0.43	.	3.7079	0.08408	0.0:0.3451:0.3048:0.35	.	98	O95057	DIRA1_HUMAN	R	98	ENSP00000325836:G98R	ENSP00000325836:G98R	G	-	1	0	DIRAS1	2668513	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	1.026000	0.30103	0.692000	0.31613	0.549000	0.68633	GGG	.	.	none		0.627	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1		
USP40	55230	hgsc.bcm.edu	37	2	234442134	234442134	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234442134G>C	ENST00000427112.2	-	10	1494	c.1459C>G	c.(1459-1461)Ccc>Gcc	p.P487A	USP40_ENST00000251722.6_Missense_Mutation_p.P487A|USP40_ENST00000450966.1_Missense_Mutation_p.P499A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	487					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CCTTCAGGGGGTCTCTGCAAC	0.348																																					p.P499A		Atlas-SNP	.											.	USP40	174	.	0			c.C1495G						PASS	.						101.0	97.0	98.0					2																	234442134		1836	4076	5912	SO:0001583	missense	55230	exon10			CAGGGGGTCTCTG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1459C>G	2.37:g.234442134G>C	ENSP00000387898:p.Pro487Ala	128.0	0.0	0		125.0	32.0	0.256	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207921	0.79240	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05513	3.43;3.43;3.43	5.23	5.23	0.72850	.	0.763029	0.12385	N	0.473527	T	0.26955	0.0660	M	0.74258	2.255	0.80722	D	1	D;D	0.71674	0.997;0.998	P;D	0.68039	0.904;0.955	T	0.00567	-1.1667	10	0.40728	T	0.16	.	18.8586	0.92264	0.0:0.0:1.0:0.0	.	487;499	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	A	499;487;487	ENSP00000415434:P499A;ENSP00000251722:P487A;ENSP00000387898:P487A	ENSP00000251722:P487A	P	-	1	0	USP40	234106873	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.406000	0.97321	2.458000	0.83093	0.586000	0.80456	CCC	.	.	none		0.348	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
STAG2	10735	hgsc.bcm.edu	37	X	123176493	123176493	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:123176493G>A	ENST00000371160.1	+	7	750	c.460G>A	c.(460-462)Gag>Aag	p.E154K	STAG2_ENST00000371144.3_Missense_Mutation_p.E154K|STAG2_ENST00000371145.3_Missense_Mutation_p.E154K|STAG2_ENST00000371157.3_Missense_Mutation_p.E154K|STAG2_ENST00000354548.5_Missense_Mutation_p.E85K|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.E154K	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	154					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGAATTCGATGAGGTAACTTA	0.323																																					p.E154K		Atlas-SNP	.											.	STAG2	309	.	0			c.G460A						PASS	.						78.0	73.0	74.0					X																	123176493		2203	4300	6503	SO:0001583	missense	10735	exon7			TTCGATGAGGTAA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.460G>A	X.37:g.123176493G>A	ENSP00000360202:p.Glu154Lys	446.0	1.0	0.00224215		257.0	68.0	0.264591	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463084	0.96257	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215	T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.74	5.74	0.90152	STAG (1);	0.000000	0.85682	D	0.000000	T	0.75087	0.3802	M	0.92077	3.27	0.80722	D	1	D;D	0.55605	0.966;0.972	P;P	0.61940	0.747;0.896	T	0.79264	-0.1875	10	0.44086	T	0.13	-12.9428	18.9534	0.92649	0.0:0.0:1.0:0.0	.	154;154	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	K	154;154;85;154;154;154;154;154;154;154	ENSP00000218089:E154K;ENSP00000397265:E154K;ENSP00000346555:E85K;ENSP00000360202:E154K;ENSP00000360199:E154K;ENSP00000360187:E154K;ENSP00000360186:E154K;ENSP00000392118:E154K	ENSP00000218089:E154K	E	+	1	0	STAG2	123004174	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	9.740000	0.98839	2.425000	0.82216	0.522000	0.50473	GAG	.	.	none		0.323	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
FAT4	79633	hgsc.bcm.edu	37	4	126336347	126336347	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336347C>A	ENST00000394329.3	+	5	6242	c.6229C>A	c.(6229-6231)Cca>Aca	p.P2077T	FAT4_ENST00000335110.5_Missense_Mutation_p.P375T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P2077>?(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGCAACTGACCCAGATAGTGG	0.418																																					p.P2077T		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6229A						PASS	.						138.0	141.0	140.0					4																	126336347		2203	4300	6503	SO:0001583	missense	79633	exon5			ACTGACCCAGATA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6229C>A	4.37:g.126336347C>A	ENSP00000377862:p.Pro2077Thr	127.0	0.0	0		108.0	8.0	0.0740741	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550366	0.27739	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.52983	0.64;0.64	5.0	4.1	0.47936	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.49047	0.1534	L	0.53729	1.69	0.39232	D	0.96369	B;B	0.28783	0.222;0.087	B;B	0.37550	0.253;0.155	T	0.54721	-0.8251	10	0.42905	T	0.14	.	14.821	0.70074	0.0:0.8556:0.1444:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	T	2077;375	ENSP00000377862:P2077T;ENSP00000335169:P375T	ENSP00000335169:P375T	P	+	1	0	FAT4	126555797	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.603000	0.46266	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
RAPGEF5	9771	hgsc.bcm.edu	37	7	22233635	22233635	+	5'Flank	SNP	G	G	A	rs375862364		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:22233635G>A	ENST00000401957.2	-	0	0				RAPGEF5_ENST00000405243.1_Missense_Mutation_p.T338M|RAPGEF5_ENST00000475788.1_5'UTR|RAPGEF5_ENST00000344041.6_Missense_Mutation_p.T185M			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						CTGAACAGTCGTCACTTCATC	0.493																																					p.T185M		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C554T						PASS	.	G	MET/THR	0,4052		0,0,2026	192.0	196.0	195.0		554	2.4	0.1	7		195	2,8352		0,2,4175	no	missense	RAPGEF5	NM_012294.3	81	0,2,6201	AA,AG,GG		0.0239,0.0,0.0161	possibly-damaging	185/731	22233635	2,12404	2026	4177	6203	SO:0001631	upstream_gene_variant	9771	exon10			ACAGTCGTCACTT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525		7.37:g.22233635G>A	Exception_encountered	103.0	0.0	0		77.0	12.0	0.155844	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000401957.2	37		.	.	.	.	.	.	.	.	.	.	G	11.73	1.724513	0.30593	0.0	2.39E-4	ENSG00000136237	ENST00000344041;ENST00000420196;ENST00000405243	D;D;D	0.85339	-1.97;-1.97;-1.97	5.31	2.44	0.29823	.	4.131740	0.00935	N	0.002779	T	0.82204	0.4986	L	0.40543	1.245	0.09310	N	1	D	0.55385	0.971	B	0.42062	0.374	T	0.69146	-0.5222	10	0.72032	D	0.01	.	9.6692	0.40002	0.0745:0.2663:0.6593:0.0	.	185	A8MQ07	.	M	185;66;338	ENSP00000343656:T185M;ENSP00000395729:T66M;ENSP00000384870:T338M	ENSP00000343656:T185M	T	-	2	0	RAPGEF5	22200160	0.005000	0.15991	0.061000	0.19648	0.976000	0.68499	0.648000	0.24828	0.213000	0.20722	0.563000	0.77884	ACG	.	.	weak		0.493	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294	
DOCK5	80005	hgsc.bcm.edu	37	8	25220581	25220581	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:25220581T>A	ENST00000276440.7	+	29	3012	c.2968T>A	c.(2968-2970)Ttt>Att	p.F990I		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	990					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CATGGAAACTTTTATCATGTT	0.458																																					p.F990I	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.T2968A						PASS	.						136.0	134.0	135.0					8																	25220581		2203	4300	6503	SO:0001583	missense	80005	exon29			GAAACTTTTATCA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.2968T>A	8.37:g.25220581T>A	ENSP00000276440:p.Phe990Ile	120.0	0.0	0		84.0	47.0	0.559524	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.392449|5.392449	0.96009|0.96009	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000276440|ENST00000444569	T|.	0.26223|.	1.75|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79281|0.79281	0.4419|0.4419	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	P;P;D|.	0.56968|.	0.94;0.898;0.978|.	P;P;P|.	0.57620|.	0.824;0.642;0.824|.	T|T	0.81795|0.81795	-0.0769|-0.0769	10|6	0.72032|.	D|.	0.01|.	.|.	15.9289|15.9289	0.79644|0.79644	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	980;765;990|.	D3DSS6;Q68DL4;Q9H7D0|.	.;.;DOCK5_HUMAN|.	I|Y	990|761	ENSP00000276440:F990I|.	ENSP00000276440:F990I|.	F|F	+|+	1|2	0|0	DOCK5|DOCK5	25276498|25276498	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	7.991000|7.991000	0.88244|0.88244	2.173000|2.173000	0.68751|0.68751	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.	none		0.458	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.P194P	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22.0	26.0	24.0		1203,612	-2.4	0.0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1203T>C	21.37:g.45712983T>C		40.0	0.0	0		63.0	24.0	0.380952	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
ENDOG	2021	hgsc.bcm.edu	37	9	131584729	131584729	+	Missense_Mutation	SNP	G	G	T	rs61737988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584729G>T	ENST00000372642.4	+	3	945	c.734G>T	c.(733-735)cGc>cTc	p.R245L	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	245					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ATTGAGCTCCGCACCTACGTG	0.587													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21105	0.0		0.001	False		,,,				2504	0.0031				p.R245L		Atlas-SNP	.											.	ENDOG	8	.	0			c.G734T						PASS	.	G	LEU/ARG,	3,4401		0,3,2199	70.0	61.0	64.0		734,	4.7	1.0	9	dbSNP_129	64	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	102,	0,22,6480	TT,TG,GG		0.2209,0.0681,0.1692	possibly-damaging,	245/298,	131584729	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			AGCTCCGCACCTA	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.734G>T	9.37:g.131584729G>T	ENSP00000361725:p.Arg245Leu	147.0	0.0	0		143.0	74.0	0.517483	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.18	3.566808	0.65651	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.66995	-0.24	5.63	4.74	0.60224	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063724	0.64402	D	0.000004	T	0.66157	0.2761	L	0.39633	1.23	0.80722	D	1	P	0.51537	0.946	P	0.49953	0.627	T	0.68232	-0.5463	10	0.52906	T	0.07	-1.808	13.8836	0.63696	0.0731:0.0:0.9269:0.0	rs61737988	245	Q14249	NUCG_HUMAN	L	245	ENSP00000361725:R245L	ENSP00000361725:R245L	R	+	2	0	ENDOG	130624550	1.000000	0.71417	0.977000	0.42913	0.284000	0.27059	6.040000	0.70980	1.384000	0.46424	-0.463000	0.05309	CGC	G|0.998;T|0.002	0.002	strong		0.587	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
SMIM11	54065	hgsc.bcm.edu	37	21	35757787	35757787	+	Silent	SNP	C	C	T	rs61747964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000399299.1_Intron|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Silent_p.H8H			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106.0	89.0	95.0		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		307.0	0.0	0		290.0	107.0	0.368966	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
MUC17	140453	hgsc.bcm.edu	37	7	100676968	100676968	+	Silent	SNP	G	G	A	rs138994021|rs71525818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100676968G>A	ENST00000306151.4	+	3	2335	c.2271G>A	c.(2269-2271)acG>acA	p.T757T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	757	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAGCAAAACGCTGTTGACCA	0.483													A|||	20	0.00399361	0.0045	0.0	5008	,	,		28523	0.0		0.0139	False		,,,				2504	0.0				p.T757T		Atlas-SNP	.											.	MUC17	804	.	0			c.G2271A						PASS	.	G		23,4383	29.0+/-57.7	0,23,2180	300.0	301.0	300.0		2271	-1.3	0.0	7	dbSNP_134	300	94,8506	52.7+/-113.3	0,94,4206	no	coding-synonymous	MUC17	NM_001040105.1		0,117,6386	AA,AG,GG		1.093,0.522,0.8996		757/4494	100676968	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAAAACGCTGTTG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2271G>A	7.37:g.100676968G>A		48.0	0.0	0		58.0	29.0	0.5	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.991;A|0.009	0.009	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CAB39L	81617	hgsc.bcm.edu	37	13	49956980	49956980	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49956980C>A	ENST00000355854.4	-	2	564	c.67G>T	c.(67-69)Gac>Tac	p.D23Y	CAB39L_ENST00000476943.1_5'UTR|CAB39L_ENST00000410043.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000409308.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000347776.5_Missense_Mutation_p.D23Y	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	23					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		GCCAAATTGTCTTTCAGGATT	0.328																																					p.D23Y		Atlas-SNP	.											.	CAB39L	35	.	0			c.G67T						PASS	.						177.0	159.0	165.0					13																	49956980		1834	4084	5918	SO:0001583	missense	81617	exon2			AATTGTCTTTCAG	AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.67G>T	13.37:g.49956980C>A	ENSP00000348113:p.Asp23Tyr	225.0	0.0	0		254.0	63.0	0.248031	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Missense_Mutation	SNP	ENST00000355854.4	37	CCDS9416.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976567	0.92982	.	.	ENSG00000102547	ENST00000355854;ENST00000347776;ENST00000378341;ENST00000409308;ENST00000410043;ENST00000457041;ENST00000413278;ENST00000409082	T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.88	5.88	0.94601	Armadillo-type fold (1);	0.189850	0.56097	D	0.000036	T	0.64294	0.2585	M	0.88979	2.995	0.80722	D	1	P	0.43909	0.821	P	0.55455	0.776	T	0.66236	-0.5974	9	.	.	.	-13.9564	19.2196	0.93791	0.0:1.0:0.0:0.0	.	23	Q9H9S4	CB39L_HUMAN	Y	23;23;20;23;23;23;23;23	ENSP00000348113:D23Y;ENSP00000261669:D23Y;ENSP00000386375:D23Y;ENSP00000386328:D23Y;ENSP00000409253:D23Y;ENSP00000404028:D23Y;ENSP00000386979:D23Y	.	D	-	1	0	CAB39L	48854981	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.327000	0.79147	2.789000	0.95967	0.591000	0.81541	GAC	.	.	none		0.328	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925	
TUB	7275	hgsc.bcm.edu	37	11	8122143	8122143	+	Missense_Mutation	SNP	C	C	T	rs139170512	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8122143C>T	ENST00000299506.2	+	10	1359	c.1210C>T	c.(1210-1212)Cgc>Tgc	p.R404C	TUB_ENST00000305253.4_Missense_Mutation_p.R459C|TUB_ENST00000534099.1_Missense_Mutation_p.R410C	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	404					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		TATCCGCCCCCGCAACGTGAG	0.537													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.001				p.R459C		Atlas-SNP	.											TUB,NS,carcinoma,-1,1	TUB	71	1	0			c.C1375T						PASS	.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	142.0	112.0	122.0		1375,1210	4.6	1.0	11	dbSNP_134	122	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	TUB	NM_003320.4,NM_177972.2	180,180	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	459/562,404/507	8122143	1,12993	2201	4296	6497	SO:0001583	missense	7275	exon11			CGCCCCCGCAACG	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.1210C>T	11.37:g.8122143C>T	ENSP00000299506:p.Arg404Cys	81.0	0.0	0		79.0	55.0	0.696203	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780775	0.70222	0.0	1.16E-4	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.85484	-1.99;-1.99;-1.99	4.59	4.59	0.56863	Tubby, C-terminal (3);	0.055535	0.64402	D	0.000001	D	0.92564	0.7638	M	0.88570	2.965	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.65874	0.939;0.931;0.935	D	0.93741	0.7050	10	0.66056	D	0.02	-18.1139	14.2881	0.66258	0.1492:0.8507:0.0:0.0	.	410;404;459	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	C	410;459;404	ENSP00000434400:R410C;ENSP00000305426:R459C;ENSP00000299506:R404C	ENSP00000299506:R404C	R	+	1	0	TUB	8078719	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.811000	0.62606	2.277000	0.76020	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	weak		0.537	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
ZNF285	26974	hgsc.bcm.edu	37	19	44890651	44890651	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44890651G>A	ENST00000330997.4	-	4	1820	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	ZNF285_ENST00000591679.1_Nonsense_Mutation_p.Q593*|ZNF285_ENST00000544719.2_Nonsense_Mutation_p.Q586*|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	586					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GTTTCTCTCTGCTCATGTAGT	0.433																																					p.Q586X		Atlas-SNP	.											.	ZNF285	86	.	0			c.C1756T						PASS	.						123.0	103.0	110.0					19																	44890651		2203	4300	6503	SO:0001587	stop_gained	26974	exon4			CTCTCTGCTCATG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1756C>T	19.37:g.44890651G>A	ENSP00000333595:p.Gln586*	89.0	0.0	0		87.0	18.0	0.206897	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Nonsense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.955111	0.73902	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	.	.	.	3.28	-2.27	0.06846	.	.	.	.	.	.	.	.	.	.	.	0.19775	N	0.999953	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	2.2056	0.03934	0.1362:0.097:0.2974:0.4695	.	.	.	.	X	609;586	.	ENSP00000333595:Q586X	Q	-	1	0	ZNF285	49582491	0.891000	0.30450	0.000000	0.03702	0.024000	0.10985	1.365000	0.34182	-0.266000	0.09339	-0.552000	0.04208	CAG	.	.	none		0.433	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
TTN	7273	hgsc.bcm.edu	37	2	179482633	179482633	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179482633G>T	ENST00000591111.1	-	203	42746	c.42522C>A	c.(42520-42522)gaC>gaA	p.D14174E	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D13247E|TTN_ENST00000460472.2_Missense_Mutation_p.D6750E|TTN_ENST00000589042.1_Missense_Mutation_p.D15815E|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D6875E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D6942E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14174	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGCAGACAGGTCTTCAGCTC	0.463																																					p.D15815E		Atlas-SNP	.											.	TTN	18412	.	0			c.C47445A						PASS	.						184.0	178.0	180.0					2																	179482633		1997	4162	6159	SO:0001583	missense	7273	exon253			AGACAGGTCTTCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42522C>A	2.37:g.179482633G>T	ENSP00000465570:p.Asp14174Glu	323.0	0.0	0		276.0	76.0	0.275362	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	10.34	1.324434	0.24080	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.63	-0.558	0.11796	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.25865	0.0630	N	0.03999	-0.3	0.33357	D	0.571856	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.15484	0.013;0.013;0.013;0.013	T	0.13415	-1.0510	9	0.87932	D	0	.	5.0288	0.14398	0.3413:0.0:0.3539:0.3048	.	6750;6875;6942;14174	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	13247;6750;6942;6875;6750	ENSP00000343764:D13247E;ENSP00000434586:D6750E;ENSP00000340554:D6942E;ENSP00000352154:D6875E	ENSP00000340554:D6942E	D	-	3	2	TTN	179190878	0.751000	0.28327	0.993000	0.49108	0.985000	0.73830	-0.159000	0.10056	-0.079000	0.12707	0.655000	0.94253	GAC	.	.	none		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ADAM32	203102	hgsc.bcm.edu	37	8	39044565	39044565	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39044565G>A	ENST00000379907.4	+	11	1179		c.e11+1		ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32							integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CAGAAGTTGTGTAAGTTTTAA	0.313																																					.		Atlas-SNP	.											.	ADAM32	70	.	0			c.1052+1G>A						PASS	.						72.0	70.0	71.0					8																	39044565		1807	4076	5883	SO:0001630	splice_region_variant	203102	exon11			AGTTGTGTAAGTT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1052+1G>A	8.37:g.39044565G>A		44.0	0.0	0		38.0	18.0	0.473684	NM_145004	Q8TC42	Splice_Site	SNP	ENST00000379907.4	37	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249507	0.39797	.	.	ENSG00000197140	ENST00000379907	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1764	0.72916	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM32	39163722	1.000000	0.71417	0.992000	0.48379	0.318000	0.28184	4.950000	0.63603	2.734000	0.93682	0.650000	0.86243	.	.	.	none		0.313	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	Intron
SPATA18	132671	hgsc.bcm.edu	37	4	52946016	52946016	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:52946016C>A	ENST00000295213.4	+	9	1660	c.1286C>A	c.(1285-1287)gCa>gAa	p.A429E	SPATA18_ENST00000419395.2_Missense_Mutation_p.A397E	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	429					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			ATTGCCTTTGCAATGCAGGCC	0.443																																					p.A429E		Atlas-SNP	.											.	SPATA18	222	.	0			c.C1286A						PASS	.						250.0	234.0	240.0					4																	52946016		2203	4300	6503	SO:0001583	missense	132671	exon9			CCTTTGCAATGCA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.1286C>A	4.37:g.52946016C>A	ENSP00000295213:p.Ala429Glu	227.0	0.0	0		191.0	45.0	0.235602	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096593	0.56075	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.32023	1.47;1.48	5.35	5.35	0.76521	.	0.051108	0.85682	D	0.000000	T	0.46367	0.1389	L	0.39633	1.23	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.87578	0.964;0.964;0.998	T	0.09618	-1.0666	10	0.27785	T	0.31	-16.3661	16.606	0.84830	0.0:1.0:0.0:0.0	.	397;429;429	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	E	429;397	ENSP00000295213:A429E;ENSP00000415309:A397E	ENSP00000295213:A429E	A	+	2	0	SPATA18	52640773	1.000000	0.71417	0.974000	0.42286	0.600000	0.36913	5.025000	0.64097	2.789000	0.95967	0.655000	0.94253	GCA	.	.	none		0.443	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
ULK2	9706	hgsc.bcm.edu	37	17	19720109	19720109	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19720109G>A	ENST00000395544.4	-	13	1548	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	ULK2_ENST00000580130.1_Intron|ULK2_ENST00000361658.2_Missense_Mutation_p.T350M	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	350					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					AAAGTCATCCGTGTCACAAGA	0.408																																					p.T350M		Atlas-SNP	.											.	ULK2	142	.	0			c.C1049T						PASS	.						127.0	116.0	120.0					17																	19720109		2203	4300	6503	SO:0001583	missense	9706	exon13			TCATCCGTGTCAC	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"""unc-51 (C. elegans)-like kinase 2"", ""unc-51-like kinase 2 (C. elegans)"""			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.1049C>T	17.37:g.19720109G>A	ENSP00000378914:p.Thr350Met	161.0	0.0	0		113.0	17.0	0.150442	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	37	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333603	0.81801	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.76709	-1.04;-1.04	5.47	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.86859	0.6034	M	0.73962	2.25	0.48762	D	0.999707	D	0.89917	1.0	D	0.83275	0.996	D	0.88117	0.2829	10	0.87932	D	0	-8.4158	13.0776	0.59095	0.0771:0.0:0.9229:0.0	.	350	Q8IYT8	ULK2_HUMAN	M	350	ENSP00000354877:T350M;ENSP00000378914:T350M	ENSP00000354877:T350M	T	-	2	0	ULK2	19660701	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.097000	0.76967	1.281000	0.44480	0.557000	0.71058	ACG	.	.	none		0.408	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683	
MYH14	79784	hgsc.bcm.edu	37	19	50812315	50812315	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50812315C>T	ENST00000596571.1	+	39	5718	c.5718C>T	c.(5716-5718)gcC>gcT	p.A1906A	MYH14_ENST00000425460.1_Silent_p.A1914A|MYH14_ENST00000376970.2_Silent_p.A1939A|MYH14_ENST00000601313.1_Silent_p.A1947A|MYH14_ENST00000598205.1_Silent_p.A1914A|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000440075.2_Silent_p.A1947A|MYH14_ENST00000262269.8_Silent_p.A1947A			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1906					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TGGAGGAGGCCGAGGAGGAGG	0.612																																					p.A1947A		Atlas-SNP	.											.	MYH14	261	.	0			c.C5841T						PASS	.						32.0	38.0	36.0					19																	50812315		2059	4204	6263	SO:0001819	synonymous_variant	79784	exon42			GGAGGCCGAGGAG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5718C>T	19.37:g.50812315C>T		187.0	0.0	0		196.0	98.0	0.5	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			.	.	none		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
XDH	7498	hgsc.bcm.edu	37	2	31588395	31588395	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:31588395C>T	ENST00000379416.3	-	23	2520	c.2472G>A	c.(2470-2472)gtG>gtA	p.V824V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	824					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GCATGCATCGCACAGGGCGGC	0.567																																					p.V824V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G2472A						PASS	.						115.0	100.0	105.0					2																	31588395		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon23			GCATCGCACAGGG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2472G>A	2.37:g.31588395C>T		140.0	0.0	0		135.0	45.0	0.333333	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.567	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
LTB	4050	hgsc.bcm.edu	37	6	31549364	31549364	+	Silent	SNP	G	G	A	rs4647186		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31549364G>A	ENST00000429299.2	-	3	259	c.252C>T	c.(250-252)agC>agT	p.S84S	LTB_ENST00000446745.2_Missense_Mutation_p.A69V|LTB_ENST00000483972.1_5'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	84			S -> R (in dbSNP:rs4647186). {ECO:0000269|Ref.7}.		cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.S84S(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGAGCCCGGGGCTGAGATCTG	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16763	0.0		0.001	False		,,,				2504	0.0				p.A69V		Atlas-SNP	.											LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C206T						PASS	.						92.0	108.0	103.0					6																	31549364		1510	2709	4219	SO:0001819	synonymous_variant	4050	exon2			CCCGGGGCTGAGA	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.252C>T	6.37:g.31549364G>A		144.0	0.0	0		92.0	31.0	0.336957	NM_009588	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889480	0.52014	.	.	ENSG00000227507	ENST00000446745	.	.	.	5.26	-2.05	0.07321	.	.	.	.	.	T	0.10078	0.0247	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.34650	-0.9820	7	0.38643	T	0.18	-10.8294	6.3303	0.21266	0.4617:0.1263:0.412:0.0	.	69	Q52LU8	.	V	69	.	ENSP00000416113:A69V	A	-	2	0	LTB	31657343	0.000000	0.05858	0.002000	0.10522	0.609000	0.37215	0.051000	0.14141	-0.159000	0.11021	-0.783000	0.03347	GCC	G|0.994;C|0.006	.	alt		0.572	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
HAP1	9001	hgsc.bcm.edu	37	17	39888636	39888636	+	Missense_Mutation	SNP	G	G	T	rs142535684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39888636G>T	ENST00000310778.5	-	3	569	c.560C>A	c.(559-561)cCt>cAt	p.P187H	RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000393939.2_Missense_Mutation_p.P187H|HAP1_ENST00000341193.5_Missense_Mutation_p.P195H|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Missense_Mutation_p.P187H			P54257	HAP1_HUMAN	huntingtin-associated protein 1	187	HAP1 N-terminal.			Missing (in Ref. 6; CAB82785). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTCCCAGACAGGTGGGAGAAG	0.582													G|||	6	0.00119808	0.0	0.0029	5008	,	,		19039	0.0		0.004	False		,,,				2504	0.0				p.P195H		Atlas-SNP	.											.	HAP1	48	.	0			c.C584A						PASS	.	G	HIS/PRO,HIS/PRO,HIS/PRO	4,4402	4.2+/-10.8	0,4,2199	33.0	33.0	33.0		584,560,560	0.2	0.4	17	dbSNP_134	33	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	77,77,77	0,14,6489	TT,TG,GG		0.1163,0.0908,0.1076	probably-damaging,probably-damaging,probably-damaging	195/603,187/595,187/620	39888636	14,12992	2203	4300	6503	SO:0001583	missense	9001	exon3			CAGACAGGTGGGA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.560C>A	17.37:g.39888636G>T	ENSP00000309392:p.Pro187His	68.0	0.0	0		93.0	43.0	0.462366	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	12.60	1.985337	0.35036	9.08E-4	0.001163	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.67171	3.0;3.19;3.14;-0.25	3.42	0.204	0.15199	.	.	.	.	.	T	0.49779	0.1577	N	0.22421	0.69	0.09310	N	1	D;D;D;D	0.61697	0.99;0.99;0.971;0.977	P;P;P;P	0.54590	0.642;0.642;0.642;0.756	T	0.45775	-0.9238	9	0.87932	D	0	0.0581	3.2202	0.06712	0.2633:0.2282:0.5085:0.0	.	187;195;187;187	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	H	187;187;187;195	ENSP00000377513:P187H;ENSP00000309392:P187H;ENSP00000334002:P187H;ENSP00000343170:P195H	ENSP00000309392:P187H	P	-	2	0	HAP1	37142162	0.031000	0.19500	0.391000	0.26233	0.448000	0.32197	0.694000	0.25512	0.254000	0.21573	0.462000	0.41574	CCT	G|0.998;T|0.002	0.002	strong		0.582	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
ZNF169	169841	hgsc.bcm.edu	37	9	97062852	97062852	+	Missense_Mutation	SNP	A	A	T	rs61154129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97062852A>T	ENST00000395395.2	+	5	1102	c.1012A>T	c.(1012-1014)Agg>Tgg	p.R338W	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	338					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				TCTACACCAGAGGACGCACTT	0.562													A|||	187	0.0373403	0.0091	0.0706	5008	,	,		20580	0.0833		0.006	False		,,,				2504	0.0368				p.R338W		Atlas-SNP	.											.	ZNF169	60	.	0			c.A1012T						PASS	.	A	TRP/ARG	48,4358	48.9+/-83.8	1,46,2156	99.0	89.0	93.0		1012	1.3	1.0	9	dbSNP_129	93	92,8508	51.1+/-111.2	1,90,4209	yes	missense	ZNF169	NM_194320.2	101	2,136,6365	TT,TA,AA		1.0698,1.0894,1.0764	probably-damaging	338/604	97062852	140,12866	2203	4300	6503	SO:0001583	missense	169841	exon5			CACCAGAGGACGC	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1012A>T	9.37:g.97062852A>T	ENSP00000378792:p.Arg338Trp	47.0	0.0	0		37.0	24.0	0.648649	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	66	0.03021978021978022	5	0.01016260162601626	17	0.04696132596685083	38	0.06643356643356643	6	0.0079155672823219	A	13.18	2.159857	0.38119	0.010894	0.010698	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.25579	1.79	2.53	1.32	0.21799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07369	0.0186	M	0.93978	3.48	0.09310	P	0.9999999999972624	D	0.71674	0.998	P	0.62813	0.907	T	0.48055	-0.9068	8	0.87932	D	0	.	6.7697	0.23587	0.7458:0.2542:0.0:0.0	rs61154129	338	Q14929	ZN169_HUMAN	W	338;147	ENSP00000378792:R338W	ENSP00000340711:R147W	R	+	1	2	ZNF169	96102673	0.000000	0.05858	0.998000	0.56505	0.364000	0.29643	-0.100000	0.10990	0.372000	0.24591	0.491000	0.48974	AGG	A|0.985;T|0.015	0.015	strong		0.562	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
EPS15	2060	hgsc.bcm.edu	37	1	51869184	51869184	+	Silent	SNP	T	T	G	rs144030750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:51869184T>G	ENST00000371733.3	-	17	1794	c.1698A>C	c.(1696-1698)ctA>ctC	p.L566L	EPS15_ENST00000396122.4_Silent_p.L243L|EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000371730.2_Silent_p.L432L	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	566					cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CAGAAGGCAGTAGTTCAGGAC	0.338			T	MLL	ALL																																p.L566L		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15	72	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1698C						PASS	.	T	,	2,4404	6.2+/-15.9	0,2,2201	95.0	92.0	93.0		756,1698	2.2	0.8	1	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	EPS15	NM_001159969.1,NM_001981.2	,	0,3,6500	GG,GT,TT		0.0116,0.0454,0.0231	,	252/583,566/897	51869184	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon17			AGGCAGTAGTTCA	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.1698A>C	1.37:g.51869184T>G		242.0	0.0	0		203.0	104.0	0.512315	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			T|0.999;G|0.001	0.001	strong		0.338	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
MUC4	4585	hgsc.bcm.edu	37	3	195515412	195515412	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515412G>A	ENST00000463781.3	-	2	3498	c.3039C>T	c.(3037-3039)agC>agT	p.S1013S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S1013S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGGGCTGGTGACAG	0.572																																					p.S1013S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	4	Deletion - In frame(4)	stomach(4)	c.C3039T						PASS	.						52.0	28.0	36.0					3																	195515412		687	1591	2278	SO:0001819	synonymous_variant	4585	exon2			GGAAGGGCTGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3039C>T	3.37:g.195515412G>A		61.0	0.0	0		72.0	26.0	0.361111	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
VWA3B	200403	hgsc.bcm.edu	37	2	98928323	98928323	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:98928323C>T	ENST00000477737.1	+	27	3767	c.3563C>T	c.(3562-3564)cCa>cTa	p.P1188L	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1188										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CTCTTCTGGCCACTGAAAGAA	0.587																																					p.P1188L		Atlas-SNP	.											.	VWA3B	138	.	0			c.C3563T						PASS	.						24.0	30.0	28.0					2																	98928323		1936	4132	6068	SO:0001583	missense	200403	exon27			TCTGGCCACTGAA	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.3563C>T	2.37:g.98928323C>T	ENSP00000417955:p.Pro1188Leu	219.0	0.0	0		202.0	53.0	0.262376	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.676780	0.29783	.	.	ENSG00000168658	ENST00000477737;ENST00000358269	T	0.08458	3.09	3.79	2.9	0.33743	.	.	.	.	.	T	0.06096	0.0158	N	0.22421	0.69	0.09310	N	0.99999	B;B	0.32829	0.386;0.164	B;B	0.30716	0.119;0.056	T	0.33979	-0.9847	9	0.46703	T	0.11	.	8.715	0.34405	0.2264:0.7736:0.0:0.0	.	580;1188	Q502W6-5;Q502W6	.;VWA3B_HUMAN	L	1188;310	ENSP00000417955:P1188L	ENSP00000351009:P310L	P	+	2	0	VWA3B	98294755	0.053000	0.20554	0.002000	0.10522	0.008000	0.06430	1.626000	0.37039	1.155000	0.42497	0.491000	0.48974	CCA	.	.	none		0.587	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
NANOS2	339345	hgsc.bcm.edu	37	19	46417625	46417625	+	Silent	SNP	A	A	G	rs142962668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46417625A>G	ENST00000341294.2	-	1	411	c.327T>C	c.(325-327)caT>caC	p.H109H		NM_001029861.2	NP_001025032.1	P60321	NANO2_HUMAN	nanos homolog 2 (Drosophila)	109					germ-line stem cell maintenance (GO:0030718)|mRNA catabolic process (GO:0006402)|multicellular organismal development (GO:0007275)|negative regulation of meiosis (GO:0045835)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	mRNA binding (GO:0003729)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	6		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		ACTTGAGCGTATGGGCCTGGT	0.657													A|||	26	0.00519169	0.0008	0.0115	5008	,	,		14495	0.0		0.0149	False		,,,				2504	0.002				p.H109H		Atlas-SNP	.											.	NANOS2	10	.	0			c.T327C						PASS	.	A		8,4398	14.3+/-33.2	0,8,2195	61.0	56.0	58.0		327	2.5	1.0	19	dbSNP_134	58	92,8508	49.8+/-109.6	1,90,4209	no	coding-synonymous	NANOS2	NM_001029861.2		1,98,6404	GG,GA,AA		1.0698,0.1816,0.7689		109/139	46417625	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	339345	exon1			GAGCGTATGGGCC	BC042883	CCDS33056.1	19q13.32	2003-12-01				ENSG00000188425			23292	protein-coding gene	gene with protein product		608228				12947200, 12690449	Standard	NM_001029861		Approved	NOS2	uc002pdu.3	P60321		ENST00000341294.2:c.327T>C	19.37:g.46417625A>G		106.0	0.0	0		78.0	40.0	0.512821	NM_001029861	Q17R30|Q4G0P8	Silent	SNP	ENST00000341294.2	37	CCDS33056.1																																																																																			A|0.993;G|0.007	0.007	strong		0.657	NANOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461685.1		
TSC22D1	8848	hgsc.bcm.edu	37	13	45147305	45147305	+	Missense_Mutation	SNP	T	T	A	rs144252895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:45147305T>A	ENST00000458659.2	-	1	3396	c.2906A>T	c.(2905-2907)gAt>gTt	p.D969V	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'UTR	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	969					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TTACCTCTCATCCTCGCCATC	0.443													T|||	2	0.000399361	0.0	0.0	5008	,	,		19730	0.0		0.002	False		,,,				2504	0.0				p.D969V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A2906T						PASS	.	T	VAL/ASP	4,4402	8.1+/-20.4	0,4,2199	48.0	47.0	47.0		2906	5.2	1.0	13	dbSNP_134	47	15,8585	9.8+/-36.6	0,15,4285	yes	missense	TSC22D1	NM_183422.3	152	0,19,6484	AA,AT,TT		0.1744,0.0908,0.1461	benign	969/1074	45147305	19,12987	2203	4300	6503	SO:0001583	missense	8848	exon1			CTCTCATCCTCGC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.2906A>T	13.37:g.45147305T>A	ENSP00000397435:p.Asp969Val	91.0	0.0	0		90.0	47.0	0.522222	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.27	3.348233	0.61183	9.08E-4	0.001744	ENSG00000102804	ENST00000458659	T	0.35421	1.31	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000012	T	0.49098	0.1537	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50499	-0.8821	10	0.62326	D	0.03	.	14.3252	0.66515	0.0:0.0:0.0:1.0	.	969	Q15714	T22D1_HUMAN	V	969	ENSP00000397435:D969V	ENSP00000397435:D969V	D	-	2	0	TSC22D1	44045305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.659000	0.68010	2.163000	0.67991	0.459000	0.35465	GAT	T|0.998;A|0.002	0.002	strong		0.443	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
PVRL2	5819	hgsc.bcm.edu	37	19	45391553	45391553	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45391553A>G	ENST00000252483.5	+	9	1534	c.1534A>G	c.(1534-1536)Atc>Gtc	p.I512V	TOMM40_ENST00000426677.2_5'Flank|TOMM40_ENST00000252487.5_5'Flank|TOMM40_ENST00000405636.2_5'Flank|TOMM40_ENST00000592434.1_5'Flank|CTB-129P6.4_ENST00000585408.1_RNA	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	512					acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		GATCAACCCCATCTATGATGC	0.577																																					p.I512V		Atlas-SNP	.											.	PVRL2	58	.	0			c.A1534G						PASS	.						100.0	95.0	97.0					19																	45391553		1973	4146	6119	SO:0001583	missense	5819	exon9			AACCCCATCTATG	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1534A>G	19.37:g.45391553A>G	ENSP00000252483:p.Ile512Val	185.0	0.0	0		198.0	114.0	0.575758	NM_001042724	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	A	6.458	0.452676	0.12283	.	.	ENSG00000130202	ENST00000252483	D	0.89415	-2.51	4.67	2.59	0.31030	.	0.128913	0.36002	N	0.002850	T	0.79782	0.4505	L	0.29908	0.895	0.33232	D	0.556026	B	0.02656	0.0	B	0.08055	0.003	T	0.73248	-0.4043	10	0.31617	T	0.26	.	7.5527	0.27806	0.8183:0.0:0.1817:0.0	.	512	Q92692	PVRL2_HUMAN	V	512	ENSP00000252483:I512V	ENSP00000252483:I512V	I	+	1	0	PVRL2	50083393	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	1.310000	0.33551	0.392000	0.25172	-0.609000	0.04063	ATC	.	.	none		0.577	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
KIAA0368	23392	hgsc.bcm.edu	37	9	114172438	114172438	+	Silent	SNP	C	C	T	rs61744546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114172438C>T	ENST00000338205.5	-	22	2652	c.2433G>A	c.(2431-2433)ctG>ctA	p.L811L	KIAA0368_ENST00000374378.3_5'Flank|RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Silent_p.L989L			Q5VYK3	ECM29_HUMAN	KIAA0368	817					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CAATTTCACCCAGGGCTGTGC	0.443													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18148	0.0		0.0089	False		,,,				2504	0.0041				p.L989L		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G2967A						PASS	.	C		1,3801		0,1,1900	53.0	53.0	53.0		2967	5.0	1.0	9	dbSNP_129	53	101,8165		0,101,4032	no	coding-synonymous	KIAA0368	NM_001080398.1		0,102,5932	TT,TC,CC		1.2219,0.0263,0.8452		989/2018	114172438	102,11966	1901	4133	6034	SO:0001819	synonymous_variant	23392	exon24			TTCACCCAGGGCT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2433G>A	9.37:g.114172438C>T		212.0	0.0	0		159.0	63.0	0.396226	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.993;T|0.007	0.007	strong		0.443	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
FOXO1	2308	hgsc.bcm.edu	37	13	41134629	41134629	+	Silent	SNP	G	G	A	rs139436481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:41134629G>A	ENST00000379561.5	-	2	1383	c.999C>T	c.(997-999)acC>acT	p.T333T	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	333	Sufficient for interaction with NLK. {ECO:0000250}.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		CATCCTGTTCGGTCATAATGG	0.473													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		21916	0.0		0.004	False		,,,				2504	0.001				p.T333T		Atlas-SNP	.											.	FOXO1	110	.	0			c.C999T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	153.0	135.0	141.0		999	-3.3	0.7	13	dbSNP_134	141	62,8538	38.3+/-94.2	0,62,4238	no	coding-synonymous	FOXO1	NM_002015.3		0,74,6429	AA,AG,GG		0.7209,0.2724,0.569		333/656	41134629	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	2308	exon2			CTGTTCGGTCATA		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.999C>T	13.37:g.41134629G>A		173.0	0.0	0		157.0	81.0	0.515924	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	37	CCDS9371.1																																																																																			G|0.996;A|0.004	0.004	strong		0.473	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388944	1388944	+	Missense_Mutation	SNP	G	G	A	rs200759023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388944G>A	ENST00000324803.4	+	1	3605	c.645G>A	c.(643-645)atG>atA	p.M215I		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	215					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			ACGTGCCCATGTGGAGTGTTC	0.657													N|||	445	0.0888578	0.1619	0.0677	5008	,	,		12756	0.001		0.0934	False		,,,				2504	0.091				p.M215I		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G645A						PASS	.	G	ILE/MET	423,3903		140,143,1880	215.0	149.0	173.0		645	0.5	0.0	4		173	744,6886		259,226,3330	no	missense	CRIPAK	NM_175918.3	10	399,369,5210	AA,AG,GG		9.751,9.7781,9.7608	benign	215/447	1388944	1167,10789	2163	3815	5978	SO:0001583	missense	285464	exon1			GCCCATGTGGAGT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.645G>A	4.37:g.1388944G>A	ENSP00000323978:p.Met215Ile	61.0	0.0	0		12.0	12.0	1	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	g	4.551	0.102411	0.08731	0.097781	0.09751	ENSG00000179979	ENST00000324803	T	0.17528	2.27	1.41	0.509	0.16977	Post-SET domain (1);	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.12156	0.007	T	0.42865	-0.9426	9	0.18710	T	0.47	.	4.0015	0.09582	0.431:0.0:0.569:0.0	.	215	Q8N1N5	CRPAK_HUMAN	I	215	ENSP00000323978:M215I	ENSP00000323978:M215I	M	+	3	0	CRIPAK	1378944	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.348000	0.02629	0.169000	0.19679	-0.506000	0.04501	ATG	.	.	weak		0.657	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SYMPK	8189	hgsc.bcm.edu	37	19	46329624	46329624	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46329624G>A	ENST00000245934.7	-	17	2433	c.2189C>T	c.(2188-2190)tCc>tTc	p.S730F	SYMPK_ENST00000598155.1_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	730					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CAGGGCCTGGGAGCGCACCTG	0.547																																					p.S730F		Atlas-SNP	.											.	SYMPK	104	.	0			c.C2189T						PASS	.						89.0	73.0	78.0					19																	46329624		2203	4300	6503	SO:0001583	missense	8189	exon17			GCCTGGGAGCGCA	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.2189C>T	19.37:g.46329624G>A	ENSP00000245934:p.Ser730Phe	64.0	0.0	0		53.0	31.0	0.584906	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	37	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990202	0.54041	.	.	ENSG00000125755	ENST00000245934	T	0.34275	1.37	4.17	4.17	0.49024	Armadillo-like helical (1);Armadillo-type fold (1);	0.287715	0.34750	N	0.003702	T	0.35799	0.0944	L	0.55481	1.735	0.50039	D	0.999846	P;B	0.47604	0.898;0.396	P;B	0.44447	0.45;0.212	T	0.25257	-1.0137	10	0.72032	D	0.01	.	9.6197	0.39714	0.0:0.0:0.7915:0.2085	.	745;730	Q4LE61;Q92797	.;SYMPK_HUMAN	F	730	ENSP00000245934:S730F	ENSP00000245934:S730F	S	-	2	0	SYMPK	51021464	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.873000	0.48475	2.339000	0.79563	0.555000	0.69702	TCC	.	.	none		0.547	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
TLN2	83660	hgsc.bcm.edu	37	15	62939591	62939591	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62939591T>C	ENST00000561311.1	+	3	312	c.82T>C	c.(82-84)Tac>Cac	p.Y28H	RP11-625H11.1_ENST00000558940.1_5'Flank|TLN2_ENST00000306829.6_Missense_Mutation_p.Y28H|RP11-625H11.1_ENST00000560347.1_5'Flank			Q9Y4G6	TLN2_HUMAN	talin 2	28					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TACAGCTGTGTACGATGCGTG	0.493																																					p.Y28H		Atlas-SNP	.											.	TLN2	253	.	0			c.T82C						PASS	.						217.0	191.0	200.0					15																	62939591		2203	4300	6503	SO:0001583	missense	83660	exon1			GCTGTGTACGATG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.82T>C	15.37:g.62939591T>C	ENSP00000453508:p.Tyr28His	102.0	0.0	0		110.0	7.0	0.0636364	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420151	0.42918	.	.	ENSG00000171914	ENST00000306829	T	0.69561	-0.41	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	L	0.51914	1.62	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76724	-0.2854	10	0.42905	T	0.14	-10.8689	15.0808	0.72113	0.0:0.0:0.0:1.0	.	28	Q9Y4G6	TLN2_HUMAN	H	28	ENSP00000303476:Y28H	ENSP00000303476:Y28H	Y	+	1	0	TLN2	60726883	1.000000	0.71417	0.970000	0.41538	0.108000	0.19459	7.988000	0.88194	2.219000	0.72066	0.533000	0.62120	TAC	.	.	none		0.493	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
CCDC168	643677	hgsc.bcm.edu	37	13	103384712	103384712	+	Missense_Mutation	SNP	G	G	A	rs17507827	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103384712G>A	ENST00000322527.2	-	1	4447	c.4448C>T	c.(4447-4449)aCg>aTg	p.T1483M		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1483			T -> M (in dbSNP:rs17507827).														ACCACGCCCCGTGATATTAAG	0.348													G|||	87	0.0173722	0.0023	0.0173	5008	,	,		19185	0.001		0.0249	False		,,,				2504	0.047				p.T6112M		Atlas-SNP	.											.	.	.	.	0			c.C18335T						PASS	.	G	MET/THR	2,1382		0,2,690	187.0	149.0	160.0		18335	-0.7	0.0	13	dbSNP_123	160	61,3119		2,57,1531	yes	missense	CCDC168	NM_001146197.1	81	2,59,2221	AA,AG,GG		1.9182,0.1445,1.3804	possibly-damaging	6112/7082	103384712	63,4501	692	1590	2282	SO:0001583	missense	643677	exon4			CGCCCCGTGATAT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.4448C>T	13.37:g.103384712G>A	ENSP00000320232:p.Thr1483Met	207.0	1.0	0.00483092		190.0	95.0	0.5	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		30	0.013736263736263736	3	0.006097560975609756	6	0.016574585635359115	0	0.0	21	0.027704485488126648	G	12.04	1.819103	0.32145	0.001445	0.019182	ENSG00000175820	ENST00000322527	T	0.03745	3.82	3.31	-0.667	0.11395	.	.	.	.	.	T	0.00580	0.0019	N	0.14661	0.345	0.09310	N	1	P	0.47350	0.894	B	0.34180	0.177	T	0.44452	-0.9327	9	0.72032	D	0.01	.	0.6482	0.00822	0.2357:0.1909:0.378:0.1953	rs17507827;rs52826516;rs17507827	1483	Q8NDH2	CC168_HUMAN	M	1483	ENSP00000320232:T1483M	ENSP00000320232:T1483M	T	-	2	0	CCDC168	102182713	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.416000	0.07097	-0.190000	0.10465	-1.136000	0.01936	ACG	G|0.983;A|0.017	0.017	strong		0.348	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
NUP214	8021	hgsc.bcm.edu	37	9	134073622	134073622	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134073622G>C	ENST00000359428.5	+	29	4885	c.4741G>C	c.(4741-4743)Gca>Cca	p.A1581P	NUP214_ENST00000451030.1_Missense_Mutation_p.A1582P|NUP214_ENST00000483497.2_Missense_Mutation_p.A407P|NUP214_ENST00000411637.2_Missense_Mutation_p.A1571P			P35658	NU214_HUMAN	nucleoporin 214kDa	1581	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CAGGACGGAGGCAGTACCACC	0.572			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.A1581P	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G4741C						PASS	.						75.0	78.0	77.0					9																	134073622		2203	4300	6503	SO:0001583	missense	8021	exon29			ACGGAGGCAGTAC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4741G>C	9.37:g.134073622G>C	ENSP00000352400:p.Ala1581Pro	98.0	0.0	0		106.0	30.0	0.283019	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989651	0.35131	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.50277	0.96;0.79;0.79;0.79;0.75	5.44	2.63	0.31362	.	0.924894	0.08948	N	0.870525	T	0.26593	0.0650	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.001;0.001;0.001;0.001;0.003	B;B;B;B;B	0.11329	0.006;0.003;0.003;0.003;0.004	T	0.26503	-1.0101	10	0.22109	T	0.4	-0.1467	7.7656	0.28978	0.0:0.1889:0.4379:0.3732	.	407;1010;1175;1571;1581	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	P	1581;1571;1582;1560;1175;1010;407;358;358	ENSP00000352400:A1581P;ENSP00000396576:A1571P;ENSP00000405014:A1582P;ENSP00000436793:A407P;ENSP00000435364:A358P	ENSP00000352400:A1581P	A	+	1	0	NUP214	133063443	0.000000	0.05858	0.033000	0.17914	0.128000	0.20619	-0.086000	0.11233	0.285000	0.22329	-0.475000	0.04921	GCA	.	.	none		0.572	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
GRAMD1A	57655	hgsc.bcm.edu	37	19	35504539	35504539	+	Missense_Mutation	SNP	C	C	T	rs201394899		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35504539C>T	ENST00000317991.5	+	9	1006	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R265C|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.R38C|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R359C|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	272						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AGTGGGTTCGCGCCGTGGCCA	0.647																																					p.R272C		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C814T						PASS	.	C	CYS/ARG,CYS/ARG	2,4180		0,2,2089	26.0	31.0	29.0		793,814	2.5	0.2	19		29	9,8429		0,9,4210	yes	missense,missense	GRAMD1A	NM_001136199.1,NM_020895.3	180,180	0,11,6299	TT,TC,CC		0.1067,0.0478,0.0872	probably-damaging,probably-damaging	265/714,272/725	35504539	11,12609	2091	4219	6310	SO:0001583	missense	57655	exon9			GGTTCGCGCCGTG	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.814C>T	19.37:g.35504539C>T	ENSP00000441032:p.Arg272Cys	92.0	0.0	0		101.0	57.0	0.564356	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509632	0.27036	4.78E-4	0.001067	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.52754	0.65;1.91;1.9	4.71	2.5	0.30297	.	0.934879	0.09007	N	0.862100	T	0.52289	0.1725	L	0.29908	0.895	0.09310	N	0.999997	P;D;D;D;P	0.76494	0.675;0.975;0.993;0.999;0.575	B;B;P;D;B	0.65987	0.039;0.249;0.616;0.94;0.068	T	0.37267	-0.9713	10	0.59425	D	0.04	.	6.9609	0.24597	0.1794:0.726:0.0:0.0946	.	272;272;38;265;359	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	C	359;38;272;265	ENSP00000423728:R38C;ENSP00000441032:R272C;ENSP00000439267:R265C	ENSP00000441032:R272C	R	+	1	0	GRAMD1A	40196379	0.680000	0.27605	0.169000	0.22859	0.103000	0.19146	1.547000	0.36190	0.542000	0.28846	0.485000	0.47835	CGC	.	.	weak		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	
RBP3	5949	hgsc.bcm.edu	37	10	48388508	48388508	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:48388508G>C	ENST00000224600.4	-	1	2483	c.2370C>G	c.(2368-2370)tcC>tcG	p.S790S	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	790	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GGATGGCCGTGGAGTAGCTGC	0.617																																					p.S790S		Atlas-SNP	.											.	RBP3	152	.	0			c.C2370G						PASS	.						28.0	26.0	27.0					10																	48388508		2201	4298	6499	SO:0001819	synonymous_variant	5949	exon1			GGCCGTGGAGTAG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2370C>G	10.37:g.48388508G>C		153.0	0.0	0		144.0	60.0	0.416667	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																			.	.	none		0.617	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
NOTCH1	4851	hgsc.bcm.edu	37	9	139413908	139413908	+	Silent	SNP	C	C	T	rs2229975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139413908C>T	ENST00000277541.6	-	5	927	c.852G>A	c.(850-852)ccG>ccA	p.P284P	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	284	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TCCACTCTGGCGGGCAGCGGC	0.617			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			C|||	612	0.122204	0.087	0.0793	5008	,	,		16798	0.0962		0.1163	False		,,,				2504	0.2331				p.P284P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.G852A						PASS	.	C		400,3480		29,342,1569	54.0	68.0	64.0		852	-10.4	0.0	9	dbSNP_98	64	1122,7160		75,972,3094	no	coding-synonymous	NOTCH1	NM_017617.3		104,1314,4663	TT,TC,CC		13.5475,10.3093,12.5144		284/2556	139413908	1522,10640	1940	4141	6081	SO:0001819	synonymous_variant	4851	exon5			CTCTGGCGGGCAG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.852G>A	9.37:g.139413908C>T		97.0	0.0	0		85.0	38.0	0.447059	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.113;G|0.000;C|0.886	0.113	strong		0.617	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860579	27860579	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27860579G>A	ENST00000359611.2	-	1	384	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	117						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)	14						TTCTTGGGGAGCAGTACGGCC	0.507																																					p.L117F		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.C349T						PASS	.						131.0	126.0	128.0					6																	27860579		2203	4300	6503	SO:0001583	missense	8336	exon1			TGGGGAGCAGTAC	X57138	CCDS4639.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000233224	ENSG00000278677		"""Histones / Replication-dependent"""	4735	protein-coding gene	gene with protein product		602796	"""H2A histone family, member N"", ""histone 1, H2am"""	H2AFN		1768865, 9439656, 12408966	Standard	NM_003514		Approved	H2A/n, H2A.1	uc003nkb.1	P0C0S8	OTTHUMG00000014494	ENST00000359611.2:c.349C>T	6.37:g.27860579G>A	ENSP00000352627:p.Leu117Phe	214.0	0.0	0		181.0	41.0	0.226519	NM_003514	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359611.2	37	CCDS4639.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.770382	0.31320	.	.	ENSG00000233224	ENST00000359611	T	0.52057	0.68	4.06	3.19	0.36642	.	0.000000	0.26130	U	0.026178	T	0.48840	0.1522	M	0.79475	2.455	0.32139	N	0.585724	.	.	.	.	.	.	T	0.54351	-0.8307	8	0.87932	D	0	.	11.3928	0.49824	0.0916:0.0:0.9084:0.0	.	.	.	.	F	117	ENSP00000352627:L117F	ENSP00000352627:L117F	L	-	1	0	HIST1H2AM	27968558	1.000000	0.71417	1.000000	0.80357	0.154000	0.21943	3.207000	0.51106	1.298000	0.44778	-0.136000	0.14681	CTC	.	.	none		0.507	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514	
RTL1	388015	hgsc.bcm.edu	37	14	101350274	101350274	+	Silent	SNP	C	C	T	rs61993320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:101350274C>T	ENST00000534062.1	-	1	910	c.852G>A	c.(850-852)ctG>ctA	p.L284L	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	284					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CTGCCACACGCAGTGCCTGGC	0.592													C|||	60	0.0119808	0.0008	0.0245	5008	,	,		18928	0.0		0.0328	False		,,,				2504	0.0092				p.L284L		Atlas-SNP	.											.	RTL1	120	.	0			c.G852A						PASS	.	C		6,1378		0,6,686	57.0	53.0	54.0		852	0.5	0.1	14	dbSNP_129	54	104,3078		0,104,1487	no	coding-synonymous	RTL1	NM_001134888.2		0,110,2173	TT,TC,CC		3.2684,0.4335,2.4091		284/1359	101350274	110,4456	692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			CACACGCAGTGCC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.852G>A	14.37:g.101350274C>T		69.0	0.0	0		49.0	22.0	0.44898	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																			C|0.983;T|0.017	0.017	strong		0.592	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
ZNF106	64397	hgsc.bcm.edu	37	15	42743209	42743209	+	Missense_Mutation	SNP	G	G	A	rs201738274		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:42743209G>A	ENST00000263805.4	-	2	1518	c.1192C>T	c.(1192-1194)Cgt>Tgt	p.R398C	ZNF106_ENST00000565611.1_Intron|ZNF106_ENST00000565380.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	398					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GGGGAATTACGTGTTTCATCA	0.408																																					p.R398C		Atlas-SNP	.											.	ZFP106	117	.	0			c.C1192T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	310.0	293.0	299.0		1192	0.3	0.0	15		299	2,8596	2.2+/-6.3	0,2,4297	no	missense	ZFP106	NM_022473.1	180	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	398/1884	42743209	2,13002	2203	4299	6502	SO:0001583	missense	64397	exon2			AATTACGTGTTTC	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1192C>T	15.37:g.42743209G>A	ENSP00000263805:p.Arg398Cys	158.0	0.0	0		187.0	37.0	0.197861	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	3.212	-0.161477	0.06502	0.0	2.33E-4	ENSG00000103994	ENST00000263805	T	0.55760	0.5	5.24	0.285	0.15705	.	1.426730	0.03878	N	0.276673	T	0.29556	0.0737	N	0.08118	0	0.09310	N	1	P;P	0.45078	0.85;0.476	B;B	0.36885	0.235;0.118	T	0.25710	-1.0124	10	0.66056	D	0.02	-0.4934	4.7175	0.12903	0.0:0.4549:0.2139:0.3312	.	181;398	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	C	398	ENSP00000263805:R398C	ENSP00000263805:R398C	R	-	1	0	ZFP106	40530501	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.176000	0.16782	0.120000	0.18254	-0.269000	0.10298	CGT	G|0.999;A|0.001	0.001	weak		0.408	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221737	67221737	+	Missense_Mutation	SNP	G	G	A	rs149684674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67221737G>A	ENST00000314586.6	-	5	671	c.431C>T	c.(430-432)cCg>cTg	p.P144L	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	144	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CACTGCAGCCGGCACTAATGA	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19157	0.0		0.0	False		,,,				2504	0.0				p.P144L		Atlas-SNP	.											LOC283849,caecum,carcinoma,0,2	EXOC3L1	52	2	0			c.C431T						PASS	.	G	LEU/PRO	1,4393		0,1,2196	60.0	70.0	67.0		431	5.7	1.0	16	dbSNP_134	67	12,8588		0,12,4288	yes	missense	EXOC3L1	NM_178516.3	98	0,13,6484	AA,AG,GG		0.1395,0.0228,0.1	probably-damaging	144/747	67221737	13,12981	2197	4300	6497	SO:0001583	missense	283849	exon5			GCAGCCGGCACTA	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.431C>T	16.37:g.67221737G>A	ENSP00000325674:p.Pro144Leu	73.0	0.0	0		83.0	45.0	0.542169	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.54	3.151062	0.57151	2.28E-4	0.001395	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.22134	2.77;1.97	5.74	5.74	0.90152	.	0.179126	0.49916	D	0.000134	T	0.46288	0.1385	M	0.77103	2.36	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69307	0.963;0.92;0.95	T	0.34329	-0.9833	10	0.46703	T	0.11	-20.7533	14.2617	0.66090	0.0:0.0:0.8505:0.1495	.	83;83;144	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	L	144;83;88	ENSP00000325674:P144L;ENSP00000439910:P83L	ENSP00000325008:P88L	P	-	2	0	EXOC3L1	65779238	0.976000	0.34144	0.962000	0.40283	0.656000	0.38851	1.800000	0.38833	2.716000	0.92895	0.650000	0.86243	CCG	G|0.999;A|0.001	0.001	strong		0.592	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
DPP4	1803	hgsc.bcm.edu	37	2	162876789	162876789	+	Silent	SNP	T	T	C	rs200990780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:162876789T>C	ENST00000360534.3	-	14	1754	c.1194A>G	c.(1192-1194)acA>acG	p.T398T	DPP4_ENST00000491591.1_5'Flank	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	398					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	AGGTGCCTTTTGTAATAAATG	0.323																																					p.T398T		Atlas-SNP	.											.	DPP4	90	.	0			c.A1194G						PASS	.						95.0	90.0	92.0					2																	162876789		2203	4300	6503	SO:0001819	synonymous_variant	1803	exon14			GCCTTTTGTAATA	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1194A>G	2.37:g.162876789T>C		85.0	0.0	0		73.0	35.0	0.479452	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			.	.	weak		0.323	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		
MUC4	4585	hgsc.bcm.edu	37	3	195506661	195506661	+	Silent	SNP	G	G	C	rs143659849	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506661G>C	ENST00000463781.3	-	2	12249	c.11790C>G	c.(11788-11790)tcC>tcG	p.S3930S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S3930S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CATGTCCTGTGGATGCCGAGG	0.582													.|||	177	0.0353435	0.0129	0.0807	5008	,	,		11453	0.0149		0.0845	False		,,,				2504	0.0041				p.S3930S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11790G						PASS	.						23.0	21.0	22.0					3																	195506661		487	1106	1593	SO:0001819	synonymous_variant	4585	exon2			TCCTGTGGATGCC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11790C>G	3.37:g.195506661G>C		203.0	0.0	0		95.0	89.0	0.936842	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.964;C|0.036	0.036	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62397114T>C	ENST00000356638.3	-	15	1796	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	GANAB_ENST00000534779.1_Missense_Mutation_p.M502V|GANAB_ENST00000346178.4_Missense_Mutation_p.M616V|GANAB_ENST00000540933.1_Missense_Mutation_p.M497V	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	594					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	GGGCGTTCCATGCCCCCAGAG	0.597													T|||	89	0.0177716	0.0008	0.0389	5008	,	,		20960	0.001		0.0547	False		,,,				2504	0.0051				p.M616V	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.A1846G						PASS	.	T	VAL/MET,VAL/MET	28,4376	31.7+/-61.6	0,28,2174	37.0	37.0	37.0		1780,1846	-4.7	0.1	11	dbSNP_131	37	362,8236	115.7+/-175.5	10,342,3947	yes	missense,missense	GANAB	NM_198334.1,NM_198335.2	21,21	10,370,6121	CC,CT,TT		4.2103,0.6358,2.9995	benign,benign	594/945,616/967	62397114	390,12612	2202	4299	6501	SO:0001583	missense	23193	exon16			GTTCCATGCCCCC	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.1780A>G	11.37:g.62397114T>C	ENSP00000349053:p.Met594Val	193.0	0.0	0		151.0	29.0	0.192053	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	53	0.024267399267399268	0	0.0	14	0.03867403314917127	0	0.0	39	0.051451187335092345	T	7.943	0.743196	0.15642	0.006358	0.042103	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.31	-4.7	0.03288	Glycoside hydrolase, superfamily (1);	0.908173	0.09646	N	0.774318	T	0.25419	0.0618	N	0.00368	-1.59	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.53961	-0.8364	10	0.29301	T	0.29	0.5168	8.9385	0.35715	0.0:0.4806:0.1198:0.3996	.	480;502;594;616	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	V	616;594;502;497	ENSP00000340466:M616V;ENSP00000349053:M594V;ENSP00000435306:M502V;ENSP00000442962:M497V	ENSP00000340466:M616V	M	-	1	0	GANAB	62153690	0.000000	0.05858	0.133000	0.22050	0.980000	0.70556	-1.352000	0.02619	-0.731000	0.04862	0.533000	0.62120	ATG	T|0.974;C|0.026	0.026	strong		0.597	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334	
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77911745C>T	ENST00000529308.1	+	6	1349	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	USP35_ENST00000530535.1_Intron|USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_Missense_Mutation_p.S94L|USP35_ENST00000441408.2_5'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			AAGGAGGACTCGAACTCGGGG	0.647													C|||	19	0.00379393	0.0015	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0082				p.S363L		Atlas-SNP	.											USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	0			c.C1088T						PASS	.	C	LEU/SER	5,3907		0,5,1951	46.0	52.0	50.0		1088	4.7	1.0	11	dbSNP_134	50	46,8202		0,46,4078	yes	missense	USP35	NM_020798.2	145	0,51,6029	TT,TC,CC		0.5577,0.1278,0.4194	benign	363/1019	77911745	51,12109	1956	4124	6080	SO:0001583	missense	57558	exon6			AGGACTCGAACTC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1088C>T	11.37:g.77911745C>T	ENSP00000431876:p.Ser363Leu	109.0	0.0	0		100.0	20.0	0.2	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	13.79	2.343705	0.41498	0.001278	0.005577	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68181	-0.24;-0.31;3.37	4.73	4.73	0.59995	Armadillo-like helical (1);	0.000000	0.52532	D	0.000071	T	0.40448	0.1117	N	0.19112	0.55	0.80722	D	1	B	0.33739	0.422	B	0.22753	0.041	T	0.43925	-0.9361	10	0.18276	T	0.48	-15.0401	17.9135	0.88942	0.0:1.0:0.0:0.0	.	363	Q9P2H5	UBP35_HUMAN	L	119;363;94	ENSP00000436001:S119L;ENSP00000431876:S363L;ENSP00000434942:S94L	ENSP00000434942:S94L	S	+	2	0	USP35	77589393	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.484000	0.66844	2.461000	0.83175	0.561000	0.74099	TCG	C|0.996;T|0.004	0.004	strong		0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
FAM171A1	221061	hgsc.bcm.edu	37	10	15256440	15256440	+	Missense_Mutation	SNP	C	C	T	rs150647132		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:15256440C>T	ENST00000378116.4	-	8	1153	c.1147G>A	c.(1147-1149)Ggc>Agc	p.G383S	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	383						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						TCGGGGCGGCCGTGGCTGGTG	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15789	0.0		0.0	False		,,,				2504	0.0				p.G383S		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1147A						PASS	.	C	SER/GLY	0,4406		0,0,2203	39.0	45.0	43.0		1147	-2.7	0.2	10	dbSNP_134	43	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FAM171A1	NM_001010924.1	56	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	383/891	15256440	10,12996	2203	4300	6503	SO:0001583	missense	221061	exon8			GGCGGCCGTGGCT	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 38"""	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1147G>A	10.37:g.15256440C>T	ENSP00000367356:p.Gly383Ser	71.0	0.0	0		73.0	34.0	0.465753	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	4.340	0.062493	0.08388	0.0	0.001163	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.32023	1.47	4.96	-2.72	0.05968	.	0.300803	0.30695	N	0.009079	T	0.15696	0.0378	N	0.19112	0.55	0.22796	N	0.998728	B	0.15141	0.012	B	0.12156	0.007	T	0.20338	-1.0278	10	0.21014	T	0.42	-16.5191	11.3681	0.49684	0.0:0.4139:0.0:0.5861	.	383	Q5VUB5	F1711_HUMAN	S	383;384	ENSP00000367356:G383S	ENSP00000367356:G383S	G	-	1	0	FAM171A1	15296446	.	.	0.169000	0.22859	0.344000	0.29017	.	.	-0.806000	0.04398	-0.983000	0.02560	GGC	C|0.999;T|0.001	0.001	strong		0.597	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
TRIM34	53840	hgsc.bcm.edu	37	11	5653866	5653866	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5653866A>G	ENST00000514226.1	+	2	642	c.305A>G	c.(304-306)gAg>gGg	p.E102G	TRIM34_ENST00000429814.2_Missense_Mutation_p.E102G|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.E102G|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.E456G	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	102					positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATCATGGAGAGAAACTCCTA	0.502																																					p.E456G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A1367G						PASS	.						75.0	69.0	71.0					11																	5653866		2201	4297	6498	SO:0001583	missense	445372	exon8			ATGGAGAGAAACT	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10063	protein-coding gene	gene with protein product		605684	"""tripartite motif-containing 34"""	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.305A>G	11.37:g.5653866A>G	ENSP00000422947:p.Glu102Gly	107.0	0.0	0		90.0	49.0	0.544444	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727557	0.69074	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	3.53	3.53	0.40419	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, B-box (3);	0.232880	0.22139	N	0.064076	T	0.76321	0.3971	H	0.97051	3.93	0.30699	N	0.750484	D;D;D	0.76494	0.999;0.998;0.983	D;D;P	0.76071	0.984;0.987;0.836	T	0.79257	-0.1878	10	0.87932	D	0	.	10.6794	0.45804	1.0:0.0:0.0:0.0	.	102;102;456	Q9BYJ4-2;Q9BYJ4;B2RNG4	.;TRI34_HUMAN;.	G	456;102;102;102;456	ENSP00000422947:E102G;ENSP00000402595:E102G;ENSP00000395982:E102G;ENSP00000346916:E456G	ENSP00000402595:E102G	E	+	2	0	TRIM34;TRIM6-TRIM34	5610442	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	8.127000	0.89593	1.847000	0.53656	0.454000	0.30748	GAG	.	.	none		0.502	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	
EXOSC8	11340	hgsc.bcm.edu	37	13	37577073	37577073	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:37577073T>C	ENST00000389704.3	+	4	386	c.121T>C	c.(121-123)Tca>Cca	p.S41P	EXOSC8_ENST00000489088.1_3'UTR|ALG5_ENST00000496689.1_5'Flank	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	41					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		CTTTTCAGGTTCAATTAGTAC	0.318																																					p.S41P		Atlas-SNP	.											.	EXOSC8	16	.	0			c.T121C						PASS	.						107.0	102.0	103.0					13																	37577073		2202	4298	6500	SO:0001583	missense	11340	exon4			TCAGGTTCAATTA	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"""CBP-interacting protein 3"", ""Opa interacting protein 2"""	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.121T>C	13.37:g.37577073T>C	ENSP00000374354:p.Ser41Pro	153.0	0.0	0		120.0	5.0	0.0416667	NM_181503	O43480|Q5TBA5	Missense_Mutation	SNP	ENST00000389704.3	37	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629298	0.67015	.	.	ENSG00000120699	ENST00000389704;ENST00000379809	T	0.63255	-0.03	5.65	4.48	0.54585	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.108320	0.64402	D	0.000003	T	0.64405	0.2595	L	0.55017	1.72	0.58432	D	0.999998	P;P	0.46064	0.864;0.872	P;P	0.51229	0.663;0.585	T	0.59941	-0.7359	10	0.24483	T	0.36	-15.5735	11.4062	0.49900	0.0:0.0701:0.0:0.9299	.	41;41	Q5JXM0;Q96B26	.;EXOS8_HUMAN	P	41	ENSP00000374354:S41P	ENSP00000369137:S41P	S	+	1	0	EXOSC8	36475073	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	1.098000	0.41479	0.533000	0.62120	TCA	.	.	none		0.318	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503	
MCCD1	401250	hgsc.bcm.edu	37	6	31496834	31496834	+	Missense_Mutation	SNP	C	C	T	rs146742941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31496834C>T	ENST00000376191.2	+	1	341	c.43C>T	c.(43-45)Cgc>Tgc	p.R15C	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	15						mitochondrion (GO:0005739)				skin(1)	1						CCATTTCCTTCGCCTCCTTCT	0.627																																					p.R15C		Atlas-SNP	.											MCCD1,NS,carcinoma,-1,1	MCCD1	3	1	0			c.C43T						PASS	.	C	CYS/ARG	0,3022		0,0,1511	173.0	128.0	144.0		43	0.8	0.1	6	dbSNP_134	144	2,5416		0,2,2707	yes	missense	MCCD1	NM_001011700.2	180	0,2,4218	TT,TC,CC		0.0369,0.0,0.0237	probably-damaging	15/120	31496834	2,8438	1511	2709	4220	SO:0001583	missense	401250	exon1			TTCCTTCGCCTCC		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.43C>T	6.37:g.31496834C>T	ENSP00000365362:p.Arg15Cys	68.0	0.0	0		46.0	25.0	0.543478	NM_001011700	A2AB29|A2RUP7|B0UZB2|Q7RTY2	Missense_Mutation	SNP	ENST00000376191.2	37	CCDS34396.1	.	.	.	.	.	.	.	.	.	.	c	0.103	-1.148811	0.01714	0.0	3.69E-4	ENSG00000204511	ENST00000376191	T	0.25250	1.81	0.748	0.748	0.18376	.	1.197690	0.06338	N	0.707425	T	0.06645	0.0170	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.41770	-0.9490	9	0.72032	D	0.01	.	.	.	.	.	15	P59942	MCCD1_HUMAN	C	15	ENSP00000365362:R15C	ENSP00000365362:R15C	R	+	1	0	MCCD1	31604813	0.000000	0.05858	0.062000	0.19696	0.029000	0.11900	-1.047000	0.03521	0.691000	0.31592	0.555000	0.69702	CGC	C|1.000;T|0.000	0.000	strong		0.627	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1		
GNAT3	346562	hgsc.bcm.edu	37	7	80117993	80117993	+	Splice_Site	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:80117993C>A	ENST00000398291.3	-	3	255		c.e3-1		CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						ATGGATGATCCTATAATTTAA	0.318																																					.		Atlas-SNP	.											.	GNAT3	65	.	0			c.162-1G>T						PASS	.						89.0	75.0	80.0					7																	80117993		1830	4083	5913	SO:0001630	splice_region_variant	346562	exon4			ATGATCCTATAAT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.162-1G>T	7.37:g.80117993C>A		76.0	0.0	0		61.0	13.0	0.213115	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Splice_Site	SNP	ENST00000398291.3	37	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390611	0.82902	.	.	ENSG00000214415	ENST00000398291	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7634	0.88470	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GNAT3	79955929	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.127000	0.77210	2.720000	0.93068	0.650000	0.86243	.	.	.	none		0.318	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	Intron
PLXNA4	91584	hgsc.bcm.edu	37	7	131883311	131883311	+	Missense_Mutation	SNP	C	C	T	rs62622406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131883311C>T	ENST00000359827.3	-	13	3633	c.2671G>A	c.(2671-2673)Gcc>Acc	p.A891T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A891T			Q9HCM2	PLXA4_HUMAN	plexin A4	891	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACATGGGAGGCGATGTCGCGA	0.577													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		19542	0.0		0.0109	False		,,,				2504	0.0041				p.A891T		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G2671A						PASS	.	C	THR/ALA	7,3955		0,7,1974	74.0	76.0	75.0		2671	5.9	1.0	7	dbSNP_129	75	113,8235		0,113,4061	yes	missense	PLXNA4	NM_020911.1	58	0,120,6035	TT,TC,CC		1.3536,0.1767,0.9748	benign	891/1895	131883311	120,12190	1981	4174	6155	SO:0001583	missense	91584	exon13			GGGAGGCGATGTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2671G>A	7.37:g.131883311C>T	ENSP00000352882:p.Ala891Thr	42.0	0.0	0		45.0	21.0	0.466667	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.07	1.531317	0.27387	0.001767	0.013536	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.75821	-0.97;-0.97	5.94	5.94	0.96194	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.168437	0.52532	D	0.000077	T	0.60586	0.2280	L	0.43923	1.385	0.36252	D	0.853963	P	0.40250	0.709	B	0.37239	0.244	T	0.66693	-0.5859	10	0.13108	T	0.6	.	20.3658	0.98878	0.0:1.0:0.0:0.0	rs62622406	891	Q9HCM2	PLXA4_HUMAN	T	891	ENSP00000323194:A891T;ENSP00000352882:A891T	ENSP00000323194:A891T	A	-	1	0	PLXNA4	131533851	0.986000	0.35501	0.999000	0.59377	0.242000	0.25591	2.642000	0.46596	2.820000	0.97059	0.650000	0.86243	GCC	C|0.991;T|0.009	0.009	strong		0.577	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
VPS52	6293	hgsc.bcm.edu	37	6	33236826	33236826	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33236826A>G	ENST00000445902.2	-	6	731	c.513T>C	c.(511-513)ctT>ctC	p.L171L	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Silent_p.L46L|RPS18_ENST00000439602.2_5'Flank	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	171					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GACCATCAACAAGCTCCCCAA	0.547																																					p.L171L		Atlas-SNP	.											.	VPS52	56	.	0			c.T513C						PASS	.						204.0	179.0	188.0					6																	33236826		1511	2709	4220	SO:0001819	synonymous_variant	6293	exon6			ATCAACAAGCTCC	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.513T>C	6.37:g.33236826A>G		165.0	0.0	0		156.0	64.0	0.410256	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			.	.	none		0.547	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S|TH_ENST00000352909.3_Silent_p.S62S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17.0	20.0	19.0		186,279,267	-1.0	0.0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.279G>A	11.37:g.2191006C>T		75.0	0.0	0		107.0	90.0	0.841121	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33548043	33548043	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33548043T>C	ENST00000290943.6	+	9	1167	c.1071T>C	c.(1069-1071)agT>agC	p.S357S		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	357										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						AAAATGACAGTCTCAGAAAGG	0.284																																					p.S356S		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T1068C						PASS	.																																			SO:0001819	synonymous_variant	441459	exon9			TGACAGTCTCAGA			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.1071T>C	9.37:g.33548043T>C		115.0	0.0	0		106.0	21.0	0.198113	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				.	.	none		0.284	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
KIAA0368	23392	hgsc.bcm.edu	37	9	114124354	114124354	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114124354C>A	ENST00000338205.5	-	49	5695	c.5476G>T	c.(5476-5478)Gag>Tag	p.E1826*	KIAA0368_ENST00000374378.3_Intron|KIAA0368_ENST00000259335.4_Nonsense_Mutation_p.E2004*			Q5VYK3	ECM29_HUMAN	KIAA0368	1832					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GCTGCTTTCTCCTGCAGTTCA	0.428																																					p.E2004X		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G6010T						PASS	.						130.0	133.0	132.0					9																	114124354		1912	4132	6044	SO:0001587	stop_gained	23392	exon51			CTTTCTCCTGCAG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.5476G>T	9.37:g.114124354C>A	ENSP00000339889:p.Glu1826*	161.0	0.0	0		128.0	28.0	0.21875	NM_001080398	O15074|Q8WU82	Nonsense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	C	47	13.552294	0.99749	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	.	.	.	5.93	5.93	0.95920	.	0.090694	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	0.3296	20.3465	0.98790	0.0:1.0:0.0:0.0	.	.	.	.	X	1826;2004;1301	.	ENSP00000259335:E2004X	E	-	1	0	KIAA0368	113164175	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.127000	0.77210	2.798000	0.96311	0.655000	0.94253	GAG	.	.	none		0.428	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
DNAJC9	23234	hgsc.bcm.edu	37	10	75006868	75006868	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75006868G>A	ENST00000372950.4	-	1	1752	c.80C>T	c.(79-81)tCc>tTc	p.S27F	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA|MRPS16_ENST00000416782.2_3'UTR|DNAJC9-AS1_ENST00000513954.1_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	27	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CTCGCCGTCGGAGGCCTCGCG	0.697																																					p.S27F		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C80T						PASS	.						13.0	13.0	13.0					10																	75006868		2188	4280	6468	SO:0001583	missense	23234	exon1			CCGTCGGAGGCCT	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.80C>T	10.37:g.75006868G>A	ENSP00000362041:p.Ser27Phe	79.0	0.0	0		88.0	42.0	0.477273	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	22.8	4.333978	0.81801	.	.	ENSG00000213551	ENST00000372950	T	0.37058	1.22	5.65	4.74	0.60224	Heat shock protein DnaJ, N-terminal (5);	0.527076	0.21432	N	0.074639	T	0.69522	0.3120	H	0.96518	3.835	0.80722	D	1	D	0.60160	0.987	D	0.65684	0.937	T	0.78851	-0.2041	10	0.87932	D	0	-22.6147	12.6301	0.56653	0.0:0.1665:0.8335:0.0	.	27	Q8WXX5	DNJC9_HUMAN	F	27	ENSP00000362041:S27F	ENSP00000362041:S27F	S	-	2	0	DNAJC9	74676874	0.888000	0.30383	0.842000	0.33263	0.371000	0.29859	4.349000	0.59385	1.377000	0.46286	0.586000	0.80456	TCC	.	.	none		0.697	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
MAML1	9794	hgsc.bcm.edu	37	5	179201226	179201226	+	Missense_Mutation	SNP	A	A	C	rs148053500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179201226A>C	ENST00000292599.3	+	5	2662	c.2399A>C	c.(2398-2400)aAc>aCc	p.N800T	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TATGGGCAGAACTCTCTGGGA	0.612													A|||	9	0.00179712	0.0015	0.0058	5008	,	,		17029	0.0		0.003	False		,,,				2504	0.0				p.N800T		Atlas-SNP	.											.	MAML1	118	.	0			c.A2399C						PASS	.	A	THR/ASN	4,4402	4.2+/-10.8	0,4,2199	35.0	36.0	35.0		2399	1.3	1.0	5	dbSNP_134	35	27,8573	19.2+/-60.6	0,27,4273	yes	missense	MAML1	NM_014757.4	65	0,31,6472	CC,CA,AA		0.314,0.0908,0.2384	possibly-damaging	800/1017	179201226	31,12975	2203	4300	6503	SO:0001583	missense	9794	exon5			GGCAGAACTCTCT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2399A>C	5.37:g.179201226A>C	ENSP00000292599:p.Asn800Thr	46.0	0.0	0		39.0	25.0	0.641026	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	A	18.11	3.550143	0.65311	9.08E-4	0.00314	ENSG00000161021	ENST00000292599	T	0.25749	1.78	4.94	1.31	0.21738	.	0.192835	0.45606	D	0.000351	T	0.26085	0.0636	L	0.58101	1.795	0.46901	D	0.999241	D	0.69078	0.997	P	0.59056	0.851	T	0.08911	-1.0699	10	0.17832	T	0.49	-16.6951	8.3868	0.32505	0.6881:0.0:0.3119:0.0	.	800	Q92585	MAML1_HUMAN	T	800	ENSP00000292599:N800T	ENSP00000292599:N800T	N	+	2	0	MAML1	179133832	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.050000	0.41297	0.260000	0.21731	0.379000	0.24179	AAC	A|0.997;C|0.003	0.003	strong		0.612	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
BIN2	51411	hgsc.bcm.edu	37	12	51695839	51695839	+	Missense_Mutation	SNP	T	T	C	rs143984628		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:51695839T>C	ENST00000267012.4	-	5	434	c.373A>G	c.(373-375)Atg>Gtg	p.M125V	BIN2_ENST00000604560.1_Missense_Mutation_p.M98V|BIN2_ENST00000544402.1_Missense_Mutation_p.M99V|BIN2_ENST00000452142.2_Intron	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	125	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						TAGATTTCCATGGTCCTTACA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		19345	0.0		0.001	False		,,,				2504	0.0				p.M125V		Atlas-SNP	.											.	BIN2	58	.	0			c.A373G						PASS	.	T	VAL/MET	0,4406		0,0,2203	152.0	121.0	131.0		373	5.5	1.0	12	dbSNP_134	131	4,8596	3.7+/-12.6	0,4,4296	yes	missense	BIN2	NM_016293.2	21	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging	125/566	51695839	4,13002	2203	4300	6503	SO:0001583	missense	51411	exon5			TTTCCATGGTCCT	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.373A>G	12.37:g.51695839T>C	ENSP00000267012:p.Met125Val	172.0	0.0	0		151.0	74.0	0.490066	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	CCDS8811.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	17.72	3.459720	0.63401	0.0	4.65E-4	ENSG00000110934	ENST00000267012;ENST00000544402	T;T	0.58652	0.32;0.32	5.48	5.48	0.80851	BAR (3);	0.000000	0.85682	D	0.000000	T	0.70029	0.3177	L	0.49778	1.585	0.40090	D	0.976241	D;D	0.69078	0.997;0.997	D;D	0.80764	0.99;0.994	T	0.70132	-0.4956	10	0.40728	T	0.16	-11.2107	14.8673	0.70427	0.0:0.0:0.0:1.0	.	99;125	F5H0W4;Q9UBW5	.;BIN2_HUMAN	V	125;99	ENSP00000267012:M125V;ENSP00000445874:M99V	ENSP00000267012:M125V	M	-	1	0	BIN2	49982106	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	4.698000	0.61789	2.227000	0.72691	0.460000	0.39030	ATG	T|1.000;C|0.000	0.000	strong		0.468	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		
SRP72	6731	hgsc.bcm.edu	37	4	57367891	57367891	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57367891G>T	ENST00000342756.5	+	19	2601	c.1880G>T	c.(1879-1881)aGa>aTa	p.R627I	SRP72_ENST00000510663.1_Missense_Mutation_p.R566I	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	627					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					ACCTCCCCAAGACCTGGCAGT	0.458																																					p.R627I		Atlas-SNP	.											.	SRP72	59	.	0			c.G1880T						PASS	.						57.0	55.0	56.0					4																	57367891		2203	4300	6503	SO:0001583	missense	6731	exon19			CCCCAAGACCTGG	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.1880G>T	4.37:g.57367891G>T	ENSP00000342181:p.Arg627Ile	243.0	0.0	0		198.0	43.0	0.217172	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.441168|4.441168	0.83993|0.83993	.|.	.|.	ENSG00000174780|ENSG00000174780	ENST00000537129|ENST00000342756;ENST00000510663	.|T;T	.|0.78481	.|-1.13;-1.18	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87273|0.87273	0.6136|0.6136	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.998	.|D;P	.|0.76575	.|0.988;0.896	D|D	0.85985|0.85985	0.1485|0.1485	6|10	0.56958|0.41790	D|T	0.05|0.15	.|.	17.5488|17.5488	0.87870|0.87870	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|566;627	.|G5E9Z8;O76094	.|.;SRP72_HUMAN	Y|I	571|627;566	.|ENSP00000342181:R627I;ENSP00000424576:R566I	ENSP00000445887:D571Y|ENSP00000342181:R627I	D|R	+|+	1|2	0|0	SRP72|SRP72	57062648|57062648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.292000|6.292000	0.72725|0.72725	2.743000|2.743000	0.94032|0.94032	0.455000|0.455000	0.32223|0.32223	GAC|AGA	.	.	none		0.458	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
CD96	10225	hgsc.bcm.edu	37	3	111286403	111286403	+	Missense_Mutation	SNP	T	T	C	rs147832650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111286403T>C	ENST00000283285.5	+	3	583	c.452T>C	c.(451-453)aTa>aCa	p.I151T	CD96_ENST00000352690.4_Missense_Mutation_p.I151T|CD96_ENST00000438817.2_Missense_Mutation_p.I151T	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	151					cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						AACCATACGATAGAAATAGAG	0.348									Opitz Trigonocephaly syndrome																												p.I151T		Atlas-SNP	.											.	CD96	75	.	0			c.T452C						PASS	.	T	THR/ILE,THR/ILE	0,4406		0,0,2203	99.0	90.0	93.0		452,452	4.2	1.0	3	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	CD96	NM_005816.4,NM_198196.2	89,89	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	151/570,151/586	111286403	4,13002	2203	4300	6503	SO:0001583	missense	10225	exon3	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	ATACGATAGAAAT	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16892	protein-coding gene	gene with protein product		606037	"""CD96 antigen"""			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.452T>C	3.37:g.111286403T>C	ENSP00000283285:p.Ile151Thr	92.0	0.0	0		72.0	43.0	0.597222	NM_005816	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	37	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115390	0.37339	0.0	4.65E-4	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.66995	1.6;-0.24;1.6	5.37	4.19	0.49359	Immunoglobulin subtype (1);	0.297277	0.29587	N	0.011726	T	0.59432	0.2193	L	0.27053	0.805	0.29717	N	0.838913	P;P;P;P	0.51351	0.906;0.944;0.906;0.906	B;P;B;B	0.50617	0.444;0.646;0.444;0.444	T	0.60667	-0.7218	10	0.87932	D	0	-14.79	8.037	0.30499	0.0:0.0921:0.0:0.9079	.	151;151;151;151	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	T	151	ENSP00000342040:I151T;ENSP00000283285:I151T;ENSP00000389801:I151T	ENSP00000283285:I151T	I	+	2	0	CD96	112769093	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.420000	0.34804	2.262000	0.75019	0.528000	0.53228	ATA	T|1.000;C|0.000	0.000	strong		0.348	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2		
FARSA	2193	hgsc.bcm.edu	37	19	13041558	13041558	+	Silent	SNP	G	G	A	rs373756496		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13041558G>A	ENST00000314606.4	-	2	171	c.153C>T	c.(151-153)atC>atT	p.I51I	CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000588025.1_Silent_p.I91I|FARSA_ENST00000423140.2_Silent_p.I51I	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	51					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	GTTCAGCCTCGATGACCTAGA	0.622																																					p.I51I		Atlas-SNP	.											.	FARSA	46	.	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	44.0	46.0	45.0		153	-6.0	0.9	19		45	0,8600		0,0,4300	no	coding-synonymous	FARSA	NM_004461.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		51/509	13041558	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2193	exon2			AGCCTCGATGACC	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.153C>T	19.37:g.13041558G>A		23.0	0.0	0		14.0	9.0	0.642857	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	37	CCDS12287.1																																																																																			.	.	weak		0.622	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
WNK3	65267	hgsc.bcm.edu	37	X	54265469	54265469	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:54265469C>T	ENST00000375159.2	-	17	3714	c.3715G>A	c.(3715-3717)Ggt>Agt	p.G1239S	WNK3_ENST00000354646.2_Missense_Mutation_p.G1239S|WNK3_ENST00000375169.3_Missense_Mutation_p.G1239S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1239					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						ATGGCTCCACCGCTTGACACA	0.448																																					p.G1239S		Atlas-SNP	.											.	WNK3	218	.	0			c.G3715A						PASS	.						63.0	59.0	60.0					X																	54265469		2203	4300	6503	SO:0001583	missense	65267	exon18			CTCCACCGCTTGA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3715G>A	X.37:g.54265469C>T	ENSP00000364301:p.Gly1239Ser	63.0	0.0	0		50.0	34.0	0.68	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486242	0.44147	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.72167	-0.44;-0.63;-0.63	5.02	3.2	0.36748	.	0.584613	0.15074	N	0.282037	T	0.65491	0.2696	L	0.27053	0.805	0.19300	N	0.999975	D;D	0.76494	0.999;0.995	P;P	0.58454	0.839;0.492	T	0.53648	-0.8409	10	0.08837	T	0.75	0.202	8.816	0.34996	0.0:0.7647:0.1477:0.0875	.	1239;1239	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	S	1239	ENSP00000364312:G1239S;ENSP00000346667:G1239S;ENSP00000364301:G1239S	ENSP00000346667:G1239S	G	-	1	0	WNK3	54282194	0.002000	0.14202	0.507000	0.27676	0.736000	0.42039	0.569000	0.23638	0.342000	0.23796	0.538000	0.68166	GGT	.	.	none		0.448	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
OXGR1	27199	hgsc.bcm.edu	37	13	97639827	97639827	+	Silent	SNP	T	T	G	rs9300380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639827T>G	ENST00000298440.1	-	4	430	c.187A>C	c.(187-189)Aga>Cga	p.R63R	OXGR1_ENST00000543457.1_Silent_p.R63R	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	63					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTCCAAGGTCTCATTTTGAAA	0.473													G|||	317	0.0632987	0.2118	0.0288	5008	,	,		21471	0.0		0.0169	False		,,,				2504	0.0				p.R63R		Atlas-SNP	.											.	OXGR1	46	.	0			c.A187C						PASS	.	G		815,3591	747.9+/-411.9	74,667,1462	121.0	113.0	116.0		187	3.3	1.0	13	dbSNP_119	116	83,8517	815.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,750,5679	GG,GT,TT		0.9651,18.4975,6.9045		63/338	97639827	898,12108	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			AAGGTCTCATTTT	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"""GPCR / Class A : Orphans"""	4531	protein-coding gene	gene with protein product	"""2-oxoglutarate receptor 1"", ""alpha-ketoglutarate receptor 1"""	606922	"""G protein-coupled receptor 80"""	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.187A>C	13.37:g.97639827T>G		173.0	0.0	0		145.0	71.0	0.489655	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			T|0.939;G|0.061	0.061	strong		0.473	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818	
SMIM11	54065	hgsc.bcm.edu	37	21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	rs34016792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000399299.1_Intron|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51.0	47.0	49.0		152	-3.9	0.0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	120.0	0.0	0		119.0	49.0	0.411765	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
CCDC67	159989	hgsc.bcm.edu	37	11	93141575	93141575	+	Missense_Mutation	SNP	T	T	C	rs371785641		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:93141575T>C	ENST00000298050.3	+	12	1605	c.1505T>C	c.(1504-1506)gTg>gCg	p.V502A	AP004242.1_ENST00000408638.1_RNA|CCDC67_ENST00000525646.1_Missense_Mutation_p.V244A	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	502					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				CAAATAAAAGTGGAACAAAAT	0.294																																					p.V502A		Atlas-SNP	.											CCDC67,NS,carcinoma,+1,1	CCDC67	57	1	0			c.T1505C						scavenged	.	T	ALA/VAL	0,3600		0,0,1800	38.0	34.0	35.0		1505	2.2	0.3	11		35	1,8127		0,1,4063	no	missense	CCDC67	NM_181645.3	64	0,1,5863	CC,CT,TT		0.0123,0.0,0.0085	benign	502/605	93141575	1,11727	1800	4064	5864	SO:0001583	missense	159989	exon12			TAAAAGTGGAACA	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1505T>C	11.37:g.93141575T>C	ENSP00000298050:p.Val502Ala	110.0	1.0	0.00909091		84.0	19.0	0.22619	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.485540	0.44147	0.0	1.23E-4	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.16897	2.31;2.31;2.31	5.86	2.18	0.27775	.	0.473884	0.25948	N	0.027261	T	0.07324	0.0185	N	0.08118	0	0.20196	N	0.999929	B;B	0.17465	0.009;0.022	B;B	0.16289	0.009;0.015	T	0.28554	-1.0040	10	0.41790	T	0.15	.	4.9184	0.13858	0.2853:0.0776:0.0:0.6372	.	502;494	Q05D60;Q6ZRU6	CCD67_HUMAN;.	A	502;502;244	ENSP00000432111:V502A;ENSP00000298050:V502A;ENSP00000435079:V244A	ENSP00000298050:V502A	V	+	2	0	CCDC67	92781223	0.992000	0.36948	0.254000	0.24359	0.935000	0.57460	0.381000	0.20619	0.112000	0.17975	0.533000	0.62120	GTG	.	.	weak		0.294	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
PIM1	5292	hgsc.bcm.edu	37	6	37138412	37138412	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37138412C>A	ENST00000373509.5	+	1	434	c.61C>A	c.(61-63)Cac>Aac	p.H21N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	112					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	CAACGACCTGCACGCCACCAA	0.726			T	BCL6	NHL																																p.H112N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C334A						PASS	.						25.0	27.0	26.0					6																	37138412		2199	4293	6492	SO:0001583	missense	5292	exon1			GACCTGCACGCCA		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.61C>A	6.37:g.37138412C>A	ENSP00000362608:p.His21Asn	18.0	0.0	0		39.0	11.0	0.282051	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236939	0.39498	.	.	ENSG00000137193	ENST00000373509	T	0.68479	-0.33	4.2	3.33	0.38152	.	0.432965	0.20921	N	0.083268	T	0.21468	0.0517	N	0.08118	0	0.29891	N	0.825193	P	0.34615	0.459	B	0.32762	0.152	T	0.17899	-1.0354	10	0.10636	T	0.68	.	12.4383	0.55612	0.0:0.915:0.0:0.085	.	112	P11309	PIM1_HUMAN	N	21	ENSP00000362608:H21N	ENSP00000362608:H21N	H	+	1	0	PIM1	37246390	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.047000	0.41269	1.080000	0.41073	0.542000	0.68232	CAC	.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
HOMEZ	57594	hgsc.bcm.edu	37	14	23746340	23746340	+	Missense_Mutation	SNP	C	C	T	rs565379852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23746340C>T	ENST00000357460.5	-	2	261	c.97G>A	c.(97-99)Ggt>Agt	p.G33S	HOMEZ_ENST00000561013.1_Missense_Mutation_p.G35S|HOMEZ_ENST00000431326.2_Missense_Mutation_p.G35S	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	33					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CTACTGAGACCGCTGGCCTCT	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		17905	0.002		0.0	False		,,,				2504	0.0				p.G33S		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G97A						PASS	.						76.0	71.0	72.0					14																	23746340		1974	4166	6140	SO:0001583	missense	57594	exon2			TGAGACCGCTGGC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.97G>A	14.37:g.23746340C>T	ENSP00000350049:p.Gly33Ser	71.0	0.0	0		63.0	29.0	0.460317	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	C	1.235	-0.622995	0.03636	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.20200	2.09;2.09	5.95	2.18	0.27775	.	0.152484	0.56097	N	0.000023	T	0.07503	0.0189	N	0.08118	0	0.22835	N	0.998674	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40478	-0.9561	10	0.02654	T	1	-7.3746	7.1207	0.25442	0.0:0.3237:0.0:0.6763	.	35;33	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	S	33;35	ENSP00000350049:G33S;ENSP00000406579:G35S	ENSP00000350049:G33S	G	-	1	0	HOMEZ	22816180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.878000	0.28126	0.494000	0.27859	-0.290000	0.09829	GGT	.	.	none		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
HIVEP1	3096	hgsc.bcm.edu	37	6	12124257	12124257	+	Missense_Mutation	SNP	C	C	G	rs372404420		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:12124257C>G	ENST00000379388.2	+	4	4561	c.4229C>G	c.(4228-4230)cCt>cGt	p.P1410R	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1410					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CCATCTTCACCTTCTCGAGTG	0.488																																					p.P1410R		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C4229G						PASS	.	C	ARG/PRO	0,4074		0,0,2037	113.0	116.0	115.0		4229	4.9	0.3	6		115	1,8369		0,1,4184	no	missense	HIVEP1	NM_002114.2	103	0,1,6221	GG,GC,CC		0.0119,0.0,0.0080	possibly-damaging	1410/2719	12124257	1,12443	2037	4185	6222	SO:0001583	missense	3096	exon4			CTTCACCTTCTCG	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4229C>G	6.37:g.12124257C>G	ENSP00000368698:p.Pro1410Arg	104.0	0.0	0		97.0	36.0	0.371134	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.931801	0.73442	0.0	1.19E-4	ENSG00000095951	ENST00000379388	T	0.09538	2.97	5.79	4.93	0.64822	.	0.460558	0.16304	N	0.220330	T	0.08044	0.0201	L	0.57536	1.79	0.80722	D	1	D	0.53462	0.96	P	0.46718	0.525	T	0.14227	-1.0480	9	.	.	.	-6.1734	9.7069	0.40220	0.1398:0.79:0.0:0.0702	.	1410	P15822	ZEP1_HUMAN	R	1410	ENSP00000368698:P1410R	.	P	+	2	0	HIVEP1	12232243	0.278000	0.24230	0.260000	0.24451	0.175000	0.22909	3.441000	0.52893	1.454000	0.47793	0.655000	0.94253	CCT	.	.	weak		0.488	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110449872	110449872	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110449872T>A	ENST00000261739.4	+	2	325	c.159T>A	c.(157-159)caT>caA	p.H53Q	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	53						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CCTTGGGACATTTGGAATCTG	0.413																																					p.H53Q		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T159A						PASS	.						129.0	115.0	120.0					12																	110449872		2203	4300	6503	SO:0001583	missense	88455	exon2			GGGACATTTGGAA	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"""Ankyrin repeat domain containing"""	21268	protein-coding gene	gene with protein product		615123	"""ankyrin repeat domain 13"""	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.159T>A	12.37:g.110449872T>A	ENSP00000261739:p.His53Gln	101.0	0.0	0		72.0	15.0	0.208333	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594305	0.86953	.	.	ENSG00000076513	ENST00000261739	T	0.66460	-0.21	6.17	1.29	0.21616	Ankyrin repeat-containing domain (3);	0.043066	0.85682	D	0.000000	T	0.64271	0.2583	L	0.39020	1.185	0.80722	D	1	D;D;D	0.61080	0.966;0.989;0.966	P;P;P	0.55055	0.69;0.767;0.69	T	0.63033	-0.6727	10	0.66056	D	0.02	-17.1926	9.0087	0.36129	0.0:0.3655:0.0:0.6345	.	53;53;53	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	Q	53	ENSP00000261739:H53Q	ENSP00000261739:H53Q	H	+	3	2	ANKRD13A	108934255	0.996000	0.38824	0.984000	0.44739	0.996000	0.88848	0.671000	0.25172	0.199000	0.20427	0.533000	0.62120	CAT	.	.	none		0.413	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
ALOX15	246	hgsc.bcm.edu	37	17	4535314	4535314	+	Missense_Mutation	SNP	G	G	A	rs34210653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4535314G>A	ENST00000570836.1	-	14	1775	c.1679C>T	c.(1678-1680)aCg>aTg	p.T560M	ALOX15_ENST00000574640.1_Missense_Mutation_p.T521M|ALOX15_ENST00000545513.1_Missense_Mutation_p.T582M|ALOX15_ENST00000293761.3_Missense_Mutation_p.T560M			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	560	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		T -> M (loss of catalytic activity; dbSNP:rs34210653). {ECO:0000269|PubMed:17959182}.		apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		CAGCCGCATCGTGCAGGGTGC	0.607													G|||	63	0.0125799	0.0023	0.0663	5008	,	,		20270	0.0		0.0109	False		,,,				2504	0.0031				p.T560M		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1679T	GRCh37	CM081155	ALOX15	M	rs34210653	PASS	.	G	MET/THR	17,4389	23.3+/-48.9	0,17,2186	59.0	54.0	56.0		1679	3.3	0.9	17	dbSNP_126	56	144,8456	72.0+/-134.6	1,142,4157	yes	missense	ALOX15	NM_001140.3	81	1,159,6343	AA,AG,GG		1.6744,0.3858,1.2379	probably-damaging	560/663	4535314	161,12845	2203	4300	6503	SO:0001583	missense	246	exon13			CGCATCGTGCAGG	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1679C>T	17.37:g.4535314G>A	ENSP00000458832:p.Thr560Met	61.0	0.0	0		63.0	32.0	0.507937	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	32	0.014652014652014652	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	10	0.013192612137203167	G	18.48	3.632894	0.67015	0.003858	0.016744	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.78126	-1.15;-1.15	4.33	3.35	0.38373	Lipoxygenase, C-terminal (3);	0.064395	0.64402	D	0.000011	T	0.51924	0.1703	M	0.85197	2.74	0.35074	D	0.762752	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.80529	-0.1342	10	0.87932	D	0	-1.2213	10.1417	0.42738	0.0:0.2025:0.7975:0.0	rs34210653	582;521;560	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	M	560;582	ENSP00000293761:T560M;ENSP00000439855:T582M	ENSP00000293761:T560M	T	-	2	0	ALOX15	4482063	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	4.166000	0.58203	1.028000	0.39785	0.655000	0.94253	ACG	G|0.988;A|0.012	0.012	strong		0.607	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
PCDHA10	56139	hgsc.bcm.edu	37	5	140235875	140235875	+	Missense_Mutation	SNP	G	G	A	rs143002904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140235875G>A	ENST00000307360.5	+	1	242	c.242G>A	c.(241-243)gGc>gAc	p.G81D	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.G81D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCAGAATGGCATTTTGTTT	0.622													.|||	19	0.00379393	0.0	0.0029	5008	,	,		17477	0.0		0.0169	False		,,,				2504	0.0				p.G81D		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G242A						PASS	.	G	,ASP/GLY,,,,,,,,,,,ASP/GLY,ASP/GLY	8,4386	11.4+/-27.6	1,6,2190	104.0	113.0	110.0		,242,,,,,,,,,,,242,242	4.3	1.0	5	dbSNP_134	110	49,8493	27.4+/-76.7	2,45,4224	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,94,,,,,,,,,,,94,94	3,51,6414	AA,AG,GG		0.5736,0.1821,0.4406	,,,,,,,,,,,,,	,81/949,,,,,,,,,,,81/845,81/686	140235875	57,12879	2197	4271	6468	SO:0001583	missense	56139	exon1			AGAATGGCATTTT	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.242G>A	5.37:g.140235875G>A	ENSP00000304234:p.Gly81Asp	91.0	0.0	0		31.0	31.0	1	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	23.3	4.399977	0.83120	0.001821	0.005736	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.40476	1.03;1.03	4.27	4.27	0.50696	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74876	0.3774	H	0.99590	4.645	0.51012	D	0.999902	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88448	0.3047	9	0.87932	D	0	.	17.329	0.87258	0.0:0.0:1.0:0.0	.	81;81;81	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	D	81	ENSP00000421030:G81D;ENSP00000304234:G81D	ENSP00000304234:G81D	G	+	2	0	PCDHA10	140216059	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.573000	0.82421	2.391000	0.81399	0.556000	0.70494	GGC	G|0.995;A|0.005	0.005	strong		0.622	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
TMEM97	27346	hgsc.bcm.edu	37	17	26646320	26646320	+	Missense_Mutation	SNP	C	C	G	rs202198126		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26646320C>G	ENST00000226230.6	+	1	200	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	TMEM97_ENST00000583381.1_Intron|TMEM97_ENST00000336687.6_5'Flank|TMEM97_ENST00000582113.1_Missense_Mutation_p.L19V	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	19					cholesterol homeostasis (GO:0042632)|regulation of cell growth (GO:0001558)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)				endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	6	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCTCTACTTCCTCAGCCACAT	0.672																																					p.L19V		Atlas-SNP	.											.	TMEM97	27	.	0			c.C55G						PASS	.	C	VAL/LEU	0,4096		0,0,2048	24.0	31.0	28.0		55	2.1	1.0	17		28	4,8312		0,4,4154	no	missense	TMEM97	NM_014573.2	32	0,4,6202	GG,GC,CC		0.0481,0.0,0.0322	benign	19/177	26646320	4,12408	2048	4158	6206	SO:0001583	missense	27346	exon1			TACTTCCTCAGCC	BC091504	CCDS11226.2	17q11.2	2014-01-28			ENSG00000109084	ENSG00000109084			28106	protein-coding gene	gene with protein product		612912				7694637, 15375745	Standard	NM_014573		Approved	MAC30	uc002hat.3	Q5BJF2	OTTHUMG00000132497	ENST00000226230.6:c.55C>G	17.37:g.26646320C>G	ENSP00000226230:p.Leu19Val	210.0	0.0	0		196.0	88.0	0.44898	NM_014573	B4DS02|Q07823	Missense_Mutation	SNP	ENST00000226230.6	37	CCDS11226.2	.	.	.	.	.	.	.	.	.	.	C	0.581	-0.836976	0.02692	0.0	4.81E-4	ENSG00000109084	ENST00000226230	.	.	.	5.41	2.06	0.26882	.	0.329557	0.33534	N	0.004806	T	0.36663	0.0975	L	0.31664	0.95	0.80722	D	1	B	0.10296	0.003	B	0.16289	0.015	T	0.21484	-1.0244	9	0.02654	T	1	-18.6822	9.5507	0.39308	0.0:0.4926:0.4306:0.0767	.	19	Q5BJF2	TMM97_HUMAN	V	19	.	ENSP00000226230:L19V	L	+	1	0	TMEM97	23670447	0.921000	0.31238	1.000000	0.80357	0.020000	0.10135	0.970000	0.29383	0.786000	0.33708	0.561000	0.74099	CTC	C|0.999;G|0.001	0.001	weak		0.672	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255675.2	NM_014573	
STAT6	6778	hgsc.bcm.edu	37	12	57496654	57496654	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57496654A>T	ENST00000300134.3	-	12	1588	c.1263T>A	c.(1261-1263)aaT>aaA	p.N421K	STAT6_ENST00000537215.2_Missense_Mutation_p.N311K|STAT6_ENST00000454075.3_Missense_Mutation_p.N421K|STAT6_ENST00000543873.2_Missense_Mutation_p.N421K|STAT6_ENST00000556155.1_Missense_Mutation_p.N421K|STAT6_ENST00000538913.2_Missense_Mutation_p.N311K	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	421					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TGGCTTTGGCATTGTTGTCTT	0.522																																					p.N421K		Atlas-SNP	.											.	STAT6	69	.	0			c.T1263A						PASS	.						144.0	115.0	125.0					12																	57496654		2203	4300	6503	SO:0001583	missense	6778	exon12			TTTGGCATTGTTG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1263T>A	12.37:g.57496654A>T	ENSP00000300134:p.Asn421Lys	114.0	0.0	0		120.0	14.0	0.116667	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.184980|4.184980	0.78677|0.78677	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000553533|ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	.|D;D;D;D;D;D	.|0.87729	.|-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.44|5.44	1.65|1.65	0.23941|0.23941	.|STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91593|0.91593	0.7344|0.7344	M|M	0.76838|0.76838	2.35|2.35	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	D|D	0.89559|0.89559	0.3805|0.3805	5|10	.|0.87932	.|D	.|0	-17.2208|-17.2208	8.3744|8.3744	0.32434|0.32434	0.762:0.0:0.238:0.0|0.762:0.0:0.238:0.0	.|.	.|421;421	.|A8K4S9;P42226	.|.;STAT6_HUMAN	S|K	122|421;311;311;421;421;311;421;311;421	.|ENSP00000300134:N421K;ENSP00000445409:N311K;ENSP00000438451:N421K;ENSP00000451742:N421K;ENSP00000444530:N311K;ENSP00000401486:N421K	.|ENSP00000300134:N421K	C|N	-|-	1|3	0|2	STAT6|STAT6	55782921|55782921	0.536000|0.536000	0.26378|0.26378	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	-0.213000|-0.213000	0.09305|0.09305	0.124000|0.124000	0.18369|0.18369	0.528000|0.528000	0.53228|0.53228	TGC|AAT	.	.	none		0.522	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
CNOT4	4850	hgsc.bcm.edu	37	7	135047811	135047811	+	Missense_Mutation	SNP	G	G	C	rs200460078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135047811G>C	ENST00000451834.1	-	12	2242	c.1959C>G	c.(1957-1959)caC>caG	p.H653Q	CNOT4_ENST00000541284.1_Missense_Mutation_p.H656Q|CNOT4_ENST00000361528.4_Missense_Mutation_p.H582Q|CNOT4_ENST00000473470.1_5'UTR|CNOT4_ENST00000423368.2_Missense_Mutation_p.H585Q			O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	0					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						AGGGGGCGCTGTGGTGGGTCT	0.587													G|||	4	0.000798722	0.0	0.0	5008	,	,		13429	0.0		0.004	False		,,,				2504	0.0				p.H656Q	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											CNOT4_ENST00000541284,NS,carcinoma,0,3	CNOT4	146	3	0			c.C1968G						PASS	.	G	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	3,4123		0,3,2060	115.0	129.0	124.0		1755,1959,1968,1746	5.0	1.0	7		124	21,8375		0,21,4177	yes	missense,missense,missense,missense	CNOT4	NM_001190847.1,NM_001190849.1,NM_001190850.1,NM_013316.3	24,24,24,24	0,24,6237	CC,CG,GG		0.2501,0.0727,0.1917	probably-damaging,probably-damaging,probably-damaging,probably-damaging	585/643,653/711,656/714,582/640	135047811	24,12498	2063	4198	6261	SO:0001583	missense	4850	exon12			GGCGCTGTGGTGG	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000451834.1:c.1959C>G	7.37:g.135047811G>C	ENSP00000388491:p.His653Gln	110.0	0.0	0		139.0	75.0	0.539568	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000451834.1	37	CCDS55167.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	18.61	3.662127	0.67700	7.27E-4	0.002501	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528	T;T;T;T	0.52295	0.67;0.69;0.68;0.68	5.92	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	P;D;D;D	0.53462	0.932;0.96;0.96;0.96	D;D;D;D	0.69142	0.917;0.962;0.944;0.944	T	0.41124	-0.9526	10	0.14656	T	0.56	-8.6859	15.0604	0.71947	0.0678:0.0:0.9322:0.0	.	653;656;585;582	E7ET38;F8VQP3;O95628-4;O95628-8	.;.;.;.	Q	656;653;585;656;582	ENSP00000445508:H656Q;ENSP00000388491:H653Q;ENSP00000406777:H585Q;ENSP00000354673:H582Q	ENSP00000262563:H656Q	H	-	3	2	CNOT4	134698351	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	1.521000	0.48983	0.557000	0.71058	CAC	G|0.998;C|0.002	0.002	strong		0.587	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316	
HN1	51155	hgsc.bcm.edu	37	17	73143748	73143748	+	Splice_Site	SNP	C	C	G	rs200749518		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73143748C>G	ENST00000409753.3	-	3	485	c.200G>C	c.(199-201)gGt>gCt	p.G67A	HN1_ENST00000481647.1_Splice_Site_p.G21A|HN1_ENST00000356033.4_Splice_Site_p.G67A|RP11-649A18.4_ENST00000579554.1_RNA|HN1_ENST00000482348.1_Splice_Site_p.G21A|HN1_ENST00000476258.1_Splice_Site_p.G21A|HN1_ENST00000405458.3_Splice_Site_p.G21A|HN1_ENST00000470924.1_Splice_Site_p.G21A|HN1_ENST00000465454.1_5'Flank|Y_RNA_ENST00000516233.1_RNA|HN1_ENST00000392566.2_Splice_Site_p.G21A|HN1_ENST00000581874.1_Splice_Site_p.G67A	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	67					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					AGACTTGGCACCTAAAAATCA	0.453																																					p.G67A		Atlas-SNP	.											.	HN1	17	.	0			c.G200C						PASS	.						58.0	60.0	59.0					17																	73143748		2203	4300	6503	SO:0001630	splice_region_variant	51155	exon3			TTGGCACCTAAAA	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"""androgen-regulated protein 2"""					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.200-1G>C	17.37:g.73143748C>G		34.0	0.0	0		24.0	14.0	0.583333	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059740	0.55325	.	.	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000356033;ENST00000409135;ENST00000392566	.	.	.	4.97	4.0	0.46444	.	0.129701	0.52532	D	0.000061	T	0.63745	0.2537	M	0.63843	1.955	0.46954	D	0.99926	D;P;D	0.56035	0.974;0.827;0.971	P;B;P	0.54499	0.754;0.418;0.721	T	0.65479	-0.6158	9	0.59425	D	0.04	.	9.2449	0.37520	0.0:0.8284:0.0:0.1716	.	67;67;67	B8ZZT7;Q9UK76-2;Q9UK76	.;.;HN1_HUMAN	A	21;67;67;67;21	.	ENSP00000348316:G67A	G	-	2	0	HN1	70655343	1.000000	0.71417	0.999000	0.59377	0.671000	0.39405	3.060000	0.49955	1.208000	0.43306	0.467000	0.42956	GGT	C|0.999;G|0.001	0.001	weak		0.453	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	Missense_Mutation
HLA-A	3105	hgsc.bcm.edu	37	6	29911213	29911213	+	Nonsense_Mutation	SNP	G	G	A	rs199474545		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911213G>A	ENST00000396634.1	+	5	853	c.512G>A	c.(511-513)tGg>tAg	p.W171*	HLA-A_ENST00000376802.2_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376809.5_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376806.5_Nonsense_Mutation_p.W171*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	171	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AAGCGCAAGTGGGAGGCGGCC	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.W171X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G512A						PASS	.						35.0	27.0	30.0					6																	29911213		1509	2705	4214	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCAAGTGGGAGGC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.512G>A	6.37:g.29911213G>A	ENSP00000379873:p.Trp171*	293.0	0.0	0		132.0	32.0	0.242424	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	31|31	5.083642|5.083642	0.94050|0.94050	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000355767|ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	.|.	.|.	.|.	3.78|3.78	-0.515|-0.515	0.11954|0.11954	.|.	.|0.000000	.|0.36815	.|U	.|0.002400	T|.	0.19644|.	0.0472|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.12604|.	-1.0541|.	4|.	0.87932|0.87932	D|D	0|0	.|.	2.0762|2.0762	0.03624|0.03624	0.1916:0.1531:0.4984:0.1569|0.1916:0.1531:0.4984:0.1569	.|.	.|.	.|.	.|.	R|X	146|171	.|.	ENSP00000348012:G146R|ENSP00000365998:W171X	G|W	+|+	1|2	0|0	HLA-A|HLA-A	30019192|30019192	0.184000|0.184000	0.23200|0.23200	0.057000|0.057000	0.19452|0.19452	0.134000|0.134000	0.20937|0.20937	0.137000|0.137000	0.15995|0.15995	-0.240000|-0.240000	0.09696|0.09696	0.485000|0.485000	0.47835|0.47835	GGG|TGG	.	.	weak		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PDCD2L	84306	hgsc.bcm.edu	37	19	34895647	34895647	+	Missense_Mutation	SNP	G	G	A	rs141960904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:34895647G>A	ENST00000246535.3	+	2	249	c.202G>A	c.(202-204)Ggc>Agc	p.G68S	PDCD2L_ENST00000587065.2_5'Flank|RP11-618P17.4_ENST00000606020.1_Missense_Mutation_p.G63S	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	68					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CCCGCTGGAAGGCTCCCCGTT	0.706													G|||	10	0.00199681	0.0	0.0072	5008	,	,		14816	0.0		0.005	False		,,,				2504	0.0				p.G68S		Atlas-SNP	.											.	PDCD2L	27	.	0			c.G202A						PASS	.	G	SER/GLY	2,4400	2.1+/-5.4	0,2,2199	23.0	22.0	22.0		202	4.0	1.0	19	dbSNP_134	22	28,8566	14.0+/-48.4	0,28,4269	yes	missense	PDCD2L	NM_032346.1	56	0,30,6468	AA,AG,GG		0.3258,0.0454,0.2308	probably-damaging	68/359	34895647	30,12966	2201	4297	6498	SO:0001583	missense	84306	exon2			CTGGAAGGCTCCC	BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.202G>A	19.37:g.34895647G>A	ENSP00000246535:p.Gly68Ser	68.0	0.0	0		76.0	37.0	0.486842	NM_032346		Missense_Mutation	SNP	ENST00000246535.3	37	CCDS12438.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	21.4	4.141095	0.77775	4.54E-4	0.003258	ENSG00000126249	ENST00000246535	.	.	.	5.04	4.0	0.46444	.	0.111834	0.64402	N	0.000014	T	0.33818	0.0876	L	0.49640	1.575	0.33769	D	0.622826	D	0.53151	0.958	P	0.45071	0.468	T	0.50825	-0.8782	9	0.16896	T	0.51	-20.8332	11.295	0.49274	0.0866:0.0:0.9134:0.0	.	68	Q9BRP1	PDD2L_HUMAN	S	68	.	ENSP00000246535:G68S	G	+	1	0	PDCD2L	39587487	1.000000	0.71417	0.995000	0.50966	0.337000	0.28794	5.910000	0.69931	1.095000	0.41419	0.313000	0.20887	GGC	G|0.998;A|0.002	0.002	strong		0.706	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346	
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCCTCTTCCGGTGCCCGCCG	0.647		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	scavenged	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0.0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	75.0	1.0	0.0133333		46.0	20.0	0.434783	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
ZC3HC1	51530	hgsc.bcm.edu	37	7	129664301	129664301	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129664301T>C	ENST00000358303.4	-	7	906	c.822A>G	c.(820-822)caA>caG	p.Q274Q	ZC3HC1_ENST00000311873.5_Silent_p.Q253Q|RNA5SP245_ENST00000364239.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000481503.1_Intron|ZC3HC1_ENST00000360708.5_Silent_p.Q274Q|RP11-306G20.1_ENST00000480018.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	274					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TCCTCATACATTGCGAACATG	0.478																																					p.Q274Q	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											.	ZC3HC1	45	.	0			c.A822G						PASS	.						73.0	67.0	69.0					7																	129664301		2203	4300	6503	SO:0001819	synonymous_variant	51530	exon7			CATACATTGCGAA	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.822A>G	7.37:g.129664301T>C		83.0	0.0	0		95.0	22.0	0.231579	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Silent	SNP	ENST00000358303.4	37	CCDS34753.1																																																																																			.	.	none		0.478	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
CYP4V2	285440	hgsc.bcm.edu	37	4	187118114	187118114	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187118114C>T	ENST00000378802.4	+	4	738	c.434C>T	c.(433-435)tCc>tTc	p.S145F		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	145					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		AAATGGCGCTCCAGGAGAAAG	0.323																																					p.S145F		Atlas-SNP	.											.	CYP4V2	49	.	0			c.C434T						PASS	.						65.0	69.0	68.0					4																	187118114		2203	4298	6501	SO:0001583	missense	285440	exon4			GGCGCTCCAGGAG	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"""Cytochrome P450s"""	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.434C>T	4.37:g.187118114C>T	ENSP00000368079:p.Ser145Phe	66.0	0.0	0		55.0	16.0	0.290909	NM_207352	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780697	0.49891	.	.	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.69806	-0.43	5.42	2.68	0.31781	.	0.512228	0.23803	N	0.044403	T	0.62048	0.2396	L	0.60904	1.88	0.09310	N	1	B	0.27013	0.166	B	0.29267	0.1	T	0.56768	-0.7924	10	0.62326	D	0.03	.	11.3683	0.49686	0.2554:0.6217:0.1229:0.0	.	145	Q6ZWL3	CP4V2_HUMAN	F	145;123	ENSP00000368079:S145F	ENSP00000274118:S123F	S	+	2	0	CYP4V2	187355108	0.014000	0.17966	0.105000	0.21289	0.973000	0.67179	1.809000	0.38922	0.320000	0.23234	-0.182000	0.12963	TCC	.	.	none		0.323	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612	
CBS	875	hgsc.bcm.edu	37	21	44488631	44488631	+	Missense_Mutation	SNP	T	T	G	rs34040148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:44488631T>G	ENST00000398165.3	-	4	563	c.304A>C	c.(304-306)Aag>Cag	p.K102Q	CBS_ENST00000359624.3_Missense_Mutation_p.K102Q|CBS_ENST00000398158.1_Missense_Mutation_p.K102Q|CBS_ENST00000398168.1_Missense_Mutation_p.K102Q|CBS_ENST00000544202.1_Missense_Mutation_p.K14Q|CBS_ENST00000470912.1_5'UTR|CBS_ENST00000352178.5_Missense_Mutation_p.K102Q	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	102			K -> N (in CBSD; 50% of activity). {ECO:0000269|PubMed:7981678}.|K -> Q (in CBSD; severe form; linked with Arg-77; dbSNP:rs34040148). {ECO:0000269|PubMed:11013450}.		cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	AGCTCACACTTCAGGCCGAAC	0.542													T|||	59	0.0117812	0.0446	0.0	5008	,	,		11993	0.0		0.0	False		,,,				2504	0.0				p.K102Q		Atlas-SNP	.											.	CBS	85	.	0			c.A304C	GRCh37	CM994315	CBS	M	rs34040148	PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	167,4239	110.8+/-149.0	1,165,2037	96.0	93.0	94.0		304,304,304	4.8	1.0	21	dbSNP_126	94	0,8600		0,0,4300	yes	missense,missense,missense	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	53,53,53	1,165,6337	GG,GT,TT		0.0,3.7903,1.284	probably-damaging,probably-damaging,probably-damaging	102/552,102/552,102/552	44488631	167,12839	2203	4300	6503	SO:0001583	missense	875	exon4			CACACTTCAGGCC	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.304A>C	21.37:g.44488631T>G	ENSP00000381231:p.Lys102Gln	101.0	0.0	0		137.0	51.0	0.372263	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	T	15.59	2.878485	0.51801	0.037903	0.0	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202;ENST00000441030	D;D;D;D;D;D;D	0.96491	-4.03;-4.03;-4.03;-4.03;-4.03;-4.03;-4.03	4.81	4.81	0.61882	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	T	0.80681	0.4669	M	0.66439	2.03	0.48395	D	0.99964	P	0.36495	0.556	B	0.36766	0.232	D	0.84529	0.0632	10	0.38643	T	0.18	-46.6496	12.8977	0.58109	0.0:0.0:0.0:1.0	rs34040148	102	P35520	CBS_HUMAN	Q	102;102;102;102;102;59;14;102	ENSP00000381225:K102Q;ENSP00000381231:K102Q;ENSP00000352643:K102Q;ENSP00000344460:K102Q;ENSP00000381234:K102Q;ENSP00000439332:K14Q;ENSP00000388235:K102Q	ENSP00000344460:K102Q	K	-	1	0	CBS	43361700	1.000000	0.71417	0.998000	0.56505	0.544000	0.35116	3.979000	0.56888	1.917000	0.55516	0.533000	0.62120	AAG	T|0.985;G|0.015	0.015	strong		0.542	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
TMEM71	137835	hgsc.bcm.edu	37	8	133764112	133764112	+	Missense_Mutation	SNP	T	T	C	rs117725783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133764112T>C	ENST00000356838.3	-	4	375	c.233A>G	c.(232-234)gAc>gGc	p.D78G	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000523829.1_Missense_Mutation_p.D78G|TMEM71_ENST00000377901.4_Missense_Mutation_p.D78G	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	78						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CAGGAAGCTGTCTTCAGTCCA	0.473													T|||	26	0.00519169	0.0	0.0072	5008	,	,		18844	0.0		0.0149	False		,,,				2504	0.0061				p.D78G		Atlas-SNP	.											.	TMEM71	55	.	0			c.A233G						PASS	.	T	GLY/ASP,GLY/ASP	17,4389	23.3+/-48.9	0,17,2186	169.0	153.0	158.0		233,233	5.8	1.0	8	dbSNP_132	158	176,8424	80.9+/-143.5	4,168,4128	yes	missense,missense	TMEM71	NM_001145153.1,NM_144649.2	94,94	4,185,6314	CC,CT,TT		2.0465,0.3858,1.4839	probably-damaging,probably-damaging	78/233,78/277	133764112	193,12813	2203	4300	6503	SO:0001583	missense	137835	exon4			AAGCTGTCTTCAG	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.233A>G	8.37:g.133764112T>C	ENSP00000349296:p.Asp78Gly	161.0	0.0	0		145.0	27.0	0.186207	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	17.79	3.475998	0.63737	0.003858	0.020465	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000519187;ENST00000519304	.	.	.	5.81	5.81	0.92471	.	0.058994	0.64402	D	0.000003	T	0.66858	0.2832	M	0.77103	2.36	0.47245	D	0.999364	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.971;0.998;0.999	T	0.77638	-0.2513	9	0.87932	D	0	-17.5053	13.9131	0.63881	0.0:0.0:0.0:1.0	.	78;78;78	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	G	78	.	ENSP00000349296:D78G	D	-	2	0	TMEM71	133833294	1.000000	0.71417	1.000000	0.80357	0.173000	0.22820	6.769000	0.74985	2.214000	0.71695	0.533000	0.62120	GAC	T|0.988;C|0.012	0.012	strong		0.473	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649	
ZNF354C	30832	hgsc.bcm.edu	37	5	178506075	178506075	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178506075A>T	ENST00000315475.6	+	5	948	c.642A>T	c.(640-642)aaA>aaT	p.K214N		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	214					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CAGGAGGAAAACCTCACATCT	0.353																																					p.K214N		Atlas-SNP	.											.	ZNF354C	77	.	0			c.A642T						PASS	.						51.0	53.0	52.0					5																	178506075		2203	4300	6503	SO:0001583	missense	30832	exon5			AGGAAAACCTCAC		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.642A>T	5.37:g.178506075A>T	ENSP00000324064:p.Lys214Asn	62.0	0.0	0		71.0	16.0	0.225352	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.254012	0.39896	.	.	ENSG00000177932	ENST00000315475	T	0.35048	1.33	3.94	-4.99	0.03010	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36082	0.0954	M	0.80847	2.515	0.09310	N	1	B	0.19073	0.033	B	0.18871	0.023	T	0.44190	-0.9344	9	0.66056	D	0.02	-3.9769	8.2749	0.31866	0.3087:0.1478:0.5435:0.0	.	214	Q86Y25	Z354C_HUMAN	N	214	ENSP00000324064:K214N	ENSP00000324064:K214N	K	+	3	2	ZNF354C	178438681	0.000000	0.05858	0.000000	0.03702	0.291000	0.27294	-0.409000	0.07160	-1.159000	0.02807	0.482000	0.46254	AAA	.	.	none		0.353	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ZNF563	147837	hgsc.bcm.edu	37	19	12429509	12429509	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12429509T>C	ENST00000293725.5	-	4	1535	c.1330A>G	c.(1330-1332)Acg>Gcg	p.T444A		NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CCATCTCCCGTATGCATTACC	0.428																																					p.T444A	GBM(39;623 795 5132 29510 31476)	Atlas-SNP	.											ZNF563,colon,carcinoma,+2,1	ZNF563	77	1	0			c.A1330G						scavenged	.						187.0	173.0	178.0					19																	12429509		2203	4300	6503	SO:0001583	missense	147837	exon4			CTCCCGTATGCAT	BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"""Zinc fingers, C2H2-type"", ""-"""	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.1330A>G	19.37:g.12429509T>C	ENSP00000293725:p.Thr444Ala	72.0	0.0	0		46.0	3.0	0.0652174	NM_145276	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.498724	0.44455	.	.	ENSG00000188868	ENST00000293725	T	0.26518	1.73	0.537	0.537	0.17144	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41442	0.1159	L	0.58510	1.815	0.20403	N	0.999909	D	0.89917	1.0	D	0.87578	0.998	T	0.13469	-1.0508	9	0.72032	D	0.01	.	6.6537	0.22977	0.0:0.0:0.0:1.0	.	444	Q8TA94	ZN563_HUMAN	A	444	ENSP00000293725:T444A	ENSP00000293725:T444A	T	-	1	0	ZNF563	12290509	0.454000	0.25728	0.020000	0.16555	0.065000	0.16274	1.380000	0.34351	0.454000	0.26884	0.260000	0.18958	ACG	.	.	none		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276	
ZNF695	57116	hgsc.bcm.edu	37	1	247162688	247162688	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247162688G>T	ENST00000339986.7	-	3	368	c.221C>A	c.(220-222)cCc>cAc	p.P74H	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Missense_Mutation_p.P74H	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CACGTTCCAGGGCTCTTTCCT	0.468																																					p.P74H		Atlas-SNP	.											.	ZNF695	55	.	0			c.C221A						PASS	.						116.0	119.0	118.0					1																	247162688		2046	4248	6294	SO:0001583	missense	57116	exon3			TTCCAGGGCTCTT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.221C>A	1.37:g.247162688G>T	ENSP00000341236:p.Pro74His	124.0	0.0	0		107.0	29.0	0.271028	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710105	0.30322	.	.	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.09911	5.35;2.93	0.149	0.149	0.14863	Krueppel-associated box (2);	.	.	.	.	T	0.35624	0.0938	M	0.91612	3.225	0.09310	N	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.91635	0.893;0.999;0.983	T	0.06862	-1.0803	8	0.87932	D	0	.	.	.	.	.	74;62;74	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	H	74	ENSP00000429736:P74H;ENSP00000341236:P74H	ENSP00000428213:P62H	P	-	2	0	ZNF695	245229311	0.448000	0.25681	0.339000	0.25562	0.341000	0.28922	1.086000	0.30853	0.192000	0.20272	0.195000	0.17529	CCC	.	.	none		0.468	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:190876283C>A	ENST00000226798.4	+	5	631	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	137					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ACCAAGAGAACAATGGGAACC	0.353																																					p.Q137K		Atlas-SNP	.											.	FRG1	76	.	0			c.C409A						PASS	.						88.0	87.0	87.0					4																	190876283		2203	4300	6503	SO:0001583	missense	2483	exon5			AGAGAACAATGGG	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.409C>A	4.37:g.190876283C>A	ENSP00000226798:p.Gln137Lys	136.0	0.0	0		162.0	9.0	0.0555556	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.202137	0.58234	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.49139	2.03;0.79	4.04	4.04	0.47022	Actin cross-linking (1);	0.103449	0.64402	D	0.000002	T	0.54902	0.1887	M	0.88377	2.95	0.80722	D	1	B	0.11235	0.004	B	0.15484	0.013	T	0.60078	-0.7333	10	0.42905	T	0.14	-3.5101	14.1451	0.65347	0.0:1.0:0.0:0.0	.	137	Q14331	FRG1_HUMAN	K	137;74	ENSP00000226798:Q137K;ENSP00000435943:Q74K	ENSP00000226798:Q137K	Q	+	1	0	FRG1	191113277	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.292000	0.78731	1.964000	0.57103	0.567000	0.79289	CAA	.	.	none		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
TSC22D1	8848	hgsc.bcm.edu	37	13	45148708	45148708	+	Silent	SNP	C	C	T	rs112613609		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:45148708C>T	ENST00000458659.2	-	1	1993	c.1503G>A	c.(1501-1503)caG>caA	p.Q501Q	TSC22D1_ENST00000501704.2_Silent_p.Q501Q|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	501	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		gttgttgttgctgctgctgct	0.512																																					p.Q501Q		Atlas-SNP	.											TSC22D1,NS,carcinoma,0,4	TSC22D1	88	4	0			c.G1503A						scavenged	.																																			SO:0001819	synonymous_variant	8848	exon1			TTGTTGCTGCTGC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1503G>A	13.37:g.45148708C>T		143.0	2.0	0.013986		142.0	6.0	0.0422535	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	37	CCDS31966.1																																																																																			.	.	none		0.512	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
ZNF560	147741	hgsc.bcm.edu	37	19	9580305	9580305	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9580305C>T	ENST00000301480.4	-	8	743		c.e8+1			NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560						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(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						CAAACACTCACCTTGGAGAAC	0.458																																					.		Atlas-SNP	.											.	ZNF560	162	.	0			c.529+1G>A						PASS	.						123.0	103.0	110.0					19																	9580305		2203	4300	6503	SO:0001630	splice_region_variant	147741	exon9			CACTCACCTTGGA	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"""Zinc fingers, C2H2-type"", ""-"""	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.529+1G>A	19.37:g.9580305C>T		80.0	0.0	0		89.0	4.0	0.0449438	NM_152476	Q495S9|Q495T1	Splice_Site	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348351	0.41599	.	.	ENSG00000198028	ENST00000301480	.	.	.	1.87	0.737	0.18314	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3266	0.26560	0.2623:0.7377:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF560	9441305	0.001000	0.12720	0.544000	0.28141	0.588000	0.36517	0.273000	0.18662	0.301000	0.22738	0.462000	0.41574	.	.	.	none		0.458	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	Intron
WNK2	65268	hgsc.bcm.edu	37	9	96024182	96024182	+	Silent	SNP	G	G	C	rs12000967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96024182G>C	ENST00000297954.4	+	12	3153	c.3153G>C	c.(3151-3153)tcG>tcC	p.S1051S	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Silent_p.S663S|WNK2_ENST00000395477.2_Silent_p.S1051S|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.S663S	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1051					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CGGTCCTCTCGCCGCCTCTGC	0.692													C|||	665	0.132788	0.2973	0.1124	5008	,	,		13886	0.001		0.1362	False		,,,				2504	0.0573				p.S1051S		Atlas-SNP	.											.	WNK2	277	.	0			c.G3153C						PASS	.	C		1193,3211		166,861,1175	37.0	35.0	36.0		3153	-0.9	1.0	9	dbSNP_120	36	944,7648		60,824,3412	no	coding-synonymous	WNK2	NM_006648.3		226,1685,4587	CC,CG,GG		10.987,27.089,16.4435		1051/2218	96024182	2137,10859	2202	4296	6498	SO:0001819	synonymous_variant	65268	exon12			CCTCTCGCCGCCT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3153G>C	9.37:g.96024182G>C		52.0	0.0	0		76.0	36.0	0.473684	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		294|294	0.1346153846153846|0.1346153846153846	144|144	0.2926829268292683|0.2926829268292683	46|46	0.1270718232044199|0.1270718232044199	1|1	0.0017482517482517483|0.0017482517482517483	103|103	0.1358839050131926|0.1358839050131926	C|C	6.678|6.678	0.493719|0.493719	0.12702|0.12702	0.27089|0.27089	0.10987|0.10987	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730	.|.	.|.	.|.	5.17|5.17	-0.945|-0.945	0.10388|0.10388	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999084|0.9999999999999084	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36138|0.36138	-0.9760|-0.9760	3|3	.|.	.|.	.|.	.|.	2.0839|2.0839	0.03641|0.03641	0.177:0.178:0.1227:0.5223|0.177:0.178:0.1227:0.5223	rs12000967|rs12000967	.|.	.|.	.|.	P|P	655|1047	.|.	.|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95064003|95064003	0.613000|0.613000	0.27009|0.27009	0.957000|0.957000	0.39632|0.39632	0.511000|0.511000	0.34104|0.34104	-0.715000|-0.715000	0.04997|0.04997	-0.302000|-0.302000	0.08869|0.08869	-0.647000|-0.647000	0.03941|0.03941	GCC|CGC	G|0.836;C|0.164	0.164	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
HPSE	10855	hgsc.bcm.edu	37	4	84222157	84222157	+	Missense_Mutation	SNP	A	A	C	rs145560091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:84222157A>C	ENST00000405413.2	-	12	1564	c.1428T>G	c.(1426-1428)gaT>gaG	p.D476E	HPSE_ENST00000513463.1_Missense_Mutation_p.D418E|HPSE_ENST00000512196.1_Missense_Mutation_p.D402E|HPSE_ENST00000311412.5_Missense_Mutation_p.D476E	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	476					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	GAAGGTATTTATCCACTTGCT	0.348																																					p.D476E		Atlas-SNP	.											.	HPSE	55	.	0			c.T1428G						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	0,4406		0,0,2203	114.0	117.0	116.0		1428,1206,1254,1428	-2.4	1.0	4	dbSNP_134	116	17,8581	12.6+/-44.7	0,17,4282	yes	missense,missense,missense,missense	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	45,45,45,45	0,17,6485	CC,CA,AA		0.1977,0.0,0.1307	benign,benign,benign,benign	476/544,402/470,418/486,476/544	84222157	17,12987	2203	4299	6502	SO:0001583	missense	10855	exon11			GTATTTATCCACT	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1428T>G	4.37:g.84222157A>C	ENSP00000384262:p.Asp476Glu	120.0	0.0	0		133.0	56.0	0.421053	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	A	6.169	0.399451	0.11696	0.0	0.001977	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.38722	1.12;1.12;1.14;1.13	4.56	-2.36	0.06663	.	0.095855	0.64402	D	0.000001	T	0.20981	0.0505	N	0.05199	-0.095	0.35589	D	0.806951	D;B;B;B	0.58620	0.983;0.059;0.097;0.014	P;B;B;B	0.54460	0.753;0.038;0.084;0.009	T	0.44726	-0.9309	10	0.02654	T	1	-21.5243	5.5816	0.17252	0.5796:0.0:0.2952:0.1252	.	402;418;418;476	E9PCA9;A9JIG7;E9PGR1;Q9Y251	.;.;.;HPSE_HUMAN	E	476;476;402;418	ENSP00000308107:D476E;ENSP00000384262:D476E;ENSP00000423265:D402E;ENSP00000421365:D418E	ENSP00000308107:D476E	D	-	3	2	HPSE	84441181	1.000000	0.71417	0.988000	0.46212	0.172000	0.22775	0.482000	0.22276	-0.153000	0.11137	-0.256000	0.11100	GAT	A|0.999;C|0.001	0.001	strong		0.348	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
MYOZ1	58529	hgsc.bcm.edu	37	10	75394457	75394457	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75394457C>A	ENST00000359322.4	-	4	651	c.287G>T	c.(286-288)gGa>gTa	p.G96V		NM_021245.3	NP_067068.1			myozenin 1											central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					GCCCAGCTGTCCCCCCACTGT	0.532																																					p.G96V		Atlas-SNP	.											.	MYOZ1	24	.	0			c.G287T						PASS	.						62.0	60.0	60.0					10																	75394457		2203	4300	6503	SO:0001583	missense	58529	exon4			AGCTGTCCCCCCA	AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"""calsarcin-2"""	605603	"""myozenin"""	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.287G>T	10.37:g.75394457C>A	ENSP00000352272:p.Gly96Val	101.0	0.0	0		80.0	29.0	0.3625	NM_021245		Missense_Mutation	SNP	ENST00000359322.4	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251231	0.80135	.	.	ENSG00000177791	ENST00000359322	T	0.66638	-0.22	6.05	6.05	0.98169	.	0.134037	0.64402	D	0.000002	T	0.78027	0.4219	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.78455	-0.2197	10	0.72032	D	0.01	-4.7931	14.7834	0.69784	0.0:0.9294:0.0:0.0706	.	96	Q9NP98	MYOZ1_HUMAN	V	96	ENSP00000352272:G96V	ENSP00000352272:G96V	G	-	2	0	MYOZ1	75064463	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.747000	0.62141	2.880000	0.98712	0.655000	0.94253	GGA	.	.	none		0.532	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1		
MTTP	4547	hgsc.bcm.edu	37	4	100518224	100518224	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100518224C>T	ENST00000265517.5	+	8	1113	c.910C>T	c.(910-912)Ctc>Ttc	p.L304F	MTTP_ENST00000511045.1_Splice_Site_p.L331F|MTTP_ENST00000457717.1_Splice_Site_p.L304F|RP11-766F14.1_ENST00000508578.1_RNA			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	304	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TGTTTTGCAGCTCTCGGAGCT	0.498																																					p.L304F		Atlas-SNP	.											.	MTTP	127	.	0			c.C910T						PASS	.						101.0	100.0	101.0					4																	100518224		2203	4300	6503	SO:0001630	splice_region_variant	4547	exon9			TTGCAGCTCTCGG		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.910-1C>T	4.37:g.100518224C>T		35.0	0.0	0		33.0	11.0	0.333333	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357959	0.41801	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.55052	0.54;0.54;0.54	5.37	4.53	0.55603	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (1);	0.061492	0.64402	D	0.000003	T	0.74068	0.3668	M	0.77616	2.38	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.75465	-0.3308	9	.	.	.	-28.4593	18.347	0.90326	0.1216:0.8784:0.0:0.0	.	331;304	E9PBP6;P55157	.;MTP_HUMAN	F	331;304;304;304	ENSP00000427679:L331F;ENSP00000400821:L304F;ENSP00000265517:L304F	.	L	+	1	0	MTTP	100737247	1.000000	0.71417	0.903000	0.35520	0.028000	0.11728	3.706000	0.54830	0.646000	0.30693	-0.808000	0.03180	CTC	.	.	none		0.498	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		Missense_Mutation
CHD8	57680	hgsc.bcm.edu	37	14	21868678	21868678	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21868678C>T	ENST00000557364.1	-	23	4727	c.4464G>A	c.(4462-4464)gtG>gtA	p.V1488V	CHD8_ENST00000430710.3_Silent_p.V1209V|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Silent_p.V1488V			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1488					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GAAGACAGTACACGAGAATGG	0.443																																					p.V1488V		Atlas-SNP	.											.	CHD8	339	.	0			c.G4464A						PASS	.						59.0	58.0	58.0					14																	21868678		1858	4104	5962	SO:0001819	synonymous_variant	57680	exon22			ACAGTACACGAGA	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.4464G>A	14.37:g.21868678C>T		70.0	0.0	0		54.0	15.0	0.277778	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	5.897	0.349646	0.11182	.	.	ENSG00000100888	ENST00000555935	D	0.84660	-1.88	4.82	-4.95	0.03048	.	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61133	-0.7124	6	.	.	.	-7.29	1.8525	0.03172	0.1838:0.1552:0.384:0.277	.	.	.	.	I	714	ENSP00000451442:V714I	.	V	-	1	0	CHD8	20938518	0.000000	0.05858	0.744000	0.31058	0.958000	0.62258	-2.646000	0.00860	-1.016000	0.03371	0.650000	0.86243	GTA	.	.	none		0.443	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
HERC4	26091	hgsc.bcm.edu	37	10	69695974	69695974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695974C>T	ENST00000395198.3	-	23	2861	c.2614G>A	c.(2614-2616)Ggt>Agt	p.G872S	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.G762S|HERC4_ENST00000412272.2_Missense_Mutation_p.G794S|HERC4_ENST00000373700.4_Missense_Mutation_p.G864S	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCTGTTGCACCAAAGTTTTCA	0.308																																					p.G872S		Atlas-SNP	.											.	HERC4	78	.	0			c.G2614A						PASS	.						138.0	129.0	132.0					10																	69695974		2203	4300	6503	SO:0001583	missense	26091	exon23			TTGCACCAAAGTT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2614G>A	10.37:g.69695974C>T	ENSP00000378624:p.Gly872Ser	68.0	0.0	0		62.0	15.0	0.241935	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153248	0.94645	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.91872	3.25	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.84384	0.0551	10	0.87932	D	0	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	S	762;794;872;864	ENSP00000277817:G762S;ENSP00000416504:G794S;ENSP00000378624:G872S;ENSP00000362804:G864S	ENSP00000277817:G762S	G	-	1	0	HERC4	69365980	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.308	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
DST	667	hgsc.bcm.edu	37	6	56420158	56420158	+	Missense_Mutation	SNP	C	C	T	rs62621210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56420158C>T	ENST00000361203.3	-	56	14495	c.14488G>A	c.(14488-14490)Gtt>Att	p.V4830I	DST_ENST00000370769.4_Missense_Mutation_p.V4832I|DST_ENST00000244364.6_Missense_Mutation_p.V2418I|DST_ENST00000446842.2_Missense_Mutation_p.V4506I|DST_ENST00000370754.5_Missense_Mutation_p.V5010I|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Missense_Mutation_p.V2744I|DST_ENST00000421834.2_Missense_Mutation_p.V2744I			Q03001	DYST_HUMAN	dystonin	4830					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCTGTTCAACATCCTTAAAT	0.363													T|||	213	0.0425319	0.115	0.0245	5008	,	,		21783	0.0		0.0278	False		,,,				2504	0.0164				p.V2418I		Atlas-SNP	.											.	DST	1427	.	0			c.G7252A						PASS	.	T	ILE/VAL	434,3276		22,390,1443	98.0	97.0	97.0		7252	4.8	1.0	6	dbSNP_129	97	356,7848		8,340,3754	yes	missense	DST	NM_015548.4	29	30,730,5197	TT,TC,CC		4.3393,11.6981,6.6309	benign	2418/5172	56420158	790,11124	1855	4102	5957	SO:0001583	missense	667	exon41			GTTCAACATCCTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.14488G>A	6.37:g.56420158C>T	ENSP00000354508:p.Val4830Ile	149.0	0.0	0		145.0	72.0	0.496552	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		88	0.040293040293040296	61	0.12398373983739837	10	0.027624309392265192	0	0.0	17	0.022427440633245383	T	12.33	1.907022	0.33628	0.116981	0.043393	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.96	4.8	0.61643	.	0.246447	0.28784	N	0.014144	T	0.05640	0.0148	N	0.02802	-0.49	0.09310	N	1.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.0;0.002;0.006;0.0;0.001	T	0.23940	-1.0174	9	0.33141	T	0.24	.	7.9146	0.29810	0.0:0.0664:0.2716:0.662	rs62621210	2744;4832;5010;4830;2418	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	I	2418;5010;4832;2744;4506;2744;4830	ENSP00000244364:V2418I;ENSP00000359790:V5010I;ENSP00000359805:V4832I;ENSP00000400883:V2744I;ENSP00000393645:V4506I;ENSP00000359824:V2744I;ENSP00000354508:V4830I	ENSP00000244364:V2418I	V	-	1	0	DST	56528117	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	2.506000	0.45433	0.505000	0.28104	-0.269000	0.10298	GTT	C|0.959;T|0.041	0.041	strong		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
MUC4	4585	hgsc.bcm.edu	37	3	195506303	195506303	+	Missense_Mutation	SNP	G	G	T	rs192584273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506303G>T	ENST00000463781.3	-	2	12607	c.12148C>A	c.(12148-12150)Cct>Act	p.P4050T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4050T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4050T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTGGTGACAGGAAGAGGGGTG	0.572													.|||	585	0.116813	0.3132	0.0922	5008	,	,		10067	0.0169		0.0845	False		,,,				2504	0.0051				p.P4050T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(2)|kidney(1)	c.C12148A						PASS	.						36.0	20.0	25.0					3																	195506303		593	1229	1822	SO:0001583	missense	4585	exon2			TGACAGGAAGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12148C>A	3.37:g.195506303G>T	ENSP00000417498:p.Pro4050Thr	160.0	0.0	0		136.0	102.0	0.75	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	167	0.07646520146520147	97	0.19715447154471544	31	0.0856353591160221	3	0.005244755244755245	36	0.047493403693931395	g	1.949	-0.441794	0.04604	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.01281	0.0	T	0.37865	-0.9687	6	.	.	.	.	4.7077	0.12858	1.0E-4:0.0:0.6463:0.3536	.	3922	E7ESK3	.	T	4050	ENSP00000417498:P4050T;ENSP00000420243:P4050T	.	P	-	1	0	MUC4	196991082	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.709000	0.05030	-0.833000	0.04245	0.064000	0.15345	CCT	G|0.925;T|0.075	0.075	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SENP5	205564	hgsc.bcm.edu	37	3	196612959	196612959	+	Missense_Mutation	SNP	C	C	T	rs151102982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196612959C>T	ENST00000323460.5	+	2	1156	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Missense_Mutation_p.H303Y	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	303					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TTCTTGTCGGCATCAGCCGTA	0.532													C|||	12	0.00239617	0.0	0.0029	5008	,	,		19282	0.0		0.007	False		,,,				2504	0.0031				p.H303Y	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.C907T						PASS	.	C	TYR/HIS	3,4403	6.2+/-15.9	0,3,2200	90.0	86.0	87.0		907	4.5	0.9	3	dbSNP_134	87	68,8532	40.8+/-97.7	1,66,4233	yes	missense	SENP5	NM_152699.4	83	1,69,6433	TT,TC,CC		0.7907,0.0681,0.5459	benign	303/756	196612959	71,12935	2203	4300	6503	SO:0001583	missense	205564	exon2			TGTCGGCATCAGC	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.907C>T	3.37:g.196612959C>T	ENSP00000327197:p.His303Tyr	69.0	0.0	0		55.0	21.0	0.381818	NM_152699	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	37	CCDS3322.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.93	2.086414	0.36855	6.81E-4	0.007907	ENSG00000119231	ENST00000323460;ENST00000445299	T;T	0.34275	1.37;1.37	5.37	4.49	0.54785	.	0.432451	0.21815	N	0.068702	T	0.12135	0.0295	N	0.14661	0.345	0.80722	D	1	P;B	0.47350	0.894;0.167	B;B	0.38562	0.276;0.04	T	0.08764	-1.0706	10	0.05351	T	0.99	-0.0265	11.2608	0.49083	0.0:0.9096:0.0:0.0904	.	303;303	B4DY82;Q96HI0	.;SENP5_HUMAN	Y	303	ENSP00000327197:H303Y;ENSP00000390231:H303Y	ENSP00000327197:H303Y	H	+	1	0	SENP5	198097356	0.364000	0.24997	0.863000	0.33907	0.985000	0.73830	2.003000	0.40844	1.381000	0.46364	0.655000	0.94253	CAT	C|0.993;T|0.007	0.007	strong		0.532	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
MAP2K2	5605	hgsc.bcm.edu	37	19	4117483	4117483	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4117483G>A	ENST00000262948.5	-	2	490	c.237C>T	c.(235-237)ggC>ggT	p.G79G	MAP2K2_ENST00000394867.4_5'UTR|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	79	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	CGTTGCCCGCGCCCAGCTCTG	0.617																																					p.G79G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.C237T						PASS	.						67.0	63.0	64.0					19																	4117483		2203	4300	6503	SO:0001819	synonymous_variant	5605	exon2			GCCCGCGCCCAGC	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.237C>T	19.37:g.4117483G>A		79.0	0.0	0		89.0	38.0	0.426966	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			.	.	none		0.617	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
PLXNB2	23654	hgsc.bcm.edu	37	22	50726134	50726134	+	Missense_Mutation	SNP	C	C	T	rs375580670		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50726134C>T	ENST00000449103.1	-	7	1710	c.1570G>A	c.(1570-1572)Gcc>Acc	p.A524T	PLXNB2_ENST00000359337.4_Missense_Mutation_p.A524T|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	524					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGTGGCTGGGCGCTGGTGACG	0.746																																					p.A524T		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G1570A						PASS	.	C	THR/ALA	0,3290		0,0,1645	3.0	4.0	4.0		1570	2.7	0.0	22		4	2,7290		0,2,3644	no	missense	PLXNB2	NM_012401.3	58	0,2,5289	TT,TC,CC		0.0274,0.0,0.0189	possibly-damaging	524/1839	50726134	2,10580	1645	3646	5291	SO:0001583	missense	23654	exon7			GCTGGGCGCTGGT		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.1570G>A	22.37:g.50726134C>T	ENSP00000409171:p.Ala524Thr	21.0	0.0	0		37.0	11.0	0.297297	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	9.673	1.147298	0.21288	0.0	2.74E-4	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.03272	3.99;3.99	4.84	2.73	0.32206	.	0.106352	0.41712	D	0.000837	T	0.06096	0.0158	M	0.69823	2.125	0.09310	N	0.99999	B	0.13145	0.007	B	0.04013	0.001	T	0.19778	-1.0295	10	0.59425	D	0.04	.	10.3837	0.44127	0.0:0.8373:0.0:0.1627	.	524	O15031	PLXB2_HUMAN	T	524	ENSP00000409171:A524T;ENSP00000352288:A524T	ENSP00000352288:A524T	A	-	1	0	PLXNB2	49068261	0.454000	0.25728	0.005000	0.12908	0.006000	0.05464	0.904000	0.28491	0.759000	0.33084	0.561000	0.74099	GCC	.	.	weak		0.746	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
POM121C	100101267	hgsc.bcm.edu	37	7	75050958	75050958	+	Silent	SNP	G	G	A	rs587702156		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75050958G>A	ENST00000257665.5	-	11	3302	c.3303C>T	c.(3301-3303)agC>agT	p.S1101S	POM121C_ENST00000453279.2_Silent_p.S859S|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	1101	Pore side. {ECO:0000255}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						CGGTGGTGGCGCTGGAGCCTG	0.637													.|||	1	0.000199681	0.0	0.0	5008	,	,		17160	0.0		0.001	False		,,,				2504	0.0				p.S859S		Atlas-SNP	.											.	POM121C	46	.	0			c.C2577T						PASS	.						7.0	10.0	9.0					7																	75050958		2158	4253	6411	SO:0001819	synonymous_variant	100101267	exon13			GGTGGCGCTGGAG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.3303C>T	7.37:g.75050958G>A		397.0	1.0	0.00251889		409.0	125.0	0.305623	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				.	.	none		0.637	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
KMT2C	58508	hgsc.bcm.edu	37	7	151878589	151878589	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151878589G>A	ENST00000262189.6	-	36	6574	c.6356C>T	c.(6355-6357)cCt>cTt	p.P2119L	KMT2C_ENST00000355193.2_Missense_Mutation_p.P2119L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2119	Pro-rich.				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)										TATGGTTCCAGGCTGGGAAAA	0.478																																					p.P2119L		Atlas-SNP	.											.	MLL3	1564	.	0			c.C6356T						PASS	.						104.0	107.0	106.0					7																	151878589		2203	4300	6503	SO:0001583	missense	58508	exon36			GTTCCAGGCTGGG	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.6356C>T	7.37:g.151878589G>A	ENSP00000262189:p.Pro2119Leu	202.0	0.0	0		130.0	74.0	0.569231	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.418230	0.42918	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84800	-1.9;-1.9	5.11	5.11	0.69529	.	0.157447	0.29551	N	0.011839	D	0.87358	0.6157	L	0.56769	1.78	0.80722	D	1	D;D	0.56521	0.961;0.976	P;P	0.51701	0.617;0.677	D	0.85101	0.0957	10	0.23891	T	0.37	.	18.558	0.91091	0.0:0.0:1.0:0.0	.	2119;1180	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	L	2119	ENSP00000262189:P2119L;ENSP00000347325:P2119L	ENSP00000262189:P2119L	P	-	2	0	MLL3	151509522	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	5.577000	0.67444	2.390000	0.81377	0.563000	0.77884	CCT	.	.	none		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
DST	667	hgsc.bcm.edu	37	6	56327856	56327856	+	Silent	SNP	C	C	T	rs144012429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56327856C>T	ENST00000244364.6	-	82	15324	c.15117G>A	c.(15115-15117)gtG>gtA	p.V5039V	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	7442					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGCAGATGGCACGGGAAAGT	0.433													C|||	57	0.0113818	0.0015	0.0159	5008	,	,		19060	0.0		0.0268	False		,,,				2504	0.0174				p.V5039V		Atlas-SNP	.											.	DST	1427	.	0			c.G15117A						PASS	.	C		36,3850		0,36,1907	142.0	133.0	136.0		15117	4.0	1.0	6	dbSNP_134	136	348,7958		7,334,3812	yes	coding-synonymous	DST	NM_015548.4		7,370,5719	TT,TC,CC		4.1897,0.9264,3.1496		5039/5172	56327856	384,11808	1943	4153	6096	SO:0001819	synonymous_variant	667	exon82			AGATGGCACGGGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000244364.6:c.15117G>A	6.37:g.56327856C>T		167.0	0.0	0		141.0	78.0	0.553191	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000244364.6	37	CCDS47443.1																																																																																			C|0.983;T|0.017	0.017	strong		0.433	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723	
MICALL2	79778	hgsc.bcm.edu	37	7	1477844	1477844	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1477844A>G	ENST00000297508.7	-	12	2375	c.2200T>C	c.(2200-2202)Tac>Cac	p.Y734H	MICALL2_ENST00000405088.4_Missense_Mutation_p.Y522H|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	734	Forms an intramolecular interaction with the N-terminal CH and LIM zinc-binding domains-containing region keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		GGGGAGAGGTAGTCGGGGTGC	0.706																																					p.Y734H		Atlas-SNP	.											.	MICALL2	63	.	0			c.T2200C						PASS	.						11.0	13.0	12.0					7																	1477844		2179	4274	6453	SO:0001583	missense	79778	exon12			AGAGGTAGTCGGG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2200T>C	7.37:g.1477844A>G	ENSP00000297508:p.Tyr734His	132.0	0.0	0		129.0	103.0	0.79845	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.525674	0.27299	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.72942	2.19;-0.7	3.95	1.41	0.22369	.	0.269934	0.19725	N	0.107484	T	0.77731	0.4174	M	0.70595	2.14	0.09310	N	0.999999	P;D	0.76494	0.481;0.999	B;D	0.75020	0.373;0.985	T	0.65022	-0.6269	10	0.52906	T	0.07	.	4.6281	0.12488	0.6909:0.1929:0.1162:0.0	.	734;522	Q8IY33;D3YTD2	MILK2_HUMAN;.	H	522;734	ENSP00000385928:Y522H;ENSP00000297508:Y734H	ENSP00000297508:Y734H	Y	-	1	0	MICALL2	1444370	0.990000	0.36364	0.011000	0.14972	0.156000	0.22039	2.693000	0.47027	0.116000	0.18110	0.374000	0.22700	TAC	.	.	none		0.706	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
CABIN1	23523	hgsc.bcm.edu	37	22	24487739	24487739	+	Missense_Mutation	SNP	G	G	A	rs117908385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:24487739G>A	ENST00000398319.2	+	24	4113	c.3728G>A	c.(3727-3729)cGc>cAc	p.R1243H	CABIN1_ENST00000405822.2_Missense_Mutation_p.R1193H|CABIN1_ENST00000263119.5_Missense_Mutation_p.R1243H	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1243					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GAGGCTGCCCGCTACCCCAAG	0.642													G|||	40	0.00798722	0.0015	0.0072	5008	,	,		17045	0.0		0.0328	False		,,,				2504	0.0				p.R1243H		Atlas-SNP	.											.	CABIN1	153	.	0			c.G3728A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	13,4393	20.2+/-43.8	0,13,2190	69.0	61.0	64.0		3728,3578,3728	5.0	1.0	22	dbSNP_132	64	156,8444	72.9+/-135.5	1,154,4145	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	29,29,29	1,167,6335	AA,AG,GG		1.814,0.2951,1.2994	probably-damaging,probably-damaging,probably-damaging	1243/2221,1193/2171,1243/2221	24487739	169,12837	2203	4300	6503	SO:0001583	missense	23523	exon24			CTGCCCGCTACCC	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3728G>A	22.37:g.24487739G>A	ENSP00000381364:p.Arg1243His	115.0	0.0	0		120.0	60.0	0.5	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	32	0.014652014652014652	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	30	0.0395778364116095	G	35	5.482768	0.96307	0.002951	0.01814	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.30182	1.54;1.54;1.54	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.65773	0.938;0.869	T	0.16571	-1.0398	10	0.52906	T	0.07	.	17.8214	0.88651	0.0:0.0:1.0:0.0	.	1193;1243	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	H	1243;1193;1243	ENSP00000263119:R1243H;ENSP00000384694:R1193H;ENSP00000381364:R1243H	ENSP00000263119:R1243H	R	+	2	0	CABIN1	22817739	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.918000	0.87506	2.531000	0.85337	0.585000	0.79938	CGC	G|0.987;A|0.013	0.013	strong		0.642	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
HIPK1	204851	hgsc.bcm.edu	37	1	114514543	114514543	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114514543G>A	ENST00000369558.1	+	15	3343	c.3111G>A	c.(3109-3111)ggG>ggA	p.G1037G	HIPK1_ENST00000369554.2_Silent_p.G992G|HIPK1_ENST00000369559.4_Silent_p.G1037G|HIPK1_ENST00000406344.1_Silent_p.G643G|HIPK1_ENST00000426820.2_Silent_p.G1037G|HIPK1_ENST00000340480.4_Silent_p.G663G|HIPK1_ENST00000369555.2_Silent_p.G992G|HIPK1_ENST00000369561.4_Silent_p.G1003G|HIPK1_ENST00000369553.1_Silent_p.G643G			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1037	Interaction with TP53.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AACGCGGGGGGACCAGTGCAG	0.542																																					p.G1037G		Atlas-SNP	.											.	HIPK1	195	.	0			c.G3111A						PASS	.						176.0	143.0	154.0					1																	114514543		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon15			CGGGGGGACCAGT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3111G>A	1.37:g.114514543G>A		222.0	1.0	0.0045045		182.0	94.0	0.516484	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	0.089	-1.170955	0.01660	.	.	ENSG00000163349	ENST00000361587	.	.	.	5.89	0.0782	0.14411	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20706	-1.0267	4	.	.	.	.	1.851	0.03169	0.2593:0.1094:0.4096:0.2218	.	.	.	.	N	318	.	.	D	+	1	0	HIPK1	114316066	0.060000	0.20803	0.994000	0.49952	0.168000	0.22595	-0.497000	0.06428	0.095000	0.17434	0.563000	0.77884	GAC	.	.	none		0.542	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
TTC3	7267	hgsc.bcm.edu	37	21	38534308	38534308	+	Missense_Mutation	SNP	C	C	G	rs377155188		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38534308C>G	ENST00000399017.2	+	31	5860	c.3113C>G	c.(3112-3114)tCt>tGt	p.S1038C	TTC3_ENST00000355666.1_Missense_Mutation_p.S1038C|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.S1038C	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1038					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTAGTTGGGTCTGGAACAACT	0.279																																					p.S1038C	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C3113G						PASS	.	C	CYS/SER,CYS/SER	0,4404		0,0,2202	50.0	47.0	48.0		3113,3113	5.1	1.0	21		48	1,8573		0,1,4286	no	missense,missense	TTC3	NM_001001894.1,NM_003316.3	112,112	0,1,6488	GG,GC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	1038/2026,1038/2026	38534308	1,12977	2202	4287	6489	SO:0001583	missense	7267	exon31			TTGGGTCTGGAAC	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3113C>G	21.37:g.38534308C>G	ENSP00000381981:p.Ser1038Cys	165.0	0.0	0		145.0	79.0	0.544828	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.86|17.86	3.493015|3.493015	0.64186|0.64186	0.0|0.0	1.17E-4|1.17E-4	ENSG00000182670|ENSG00000182670	ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T;T;T	.|0.15834	.|2.39;2.39;2.68;2.68;2.68	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.64402	.|D	.|0.000013	T|T	0.40222|0.40222	0.1108|0.1108	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.996	T|T	0.19679|0.19679	-1.0298|-1.0298	5|10	.|0.87932	.|D	.|0	-23.3456|-23.3456	14.2622|14.2622	0.66092|0.66092	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|96;1038	.|Q5GIT6;P53804	.|.;TTC3_HUMAN	V|C	194|1038;1020;1038;1038;1038	.|ENSP00000403943:S1038C;ENSP00000391891:S1020C;ENSP00000347889:S1038C;ENSP00000381981:S1038C;ENSP00000346791:S1038C	.|ENSP00000346791:S1038C	L|S	+|+	1|2	2|0	TTC3|TTC3	37456178|37456178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	3.437000|3.437000	0.52863|0.52863	2.502000|2.502000	0.84385|0.84385	0.557000|0.557000	0.71058|0.71058	CTG|TCT	.	.	weak		0.279	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
METTL20	254013	hgsc.bcm.edu	37	12	31815167	31815167	+	Missense_Mutation	SNP	G	G	T	rs61736289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31815167G>T	ENST00000357721.3	+	2	495	c.280G>T	c.(280-282)Gca>Tca	p.A94S	METTL20_ENST00000395763.3_Missense_Mutation_p.A94S|METTL20_ENST00000412352.2_Missense_Mutation_p.A94S|METTL20_ENST00000538463.1_Missense_Mutation_p.A94S|METTL20_ENST00000538391.1_Missense_Mutation_p.A94S	NM_001135863.1	NP_001129335.1	Q8IXQ9	MET20_HUMAN	methyltransferase like 20	94						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			lung(2)|stomach(1)	3						TCCTTACTGGGCAATCTACTG	0.527													G|||	113	0.0225639	0.0023	0.0504	5008	,	,		19695	0.001		0.0596	False		,,,				2504	0.0143				p.A94S		Atlas-SNP	.											.	METTL20	23	.	0			c.G280T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	40,4366	43.1+/-76.7	0,40,2163	64.0	67.0	66.0		280,280,280	4.4	1.0	12	dbSNP_129	66	438,8162	133.5+/-191.0	10,418,3872	yes	missense,missense,missense	METTL20	NM_001135863.1,NM_001135864.1,NM_173802.3	99,99,99	10,458,6035	TT,TG,GG		5.093,0.9079,3.6752	probably-damaging,probably-damaging,probably-damaging	94/263,94/263,94/263	31815167	478,12528	2203	4300	6503	SO:0001583	missense	254013	exon2			TACTGGGCAATCT	BC039535	CCDS8724.1	12p11.21	2011-03-03	2011-03-03	2011-03-03	ENSG00000139160	ENSG00000139160			28739	protein-coding gene	gene with protein product		615256	"""chromosome 12 open reading frame 72"""	C12orf72			Standard	NM_173802		Approved	DKFZp451L235, MGC50559	uc001rkm.3	Q8IXQ9		ENST00000357721.3:c.280G>T	12.37:g.31815167G>T	ENSP00000350353:p.Ala94Ser	60.0	0.0	0		48.0	23.0	0.479167	NM_173802	D3DUW3	Missense_Mutation	SNP	ENST00000357721.3	37	CCDS8724.1	61	0.027930402930402932	1	0.0020325203252032522	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	G	26.6	4.751076	0.89753	0.009079	0.05093	ENSG00000139160	ENST00000412352;ENST00000395763;ENST00000538463;ENST00000357721;ENST00000538391	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.73962	2.25	0.80722	D	1	D	0.54397	0.966	P	0.49140	0.601	T	0.55964	-0.8057	9	0.37606	T	0.19	-10.4463	17.1676	0.86821	0.0:0.0:1.0:0.0	rs61736289	94	Q8IXQ9	MET20_HUMAN	S	94	.	ENSP00000350353:A94S	A	+	1	0	METTL20	31706434	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.907000	0.92634	2.277000	0.76020	0.561000	0.74099	GCA	G|0.968;T|0.032	0.032	strong		0.527	METTL20-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402196.1	NM_173802	
TTC21A	199223	hgsc.bcm.edu	37	3	39156124	39156124	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39156124G>A	ENST00000431162.2	+	6	741	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	TTC21A_ENST00000301819.6_Missense_Mutation_p.V203M|TTC21A_ENST00000440121.1_Missense_Mutation_p.V162M			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	203										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCTGGAGGTGGTGAACCAGAT	0.552																																					p.V203M		Atlas-SNP	.											.	TTC21A	96	.	0			c.G607A						PASS	.						136.0	133.0	134.0					3																	39156124		2028	4185	6213	SO:0001583	missense	199223	exon6			GAGGTGGTGAACC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.607G>A	3.37:g.39156124G>A	ENSP00000398211:p.Val203Met	141.0	0.0	0		128.0	19.0	0.148438	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742688	0.69418	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.64618	-0.11;-0.11;2.27	5.0	5.0	0.66597	Tetratricopeptide-like helical (1);	0.183014	0.35615	N	0.003092	T	0.73690	0.3619	M	0.72118	2.19	0.28282	N	0.923935	D;D;D;D;D	0.61080	0.967;0.989;0.989;0.981;0.989	P;D;D;P;D	0.63192	0.805;0.912;0.912;0.819;0.912	T	0.69439	-0.5145	10	0.54805	T	0.06	-18.6922	10.7065	0.45958	0.0894:0.0:0.9106:0.0	.	162;203;203;203;203	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	M	203;203;203;162	ENSP00000301819:V203M;ENSP00000398211:V203M;ENSP00000410882:V162M	ENSP00000301819:V203M	V	+	1	0	TTC21A	39131128	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.201000	0.51059	2.316000	0.78162	0.561000	0.74099	GTG	.	.	none		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
PTPRM	5797	hgsc.bcm.edu	37	18	8253407	8253407	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:8253407T>A	ENST00000332175.8	+	17	3747	c.2710T>A	c.(2710-2712)Tac>Aac	p.Y904N	PTPRM_ENST00000400053.4_Missense_Mutation_p.Y842N|PTPRM_ENST00000444013.1_Missense_Mutation_p.Y691N|PTPRM_ENST00000580170.1_Missense_Mutation_p.Y917N|PTPRM_ENST00000400060.4_Missense_Mutation_p.Y918N	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	904	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CAAGGAGGAATACGAGGTGAG	0.557																																					p.Y917N		Atlas-SNP	.											.	PTPRM	185	.	0			c.T2749A						PASS	.						43.0	30.0	34.0					18																	8253407		2203	4300	6503	SO:0001583	missense	5797	exon19			GAGGAATACGAGG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2710T>A	18.37:g.8253407T>A	ENSP00000331418:p.Tyr904Asn	104.0	0.0	0		86.0	19.0	0.22093	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243448	0.79912	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.93	5.93	0.95920	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.85682	D	0.000000	T	0.72170	0.3427	H	0.95679	3.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	T	0.81466	-0.0920	10	0.87932	D	0	.	16.3695	0.83350	0.0:0.0:0.0:1.0	.	691;917;904	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	N	904;918;842;691	ENSP00000331418:Y904N;ENSP00000382933:Y918N;ENSP00000382927:Y842N;ENSP00000387608:Y691N	ENSP00000331418:Y904N	Y	+	1	0	PTPRM	8243407	1.000000	0.71417	0.693000	0.30195	0.951000	0.60555	8.033000	0.88852	2.261000	0.74972	0.459000	0.35465	TAC	.	.	none		0.557	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
C2orf61	285051	hgsc.bcm.edu	37	2	47357129	47357129	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47357129C>T	ENST00000445927.2	-	5	596	c.470G>A	c.(469-471)tGt>tAt	p.C157Y	C2orf61_ENST00000294947.2_Missense_Mutation_p.C157Y|RP11-761B3.1_ENST00000422269.1_3'UTR	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	157										endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCGAAATACACAGCTCCTATA	0.259																																					p.C157Y		Atlas-SNP	.											.	C2orf61	31	.	0			c.G470A						PASS	.						77.0	81.0	80.0					2																	47357129		2203	4300	6503	SO:0001583	missense	285051	exon5			AATACACAGCTCC	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.470G>A	2.37:g.47357129C>T	ENSP00000408527:p.Cys157Tyr	93.0	0.0	0		186.0	27.0	0.145161	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.371|7.371	0.626725|0.626725	0.14257|0.14257	.|.	.|.	ENSG00000239605|ENSG00000239605	ENST00000445927;ENST00000294947|ENST00000449846	T;T|.	0.29397|.	1.57;1.6|.	5.07|5.07	0.0874|0.0874	0.14450|0.14450	.|.	0.377447|.	0.22845|.	N|.	0.054930|.	T|T	0.16171|0.16171	0.0389|0.0389	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999995|0.999995	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.21552|0.21552	-1.0242|-1.0242	10|5	0.02654|.	T|.	1|.	-5.7694|-5.7694	0.8202|0.8202	0.01110|0.01110	0.4569:0.1806:0.1051:0.2573|0.4569:0.1806:0.1051:0.2573	.|.	157|.	Q8N801|.	CB061_HUMAN|.	Y|M	157|37	ENSP00000408527:C157Y;ENSP00000294947:C157Y|.	ENSP00000294947:C157Y|.	C|V	-|-	2|1	0|0	C2orf61|C2orf61	47210633|47210633	0.159000|0.159000	0.22864|0.22864	0.705000|0.705000	0.30386|0.30386	0.479000|0.479000	0.33129|0.33129	0.539000|0.539000	0.23175|0.23175	0.794000|0.794000	0.33899|0.33899	-0.521000|-0.521000	0.04368|0.04368	TGT|GTG	.	.	none		0.259	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649	
DUOX2	50506	hgsc.bcm.edu	37	15	45400296	45400296	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45400296A>G	ENST00000603300.1	-	13	1725	c.1523T>C	c.(1522-1524)tTt>tCt	p.F508S	DUOX2_ENST00000389039.6_Missense_Mutation_p.F508S	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	508	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CAGCCGTACAAACTGGTCGAG	0.612																																					p.F508S		Atlas-SNP	.											.	DUOX2	137	.	0			c.T1523C						PASS	.						86.0	87.0	87.0					15																	45400296		2198	4298	6496	SO:0001583	missense	50506	exon13			CGTACAAACTGGT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1523T>C	15.37:g.45400296A>G	ENSP00000475084:p.Phe508Ser	88.0	0.0	0		109.0	73.0	0.669725	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593116	0.86953	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.86892	0.6042	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90760	0.4664	9	0.87932	D	0	-8.369	14.7402	0.69448	1.0:0.0:0.0:0.0	.	508;70	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	S	508	.	ENSP00000373691:F508S	F	-	2	0	DUOX2	43187588	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	9.106000	0.94253	2.080000	0.62538	0.533000	0.62120	TTT	.	.	none		0.612	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
DNAH9	1770	hgsc.bcm.edu	37	17	11543610	11543610	+	Missense_Mutation	SNP	A	A	G	rs61740059	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:11543610A>G	ENST00000262442.4	+	10	1878	c.1810A>G	c.(1810-1812)Atg>Gtg	p.M604V	DNAH9_ENST00000454412.2_Missense_Mutation_p.M604V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	604	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GCACAAGAACATGCCCACCGT	0.602													A|||	67	0.0133786	0.0015	0.0216	5008	,	,		18384	0.0		0.0219	False		,,,				2504	0.0286				p.M604V		Atlas-SNP	.											.	DNAH9	695	.	0			c.A1810G						PASS	.	A	VAL/MET	16,4390	24.3+/-50.5	0,16,2187	130.0	123.0	125.0		1810	5.4	1.0	17	dbSNP_129	125	277,8323	104.2+/-165.2	5,267,4028	yes	missense	DNAH9	NM_001372.3	21	5,283,6215	GG,GA,AA		3.2209,0.3631,2.2528	possibly-damaging	604/4487	11543610	293,12713	2203	4300	6503	SO:0001583	missense	1770	exon10			AAGAACATGCCCA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.1810A>G	17.37:g.11543610A>G	ENSP00000262442:p.Met604Val	73.0	0.0	0		66.0	28.0	0.424242	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	18.65	3.669200	0.67814	0.003631	0.032209	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.55930	0.49;0.49	5.4	5.4	0.78164	Dynein heavy chain, domain-1 (1);	0.554792	0.19401	N	0.115180	T	0.47358	0.1441	M	0.86268	2.805	0.80722	D	1	P	0.52316	0.952	P	0.56127	0.792	T	0.66352	-0.5945	10	0.52906	T	0.07	.	13.6437	0.62267	1.0:0.0:0.0:0.0	rs61740059	604	Q9NYC9	DYH9_HUMAN	V	604	ENSP00000262442:M604V;ENSP00000414874:M604V	ENSP00000262442:M604V	M	+	1	0	DNAH9	11484335	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.050000	0.64251	2.049000	0.60858	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.602	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
FIGNL1	63979	hgsc.bcm.edu	37	7	50513721	50513721	+	Missense_Mutation	SNP	A	A	C	rs146680091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:50513721A>C	ENST00000419119.1	-	2	2818	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	FIGNL1_ENST00000356889.4_Missense_Mutation_p.L422W|FIGNL1_ENST00000433017.1_Missense_Mutation_p.L422W|FIGNL1_ENST00000395556.2_Missense_Mutation_p.L422W			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	422					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				GTCTGGCCTCAACATGGGCCA	0.433													A|||	4	0.000798722	0.0	0.0014	5008	,	,		21003	0.0		0.003	False		,,,				2504	0.0				p.L422W		Atlas-SNP	.											.	FIGNL1	73	.	0			c.T1265G						PASS	.	A	TRP/LEU,TRP/LEU	3,4403	6.2+/-15.9	0,3,2200	82.0	89.0	86.0		1265,1265	6.0	1.0	7	dbSNP_134	86	33,8567	19.8+/-62.0	0,33,4267	yes	missense,missense	FIGNL1	NM_001042762.1,NM_022116.3	61,61	0,36,6467	CC,CA,AA		0.3837,0.0681,0.2768	probably-damaging,probably-damaging	422/675,422/675	50513721	36,12970	2203	4300	6503	SO:0001583	missense	63979	exon4			GGCCTCAACATGG	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1265T>G	7.37:g.50513721A>C	ENSP00000410811:p.Leu422Trp	154.0	0.0	0		110.0	75.0	0.681818	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.262784	0.80358	6.81E-4	0.003837	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65	5.99	5.99	0.97316	.	0.227384	0.36740	N	0.002426	D	0.95652	0.8586	L	0.47190	1.495	0.80722	D	1	D	0.71674	0.998	D	0.65874	0.939	D	0.95189	0.8306	10	0.41790	T	0.15	-3.4226	15.6754	0.77316	1.0:0.0:0.0:0.0	.	422	Q6PIW4	FIGL1_HUMAN	W	422	ENSP00000349356:L422W;ENSP00000378924:L422W;ENSP00000399997:L422W;ENSP00000410811:L422W	ENSP00000349356:L422W	L	-	2	0	FIGNL1	50481215	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTG	A|0.997;C|0.003	0.003	strong		0.433	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762	
ZNF136	7695	hgsc.bcm.edu	37	19	12298164	12298164	+	Missense_Mutation	SNP	G	G	A	rs200700405		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12298164G>A	ENST00000343979.4	+	4	1111	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	ZNF136_ENST00000398616.2_Missense_Mutation_p.R258Q	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	324					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						CCCTCCCTTCGACTACATGAA	0.428																																					p.R324Q		Atlas-SNP	.											ZNF136,colon,carcinoma,+1,1	ZNF136	57	1	0			c.G971A						PASS	.						92.0	93.0	92.0					19																	12298164		2203	4300	6503	SO:0001583	missense	7695	exon4			CCCTTCGACTACA	U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"""Zinc fingers, C2H2-type"", ""-"""	12920	protein-coding gene	gene with protein product		604078	"""zinc finger protein 136 (clone pHZ-20)"""			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.971G>A	19.37:g.12298164G>A	ENSP00000344162:p.Arg324Gln	36.0	0.0	0		39.0	22.0	0.564103	NM_003437		Missense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.676518	0.29783	.	.	ENSG00000196646	ENST00000343979;ENST00000398616	T;T	0.07444	3.19;3.19	1.25	0.00598	0.14064	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02571	0.0078	N	0.10685	0.025	0.09310	N	1	B	0.33857	0.429	B	0.15052	0.012	T	0.42292	-0.9460	8	.	.	.	.	1.9912	0.03447	0.4876:0.0:0.254:0.2584	.	324	P52737	ZN136_HUMAN	Q	324;258	ENSP00000344162:R324Q;ENSP00000381617:R258Q	.	R	+	2	0	ZNF136	12159164	0.000000	0.05858	0.007000	0.13788	0.997000	0.91878	-1.017000	0.03630	-0.007000	0.14345	0.655000	0.94253	CGA	G|0.999;A|0.001	0.001	weak		0.428	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080938	57080938	+	Silent	SNP	C	C	A	rs145901431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57080938C>A	ENST00000532437.1	-	4	1535	c.1224G>T	c.(1222-1224)ggG>ggT	p.G408G	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Silent_p.G408G			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	408	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CCTCCTCCTCCCCGCCAGATG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16354	0.0		0.004	False		,,,				2504	0.001				p.G408G		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G1224T						PASS	.	C		0,4398		0,0,2199	23.0	24.0	24.0		1224	0.8	0.0	11	dbSNP_134	24	27,8561		0,27,4267	yes	coding-synonymous	TNKS1BP1	NM_033396.2		0,27,6466	AA,AC,CC		0.3144,0.0,0.2079		408/1730	57080938	27,12959	2199	4294	6493	SO:0001819	synonymous_variant	85456	exon5			CTCCTCCCCGCCA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1224G>T	11.37:g.57080938C>A		66.0	0.0	0		50.0	41.0	0.82	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.998;A|0.002	0.002	strong		0.647	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
SERPIND1	3053	hgsc.bcm.edu	37	22	21133831	21133831	+	Missense_Mutation	SNP	C	C	A	rs5903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:21133831C>A	ENST00000215727.5	+	2	514	c.231C>A	c.(229-231)gaC>gaA	p.D77E	PI4KA_ENST00000572273.1_Intron|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.D77E	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	77	2 X 11 AA approximate repeats, Asp/Glu- rich (acidic) (hirudin-like).|Chemotactic activity.				blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	AGGAGGACGACGACTATCTGG	0.507													C|||	17	0.00339457	0.0	0.0043	5008	,	,		20196	0.0		0.0119	False		,,,				2504	0.002				p.D77E		Atlas-SNP	.											.	SERPIND1	92	.	0			c.C231A						PASS	.	C	GLU/ASP,	10,4396	16.8+/-37.8	0,10,2193	79.0	69.0	72.0		231,	-11.5	0.4	22	dbSNP_52	72	83,8517	48.5+/-108.0	0,83,4217	yes	missense,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	45,	0,93,6410	AA,AC,CC		0.9651,0.227,0.7151	benign,	77/500,	21133831	93,12913	2203	4300	6503	SO:0001583	missense	3053	exon2			GGACGACGACTAT	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"""Serine (or cysteine) peptidase inhibitors"""	4838	protein-coding gene	gene with protein product	"""heparin cofactor II"""	142360	"""serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"""	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.231C>A	22.37:g.21133831C>A	ENSP00000215727:p.Asp77Glu	126.0	0.0	0		133.0	65.0	0.488722	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	37	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	C	4.885	0.164489	0.09287	0.00227	0.009651	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.81739	-1.53;-1.53	5.75	-11.5	0.00074	.	0.295809	0.41500	N	0.000877	T	0.34135	0.0887	N	0.04018	-0.295	0.22034	N	0.999407	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.55579	-0.8119	10	0.02654	T	1	.	7.576	0.27937	0.0539:0.4378:0.3104:0.1979	.	77;77	Q8IVC0;P05546	.;HEP2_HUMAN	E	77	ENSP00000215727:D77E;ENSP00000384050:D77E	ENSP00000215727:D77E	D	+	3	2	SERPIND1	19463831	0.000000	0.05858	0.378000	0.26068	0.923000	0.55619	-2.171000	0.01267	-1.815000	0.01222	-1.021000	0.02439	GAC	A|0.004;C|0.984;T|0.013	0.004	strong		0.507	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185	
C14orf39	317761	hgsc.bcm.edu	37	14	60945066	60945066	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60945066T>C	ENST00000321731.3	-	5	434	c.275A>G	c.(274-276)tAt>tGt	p.Y92C		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	92					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GTCCTGCATATAATCTTCATG	0.279																																					p.Y92C		Atlas-SNP	.											.	C14orf39	79	.	0			c.A275G						PASS	.						78.0	76.0	77.0					14																	60945066		2201	4294	6495	SO:0001583	missense	317761	exon5			TGCATATAATCTT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.275A>G	14.37:g.60945066T>C	ENSP00000324920:p.Tyr92Cys	200.0	0.0	0		166.0	90.0	0.542169	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016056	0.35606	.	.	ENSG00000179008	ENST00000321731;ENST00000555476	T;T	0.59364	1.7;0.27	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000006	T	0.71187	0.3310	M	0.69823	2.125	0.35794	D	0.822654	D	0.89917	1.0	D	0.73380	0.98	T	0.77770	-0.2463	10	0.44086	T	0.13	-10.7904	9.2845	0.37749	0.1605:0.0:0.0:0.8395	.	92	Q8N1H7	S6OS1_HUMAN	C	92;63	ENSP00000324920:Y92C;ENSP00000451665:Y63C	ENSP00000324920:Y92C	Y	-	2	0	C14orf39	60014819	1.000000	0.71417	0.997000	0.53966	0.107000	0.19398	2.294000	0.43567	2.237000	0.73441	0.528000	0.53228	TAT	.	.	none		0.279	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
C3	718	hgsc.bcm.edu	37	19	6718146	6718146	+	Missense_Mutation	SNP	T	T	G	rs147859257	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6718146T>G	ENST00000245907.6	-	4	555	c.463A>C	c.(463-465)Aag>Cag	p.K155Q		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	155			K -> Q (in ARMD9; results in resistance to proteolytic inactivation by CFH and CFI). {ECO:0000269|PubMed:24036952}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GGTAGCAGCTTGTGGTTGACG	0.652													T|||	2	0.000399361	0.0	0.0	5008	,	,		18237	0.0		0.002	False		,,,				2504	0.0				p.K155Q		Atlas-SNP	.											.	C3	192	.	0			c.A463C						PASS	.	T	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	94.0	88.0	90.0		463	1.3	0.4	19	dbSNP_134	90	37,8563	25.1+/-72.6	0,37,4263	yes	missense	C3	NM_000064.2	53	0,38,6465	GG,GT,TT		0.4302,0.0227,0.2922	possibly-damaging	155/1664	6718146	38,12968	2203	4300	6503	SO:0001583	missense	718	exon4			GCAGCTTGTGGTT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.463A>C	19.37:g.6718146T>G	ENSP00000245907:p.Lys155Gln	97.0	0.0	0		87.0	47.0	0.54023	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	9.992	1.231149	0.22626	2.27E-4	0.004302	ENSG00000125730	ENST00000245907	T	0.73681	-0.77	4.56	1.27	0.21489	Alpha-2-macroglobulin, N-terminal (1);	0.839580	0.11137	N	0.595772	T	0.69305	0.3096	L	0.58354	1.805	0.20074	N	0.999934	B	0.25235	0.121	B	0.32022	0.139	T	0.57359	-0.7825	10	0.33940	T	0.23	.	7.5787	0.27952	0.0:0.2731:0.0:0.7269	.	155	P01024	CO3_HUMAN	Q	155	ENSP00000245907:K155Q	ENSP00000245907:K155Q	K	-	1	0	C3	6669146	0.002000	0.14202	0.358000	0.25811	0.607000	0.37147	-0.429000	0.06982	-0.030000	0.13804	0.248000	0.18094	AAG	T|0.998;G|0.002	0.002	strong		0.652	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
FFAR3	2865	hgsc.bcm.edu	37	19	35850408	35850408	+	Missense_Mutation	SNP	C	C	T	rs138920343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35850408C>T	ENST00000327809.4	+	2	817	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	FFAR3_ENST00000594310.1_Missense_Mutation_p.R206C	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	206					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CTGCTACAGCCGCCTGGTGTG	0.652																																					p.R206C	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											.	FFAR3	40	.	0			c.C616T						PASS	.	C	CYS/ARG	7,4375		0,7,2184	14.0	13.0	13.0		616	5.1	1.0	19	dbSNP_134	13	61,8409		0,61,4174	no	missense	FFAR3	NM_005304.3	180	0,68,6358	TT,TC,CC		0.7202,0.1597,0.5291	probably-damaging	206/347	35850408	68,12784	2191	4235	6426	SO:0001583	missense	2865	exon2			TACAGCCGCCTGG	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.616C>T	19.37:g.35850408C>T	ENSP00000328230:p.Arg206Cys	417.0	0.0	0		405.0	113.0	0.279012	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633388	0.67015	0.001597	0.007202	ENSG00000185897	ENST00000327809	T	0.39592	1.07	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.264721	0.41001	U	0.000964	T	0.49558	0.1564	M	0.71581	2.175	0.18873	N	0.999988	D	0.76494	0.999	D	0.63033	0.91	T	0.49570	-0.8926	10	0.37606	T	0.19	-16.7142	11.2036	0.48756	0.1836:0.8164:0.0:0.0	.	206	O14843	FFAR3_HUMAN	C	206	ENSP00000328230:R206C	ENSP00000328230:R206C	R	+	1	0	FFAR3	40542248	0.097000	0.21791	1.000000	0.80357	0.990000	0.78478	2.128000	0.42045	2.385000	0.81259	0.455000	0.32223	CGC	C|0.997;T|0.003	0.003	strong		0.652	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
NEUROD6	63974	hgsc.bcm.edu	37	7	31378795	31378795	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31378795G>A	ENST00000297142.3	-	2	410	c.88C>T	c.(88-90)Caa>Taa	p.Q30*		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	30					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	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)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						TTCTTAATTTGCTTCTGGTCC	0.433																																					p.Q30X		Atlas-SNP	.											.	NEUROD6	84	.	0			c.C88T						PASS	.						136.0	148.0	144.0					7																	31378795		2203	4300	6503	SO:0001587	stop_gained	63974	exon2			TAATTTGCTTCTG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.88C>T	7.37:g.31378795G>A	ENSP00000297142:p.Gln30*	82.0	0.0	0		61.0	12.0	0.196721	NM_022728	Q548T9|Q9H3H6	Nonsense_Mutation	SNP	ENST00000297142.3	37	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	37	6.007479	0.97195	.	.	ENSG00000164600	ENST00000297142	.	.	.	5.28	5.28	0.74379	.	0.240470	0.36101	N	0.002799	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-2.4487	18.9485	0.92632	0.0:0.0:1.0:0.0	.	.	.	.	X	30	.	ENSP00000297142:Q30X	Q	-	1	0	NEUROD6	31345320	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.750000	0.62162	2.485000	0.83878	0.650000	0.86243	CAA	.	.	none		0.433	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
SLC45A3	85414	hgsc.bcm.edu	37	1	205628616	205628616	+	Missense_Mutation	SNP	C	C	T	rs137949511	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205628616C>T	ENST00000367145.3	-	5	1703	c.1408G>A	c.(1408-1410)Gta>Ata	p.V470I	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	470					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			ACCACACGTACGGAGACATCA	0.677			T	"""ETV1, ETV5, ELK4, ERG"""	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	21	0.00419329	0.0	0.0043	5008	,	,		18353	0.0		0.0119	False		,,,				2504	0.0061				p.V470I		Atlas-SNP	.		Dom	yes		1	1q32	85414	"""solute carrier family 45, member 3"""		E	.	SLC45A3	54	.	0			c.G1408A						PASS	.	C	ILE/VAL	8,4396	14.3+/-33.2	0,8,2194	38.0	38.0	38.0		1408	-1.4	0.4	1	dbSNP_134	38	78,8520	44.5+/-102.8	0,78,4221	yes	missense	SLC45A3	NM_033102.2	29	0,86,6415	TT,TC,CC		0.9072,0.1817,0.6614	benign	470/554	205628616	86,12916	2202	4299	6501	SO:0001583	missense	85414	exon5			CACGTACGGAGAC	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"""Solute carriers"""	8642	protein-coding gene	gene with protein product		605097	"""prostate cancer associated protein 6"", ""prostate cancer associated protein 2"", ""prostate cancer associated protein 8"""	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1408G>A	1.37:g.205628616C>T	ENSP00000356113:p.Val470Ile	115.0	0.0	0	2153	128.0	71.0	0.554688	NM_033102	A8K2U9	Missense_Mutation	SNP	ENST00000367145.3	37	CCDS1458.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.983	-0.209897	0.06140	0.001817	0.009072	ENSG00000158715	ENST00000367145	T	0.44482	0.92	5.48	-1.36	0.09085	.	0.387498	0.26341	N	0.024935	T	0.13072	0.0317	N	0.14661	0.345	0.09310	N	1	B	0.22211	0.066	B	0.13407	0.009	T	0.20538	-1.0272	10	0.14656	T	0.56	-17.1135	7.4464	0.27213	0.0:0.4405:0.1634:0.3962	.	470	Q96JT2	S45A3_HUMAN	I	470	ENSP00000356113:V470I	ENSP00000356113:V470I	V	-	1	0	SLC45A3	203895239	0.023000	0.18921	0.369000	0.25952	0.167000	0.22549	-0.027000	0.12371	-0.144000	0.11314	-0.339000	0.08088	GTA	C|0.994;T|0.006	0.006	strong		0.677	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102	
C9orf3	84909	hgsc.bcm.edu	37	9	97717527	97717527	+	Missense_Mutation	SNP	C	C	T	rs143555020		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97717527C>T	ENST00000375315.2	+	7	1730	c.1730C>T	c.(1729-1731)cCg>cTg	p.P577L	C9orf3_ENST00000297979.5_Missense_Mutation_p.P478L	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	577					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		GGACTTAATCCGGAGAAGATC	0.398													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20468	0.0		0.0	False		,,,				2504	0.0				p.P577L		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1730T						PASS	.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	125.0	110.0	115.0		1730,1433	4.1	1.0	9	dbSNP_134	115	0,8600		0,0,4300	no	missense,missense	C9orf3	NM_001193329.1,NM_032823.5	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	577/820,478/721	97717527	1,13005	2203	4300	6503	SO:0001583	missense	84909	exon7			TTAATCCGGAGAA	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.1730C>T	9.37:g.97717527C>T	ENSP00000364464:p.Pro577Leu	51.0	0.0	0		32.0	7.0	0.21875	NM_001193329	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.54	1.377611	0.24944	2.27E-4	0.0	ENSG00000148120	ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	5.0	4.11	0.48088	.	0.210223	0.39759	N	0.001269	T	0.22781	0.0550	M	0.84082	2.675	0.80722	D	1	D;P;D	0.76494	0.998;0.848;0.999	P;B;P	0.62435	0.835;0.361;0.902	T	0.01508	-1.1337	10	0.87932	D	0	-10.1413	11.284	0.49212	0.0:0.9136:0.0:0.0864	.	577;478;478	Q8N6M6;Q8N6M6-4;Q8N6M6-2	AMPO_HUMAN;.;.	L	478;577;301;359	ENSP00000297979:P478L;ENSP00000364464:P577L;ENSP00000402171:P301L;ENSP00000401854:P359L	ENSP00000297979:P478L	P	+	2	0	C9orf3	96757348	0.442000	0.25633	0.980000	0.43619	0.172000	0.22775	2.770000	0.47662	1.483000	0.48342	-0.126000	0.14955	CCG	C|1.000;T|0.000	0.000	strong		0.398	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	
HSDL2	84263	hgsc.bcm.edu	37	9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	rs41280175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000262542.7_5'UTR	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128.0	126.0	126.0		272,272	3.2	1.0	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18572	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 13C, member 1"""		"""chromosome 9 open reading frame 99"""	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	63.0	0.0	0		43.0	26.0	0.604651	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303	
SNTB2	6645	hgsc.bcm.edu	37	16	69318149	69318149	+	Splice_Site	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69318149T>C	ENST00000336278.4	+	5	1383		c.e5+2			NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)							cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		TCTCTCTAGGTAGAGATGCTG	0.423																																					.	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.1345+2T>C						PASS	.						70.0	64.0	66.0					16																	69318149		2198	4300	6498	SO:0001630	splice_region_variant	6645	exon5			TCTAGGTAGAGAT	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"""syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"""	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.1345+2T>C	16.37:g.69318149T>C		85.0	0.0	0		88.0	4.0	0.0454545	NM_006750	Q9BY09	Splice_Site	SNP	ENST00000336278.4	37	CCDS10873.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.346898	0.82022	.	.	ENSG00000168807	ENST00000336278;ENST00000467311	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7976	0.69889	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNTB2	67875650	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.857000	0.86963	1.975000	0.57531	0.533000	0.62120	.	.	.	none		0.423	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		Intron
MKNK1	8569	hgsc.bcm.edu	37	1	47028362	47028362	+	Missense_Mutation	SNP	C	C	T	rs55791614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47028362C>T	ENST00000371946.4	-	11	1085	c.922G>A	c.(922-924)Gac>Aac	p.D308N	MKNK1_ENST00000371945.4_Missense_Mutation_p.D267N|MKNK1_ENST00000428112.2_Missense_Mutation_p.D267N|MKNK1_ENST00000371944.4_Missense_Mutation_p.D172N|MKNK1_ENST00000341183.5_Missense_Mutation_p.D267N|MKNK1-AS1_ENST00000602433.1_RNA	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	308	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs55791614). {ECO:0000269|PubMed:17344846}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					CAGCCACAGTCGGCCCCGCAG	0.662													C|||	10	0.00199681	0.0	0.0043	5008	,	,		16040	0.0		0.005	False		,,,				2504	0.002				p.D308N		Atlas-SNP	.											.	MKNK1	36	.	0			c.G922A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	11,4385		0,11,2187	27.0	24.0	25.0		799,922,799	4.5	1.0	1	dbSNP_129	25	60,8500		1,58,4221	no	missense,missense,missense	MKNK1	NM_001135553.1,NM_003684.4,NM_198973.2	23,23,23	1,69,6408	TT,TC,CC		0.7009,0.2502,0.548	benign,benign,benign	267/425,308/466,267/348	47028362	71,12885	2198	4280	6478	SO:0001583	missense	8569	exon11			CACAGTCGGCCCC	AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.922G>A	1.37:g.47028362C>T	ENSP00000361014:p.Asp308Asn	181.0	0.0	0		171.0	104.0	0.608187	NM_003684	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	37	CCDS538.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.55	2.866573	0.51588	0.002502	0.007009	ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.42	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086825	0.85682	D	0.000000	T	0.08358	0.0208	N	0.12502	0.225	0.80722	D	1	B;B;B;B;B;P	0.42649	0.102;0.245;0.102;0.083;0.193;0.786	B;B;B;B;B;B	0.37888	0.031;0.054;0.031;0.018;0.09;0.26	T	0.09596	-1.0667	10	0.32370	T	0.25	.	13.8642	0.63578	0.0:0.9252:0.0:0.0748	rs55791614	172;172;267;267;267;308	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5	.;.;.;.;.;MKNK1_HUMAN	N	308;267;172;267;267	ENSP00000361014:D308N;ENSP00000361013:D267N;ENSP00000361012:D172N;ENSP00000339573:D267N;ENSP00000411135:D267N	ENSP00000339573:D267N	D	-	1	0	MKNK1	46800949	0.994000	0.37717	0.977000	0.42913	0.672000	0.39443	3.119000	0.50422	2.826000	0.97356	0.563000	0.77884	GAC	C|0.996;T|0.004	0.004	strong		0.662	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684	
CDC20B	166979	hgsc.bcm.edu	37	5	54424381	54424381	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54424381G>A	ENST00000381375.2	-	7	907	c.762C>T	c.(760-762)taC>taT	p.Y254Y	CDC20B_ENST00000296733.1_Silent_p.Y254Y|CDC20B_ENST00000322374.6_Silent_p.Y254Y|CDC20B_ENST00000334206.5_Silent_p.Y254Y			Q86Y33	CD20B_HUMAN	cell division cycle 20B	254										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			CATTCCAGATGTATACAGCAG	0.383																																					p.Y254Y		Atlas-SNP	.											.	CDC20B	61	.	0			c.C762T						PASS	.						145.0	151.0	149.0					5																	54424381		2203	4300	6503	SO:0001819	synonymous_variant	166979	exon7			CCAGATGTATACA	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.762C>T	5.37:g.54424381G>A		199.0	0.0	0		184.0	64.0	0.347826	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			.	.	none		0.383	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
PPP6R3	55291	hgsc.bcm.edu	37	11	68377475	68377475	+	Missense_Mutation	SNP	A	A	G	rs79540432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68377475A>G	ENST00000393800.2	+	23	2808	c.2554A>G	c.(2554-2556)Agc>Ggc	p.S852G	PPP6R3_ENST00000529710.1_Missense_Mutation_p.S772G|PPP6R3_ENST00000524904.1_Missense_Mutation_p.S846G|PPP6R3_ENST00000393801.3_Missense_Mutation_p.S858G|PPP6R3_ENST00000534534.1_Missense_Mutation_p.S620G|PPP6R3_ENST00000265636.5_Missense_Mutation_p.S772G|PPP6R3_ENST00000265637.4_Missense_Mutation_p.S806G|PPP6R3_ENST00000524845.1_Missense_Mutation_p.S823G|PPP6R3_ENST00000393799.2_Missense_Mutation_p.S858G|PPP6R3_ENST00000527403.2_Missense_Mutation_p.S817G	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	852					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GCCTCCCAGCAGCAGTCCCGA	0.622													A|||	19	0.00379393	0.0008	0.0086	5008	,	,		18142	0.0		0.0119	False		,,,				2504	0.0				p.S858G		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A2572G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	10,4390	17.9+/-39.9	0,10,2190	53.0	52.0	52.0		2572,2554,2536,2467,2314,2314	3.8	1.0	11	dbSNP_131	52	111,8477	58.3+/-119.8	3,105,4186	yes	missense,missense,missense,missense,missense,missense	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	56,56,56,56,56,56	3,115,6376	GG,GA,AA		1.2925,0.2273,0.9316	benign,benign,benign,benign,benign,benign	858/880,852/874,846/868,823/845,772/792,772/794	68377475	121,12867	2200	4294	6494	SO:0001583	missense	55291	exon24			CCCAGCAGCAGTC	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2554A>G	11.37:g.68377475A>G	ENSP00000377389:p.Ser852Gly	57.0	0.0	0		58.0	41.0	0.706897	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	A	11.52	1.663897	0.29515	0.002273	0.012925	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.96	3.76	0.43208	.	0.236035	0.35207	N	0.003362	T	0.38241	0.1033	L	0.47716	1.5	0.38584	D	0.950242	B;B;B;B;B;B;B;B	0.19200	0.031;0.034;0.0;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.24006	0.05;0.011;0.002;0.001;0.004;0.002;0.003;0.001	T	0.48681	-0.9014	10	0.44086	T	0.13	.	12.9887	0.58606	0.8559:0.1441:0.0:0.0	.	535;620;772;823;846;852;858;772	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	G	858;852;620;823;806;846;858;772;772;817;559	ENSP00000377388:S858G;ENSP00000377389:S852G;ENSP00000434429:S620G;ENSP00000431415:S823G;ENSP00000265637:S806G;ENSP00000433058:S846G;ENSP00000377390:S858G;ENSP00000265636:S772G;ENSP00000437329:S772G;ENSP00000433565:S817G;ENSP00000436209:S559G	ENSP00000265636:S772G	S	+	1	0	PPP6R3	68134051	1.000000	0.71417	0.997000	0.53966	0.357000	0.29423	4.276000	0.58933	1.861000	0.53984	0.459000	0.35465	AGC	A|0.992;G|0.008	0.008	strong		0.622	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
CACNB4	785	hgsc.bcm.edu	37	2	152955482	152955482	+	Missense_Mutation	SNP	G	G	C	rs200662010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152955482G>C	ENST00000539935.1	-	1	111	c.44C>G	c.(43-45)cCg>cGg	p.P15R	AC079790.2_ENST00000420365.1_RNA|CACNB4_ENST00000201943.5_Missense_Mutation_p.P15R|CACNB4_ENST00000427385.1_5'Flank	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	15					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GGGGGAGTGCGGCCCGTCCGC	0.721													G|||	2	0.000399361	0.0	0.0029	5008	,	,		9469	0.0		0.0	False		,,,				2504	0.0				p.P15R		Atlas-SNP	.											.	CACNB4	108	.	0			c.C44G						PASS	.	G	ARG/PRO,ARG/PRO	4,3898		0,4,1947	11.0	16.0	14.0		44,44	-0.1	1.0	2		14	26,8102		0,26,4038	yes	missense,missense	CACNB4	NM_000726.3,NM_001145798.1	103,103	0,30,5985	CC,CG,GG		0.3199,0.1025,0.2494	benign,benign	15/521,15/459	152955482	30,12000	1951	4064	6015	SO:0001583	missense	785	exon1			GAGTGCGGCCCGT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.44C>G	2.37:g.152955482G>C	ENSP00000438949:p.Pro15Arg	117.0	0.0	0		124.0	61.0	0.491935	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	4.250	0.045444	0.08196	0.001025	0.003199	ENSG00000182389	ENST00000539935;ENST00000201943;ENST00000339254	T;T	0.71461	-0.57;-0.57	4.55	-0.0829	0.13696	.	0.952431	0.08719	N	0.903787	T	0.49321	0.1550	N	0.14661	0.345	0.80722	D	1	B;B	0.20671	0.0;0.047	B;B	0.19148	0.0;0.024	T	0.36962	-0.9726	10	0.52906	T	0.07	-4.6977	4.2846	0.10848	0.0937:0.2947:0.4771:0.1345	.	15;15	A7BJ74;O00305	.;CACB4_HUMAN	R	15	ENSP00000438949:P15R;ENSP00000201943:P15R	ENSP00000201943:P15R	P	-	2	0	CACNB4	152663728	0.980000	0.34600	0.997000	0.53966	0.024000	0.10985	-0.208000	0.09371	0.025000	0.15241	-0.176000	0.13171	CCG	G|1.000;C|0.000	0.000	strong		0.721	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	
HAUS4	54930	hgsc.bcm.edu	37	14	23421593	23421593	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23421593G>A	ENST00000206474.7	-	4	526	c.274C>T	c.(274-276)Ctt>Ttt	p.L92F	RP11-298I3.5_ENST00000555074.1_Intron|HAUS4_ENST00000342454.8_Missense_Mutation_p.L92F|HAUS4_ENST00000554446.1_5'UTR|HAUS4_ENST00000490506.1_5'UTR|HAUS4_ENST00000555367.1_Missense_Mutation_p.L92F|HAUS4_ENST00000347758.2_Missense_Mutation_p.L92F|RP11-298I3.1_ENST00000548322.1_RNA|HAUS4_ENST00000397409.4_Missense_Mutation_p.L92F|HAUS4_ENST00000541587.1_Missense_Mutation_p.L92F|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000555986.1_Missense_Mutation_p.L92F			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	92					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|cervix(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)	14						TAGTCCACAAGCAACTCTTGA	0.433																																					p.L92F		Atlas-SNP	.											.	HAUS4	34	.	0			c.C274T						PASS	.						229.0	218.0	222.0					14																	23421593		2203	4300	6503	SO:0001583	missense	54930	exon4			CCACAAGCAACTC	AK000431	CCDS9580.1, CCDS53886.1	14q11.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000092036	ENSG00000092036		"""HAUS augmin-like complex subunits"""	20163	protein-coding gene	gene with protein product		613431	"""chromosome 14 open reading frame 94"""	C14orf94		19427217	Standard	NM_017815		Approved	FLJ20424	uc001wht.3	Q9H6D7	OTTHUMG00000028710	ENST00000206474.7:c.274C>T	14.37:g.23421593G>A	ENSP00000206474:p.Leu92Phe	206.0	0.0	0		183.0	97.0	0.530055	NM_001166270	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	37	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260380	0.80246	.	.	ENSG00000092036	ENST00000206474;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555040;ENST00000556915;ENST00000554516;ENST00000557591	.	.	.	5.71	5.71	0.89125	.	0.124104	0.53938	D	0.000054	T	0.69214	0.3086	L	0.59436	1.845	0.32357	N	0.557748	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.996;0.997	T	0.75453	-0.3312	9	0.72032	D	0.01	-7.2977	15.3637	0.74503	0.0:0.0:1.0:0.0	.	92;92;92	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	F	92	.	ENSP00000206474:L92F	L	-	1	0	HAUS4	22491433	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.932000	0.56537	2.694000	0.91930	0.655000	0.94253	CTT	.	.	none		0.433	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3		
SCIN	85477	hgsc.bcm.edu	37	7	12617727	12617727	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12617727A>C	ENST00000297029.5	+	2	339	c.238A>C	c.(238-240)Atc>Ctc	p.I80L		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	80	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AGCTGCTGCCATCTTCACTGT	0.418																																					p.I80L		Atlas-SNP	.											.	SCIN	105	.	0			c.A238C						PASS	.						116.0	98.0	104.0					7																	12617727		692	1591	2283	SO:0001583	missense	85477	exon2			GCTGCCATCTTCA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.238A>C	7.37:g.12617727A>C	ENSP00000297029:p.Ile80Leu	144.0	0.0	0		148.0	64.0	0.432432	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275863	0.80580	.	.	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.51574	0.7;0.7	4.93	3.76	0.43208	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.67953	2.075	0.80722	D	1	B	0.26708	0.157	P	0.46026	0.501	T	0.61705	-0.7008	10	0.72032	D	0.01	-9.0734	11.05	0.47880	0.8607:0.0:0.0:0.1393	.	80	Q9Y6U3	ADSV_HUMAN	L	80;107	ENSP00000297029:I80L;ENSP00000404380:I107L	ENSP00000297029:I80L	I	+	1	0	SCIN	12584252	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.286000	0.78671	0.884000	0.36064	-0.481000	0.04817	ATC	.	.	none		0.418	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33405994	33405994	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33405994G>A	ENST00000418600.2	+	8	1413	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.A438T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.A379T|MIR5004_ENST00000579078.1_RNA	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	438					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CTTGGAGCCCGCCCTGAATGT	0.512																																					p.A438T		Atlas-SNP	.											SYNGAP1_ENST00000293748,right_lower_lobe,carcinoma,0,2	SYNGAP1	202	2	0			c.G1312A						scavenged	.						160.0	155.0	157.0					6																	33405994		2203	4300	6503	SO:0001583	missense	8831	exon8			GAGCCCGCCCTGA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1312G>A	6.37:g.33405994G>A	ENSP00000403636:p.Ala438Thr	276.0	2.0	0.00724638		285.0	149.0	0.522807	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	14.39	2.522340	0.44866	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.16457	2.34;2.43;2.43	4.86	3.99	0.46301	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.246616	0.33712	N	0.004627	T	0.03095	0.0091	N	0.14661	0.345	0.31709	N	0.639723	B;P;P;B	0.36660	0.428;0.564;0.564;0.026	B;B;B;B	0.19666	0.011;0.026;0.026;0.003	T	0.27502	-1.0072	10	0.72032	D	0.01	.	11.1118	0.48237	0.0904:0.0:0.9096:0.0	.	438;438;438;438	Q96PV0;Q96PV0-2;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.;.	T	438;438;438;379	ENSP00000293748:A438T;ENSP00000403636:A438T;ENSP00000412475:A379T	ENSP00000293748:A438T	A	+	1	0	SYNGAP1	33513972	0.968000	0.33430	0.858000	0.33744	0.950000	0.60333	1.961000	0.40432	1.255000	0.44051	0.650000	0.86243	GCC	.	.	none		0.512	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
ZC3H4	23211	hgsc.bcm.edu	37	19	47571039	47571039	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47571039G>A	ENST00000253048.5	-	15	2523	c.2486C>T	c.(2485-2487)tCc>tTc	p.S829F	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	829							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GGGTCGGCTGGACGTCTGCTG	0.622																																					p.S829F		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C2486T						PASS	.						17.0	19.0	18.0					19																	47571039		2045	4167	6212	SO:0001583	missense	23211	exon15			CGGCTGGACGTCT	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2486C>T	19.37:g.47571039G>A	ENSP00000253048:p.Ser829Phe	46.0	0.0	0		33.0	6.0	0.181818	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029641	0.54790	.	.	ENSG00000130749	ENST00000253048	T	0.19532	2.14	5.58	5.58	0.84498	.	0.329705	0.30201	N	0.010169	T	0.41650	0.1168	L	0.47716	1.5	0.51233	D	0.999918	D	0.71674	0.998	D	0.71870	0.975	T	0.12604	-1.0541	10	0.66056	D	0.02	.	18.3514	0.90339	0.0:0.0:1.0:0.0	.	829	Q9UPT8	ZC3H4_HUMAN	F	829	ENSP00000253048:S829F	ENSP00000253048:S829F	S	-	2	0	ZC3H4	52262879	1.000000	0.71417	0.103000	0.21229	0.293000	0.27360	5.684000	0.68197	2.642000	0.89623	0.655000	0.94253	TCC	.	.	none		0.622	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
SLCO1C1	53919	hgsc.bcm.edu	37	12	20876168	20876168	+	Missense_Mutation	SNP	C	C	T	rs144285413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:20876168C>T	ENST00000266509.2	+	9	1534	c.1166C>T	c.(1165-1167)tCc>tTc	p.S389F	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.S389F|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.S271F|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.S389F|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.S340F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	389					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	CAGTCATCCTCCAGGGCCAAC	0.443													C|||	20	0.00399361	0.0008	0.0058	5008	,	,		19476	0.0		0.0139	False		,,,				2504	0.001				p.S389F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C1166T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	159.0	138.0	145.0		812,1019,1166,1166	4.5	0.9	12	dbSNP_134	145	59,8541	35.9+/-90.5	0,59,4241	yes	missense,missense,missense,missense	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	155,155,155,155	0,67,6436	TT,TC,CC		0.686,0.1816,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	271/613,340/664,389/731,389/713	20876168	67,12939	2203	4300	6503	SO:0001583	missense	53919	exon9			CATCCTCCAGGGC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1166C>T	12.37:g.20876168C>T	ENSP00000266509:p.Ser389Phe	296.0	0.0	0		213.0	111.0	0.521127	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	21.6	4.166506	0.78339	0.001816	0.00686	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	4.54	4.54	0.55810	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.69387	0.3105	M	0.92026	3.265	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.997;0.997	T	0.80690	-0.1270	10	0.87932	D	0	.	17.8397	0.88712	0.0:1.0:0.0:0.0	.	271;340;389;389	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	F	389;340;389;389;271	ENSP00000444149:S389F;ENSP00000438665:S340F;ENSP00000266509:S389F;ENSP00000370964:S389F;ENSP00000444527:S271F	ENSP00000266509:S389F	S	+	2	0	SLCO1C1	20767435	1.000000	0.71417	0.949000	0.38748	0.767000	0.43475	7.278000	0.78587	2.510000	0.84645	0.561000	0.74099	TCC	C|0.994;T|0.006	0.006	strong		0.443	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
TTN	7273	hgsc.bcm.edu	37	2	179643775	179643775	+	Missense_Mutation	SNP	C	C	T	rs36021856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179643775C>T	ENST00000591111.1	-	24	4258	c.4034G>A	c.(4033-4035)gGc>gAc	p.G1345D	TTN_ENST00000342992.6_Missense_Mutation_p.G1345D|TTN_ENST00000460472.2_Missense_Mutation_p.G1299D|TTN_ENST00000589042.1_Missense_Mutation_p.G1345D|TTN_ENST00000359218.5_Missense_Mutation_p.G1299D|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.G1345D|TTN_ENST00000342175.6_Missense_Mutation_p.G1299D			Q8WZ42	TITIN_HUMAN	titin	33541	Ig-like 5.		G -> D (in dbSNP:rs36021856). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTAGCTCTGCCATCTTGTAG	0.398													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21020	0.0		0.0159	False		,,,				2504	0.0				p.G1345D		Atlas-SNP	.											.	TTN	18412	.	0			c.G4034A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	3,4403	6.2+/-15.9	0,3,2200	136.0	120.0	125.0		3896,4034,4034,3896,3896	5.7	1.0	2	dbSNP_126	125	63,8537	38.8+/-94.9	1,61,4238	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	94,94,94,94,94	1,64,6438	TT,TC,CC		0.7326,0.0681,0.5075	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1299/26927,1345/33424,1345/5605,1299/27052,1299/27119	179643775	66,12940	2203	4300	6503	SO:0001583	missense	7273	exon24			GCTCTGCCATCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4034G>A	2.37:g.179643775C>T	ENSP00000465570:p.Gly1345Asp	174.0	0.0	0		144.0	76.0	0.527778	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	17.13	3.311645	0.60414	6.81E-4	0.007326	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73194	0.3556	M	0.77616	2.38	0.49389	D	0.999784	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.80845	-0.1200	9	0.87932	D	0	.	19.8946	0.96949	0.0:1.0:0.0:0.0	rs36021856	1299;1299;1299;1345;1345	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	D	1345;1299;1299;1299;1299;1345	ENSP00000343764:G1345D;ENSP00000434586:G1299D;ENSP00000340554:G1299D;ENSP00000352154:G1299D;ENSP00000354117:G1345D	ENSP00000340554:G1299D	G	-	2	0	TTN	179352020	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.711000	0.92665	0.655000	0.94253	GGC	C|0.993;T|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RANBP3	8498	hgsc.bcm.edu	37	19	5915300	5915300	+	IGR	SNP	C	C	A	rs147363394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5915300C>A	ENST00000340578.6	-	0	3233				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000452990.2_Missense_Mutation_p.F152L|CAPS_ENST00000588776.1_Missense_Mutation_p.F265L|CAPS_ENST00000222125.5_Missense_Mutation_p.F179L	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						ATGAGGAGTTCGTGGCCATGA	0.657													C|||	5	0.000998403	0.0	0.0043	5008	,	,		16061	0.0		0.002	False		,,,				2504	0.0				p.F179L		Atlas-SNP	.											.	CAPS	14	.	0			c.C537A						PASS	.	C	LEU/PHE,LEU/PHE	1,4401	2.1+/-5.4	0,1,2200	74.0	59.0	64.0		537,456	-10.0	0.5	19	dbSNP_134	64	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	22,22	0,12,6489	AA,AC,CC		0.1279,0.0227,0.0923	probably-damaging,probably-damaging	179/190,152/163	5915300	12,12990	2201	4300	6501	SO:0001628	intergenic_variant	828	exon5			GGAGTTCGTGGCC	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5915300C>A		97.0	0.0	0		111.0	57.0	0.513514	NM_004058	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	22.2	4.252906	0.80135	2.27E-4	0.001279	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.69175	-0.25;-0.38	5.3	-10.0	0.00425	EF-hand-like domain (1);	0.000000	0.64402	D	0.000007	T	0.80374	0.4611	M	0.90425	3.115	0.34295	D	0.683746	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.88488	0.3073	10	0.87932	D	0	-13.7929	17.3435	0.87304	0.0:0.6317:0.0:0.3683	.	312;179	Q8NF12;Q13938	.;CAYP1_HUMAN	L	312;179;152	ENSP00000222125:F179L;ENSP00000403263:F152L	ENSP00000222125:F179L	F	+	3	2	CAPS	5866300	0.002000	0.14202	0.526000	0.27913	0.946000	0.59487	-2.224000	0.01213	-2.213000	0.00735	-1.036000	0.02392	TTC	C|0.999;A|0.001	0.001	strong		0.657	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
LILRB2	10288	hgsc.bcm.edu	37	19	54783836	54783836	+	Silent	SNP	G	G	A	rs111453734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54783836G>A	ENST00000391749.4	-	4	436	c.165C>T	c.(163-165)gcC>gcT	p.A55A	LILRB2_ENST00000314446.5_Silent_p.A55A|LILRB2_ENST00000434421.1_Intron|LILRB2_ENST00000391748.1_Silent_p.A55A|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000391746.1_Silent_p.A55A|LILRB2_ENST00000471216.1_5'UTR	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	55	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTACTCCTGGGCTTCAAGGC	0.547													.|||	8	0.00159744	0.0008	0.0072	5008	,	,		19344	0.0		0.002	False		,,,				2504	0.0				p.A55A		Atlas-SNP	.											.	LILRB2	94	.	0			c.C165T						PASS	.	G	,	6,4400	9.9+/-24.2	0,6,2197	173.0	172.0	172.0		165,165	-4.8	0.0	19	dbSNP_132	172	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous,coding-synonymous	LILRB2	NM_001080978.2,NM_005874.3	,	0,32,6471	AA,AG,GG		0.3023,0.1362,0.246	,	55/598,55/599	54783836	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	10288	exon4			CTCCTGGGCTTCA	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.165C>T	19.37:g.54783836G>A		92.0	0.0	0		84.0	49.0	0.583333	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
BCAS3	54828	hgsc.bcm.edu	37	17	58952044	58952044	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:58952044G>A	ENST00000390652.5	+	9	637	c.606G>A	c.(604-606)caG>caA	p.Q202Q	BCAS3_ENST00000407086.3_Silent_p.Q202Q|BCAS3_ENST00000408905.3_Silent_p.Q202Q|BCAS3_ENST00000588462.1_Silent_p.Q202Q|BCAS3_ENST00000589222.1_Silent_p.Q202Q	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TAGTCTTGCAGGAGAAAATTG	0.328																																					p.Q202Q		Atlas-SNP	.											.	BCAS3	90	.	0			c.G606A						PASS	.						110.0	101.0	104.0					17																	58952044		1820	4081	5901	SO:0001819	synonymous_variant	54828	exon9			CTTGCAGGAGAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.606G>A	17.37:g.58952044G>A		48.0	0.0	0		49.0	25.0	0.510204	NM_001099432		Silent	SNP	ENST00000390652.5	37	CCDS45749.1																																																																																			.	.	none		0.328	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	
CASZ1	54897	hgsc.bcm.edu	37	1	10703243	10703243	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10703243T>A	ENST00000377022.3	-	19	4311	c.3994A>T	c.(3994-3996)Aac>Tac	p.N1332Y	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1332					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CGGTCGAAGTTCTTCCCCAGC	0.662																																					p.N1332Y		Atlas-SNP	.											.	CASZ1	150	.	0			c.A3994T						PASS	.						52.0	60.0	57.0					1																	10703243		2085	4210	6295	SO:0001583	missense	54897	exon19			CGAAGTTCTTCCC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.3994A>T	1.37:g.10703243T>A	ENSP00000366221:p.Asn1332Tyr	59.0	0.0	0		51.0	16.0	0.313726	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666405	0.88251	.	.	ENSG00000130940	ENST00000377022	.	.	.	4.77	4.77	0.60923	.	0.000000	0.49305	U	0.000149	T	0.68705	0.3030	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71523	-0.4567	9	0.62326	D	0.03	-26.2009	14.3215	0.66489	0.0:0.0:0.0:1.0	.	1332	Q86V15	CASZ1_HUMAN	Y	1332	.	ENSP00000366221:N1332Y	N	-	1	0	CASZ1	10625830	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.530000	0.81962	1.783000	0.52377	0.459000	0.35465	AAC	.	.	none		0.662	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
SHPRH	257218	hgsc.bcm.edu	37	6	146267376	146267376	+	Silent	SNP	T	T	C	rs201477770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:146267376T>C	ENST00000367505.2	-	7	1578	c.1314A>G	c.(1312-1314)caA>caG	p.Q438Q	SHPRH_ENST00000275233.7_Silent_p.Q438Q|SHPRH_ENST00000367503.3_Silent_p.Q438Q|SHPRH_ENST00000438092.2_Silent_p.Q438Q			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	438	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		Q -> R (in an ovarian cancer cell line). {ECO:0000269|PubMed:12837266}.		DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TACGAGGGCATTGAACTTTTT	0.313													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16466	0.0		0.0	False		,,,				2504	0.0				p.Q438Q		Atlas-SNP	.											.	SHPRH	169	.	0			c.A1314G						PASS	.	T	,	0,3650		0,0,1825	165.0	146.0	152.0		1314,1314	-6.0	0.9	6	dbSNP_134	152	1,8145		0,1,4072	no	coding-synonymous,coding-synonymous	SHPRH	NM_001042683.2,NM_173082.3	,	0,1,5897	CC,CT,TT		0.0123,0.0,0.0085	,	438/1684,438/1660	146267376	1,11795	1825	4073	5898	SO:0001819	synonymous_variant	257218	exon7			AGGGCATTGAACT	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1314A>G	6.37:g.146267376T>C		57.0	0.0	0		20.0	10.0	0.5	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	37	CCDS43513.2																																																																																			T|1.000;C|0.000	0.000	strong		0.313	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
ANO7	50636	hgsc.bcm.edu	37	2	242147054	242147054	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242147054G>A	ENST00000274979.8	+	11	1311	c.1208G>A	c.(1207-1209)tGg>tAg	p.W403*	ANO7_ENST00000402430.3_Nonsense_Mutation_p.W402*	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	403					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						TGCCCTTTCTGGCTGCTCTCC	0.617																																					p.W403X		Atlas-SNP	.											.	ANO7	136	.	0			c.G1208A						PASS	.						108.0	102.0	104.0					2																	242147054		2203	4300	6503	SO:0001587	stop_gained	50636	exon11			CTTTCTGGCTGCT	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1208G>A	2.37:g.242147054G>A	ENSP00000274979:p.Trp403*	50.0	0.0	0		49.0	11.0	0.22449	NM_001001891	Q6IWH6	Nonsense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.809907	0.70797	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	.	.	.	2.49	2.49	0.30216	.	0.451423	0.21800	U	0.068929	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4445	0.55643	0.0:0.0:1.0:0.0	.	.	.	.	X	403;402	.	ENSP00000274979:W403X	W	+	2	0	ANO7	241795727	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	6.347000	0.73004	1.315000	0.45114	0.313000	0.20887	TGG	.	.	none		0.617	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
JSRP1	126306	hgsc.bcm.edu	37	19	2253687	2253687	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2253687G>A	ENST00000300961.6	-	5	432	c.368C>T	c.(367-369)tCg>tTg	p.S123L	JSRP1_ENST00000586471.2_Missense_Mutation_p.S123L|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	123	Pro-rich.				protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGTTGAGCGACAGGTCTCC	0.756																																					p.S123L		Atlas-SNP	.											.	JSRP1	18	.	0			c.C368T						PASS	.						7.0	10.0	9.0					19																	2253687		1985	3928	5913	SO:0001583	missense	126306	exon5			TTGAGCGACAGGT	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.368C>T	19.37:g.2253687G>A	ENSP00000300961:p.Ser123Leu	15.0	0.0	0		20.0	9.0	0.45	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051013	0.75960	.	.	ENSG00000167476	ENST00000300961	T	0.42513	0.97	4.89	4.89	0.63831	.	1.031560	0.07762	N	0.950312	T	0.30070	0.0753	N	0.19112	0.55	0.09310	N	1	B	0.28584	0.216	B	0.21546	0.035	T	0.12993	-1.0526	10	0.72032	D	0.01	-7.5515	9.2315	0.37439	0.1:0.0:0.9:0.0	.	123	Q96MG2	JSPR1_HUMAN	L	123	ENSP00000300961:S123L	ENSP00000300961:S123L	S	-	2	0	JSRP1	2204687	0.687000	0.27671	0.017000	0.16124	0.777000	0.43975	4.762000	0.62250	2.251000	0.74343	0.561000	0.74099	TCG	.	.	none		0.756	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
TMEM151A	256472	hgsc.bcm.edu	37	11	66062014	66062014	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66062014G>A	ENST00000327259.4	+	2	441	c.297G>A	c.(295-297)ctG>ctA	p.L99L		NM_153266.3	NP_694998.1	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	99						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(4)|lung(6)	11						ATGGCTACCTGTACATCCCGC	0.731																																					p.L99L		Atlas-SNP	.											.	TMEM151A	39	.	0			c.G297A						PASS	.						66.0	47.0	53.0					11																	66062014		2197	4291	6488	SO:0001819	synonymous_variant	256472	exon2			CTACCTGTACATC	BC033898	CCDS8133.1	11q13.2	2007-10-25	2007-10-25	2007-10-25	ENSG00000179292	ENSG00000179292			28497	protein-coding gene	gene with protein product			"""transmembrane protein 151"""	TMEM151		12477932	Standard	NM_153266		Approved	MGC33486	uc001ohl.3	Q8N4L1	OTTHUMG00000166920	ENST00000327259.4:c.297G>A	11.37:g.66062014G>A		52.0	0.0	0		68.0	38.0	0.558824	NM_153266	Q8ND14	Silent	SNP	ENST00000327259.4	37	CCDS8133.1																																																																																			.	.	none		0.731	TMEM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391897.1	NM_153266	
GRK7	131890	hgsc.bcm.edu	37	3	141497368	141497368	+	Missense_Mutation	SNP	G	G	A	rs34429284		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141497368G>A	ENST00000264952.2	+	1	379	c.242G>A	c.(241-243)cGc>cAc	p.R81H		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	81	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> H (in dbSNP:rs34429284). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CCCACGTTCCGCAAGGCGGCA	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		18091	0.0		0.0	False		,,,				2504	0.001				p.R81H		Atlas-SNP	.											.	GRK7	65	.	0			c.G242A						PASS	.	G	HIS/ARG	3,4401		0,3,2199	27.0	26.0	27.0		242	-4.7	0.0	3	dbSNP_126	27	26,8568		0,26,4271	yes	missense	GRK7	NM_139209.2	29	0,29,6470	AA,AG,GG		0.3025,0.0681,0.2231	possibly-damaging	81/554	141497368	29,12969	2202	4297	6499	SO:0001583	missense	131890	exon1			CGTTCCGCAAGGC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.242G>A	3.37:g.141497368G>A	ENSP00000264952:p.Arg81His	120.0	0.0	0		108.0	46.0	0.425926	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	G	3.233	-0.157014	0.06544	6.81E-4	0.003025	ENSG00000114124	ENST00000264952	T	0.02236	4.38	4.33	-4.7	0.03288	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.921148	0.09093	N	0.849577	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	P	0.45594	0.862	B	0.39562	0.303	T	0.47886	-0.9082	10	0.35671	T	0.21	1.776	7.5979	0.28058	0.3685:0.0:0.4911:0.1404	rs34429284	81	Q8WTQ7	GRK7_HUMAN	H	81	ENSP00000264952:R81H	ENSP00000264952:R81H	R	+	2	0	GRK7	142980058	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.737000	0.04877	-1.006000	0.03412	-0.982000	0.02568	CGC	G|0.998;A|0.002	0.002	strong		0.647	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
INHBA	3624	hgsc.bcm.edu	37	7	41729843	41729843	+	Missense_Mutation	SNP	C	C	T	rs138819536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:41729843C>T	ENST00000242208.4	-	3	932	c.686G>A	c.(685-687)cGg>cAg	p.R229Q	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_Missense_Mutation_p.R229Q|INHBA_ENST00000464515.1_5'UTR	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	229					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTCCAGCAACCGCTGGATGCT	0.572										TSP Lung(11;0.080)			C|||	3	0.000599042	0.0008	0.0	5008	,	,		18089	0.0		0.002	False		,,,				2504	0.0				p.R229Q		Atlas-SNP	.											INHBA,NS,carcinoma,0,1	INHBA	118	1	0			c.G686A						PASS	.	C	GLN/ARG	4,4402		0,4,2199	52.0	50.0	51.0		686	6.1	1.0	7	dbSNP_134	51	30,8570		0,30,4270	yes	missense	INHBA	NM_002192.2	43	0,34,6469	TT,TC,CC		0.3488,0.0908,0.2614	possibly-damaging	229/427	41729843	34,12972	2203	4300	6503	SO:0001583	missense	3624	exon3			AGCAACCGCTGGA		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.686G>A	7.37:g.41729843C>T	ENSP00000242208:p.Arg229Gln	82.0	0.0	0		54.0	43.0	0.796296	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	.	18.81	3.702318	0.68501	9.08E-4	0.003488	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.68025	-0.3;-0.3	6.06	6.06	0.98353	Transforming growth factor-beta, N-terminal (1);	0.420201	0.27686	N	0.018263	T	0.61248	0.2332	L	0.43152	1.355	0.43714	D	0.996185	P	0.44478	0.836	B	0.39503	0.301	T	0.56902	-0.7902	10	0.19147	T	0.46	-17.7159	20.6208	0.99490	0.0:1.0:0.0:0.0	.	229	P08476	INHBA_HUMAN	Q	229	ENSP00000242208:R229Q;ENSP00000397197:R229Q	ENSP00000242208:R229Q	R	-	2	0	INHBA	41696368	0.946000	0.32159	0.988000	0.46212	0.992000	0.81027	2.752000	0.47516	2.882000	0.98803	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.572	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
GPR149	344758	hgsc.bcm.edu	37	3	154147336	154147336	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:154147336C>T	ENST00000389740.2	-	1	168	c.69G>A	c.(67-69)acG>acA	p.T23T		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	23					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTAAAAGGTCCGTAGAATTAT	0.363																																					p.T23T		Atlas-SNP	.											GPR149,NS,carcinoma,-1,1	GPR149	134	1	0			c.G69A						PASS	.						77.0	77.0	77.0					3																	154147336		1836	4087	5923	SO:0001819	synonymous_variant	344758	exon1			AAGGTCCGTAGAA	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.69G>A	3.37:g.154147336C>T		167.0	0.0	0		146.0	33.0	0.226027	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			.	.	none		0.363	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
RADIL	55698	hgsc.bcm.edu	37	7	4856904	4856904	+	Missense_Mutation	SNP	T	T	C	rs201312293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4856904T>C	ENST00000399583.3	-	7	1881	c.1694A>G	c.(1693-1695)tAc>tGc	p.Y565C	RADIL_ENST00000536091.1_Silent_p.V511V|RADIL_ENST00000538469.1_Missense_Mutation_p.Y325C	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	565	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CTGGAAGGCGTACAGCACCAC	0.632													T|||	7	0.00139776	0.0	0.0058	5008	,	,		16847	0.0		0.003	False		,,,				2504	0.0				p.Y565C		Atlas-SNP	.											RADIL,right_upper_lobe,carcinoma,0,1	RADIL	110	1	0			c.A1694G						PASS	.	T	CYS/TYR	9,4395	12.9+/-30.5	0,9,2193	67.0	74.0	71.0		1694	4.5	0.9	7		71	48,8550	30.7+/-82.3	0,48,4251	yes	missense	RADIL	NM_018059.4	194	0,57,6444	CC,CT,TT		0.5583,0.2044,0.4384	probably-damaging	565/1076	4856904	57,12945	2202	4299	6501	SO:0001583	missense	55698	exon7			AAGGCGTACAGCA	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1694A>G	7.37:g.4856904T>C	ENSP00000382492:p.Tyr565Cys	124.0	0.0	0		100.0	65.0	0.65	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	t	18.25	3.583364	0.65992	0.002044	0.005583	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.42900	0.96;0.96	5.7	4.54	0.55810	Dilute (1);	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.52660	-0.8546	10	0.46703	T	0.11	-18.0204	10.6794	0.45804	0.0:0.0759:0.0:0.9241	.	565	Q96JH8	RADIL_HUMAN	C	565;536;299;325	ENSP00000382492:Y565C;ENSP00000442966:Y325C	ENSP00000320946:Y536C	Y	-	2	0	RADIL	4823430	1.000000	0.71417	0.867000	0.34043	0.958000	0.62258	2.542000	0.45744	0.987000	0.38709	0.375000	0.23000	TAC	T|0.997;C|0.003	0.003	strong		0.632	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
KIF21B	23046	hgsc.bcm.edu	37	1	200978027	200978027	+	Missense_Mutation	SNP	G	G	A	rs140589352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:200978027G>A	ENST00000422435.2	-	3	633	c.317C>T	c.(316-318)tCg>tTg	p.S106L	KIF21B_ENST00000360529.5_Missense_Mutation_p.S106L|KIF21B_ENST00000332129.2_Missense_Mutation_p.S106L|KIF21B_ENST00000461742.2_Missense_Mutation_p.S106L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	106	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CTCCTCCTCCGACGTTGCCAT	0.642													G|||	42	0.00838658	0.0	0.013	5008	,	,		20340	0.0		0.0179	False		,,,				2504	0.0153				p.S106L		Atlas-SNP	.											.	KIF21B	208	.	0			c.C317T						PASS	.	G	LEU/SER	13,4393	20.2+/-43.8	0,13,2190	118.0	103.0	108.0		317	4.7	0.0	1	dbSNP_134	108	193,8407	85.0+/-147.5	3,187,4110	yes	missense	KIF21B	NM_017596.2	145	3,200,6300	AA,AG,GG		2.2442,0.2951,1.5839	benign	106/1625	200978027	206,12800	2203	4300	6503	SO:0001583	missense	23046	exon3			TCCTCCGACGTTG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.317C>T	1.37:g.200978027G>A	ENSP00000411831:p.Ser106Leu	42.0	0.0	0		51.0	26.0	0.509804	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	G	10.10	1.257053	0.22965	0.002951	0.022442	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.57	4.66	0.58398	Kinesin, motor domain (4);	0.322422	0.29073	N	0.013235	T	0.52208	0.1720	M	0.68952	2.095	0.09310	N	0.999999	P;P;B;P	0.42248	0.774;0.774;0.0;0.733	B;B;B;B	0.31869	0.094;0.137;0.002;0.131	T	0.55296	-0.8163	10	0.27082	T	0.32	.	14.3505	0.66699	0.0714:0.0:0.9286:0.0	.	106;106;106;106	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	L	106	ENSP00000328494:S106L;ENSP00000353724:S106L;ENSP00000433808:S106L;ENSP00000411831:S106L	ENSP00000328494:S106L	S	-	2	0	KIF21B	199244650	0.791000	0.28800	0.014000	0.15608	0.324000	0.28378	4.731000	0.62022	1.348000	0.45733	0.650000	0.86243	TCG	G|0.987;A|0.013	0.013	strong		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
SHROOM3	57619	hgsc.bcm.edu	37	4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	rs76656494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168.0	168.0	168.0		1691	4.4	1.0	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	79.0	0.0	0		50.0	26.0	0.52	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
KRT84	3890	hgsc.bcm.edu	37	12	52778829	52778829	+	Missense_Mutation	SNP	C	C	A	rs140632920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52778829C>A	ENST00000257951.3	-	1	607	c.541G>T	c.(541-543)Gac>Tac	p.D181Y	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	181	Coil 1A.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTACCTTGTCAATGAAGGAG	0.488													C|||	7	0.00139776	0.0	0.0	5008	,	,		22209	0.0		0.006	False		,,,				2504	0.001				p.D181Y		Atlas-SNP	.											.	KRT84	61	.	0			c.G541T						PASS	.	C	TYR/ASP	3,4403	6.2+/-15.9	0,3,2200	216.0	219.0	218.0		541	5.0	1.0	12	dbSNP_134	218	22,8578	16.0+/-53.3	0,22,4278	yes	missense	KRT84	NM_033045.3	160	0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922	probably-damaging	181/601	52778829	25,12981	2203	4300	6503	SO:0001583	missense	3890	exon1			CCTTGTCAATGAA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.541G>T	12.37:g.52778829C>A	ENSP00000257951:p.Asp181Tyr	111.0	0.0	0		98.0	55.0	0.561224	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.2	4.119953	0.77323	6.81E-4	0.002558	ENSG00000161849	ENST00000257951	D	0.92299	-3.01	5.03	5.03	0.67393	Filament (1);	0.000000	0.52532	D	0.000066	D	0.97695	0.9244	H	0.97315	3.98	0.58432	D	0.999998	D	0.76494	0.999	D	0.77004	0.989	D	0.98708	1.0703	10	0.87932	D	0	.	18.9362	0.92586	0.0:1.0:0.0:0.0	.	181	Q9NSB2	KRT84_HUMAN	Y	181	ENSP00000257951:D181Y	ENSP00000257951:D181Y	D	-	1	0	KRT84	51065096	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.612000	0.82975	2.790000	0.95986	0.609000	0.83330	GAC	C|0.998;A|0.002	0.002	strong		0.488	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	AP5Z1_ENST00000490487.1_3'UTR|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15.0	20.0	18.0		2379	-9.4	0.0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.2379G>T	7.37:g.4830971G>T		142.0	0.0	0		153.0	39.0	0.254902	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
PDLIM5	10611	hgsc.bcm.edu	37	4	95496940	95496940	+	Silent	SNP	G	G	A	rs115743950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:95496940G>A	ENST00000317968.4	+	5	601	c.465G>A	c.(463-465)gcG>gcA	p.A155A	PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Silent_p.A33A|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000380180.3_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	155					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)	p.A155A(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		CAGCCCATGCGACCACCTCAT	0.552													G|||	20	0.00399361	0.0023	0.0043	5008	,	,		20003	0.0		0.0089	False		,,,				2504	0.0051				p.A155A		Atlas-SNP	.											PDLIM5,NS,carcinoma,+1,2	PDLIM5	76	2	1	Substitution - coding silent(1)	kidney(1)	c.G465A						PASS	.	G	,,,	16,4390	24.3+/-50.5	0,16,2187	295.0	249.0	265.0		,,,465	2.9	1.0	4	dbSNP_132	265	140,8460	70.0+/-132.6	0,140,4160	no	intron,intron,intron,coding-synonymous	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,	0,156,6347	AA,AG,GG		1.6279,0.3631,1.1994	,,,	,,,155/597	95496940	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	10611	exon5			CCATGCGACCACC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.465G>A	4.37:g.95496940G>A		203.0	0.0	0		205.0	115.0	0.560976	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	37	CCDS3641.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
HIST1H3G	8355	hgsc.bcm.edu	37	6	26271208	26271208	+	Silent	SNP	T	T	C	rs141036055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26271208T>C	ENST00000305910.3	-	1	404	c.405A>G	c.(403-405)agA>agG	p.R135R	HIST1H2BI_ENST00000377733.2_5'Flank	NM_003534.2	NP_003525.1	P68431	H31_HUMAN	histone cluster 1, H3g	135				Missing (in Ref. 2; AAA52651). {ECO:0000305}.	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)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12						ACCTCTACGCTCTCTCCCCAC	0.483													T|||	2	0.000399361	0.0	0.0	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.002				p.R135R		Atlas-SNP	.											.	HIST1H3G	20	.	0			c.A405G						PASS	.	T		0,4406		0,0,2203	61.0	64.0	63.0		405	1.5	1.0	6	dbSNP_134	63	11,8589		0,11,4289	no	coding-synonymous	HIST1H3G	NM_003534.2		0,11,6492	CC,CT,TT		0.1279,0.0,0.0846		135/137	26271208	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	8355	exon1			CTACGCTCTCTCC	Z80785	CCDS4602.1	6p22.1	2011-07-22	2006-10-11	2003-03-14	ENSG00000256018			"""Histones / Replication-dependent"""	4772	protein-coding gene	gene with protein product		602815	"""H3 histone family, member H"", ""histone 1, H3g"""	H3FH		9119399, 12408966	Standard	NM_003534		Approved	H3/h	uc003nhi.3	P68431	OTTHUMG00000014436	ENST00000305910.3:c.405A>G	6.37:g.26271208T>C		84.0	0.0	0		50.0	22.0	0.44	NM_003534	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000305910.3	37	CCDS4602.1																																																																																			T|0.999;C|0.001	0.001	strong		0.483	HIST1H3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040099.2	NM_003534	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801871	185801871	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185801871A>T	ENST00000302277.6	+	4	2342	c.1748A>T	c.(1747-1749)aAa>aTa	p.K583I		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	583							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						ATAAGGTTGAAAGAGACCCAT	0.294																																					p.K583I		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1748T						PASS	.						34.0	41.0	39.0					2																	185801871		2180	4278	6458	SO:0001583	missense	91752	exon4			GGTTGAAAGAGAC	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1748A>T	2.37:g.185801871A>T	ENSP00000303252:p.Lys583Ile	69.0	0.0	0		60.0	20.0	0.333333	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.647690	0.67358	.	.	ENSG00000170396	ENST00000302277	T	0.10005	2.92	5.5	5.5	0.81552	.	0.097775	0.44902	D	0.000416	T	0.29491	0.0735	L	0.58101	1.795	0.34076	D	0.659021	D	0.89917	1.0	D	0.73380	0.98	T	0.40459	-0.9562	10	0.87932	D	0	-23.4158	14.793	0.69857	1.0:0.0:0.0:0.0	.	583	Q7Z570	Z804A_HUMAN	I	583	ENSP00000303252:K583I	ENSP00000303252:K583I	K	+	2	0	ZNF804A	185510116	1.000000	0.71417	0.489000	0.27452	0.972000	0.66771	3.815000	0.55651	2.083000	0.62718	0.528000	0.53228	AAA	.	.	none		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
NSMAF	8439	hgsc.bcm.edu	37	8	59508166	59508166	+	Silent	SNP	A	A	G	rs149564750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59508166A>G	ENST00000038176.3	-	22	2057	c.1845T>C	c.(1843-1845)aaT>aaC	p.N615N	NSMAF_ENST00000427130.2_Silent_p.N646N	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	615					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGGTGATGTTATTCCAGGCCA	0.403													A|||	24	0.00479233	0.0	0.0101	5008	,	,		18010	0.0		0.0139	False		,,,				2504	0.0031				p.N646N		Atlas-SNP	.											.	NSMAF	156	.	0			c.T1938C						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	196.0	181.0	186.0		1938,1845	1.1	0.8	8	dbSNP_134	186	79,8521	44.9+/-103.4	1,77,4222	no	coding-synonymous,coding-synonymous	NSMAF	NM_001144772.1,NM_003580.3	,	1,83,6419	GG,GA,AA		0.9186,0.1362,0.6535	,	646/949,615/918	59508166	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	8439	exon22			GATGTTATTCCAG	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1845T>C	8.37:g.59508166A>G		270.0	0.0	0		185.0	41.0	0.221622	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
ARHGAP6	395	hgsc.bcm.edu	37	X	11682921	11682921	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:11682921C>A	ENST00000337414.4	-	1	900	c.28G>T	c.(28-30)Gtc>Ttc	p.V10F	ARHGAP6_ENST00000380732.3_Missense_Mutation_p.V10F|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.V10F	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	10					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CAGGAGAAGACGCTGTGGAGC	0.677																																					p.V10F		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.G28T						PASS	.						8.0	10.0	10.0					X																	11682921		1777	3411	5188	SO:0001583	missense	395	exon1			AGAAGACGCTGTG	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"""Rho GTPase activating proteins"""	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.28G>T	X.37:g.11682921C>A	ENSP00000338967:p.Val10Phe	114.0	0.0	0		110.0	37.0	0.336364	NM_006125	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634288	0.87660	.	.	ENSG00000047648	ENST00000337414;ENST00000380718;ENST00000380732	T;T;T	0.44881	1.35;1.19;0.91	4.82	4.82	0.62117	.	.	.	.	.	T	0.50548	0.1622	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.56595	-0.7953	9	0.87932	D	0	.	14.4354	0.67277	0.0:1.0:0.0:0.0	.	10;10	O43182-2;O43182	.;RHG06_HUMAN	F	10	ENSP00000338967:V10F;ENSP00000370094:V10F;ENSP00000370108:V10F	ENSP00000338967:V10F	V	-	1	0	ARHGAP6	11592842	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.516000	0.53436	1.987000	0.57996	0.594000	0.82650	GTC	.	.	none		0.677	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156817	26156817	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26156817G>A	ENST00000304218.3	+	1	259	c.199G>A	c.(199-201)Gca>Aca	p.A67T	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	67	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GAAAGCGCTGGCAGCCGCTGG	0.617																																					p.A67T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G199A						PASS	.						35.0	38.0	37.0					6																	26156817		2203	4300	6503	SO:0001583	missense	3008	exon1			GCGCTGGCAGCCG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.199G>A	6.37:g.26156817G>A	ENSP00000307705:p.Ala67Thr	90.0	0.0	0		72.0	10.0	0.138889	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	19.26	3.794164	0.70452	.	.	ENSG00000168298	ENST00000304218	T	0.10477	2.87	5.11	5.11	0.69529	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.416196	0.25863	N	0.027820	T	0.15089	0.0364	L	0.60957	1.885	0.53688	D	0.999973	B	0.33379	0.41	P	0.47528	0.549	T	0.01643	-1.1305	10	0.42905	T	0.14	-2.9473	17.8759	0.88825	0.0:0.0:1.0:0.0	.	67	P10412	H14_HUMAN	T	67	ENSP00000307705:A67T	ENSP00000307705:A67T	A	+	1	0	HIST1H1E	26264796	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.534000	0.67167	2.542000	0.85734	0.561000	0.74099	GCA	.	.	none		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
BRWD1	54014	hgsc.bcm.edu	37	21	40608530	40608530	+	Silent	SNP	A	A	C	rs143020455		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40608530A>C	ENST00000333229.2	-	23	3084	c.2757T>G	c.(2755-2757)ccT>ccG	p.P919P	BRWD1_ENST00000380800.3_Silent_p.P919P|BRWD1_ENST00000342449.3_Silent_p.P919P	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	919					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CCTCCTTCTTAGGCTTATTTT	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		21667	0.0		0.0	False		,,,				2504	0.0				p.P919P	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.T2757G						PASS	.	A	,	0,4406		0,0,2203	122.0	110.0	114.0		2757,2757	4.2	1.0	21	dbSNP_134	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	0,8,6495	CC,CA,AA		0.093,0.0,0.0615	,	919/2321,919/2270	40608530	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon23			CTTCTTAGGCTTA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2757T>G	21.37:g.40608530A>C		107.0	0.0	0		115.0	56.0	0.486957	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			A|0.999;C|0.001	0.001	strong		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121996C>T	ENST00000271588.4	+	96	15240	c.15011C>T	c.(15010-15012)aCt>aTt	p.T5004I	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTGAAGTCACTGTAAAGGTA	0.433													C|||	10	0.00199681	0.0	0.0014	5008	,	,		18553	0.0		0.008	False		,,,				2504	0.001				p.T5004I		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15011T						PASS	.	C	ILE/THR	4,4402	2.1+/-5.4	0,4,2199	196.0	170.0	179.0		15011	2.9	0.0	1	dbSNP_133	179	29,8571	9.1+/-34.3	1,27,4272	yes	missense	HMCN1	NM_031935.2	89	1,31,6471	TT,TC,CC		0.3372,0.0908,0.2537	benign	5004/5636	186121996	33,12973	2203	4300	6503	SO:0001583	missense	83872	exon96			AAGTCACTGTAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15011C>T	1.37:g.186121996C>T	ENSP00000271588:p.Thr5004Ile	215.0	0.0	0		170.0	88.0	0.517647	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.698	0.909113	0.17833	9.08E-4	0.003372	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31510	1.49;1.49	5.9	2.9	0.33743	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.27316	0.175	B	0.30855	0.121	T	0.34601	-0.9822	10	0.29301	T	0.29	.	9.0753	0.36517	0.4557:0.2514:0.2928:0.0	.	5004	Q96RW7	HMCN1_HUMAN	I	5004	ENSP00000271588:T5004I;ENSP00000356462:T5004I	ENSP00000271588:T5004I	T	+	2	0	HMCN1	184388619	0.000000	0.05858	0.026000	0.17262	0.758000	0.43043	0.220000	0.17660	0.314000	0.23086	0.650000	0.86243	ACT	C|0.996;T|0.004	0.004	strong		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
ZNF85	7639	hgsc.bcm.edu	37	19	21132453	21132453	+	Missense_Mutation	SNP	C	C	G	rs146063134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21132453C>G	ENST00000328178.8	+	4	1246	c.1133C>G	c.(1132-1134)gCc>gGc	p.A378G	ZNF85_ENST00000345030.6_Missense_Mutation_p.A345G|ZNF85_ENST00000601023.1_Missense_Mutation_p.A319G	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	378					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						TGTGGAAAAGCCTTTAATCAT	0.348													.|||	2	0.000399361	0.0	0.0	5008	,	,		19410	0.0		0.001	False		,,,				2504	0.001				p.A408G		Atlas-SNP	.											.	ZNF85	72	.	0			c.C1223G						PASS	.	C	GLY/ALA	0,4394		0,0,2197	39.0	42.0	41.0		1133	1.4	0.0	19	dbSNP_134	41	6,8586		0,6,4290	no	missense	ZNF85	NM_003429.4	60	0,6,6487	GG,GC,CC		0.0698,0.0,0.0462	possibly-damaging	378/596	21132453	6,12980	2197	4296	6493	SO:0001583	missense	7639	exon5			GAAAAGCCTTTAA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1133C>G	19.37:g.21132453C>G	ENSP00000329793:p.Ala378Gly	41.0	0.0	0		18.0	8.0	0.444444	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	12.01	1.809319	0.31961	0.0	6.98E-4	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.19669	2.13;2.13	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31071	0.0785	L	0.41573	1.285	0.58432	D	0.999999	B;D;P	0.63046	0.289;0.992;0.898	B;D;P	0.77004	0.17;0.989;0.808	T	0.05632	-1.0873	9	0.66056	D	0.02	.	6.8304	0.23907	0.0:0.4775:0.5225:0.0	.	345;319;378	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	G	378;345;253	ENSP00000329793:A378G;ENSP00000342340:A345G	ENSP00000329793:A378G	A	+	2	0	ZNF85	20924293	0.001000	0.12720	0.039000	0.18376	0.129000	0.20672	0.077000	0.14738	0.681000	0.31386	0.462000	0.41574	GCC	C|0.999;G|0.001	0.001	strong		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
LIMS1	3987	hgsc.bcm.edu	37	2	109276110	109276110	+	Missense_Mutation	SNP	G	G	A	rs146149508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:109276110G>A	ENST00000393310.1	+	2	213	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	LIMS1_ENST00000542845.1_Missense_Mutation_p.G78S|LIMS1_ENST00000332345.6_Missense_Mutation_p.G16S|LIMS1_ENST00000409441.1_Missense_Mutation_p.G53S|LIMS1_ENST00000393314.2_Missense_Mutation_p.G78S|LIMS1_ENST00000338045.3_Missense_Mutation_p.G16S|LIMS1_ENST00000410093.1_Missense_Mutation_p.G20S|LIMS1_ENST00000544547.1_Missense_Mutation_p.G28S|LIMS1_ENST00000462817.1_3'UTR	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	16	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						CTGCAAGGGCGGCTTTGCGCC	0.572													G|||	11	0.00219649	0.0	0.0043	5008	,	,		24021	0.0		0.008	False		,,,				2504	0.0				p.G78S		Atlas-SNP	.											.	LIMS1	38	.	0			c.G232A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	9,4397	14.3+/-33.2	0,9,2194	117.0	90.0	99.0		58,82,157,232,46,46	4.6	0.8	2	dbSNP_134	99	93,8507	52.3+/-112.8	0,93,4207	no	missense,missense,missense,missense,missense,missense	LIMS1	NM_001193482.1,NM_001193483.2,NM_001193484.1,NM_001193485.2,NM_001193488.1,NM_004987.5	56,56,56,56,56,56	0,102,6401	AA,AG,GG		1.0814,0.2043,0.7843	benign,benign,benign,benign,benign,benign	20/330,28/338,53/363,78/388,16/326,16/326	109276110	102,12904	2203	4300	6503	SO:0001583	missense	3987	exon2			AAGGGCGGCTTTG		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983	ENST00000393310.1:c.46G>A	2.37:g.109276110G>A	ENSP00000376987:p.Gly16Ser	630.0	0.0	0		859.0	303.0	0.352736	NM_001193485	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Missense_Mutation	SNP	ENST00000393310.1	37	CCDS2078.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017490	0.75161	0.002043	0.010814	ENSG00000169756	ENST00000544547;ENST00000428064;ENST00000332345;ENST00000393310;ENST00000410093;ENST00000409441;ENST00000338045;ENST00000542845;ENST00000393314	D;D;D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	4.63	4.63	0.57726	Zinc finger, LIM-type (5);	0.160833	0.41605	D	0.000860	T	0.81978	0.4937	L	0.45744	1.44	0.80722	D	1	P;P;B;B	0.44946	0.846;0.53;0.377;0.377	P;B;B;B	0.45195	0.473;0.124;0.087;0.087	T	0.83289	-0.0034	10	0.33141	T	0.24	.	17.6679	0.88208	0.0:0.0:1.0:0.0	.	78;53;16;28	B7Z7R3;B7Z907;P48059;B7Z483	.;.;LIMS1_HUMAN;.	S	28;28;16;16;20;53;16;78;78	ENSP00000437912:G28S;ENSP00000390862:G28S;ENSP00000331775:G16S;ENSP00000376987:G16S;ENSP00000386926:G20S;ENSP00000387264:G53S;ENSP00000337598:G16S;ENSP00000446121:G78S;ENSP00000376990:G78S	ENSP00000331775:G16S	G	+	1	0	LIMS1	108642542	1.000000	0.71417	0.842000	0.33263	0.932000	0.56968	6.498000	0.73679	2.392000	0.81423	0.563000	0.77884	GGC	G|0.994;A|0.006	0.006	strong		0.572	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987	
R3HDM1	23518	hgsc.bcm.edu	37	2	136467084	136467084	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136467084G>A	ENST00000264160.4	+	21	2806	c.2436G>A	c.(2434-2436)caG>caA	p.Q812Q	R3HDM1_ENST00000409606.1_Silent_p.Q813Q|R3HDM1_ENST00000410054.1_Silent_p.Q757Q|R3HDM1_ENST00000329971.3_Silent_p.Q683Q|R3HDM1_ENST00000409478.1_Silent_p.Q684Q	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	812							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		GTTCCCAGCAGCTTCAAGGCC	0.383																																					p.Q812Q		Atlas-SNP	.											.	R3HDM1	84	.	0			c.G2436A						PASS	.						123.0	107.0	112.0					2																	136467084		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon21			CCAGCAGCTTCAA	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.2436G>A	2.37:g.136467084G>A		425.0	1.0	0.00235294		307.0	149.0	0.485342	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.684|8.684	0.905766|0.905766	0.17760|0.17760	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000429703|ENST00000445855	.|.	.|.	.|.	5.61|5.61	4.72|4.72	0.59763|0.59763	.|.	.|.	.|.	.|.	.|.	T|T	0.60612|0.60612	0.2282|0.2282	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57329|0.57329	-0.7830|-0.7830	4|4	.|.	.|.	.|.	0.2051|0.2051	9.5268|9.5268	0.39169|0.39169	0.0734:0.0:0.7872:0.1394|0.0734:0.0:0.7872:0.1394	.|.	.|.	.|.	.|.	T|N	536|108	.|.	.|.	A|S	+|+	1|2	0|0	R3HDM1|R3HDM1	136183554|136183554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.615000|2.615000	0.46368|0.46368	2.647000|2.647000	0.89833|0.89833	0.644000|0.644000	0.83932|0.83932	GCT|AGC	.	.	none		0.383	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	
SORCS1	114815	hgsc.bcm.edu	37	10	108380256	108380256	+	Missense_Mutation	SNP	G	G	A	rs144056795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:108380256G>A	ENST00000263054.6	-	20	2733	c.2726C>T	c.(2725-2727)gCg>gTg	p.A909V	SORCS1_ENST00000369698.1_Missense_Mutation_p.A444V|SORCS1_ENST00000478809.2_5'Flank|SORCS1_ENST00000344440.6_Missense_Mutation_p.A909V	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	909					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.A909V(2)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CACTGCCGTCGCATTGACCTC	0.562													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19875	0.0		0.0	False		,,,				2504	0.0				p.A909V		Atlas-SNP	.											SORCS1_ENST00000344440,right_upper_lobe,carcinoma,+1,3	SORCS1	534	3	2	Substitution - Missense(2)	endometrium(2)	c.C2726T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	18,4388	25.3+/-52.1	0,18,2185	166.0	135.0	146.0		2726,2726,2726,2726,2726,2726	5.8	0.7	10	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	64,64,64,64,64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign,benign,benign,benign,benign	909/1199,909/1180,909/1131,909/1160,909/1180,909/1169	108380256	18,12988	2203	4300	6503	SO:0001583	missense	114815	exon20			GCCGTCGCATTGA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2726C>T	10.37:g.108380256G>A	ENSP00000263054:p.Ala909Val	98.0	0.0	0		112.0	25.0	0.223214	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.29	1.594477	0.28445	0.004085	0.0	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.40476	1.03;1.03;1.03	5.75	5.75	0.90469	PKD/Chitinase domain (1);PKD domain (1);	0.224860	0.40728	N	0.001035	T	0.29556	0.0737	N	0.13043	0.29	0.45962	D	0.998782	B;B;B;B;B	0.19445	0.021;0.036;0.036;0.021;0.036	B;B;B;B;B	0.14023	0.005;0.01;0.01;0.005;0.01	T	0.08576	-1.0715	9	.	.	.	-18.823	19.9548	0.97216	0.0:0.0:1.0:0.0	.	909;909;909;909;909	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	V	444;909;909	ENSP00000358712:A444V;ENSP00000263054:A909V;ENSP00000345964:A909V	.	A	-	2	0	SORCS1	108370246	1.000000	0.71417	0.676000	0.29932	0.232000	0.25224	5.920000	0.70017	2.714000	0.92807	0.655000	0.94253	GCG	G|0.999;A|0.001	0.001	strong		0.562	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
AMBN	258	hgsc.bcm.edu	37	4	71469006	71469006	+	Silent	SNP	C	C	T	rs113360877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71469006C>T	ENST00000322937.6	+	10	781	c.678C>T	c.(676-678)caC>caT	p.H226H	AMBN_ENST00000449493.2_Silent_p.H211H	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	226					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			TGATTTCTCACGGACCAATGC	0.318													C|||	29	0.00579073	0.0008	0.0086	5008	,	,		14320	0.001		0.0179	False		,,,				2504	0.0031				p.H226H		Atlas-SNP	.											.	AMBN	73	.	0			c.C678T						PASS	.	C		14,4390	21.2+/-45.6	0,14,2188	77.0	74.0	75.0		678	1.8	1.0	4	dbSNP_132	75	186,8406	84.2+/-146.7	1,184,4111	no	coding-synonymous	AMBN	NM_016519.5		1,198,6299	TT,TC,CC		2.1648,0.3179,1.5389		226/448	71469006	200,12796	2202	4296	6498	SO:0001819	synonymous_variant	258	exon10			TTCTCACGGACCA	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.678C>T	4.37:g.71469006C>T		186.0	0.0	0		149.0	65.0	0.436242	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																			C|0.987;T|0.013	0.013	strong		0.318	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62856646	62856646	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:62856646G>A	ENST00000584306.1	-	11	4148	c.3618C>T	c.(3616-3618)ctC>ctT	p.L1206L	LRRC37A3_ENST00000334962.5_Silent_p.L183L|LRRC37A3_ENST00000400877.3_Silent_p.L244L|LRRC37A3_ENST00000319651.5_Silent_p.L1206L|LRRC37A3_ENST00000339474.5_Silent_p.L324L	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1206						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CTGGACTTCCGAGCCTTTTTT	0.562																																					p.L1206L		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.C3618T						PASS	.																																			SO:0001819	synonymous_variant	374819	exon11			ACTTCCGAGCCTT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.3618C>T	17.37:g.62856646G>A		38.0	0.0	0		38.0	21.0	0.552632	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	37	CCDS32708.1																																																																																			.	.	none		0.562	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
FAM102A	399665	hgsc.bcm.edu	37	9	130742271	130742271	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742271C>T	ENST00000373095.1	-	1	521	c.146G>A	c.(145-147)aGg>aAg	p.R49K		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	49										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						CAGCTCCTACCTTGACGACAA	0.632																																					p.R49K		Atlas-SNP	.											.	FAM102A	32	.	0			c.G146A						PASS	.						63.0	67.0	66.0					9																	130742271		2203	4300	6503	SO:0001630	splice_region_variant	399665	exon1			TCCTACCTTGACG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.146+1G>A	9.37:g.130742271C>T		68.0	0.0	0		72.0	17.0	0.236111	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	36	5.857711	0.97030	.	.	ENSG00000167106	ENST00000373095	T	0.39787	1.06	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.79011	2.435	0.80722	D	1	P	0.45634	0.863	P	0.45538	0.484	T	0.57946	-0.7723	9	.	.	.	-30.8032	16.9987	0.86376	0.0:1.0:0.0:0.0	.	49	Q5T9C2	F102A_HUMAN	K	49	ENSP00000362187:R49K	.	R	-	2	0	FAM102A	129782092	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.487000	0.81328	2.244000	0.73946	0.462000	0.41574	AGG	.	.	none		0.632	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		Missense_Mutation
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Intron	SNP	T	T	G	rs143144671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron|ETFB_ENST00000354232.4_Missense_Mutation_p.E40A	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		ATCCAGCCATTCCTGGGTACC	0.522													t|||	4	0.000798722	0.0	0.0029	5008	,	,		18122	0.0		0.002	False		,,,				2504	0.0				p.E40A		Atlas-SNP	.											.	ETFB	46	.	0			c.A119C						PASS	.	T	ALA/GLU,	3,4403	6.2+/-15.9	0,3,2200	88.0	83.0	85.0		119,	-3.9	0.0	19	dbSNP_134	85	31,8569	21.6+/-65.8	0,31,4269	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	107,	0,34,6469	GG,GT,TT		0.3605,0.0681,0.2614	possibly-damaging,	40/347,	51857774	34,12972	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			AGCCATTCCTGGG	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-212A>C	19.37:g.51857774T>G		106.0	0.0	0		94.0	65.0	0.691489	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	t	12.37	1.918726	0.33908	6.81E-4	0.003605	ENSG00000105379	ENST00000354232	D	0.85339	-1.97	2.49	-3.88	0.04205	.	.	.	.	.	T	0.68430	0.3000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50558	-0.8814	7	.	.	.	.	4.1225	0.10112	0.0:0.1914:0.3562:0.4524	.	40	P38117-2	.	A	40	ENSP00000346173:E40A	.	E	-	2	0	ETFB	56549586	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.697000	0.05098	-1.056000	0.03205	-0.319000	0.08680	GAA	T|0.998;G|0.002	0.002	strong		0.522	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092948	1092948	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092948C>G	ENST00000441003.2	+	30	4794	c.4767C>G	c.(4765-4767)acC>acG	p.T1589T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1590T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1590T(2)|p.T1589T(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tcaccaccaccactacggtga	0.627																																					p.T1589T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,12	MUC2	614	12	4	Substitution - coding silent(4)	endometrium(2)|kidney(2)	c.C4767G						scavenged	.																																			SO:0001819	synonymous_variant	4583	exon30			CACCACCACTACG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4767C>G	11.37:g.1092948C>G		37.0	0.0	0		56.0	4.0	0.0714286	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
UMODL1	89766	hgsc.bcm.edu	37	21	43531345	43531345	+	Intron	SNP	G	G	A	rs76618631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43531345G>A	ENST00000408910.2	+	11	1899				C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Silent_p.A599A|UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000408989.2_Silent_p.A671A	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CCAGCCAGGCGAGCCCCAGCC	0.726													G|||	104	0.0207668	0.0734	0.0072	5008	,	,		10161	0.0		0.002	False		,,,				2504	0.0				p.A671A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G2013A						PASS	.	G	,,,	161,3347		2,157,1595	4.0	7.0	6.0		,1797,,2013	0.1	0.0	21	dbSNP_131	6	1,7635		0,1,3817	no	intron,coding-synonymous,intron,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	2,158,5412	AA,AG,GG		0.0131,4.5895,1.4537	,,,	,599/1375,,671/1447	43531345	162,10982	1754	3818	5572	SO:0001627	intron_variant	89766	exon11			CCAGGCGAGCCCC		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1899+114G>A	21.37:g.43531345G>A		27.0	0.0	0		35.0	14.0	0.4	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			G|0.983;A|0.017	0.017	strong		0.726	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
PABPC1	26986	hgsc.bcm.edu	37	8	101721785	101721785	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:101721785T>A	ENST00000318607.5	-	8	2275	c.1147A>T	c.(1147-1149)Atg>Ttg	p.M383L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Missense_Mutation_p.M351L|PABPC1_ENST00000519004.1_Missense_Mutation_p.M338L	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	383					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ATTCTCTGCATATACTGGTTA	0.493																																					p.M383L		Atlas-SNP	.											.	PABPC1	76	.	0			c.A1147T						PASS	.						168.0	142.0	151.0					8																	101721785		2203	4300	6503	SO:0001583	missense	26986	exon8			TCTGCATATACTG	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1147A>T	8.37:g.101721785T>A	ENSP00000313007:p.Met383Leu	256.0	0.0	0		220.0	73.0	0.331818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.08|19.08	3.757792|3.757792	0.69648|0.69648	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596	T;T;T|.	0.32023|.	1.52;1.47;2.53|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76601|0.76601	0.4010|0.4010	M|M	0.84846|0.84846	2.72|2.72	0.58432|0.58432	D|D	0.999995|0.999995	B;B;B|.	0.21452|.	0.043;0.056;0.025|.	B;B;B|.	0.23150|.	0.033;0.044;0.019|.	T|T	0.75736|0.75736	-0.3213|-0.3213	10|6	0.48119|0.23891	T|T	0.1|0.37	.|.	15.3415|15.3415	0.74300|0.74300	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	351;383;383|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	L|F	383;383;338;351|215	ENSP00000313007:M383L;ENSP00000429594:M338L;ENSP00000429395:M351L|.	ENSP00000313007:M383L|ENSP00000430068:Y215F	M|Y	-|-	1|2	0|0	PABPC1|PABPC1	101790961|101790961	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.968000|7.968000	0.87980|0.87980	2.083000|2.083000	0.62718|0.62718	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.	none		0.493	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
NBAS	51594	hgsc.bcm.edu	37	2	15607853	15607853	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:15607853G>A	ENST00000281513.5	-	18	1978	c.1953C>T	c.(1951-1953)gcC>gcT	p.A651A	NBAS_ENST00000441750.1_Silent_p.A651A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	651					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TTTTATTCTTGGCAGGCTCTT	0.343																																					p.A651A		Atlas-SNP	.											.	NBAS	246	.	0			c.C1953T						PASS	.						106.0	99.0	101.0					2																	15607853		2202	4299	6501	SO:0001819	synonymous_variant	51594	exon18			ATTCTTGGCAGGC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1953C>T	2.37:g.15607853G>A		211.0	1.0	0.00473934		246.0	136.0	0.552846	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			.	.	none		0.343	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
PDIA4	9601	hgsc.bcm.edu	37	7	148709061	148709061	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:148709061G>A	ENST00000286091.4	-	6	1088	c.856C>T	c.(856-858)Ccc>Tcc	p.P286S		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	286	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			TCCTTGGAGGGAGGCCCGGAC	0.577																																					p.P286S		Atlas-SNP	.											.	PDIA4	57	.	0			c.C856T						PASS	.						80.0	76.0	77.0					7																	148709061		2203	4300	6503	SO:0001583	missense	9601	exon6			TGGAGGGAGGCCC	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.856C>T	7.37:g.148709061G>A	ENSP00000286091:p.Pro286Ser	70.0	0.0	0		60.0	10.0	0.166667	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	g	12.18	1.862013	0.32884	.	.	ENSG00000155660	ENST00000286091	T	0.19394	2.15	5.14	5.14	0.70334	Thioredoxin-like fold (2);	0.100995	0.64402	D	0.000001	T	0.13114	0.0318	N	0.21583	0.68	0.80722	D	1	P	0.36282	0.546	B	0.22386	0.039	T	0.11567	-1.0582	10	0.16896	T	0.51	.	18.7073	0.91643	0.0:0.0:1.0:0.0	.	286	P13667	PDIA4_HUMAN	S	286	ENSP00000286091:P286S	ENSP00000286091:P286S	P	-	1	0	PDIA4	148339994	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.052000	0.71080	2.423000	0.82170	0.639000	0.83563	CCC	.	.	none		0.577	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
KIF18A	81930	hgsc.bcm.edu	37	11	28045367	28045367	+	Silent	SNP	G	G	A	rs35440657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:28045367G>A	ENST00000263181.6	-	16	2825	c.2535C>T	c.(2533-2535)gaC>gaT	p.D845D		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	845					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.D845D(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						CAGAATTTACGTCTGCAGTTA	0.318													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17656	0.0		0.0089	False		,,,				2504	0.002				p.D845D		Atlas-SNP	.											KIF18A,caecum,carcinoma,0,1	KIF18A	92	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C2535T						PASS	.	G		3,4399	6.2+/-15.9	0,3,2198	127.0	115.0	119.0		2535	-5.2	0.0	11	dbSNP_126	119	66,8532	40.3+/-97.0	0,66,4233	no	coding-synonymous	KIF18A	NM_031217.3		0,69,6431	AA,AG,GG		0.7676,0.0682,0.5308		845/899	28045367	69,12931	2201	4299	6500	SO:0001819	synonymous_variant	81930	exon16			ATTTACGTCTGCA	AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2535C>T	11.37:g.28045367G>A		143.0	0.0	0		115.0	20.0	0.173913	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Silent	SNP	ENST00000263181.6	37	CCDS7867.1																																																																																			G|0.995;A|0.005	0.005	strong		0.318	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
CLCF1	23529	hgsc.bcm.edu	37	11	67132804	67132804	+	Missense_Mutation	SNP	G	G	A	rs78755659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67132804G>A	ENST00000312438.7	-	3	678	c.481C>T	c.(481-483)Ccg>Tcg	p.P161S	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Missense_Mutation_p.P151S|RN7SKP239_ENST00000364814.1_RNA|CLCF1_ENST00000528474.1_Missense_Mutation_p.P151S	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	161					B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			CCAGGCAGCGGCTGGGGCAGT	0.657													g|||	64	0.0127796	0.0	0.0058	5008	,	,		17140	0.0		0.0179	False		,,,				2504	0.0429				p.P161S		Atlas-SNP	.											.	CLCF1	15	.	0			c.C481T						PASS	.		SER/PRO,SER/PRO	9,4389		0,9,2190	20.0	21.0	21.0		451,481	4.3	1.0	11	dbSNP_131	21	91,8483		1,89,4197	yes	missense,missense	CLCF1	NM_001166212.1,NM_013246.2	74,74	1,98,6387	AA,AG,GG		1.0613,0.2046,0.7709	benign,benign	151/216,161/226	67132804	100,12872	2199	4287	6486	SO:0001583	missense	23529	exon3			GCAGCGGCTGGGG	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"""B-cell stimulating factor 3"", ""cold-induced sweating syndrome 2"", ""novel neurotrophin-1"""	607672	"""CRLF1 associated cytokine-like factor 1"""			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.481C>T	11.37:g.67132804G>A	ENSP00000309338:p.Pro161Ser	86.0	0.0	0		81.0	20.0	0.246914	NM_013246	B4DNT4|Q6NZA4	Missense_Mutation	SNP	ENST00000312438.7	37	CCDS31617.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	g	11.26	1.587561	0.28268	0.002046	0.010613	ENSG00000175505	ENST00000312438;ENST00000533438;ENST00000528474	T;T;T	0.75260	-0.92;-0.92;-0.92	4.27	4.27	0.50696	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.64402	D	0.000001	T	0.58409	0.2120	L	0.29908	0.895	0.30105	N	0.807084	P	0.45212	0.853	P	0.52109	0.69	T	0.68981	-0.5266	10	0.87932	D	0	-7.0213	13.0463	0.58928	0.0:0.1625:0.8375:0.0	.	161	Q9UBD9	CLCF1_HUMAN	S	161;151;151	ENSP00000309338:P161S;ENSP00000434122:P151S;ENSP00000432553:P151S	ENSP00000309338:P161S	P	-	1	0	CLCF1	66889380	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.795000	0.55499	2.320000	0.78422	0.556000	0.70494	CCG	G|0.992;A|0.008	0.008	strong		0.657	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246	
ANGPTL2	23452	hgsc.bcm.edu	37	9	129870763	129870763	+	Missense_Mutation	SNP	C	C	T	rs370920897		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:129870763C>T	ENST00000373425.3	-	2	865	c.248G>A	c.(247-249)cGa>cAa	p.R83Q	RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000491991.1_5'Flank|RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000259351.5_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	83					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CTTATGCACTCGGTTCTCCAG	0.592																																					p.R83Q		Atlas-SNP	.											ANGPTL2,colon,carcinoma,-1,1	ANGPTL2	46	1	0			c.G248A						PASS	.	C	,,,GLN/ARG,	1,4405	2.1+/-5.4	0,1,2202	63.0	53.0	56.0		,,,248,	4.9	1.0	9		56	0,8600		0,0,4300	no	intron,intron,intron,missense,intron	RALGPS1,ANGPTL2	NM_001190728.1,NM_001190729.1,NM_001190730.1,NM_012098.2,NM_014636.2	,,,43,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,probably-damaging,	,,,83/494,	129870763	1,13005	2203	4300	6503	SO:0001583	missense	23452	exon2			TGCACTCGGTTCT	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.248G>A	9.37:g.129870763C>T	ENSP00000362524:p.Arg83Gln	52.0	0.0	0		63.0	14.0	0.222222	NM_012098	Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	37	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291664	0.80914	2.27E-4	0.0	ENSG00000136859	ENST00000373425	T	0.40225	1.04	4.87	4.87	0.63330	.	0.119965	0.52532	D	0.000062	T	0.47060	0.1425	M	0.70275	2.135	0.80722	D	1	D	0.53885	0.963	P	0.45660	0.489	T	0.47898	-0.9081	10	0.12103	T	0.63	.	18.0259	0.89269	0.0:1.0:0.0:0.0	.	83	Q9UKU9	ANGL2_HUMAN	Q	83	ENSP00000362524:R83Q	ENSP00000362524:R83Q	R	-	2	0	ANGPTL2	128910584	1.000000	0.71417	0.995000	0.50966	0.749000	0.42624	7.818000	0.86416	2.259000	0.74868	0.655000	0.94253	CGA	.	.	weak		0.592	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098	
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28995211C>T	ENST00000311008.11	+	11	1802	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G	LAT_ENST00000564277.1_5'Flank|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000395461.3_5'Flank|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000565975.1_Silent_p.G520G|SPNS1_ENST00000352260.7_Silent_p.G401G|SPNS1_ENST00000323081.8_Silent_p.G402G|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000395456.2_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	475					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACTGGGCGGCGCAGCCTTCC	0.672													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18700	0.0		0.008	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1425T						PASS	.	C	,,,,	7,4387	12.9+/-30.5	0,7,2190	48.0	51.0	50.0		1425,1203,1206,1269,1425	-9.2	0.1	16	dbSNP_132	50	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	1,79,6417	TT,TC,CC		0.8605,0.1593,0.6234	,,,,	475/529,401/455,402/456,423/477,475/529	28995211	81,12913	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			GGGCGGCGCAGCC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1425C>T	16.37:g.28995211C>T		56.0	0.0	0		65.0	33.0	0.507692	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.995;T|0.005	0.005	strong		0.672	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
MYO1F	4542	hgsc.bcm.edu	37	19	8616999	8616999	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8616999C>T	ENST00000338257.8	-	7	821	c.554G>A	c.(553-555)gGc>gAc	p.G185D	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	185	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						GGAGATCTTGCCCCCATCTGG	0.562																																					p.G185D		Atlas-SNP	.											.	MYO1F	128	.	0			c.G554A						PASS	.						100.0	102.0	102.0					19																	8616999		1977	4203	6180	SO:0001583	missense	4542	exon7			ATCTTGCCCCCAT	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.554G>A	19.37:g.8616999C>T	ENSP00000344871:p.Gly185Asp	121.0	0.0	0		102.0	23.0	0.22549	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316297	0.81469	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.95885	-3.84	3.93	3.93	0.45458	Myosin head, motor domain (2);	0.064498	0.64402	D	0.000010	D	0.98695	0.9562	H	0.98721	4.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.99301	1.0901	10	0.87932	D	0	.	15.1284	0.72500	0.0:1.0:0.0:0.0	.	185;185;185	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	D	230;185	ENSP00000344871:G185D	ENSP00000304899:G230D	G	-	2	0	MYO1F	8522999	1.000000	0.71417	0.986000	0.45419	0.850000	0.48378	7.651000	0.83577	2.048000	0.60808	0.460000	0.39030	GGC	.	.	none		0.562	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
GOLGB1	2804	hgsc.bcm.edu	37	3	121413362	121413362	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121413362T>C	ENST00000340645.5	-	13	6118	c.5993A>G	c.(5992-5994)cAg>cGg	p.Q1998R	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q2003R	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1998					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GGGTTCTTTCTGAGCACCTTG	0.378																																					p.Q2003R		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6008G						PASS	.						166.0	176.0	172.0					3																	121413362		2203	4300	6503	SO:0001583	missense	2804	exon13			TCTTTCTGAGCAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5993A>G	3.37:g.121413362T>C	ENSP00000341848:p.Gln1998Arg	123.0	0.0	0		87.0	41.0	0.471264	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.356523	0.41700	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.25912	1.81;1.77	5.21	5.21	0.72293	.	0.130327	0.35525	N	0.003143	T	0.46444	0.1393	M	0.72894	2.215	0.45837	D	0.998705	D;D;D;D	0.76494	0.996;0.996;0.959;0.999	D;D;P;D	0.75484	0.922;0.986;0.564;0.953	T	0.35549	-0.9784	10	0.17832	T	0.49	.	13.0741	0.59077	0.0:0.0:0.0:1.0	.	1923;2003;2003;1998	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	R	1998;2003	ENSP00000341848:Q1998R;ENSP00000377275:Q2003R	ENSP00000341848:Q1998R	Q	-	2	0	GOLGB1	122896052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.173000	0.50839	2.174000	0.68829	0.533000	0.62120	CAG	.	.	none		0.378	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
MTUS1	57509	hgsc.bcm.edu	37	8	17611916	17611916	+	Silent	SNP	C	C	T	rs61740538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17611916C>T	ENST00000262102.6	-	2	1625	c.1401G>A	c.(1399-1401)tcG>tcA	p.S467S	MTUS1_ENST00000519263.1_Silent_p.S467S|MTUS1_ENST00000381869.3_Silent_p.S467S|MTUS1_ENST00000381862.3_Silent_p.S467S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	467					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		GTGCCTCCTTCGAGTCTGGTA	0.398													C|||	34	0.00678914	0.0015	0.0086	5008	,	,		19744	0.0		0.0229	False		,,,				2504	0.0031				p.S467S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G1401A						PASS	.	C	,	9,3729		0,9,1860	154.0	146.0	149.0		1401,1401	2.8	0.0	8	dbSNP_129	149	219,8015		4,211,3902	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	4,220,5762	TT,TC,CC		2.6597,0.2408,1.9044	,	467/1271,467/1217	17611916	228,11744	1869	4117	5986	SO:0001819	synonymous_variant	57509	exon2			CTCCTTCGAGTCT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1401G>A	8.37:g.17611916C>T		214.0	0.0	0		145.0	26.0	0.17931	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.982;T|0.018	0.018	strong		0.398	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:24954303G>C	ENST00000217456.2	-	4	689	c.399C>G	c.(397-399)gcC>gcG	p.A133A	RNU6-1257P_ENST00000384625.1_RNA|APMAP_ENST00000447138.1_Silent_p.A133A	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	133					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										AACCAAACCGGGCAATGGTCT	0.448													G|||	3	0.000599042	0.0	0.0	5008	,	,		19675	0.0		0.001	False		,,,				2504	0.002				p.A133A		Atlas-SNP	.											.	APMAP	3	.	0			c.C399G						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	107.0	92.0	97.0		399	0.0	1.0	20	dbSNP_134	97	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	C20orf3	NM_020531.2		0,13,6490	CC,CG,GG		0.1279,0.0454,0.1		133/417	24954303	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			AAACCGGGCAATG	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.399C>G	20.37:g.24954303G>C		131.0	0.0	0		116.0	62.0	0.534483	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103322	0.20632	4.54E-4	0.001279	ENSG00000101474	ENST00000451442	.	.	.	5.43	0.0444	0.14225	.	.	.	.	.	T	0.50360	0.1611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33752	-0.9856	4	.	.	.	-17.6727	5.067	0.14587	0.3047:0.2599:0.4354:0.0	.	.	.	.	R	118	.	.	P	-	2	0	C20orf3	24902303	0.804000	0.28969	0.963000	0.40424	0.854000	0.48673	-0.233000	0.09041	-0.200000	0.10300	-0.150000	0.13652	CCC	G|0.998;C|0.002	0.002	strong		0.448	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
PCDH18	54510	hgsc.bcm.edu	37	4	138452706	138452706	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:138452706A>T	ENST00000344876.4	-	1	923	c.537T>A	c.(535-537)aaT>aaA	p.N179K	PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.N179K|PCDH18_ENST00000507846.1_5'UTR|PCDH18_ENST00000510305.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	179	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TAAAAAAATCATTGGCAGAGA	0.483																																					p.N179K		Atlas-SNP	.											.	PCDH18	229	.	0			c.T537A						PASS	.						60.0	59.0	60.0					4																	138452706		2203	4300	6503	SO:0001583	missense	54510	exon1			AAAATCATTGGCA	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.537T>A	4.37:g.138452706A>T	ENSP00000355082:p.Asn179Lys	167.0	0.0	0		119.0	31.0	0.260504	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072697	0.36566	.	.	ENSG00000189184	ENST00000344876;ENST00000412923	T;T	0.50813	0.73;0.73	5.89	0.536	0.17138	Cadherin (4);Cadherin-like (1);	0.000000	0.46145	D	0.000304	T	0.65544	0.2701	M	0.87827	2.91	0.80722	D	1	D;D	0.71674	0.998;0.992	P;P	0.61201	0.885;0.739	T	0.69476	-0.5135	10	0.87932	D	0	.	10.9316	0.47222	0.5396:0.0:0.4604:0.0	.	179;179	Q9HCL0-2;Q9HCL0	.;PCD18_HUMAN	K	179	ENSP00000355082:N179K;ENSP00000390688:N179K	ENSP00000355082:N179K	N	-	3	2	PCDH18	138672156	1.000000	0.71417	0.930000	0.37139	0.304000	0.27724	1.063000	0.30567	0.078000	0.16900	0.455000	0.32223	AAT	.	.	none		0.483	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
GAD1	2571	hgsc.bcm.edu	37	2	171716266	171716266	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171716266G>C	ENST00000358196.3	+	17	2209	c.1659G>C	c.(1657-1659)atG>atC	p.M553I		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	553					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						GTACGACCATGGTTGGCTACC	0.493																																					p.M553I		Atlas-SNP	.											.	GAD1	79	.	0			c.G1659C						PASS	.						78.0	71.0	73.0					2																	171716266		2203	4300	6503	SO:0001583	missense	2571	exon17			GACCATGGTTGGC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1659G>C	2.37:g.171716266G>C	ENSP00000350928:p.Met553Ile	99.0	0.0	0		90.0	19.0	0.211111	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785893	0.90282	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.93328	3.405	0.80722	D	1	P	0.50528	0.936	P	0.51016	0.656	T	0.74914	-0.3502	10	0.87932	D	0	-23.7109	19.6956	0.96023	0.0:0.0:1.0:0.0	.	553	Q99259	DCE1_HUMAN	I	553	ENSP00000350928:M553I	ENSP00000350928:M553I	M	+	3	0	GAD1	171424512	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.420000	0.97426	2.729000	0.93468	0.585000	0.79938	ATG	.	.	none		0.493	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
ARHGEF1	9138	hgsc.bcm.edu	37	19	42409189	42409189	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42409189G>A	ENST00000354532.3	+	23	2397		c.e23+1		ARHGEF1_ENST00000337665.4_Splice_Site|ARHGEF1_ENST00000347545.4_Splice_Site|ARHGEF1_ENST00000378152.4_Splice_Site|ARHGEF1_ENST00000599846.1_Splice_Site	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1						cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		AGCGGAAAAAGTGAGGGGGGG	0.602																																					.		Atlas-SNP	.											ARHGEF1,NS,carcinoma,+1,1	ARHGEF1	95	1	0			c.2249+1G>A						PASS	.						46.0	45.0	45.0					19																	42409189		2203	4300	6503	SO:0001630	splice_region_variant	9138	exon23			GAAAAAGTGAGGG	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.2249+1G>A	19.37:g.42409189G>A		78.0	0.0	0		78.0	16.0	0.205128	NM_004706	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Splice_Site	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946544	0.53186	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000337665;ENST00000378152	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1593	0.72771	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGEF1	47101029	1.000000	0.71417	0.160000	0.22671	0.018000	0.09664	5.579000	0.67457	2.229000	0.72834	0.585000	0.79938	.	.	.	none		0.602	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002	Intron
CNTNAP4	85445	hgsc.bcm.edu	37	16	76461498	76461498	+	Splice_Site	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:76461498T>G	ENST00000476707.1	+	3	686		c.e3+2		CNTNAP4_ENST00000469589.1_Splice_Site|CNTNAP4_ENST00000377504.4_Splice_Site|CNTNAP4_ENST00000478060.1_Splice_Site|CNTNAP4_ENST00000307431.8_Splice_Site			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4						cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTGCATACAGTAAGTGTTTGT	0.388																																					.		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.537+2T>G						PASS	.						76.0	71.0	73.0					16																	76461498		2198	4300	6498	SO:0001630	splice_region_variant	85445	exon4			ATACAGTAAGTGT	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.547+2T>G	16.37:g.76461498T>G		134.0	0.0	0		168.0	74.0	0.440476	NM_033401	E9PFZ6|Q86YZ7	Splice_Site	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	T	24.5	4.533056	0.85812	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8097	0.69985	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTNAP4	75018999	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.720000	0.84759	2.232000	0.73038	0.533000	0.62120	.	.	.	none		0.388	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	Intron
ZCWPW2	152098	hgsc.bcm.edu	37	3	28454627	28454627	+	Missense_Mutation	SNP	A	A	G	rs148504648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:28454627A>G	ENST00000383768.2	+	3	256	c.68A>G	c.(67-69)aAc>aGc	p.N23S	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.N23S			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	23							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TCAGTGGAAAACATGTATGTA	0.323													A|||	2	0.000399361	0.0	0.0	5008	,	,		19875	0.0		0.002	False		,,,				2504	0.0				p.N23S		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.A68G						PASS	.	A	SER/ASN	6,4400	9.9+/-24.2	0,6,2197	109.0	107.0	108.0		68	0.1	0.0	3	dbSNP_134	108	25,8575	17.3+/-56.4	0,25,4275	yes	missense	ZCWPW2	NM_001040432.1	46	0,31,6472	GG,GA,AA		0.2907,0.1362,0.2384	benign	23/357	28454627	31,12975	2203	4300	6503	SO:0001583	missense	152098	exon2			TGGAAAACATGTA	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.68A>G	3.37:g.28454627A>G	ENSP00000373278:p.Asn23Ser	131.0	0.0	0		83.0	28.0	0.337349	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	16.03	3.007777	0.54361	0.001362	0.002907	ENSG00000206559	ENST00000420223;ENST00000383768;ENST00000421010	T;T	0.32988	1.43;1.43	5.37	0.0559	0.14317	.	0.328394	0.26474	N	0.024175	T	0.18383	0.0441	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.15350	-1.0440	10	0.36615	T	0.2	-2.9798	7.7479	0.28879	0.5196:0.0:0.4804:0.0	.	23	Q504Y3	ZCPW2_HUMAN	S	23	ENSP00000373278:N23S;ENSP00000412386:N23S	ENSP00000373278:N23S	N	+	2	0	ZCWPW2	28429631	0.001000	0.12720	0.033000	0.17914	0.962000	0.63368	-0.160000	0.10041	0.000000	0.14550	0.482000	0.46254	AAC	A|0.998;G|0.002	0.002	strong		0.323	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
PGAP1	80055	hgsc.bcm.edu	37	2	197711870	197711870	+	Silent	SNP	G	G	A	rs149815494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:197711870G>A	ENST00000354764.4	-	22	2121	c.2007C>T	c.(2005-2007)gcC>gcT	p.A669A		NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	669					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTAAAATGACGGCATCTAATT	0.373													G|||	17	0.00339457	0.0	0.0	5008	,	,		16262	0.0		0.0169	False		,,,				2504	0.0				p.A669A		Atlas-SNP	.											.	PGAP1	84	.	0			c.C2007T						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	138.0	143.0	141.0		2007	3.1	1.0	2	dbSNP_134	141	87,8513	49.8+/-109.6	1,85,4214	no	coding-synonymous	PGAP1	NM_024989.3		1,95,6407	AA,AG,GG		1.0116,0.227,0.7458		669/923	197711870	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	80055	exon22			AATGACGGCATCT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.2007C>T	2.37:g.197711870G>A		204.0	0.0	0		147.0	59.0	0.401361	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Silent	SNP	ENST00000354764.4	37	CCDS2318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.373	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
C14orf37	145407	hgsc.bcm.edu	37	14	58605043	58605043	+	Missense_Mutation	SNP	G	G	A	rs61741199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605043G>A	ENST00000267485.7	-	2	1228	c.1034C>T	c.(1033-1035)aCa>aTa	p.T345I	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	345						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TACTTGTGCTGTCTGAGACAT	0.547													G|||	351	0.0700879	0.1437	0.0432	5008	,	,		20918	0.0		0.0577	False		,,,				2504	0.0746				p.T345I		Atlas-SNP	.											.	C14orf37	87	.	0			c.C1034T						PASS	.	G	ILE/THR	516,3890	237.1+/-249.0	31,454,1718	155.0	152.0	153.0		1034	3.7	0.2	14	dbSNP_129	153	483,8117	140.1+/-196.7	12,459,3829	yes	missense	C14orf37	NM_001001872.2	89	43,913,5547	AA,AG,GG		5.6163,11.7113,7.6811	benign	345/775	58605043	999,12007	2203	4300	6503	SO:0001583	missense	145407	exon2			TGTGCTGTCTGAG		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1034C>T	14.37:g.58605043G>A	ENSP00000267485:p.Thr345Ile	139.0	0.0	0		112.0	112.0	1	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	123	0.05631868131868132	62	0.12601626016260162	15	0.04143646408839779	0	0.0	46	0.06068601583113457	G	11.64	1.698404	0.30142	0.117113	0.056163	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21191	2.02	5.6	3.72	0.42706	.	0.558344	0.18393	N	0.142606	T	0.00144	0.0004	L	0.46157	1.445	0.58432	P	9.000000000036756E-6	B;P;B;B	0.38597	0.084;0.639;0.084;0.084	B;B;B;B	0.32928	0.066;0.155;0.066;0.066	T	0.12400	-1.0549	9	0.11794	T	0.64	-0.2219	6.3844	0.21552	0.1574:0.1953:0.6473:0.0	.	383;345;345;345	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	I	345;383	ENSP00000267485:T345I	ENSP00000267485:T345I	T	-	2	0	C14orf37	57674796	0.050000	0.20438	0.200000	0.23457	0.367000	0.29736	0.079000	0.14782	1.302000	0.44855	0.655000	0.94253	ACA	G|0.928;A|0.072	0.072	strong		0.547	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
ICAM3	3385	hgsc.bcm.edu	37	19	10445806	10445806	+	Silent	SNP	C	C	T	rs3181047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10445806C>T	ENST00000160262.5	-	4	1081	c.873G>A	c.(871-873)gaG>gaA	p.E291E	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Silent_p.E214E	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	291	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			TGCAGACGATCTCCCGGGCAC	0.662													C|||	45	0.00898562	0.0	0.0	5008	,	,		14325	0.0377		0.004	False		,,,				2504	0.0031				p.E291E		Atlas-SNP	.											.	ICAM3	29	.	0			c.G873A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	106.0	113.0	110.0		873	-4.6	0.0	19	dbSNP_105	110	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ICAM3	NM_002162.3		0,9,6494	TT,TC,CC		0.0698,0.0681,0.0692		291/548	10445806	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon4			GACGATCTCCCGG		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.873G>A	19.37:g.10445806C>T		93.0	0.0	0		90.0	47.0	0.522222	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			C|0.995;T|0.005	0.005	strong		0.662	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
ZNF304	57343	hgsc.bcm.edu	37	19	57868483	57868483	+	Missense_Mutation	SNP	G	G	A	rs45612632	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57868483G>A	ENST00000282286.5	+	3	1419	c.1246G>A	c.(1246-1248)Gca>Aca	p.A416T	ZNF304_ENST00000598744.1_Missense_Mutation_p.A374T|ZNF304_ENST00000443917.2_Missense_Mutation_p.A463T|ZNF304_ENST00000391705.3_Missense_Mutation_p.A416T			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TCATACCGGGGCAAGGCCCTA	0.443													G|||	65	0.0129792	0.0015	0.0101	5008	,	,		21870	0.0		0.0358	False		,,,				2504	0.0204				p.A416T		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1246A						PASS	.	G	THR/ALA	19,4387	25.3+/-52.1	1,17,2185	50.0	53.0	52.0		1246	3.0	0.9	19	dbSNP_127	52	261,8339	99.9+/-161.4	4,253,4043	yes	missense	ZNF304	NM_020657.2	58	5,270,6228	AA,AG,GG		3.0349,0.4312,2.1529	possibly-damaging	416/660	57868483	280,12726	2203	4300	6503	SO:0001583	missense	57343	exon3			ACCGGGGCAAGGC	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1246G>A	19.37:g.57868483G>A	ENSP00000282286:p.Ala416Thr	67.0	0.0	0		73.0	50.0	0.684932	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	30	0.013736263736263736	0	0.0	3	0.008287292817679558	0	0.0	27	0.03562005277044855	G	20.5	3.996773	0.74818	0.004312	0.030349	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.17213	2.29;2.29;2.29	4.03	2.96	0.34315	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.11364	0.135	0.25176	N	0.990242	P;P	0.35272	0.493;0.493	B;B	0.35413	0.202;0.202	T	0.21042	-1.0257	9	0.87932	D	0	.	12.651	0.56761	0.0:0.0:0.8326:0.1674	rs45612632	416;463	Q9HCX3;E7EQD3	ZN304_HUMAN;.	T	416;416;463	ENSP00000282286:A416T;ENSP00000375586:A416T;ENSP00000401642:A463T	ENSP00000282286:A416T	A	+	1	0	ZNF304	62560295	0.976000	0.34144	0.873000	0.34254	0.992000	0.81027	4.167000	0.58209	1.234000	0.43709	0.650000	0.86243	GCA	G|0.981;A|0.019	0.019	strong		0.443	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						PASS	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42.0	41.0	41.0		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	76.0	0.0	0		42.0	15.0	0.357143	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133.0	134.0	134.0		,2547	-12.3	0.0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2547G>T	18.37:g.28710615C>A		246.0	0.0	0		201.0	85.0	0.422886	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
MUC5B	727897	hgsc.bcm.edu	37	11	1270647	1270647	+	Missense_Mutation	SNP	G	G	C	rs185838223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270647G>C	ENST00000529681.1	+	31	12595	c.12537G>C	c.(12535-12537)caG>caC	p.Q4179H	MUC5B_ENST00000447027.1_Missense_Mutation_p.Q4182H|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4179	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCAGGCCCAGCCTGGTGTCC	0.667													G|||	246	0.0491214	0.0598	0.1066	5008	,	,		16942	0.003		0.0497	False		,,,				2504	0.0409				p.Q4179H		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12537C						PASS	.	G	HIS/GLN	237,3547		17,203,1672	44.0	53.0	50.0		12537	-7.2	0.0	11		50	432,7746		13,406,3670	no	missense	MUC5B	NM_002458.2	24	30,609,5342	CC,CG,GG		5.2825,6.2632,5.5927	benign	4179/5763	1270647	669,11293	1892	4089	5981	SO:0001583	missense	727897	exon31			GGCCCAGCCTGGT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.12537G>C	11.37:g.1270647G>C	ENSP00000436812:p.Gln4179His	731.0	0.0	0		732.0	153.0	0.209016	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	96	0.04395604395604396	20	0.04065040650406504	33	0.09116022099447514	0	0.0	43	0.05672823218997362	g	7.941	0.742802	0.15642	0.062632	0.052825	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.28	3.62	-7.25	0.01470	.	.	.	.	.	T	0.00412	0.0013	N	0.05441	-0.05	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.16041	-1.0416	9	0.87932	D	0	.	24.3801	0.99989	0.0:0.8733:0.1267:0.0	.	4652;4182	A7Y9J9;E9PBJ0	.;.	H	4179;4182;4123;4029	ENSP00000436812:Q4179H;ENSP00000415793:Q4182H	ENSP00000343037:Q4123H	Q	+	3	2	MUC5B	1227223	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.783000	0.04638	-1.952000	0.01027	0.393000	0.25936	CAG	G|0.952;C|0.048	0.048	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128796860	128796860	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:128796860C>A	ENST00000274487.4	+	2	284	c.139C>A	c.(139-141)Ccg>Acg	p.P47T	ADAMTS19-AS1_ENST00000502827.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	47						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GCGCCGGGAGCCGGTGGACCC	0.761																																					p.P47T		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.C139A						PASS	.						1.0	1.0	1.0					5																	128796860		985	2022	3007	SO:0001583	missense	171019	exon2			CGGGAGCCGGTGG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.139C>A	5.37:g.128796860C>A	ENSP00000274487:p.Pro47Thr	8.0	0.0	0		14.0	13.0	0.928571	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266920	0.40095	.	.	ENSG00000145808	ENST00000274487	T	0.64618	-0.11	3.54	2.64	0.31445	.	0.215910	0.23754	N	0.044896	T	0.35566	0.0936	N	0.08118	0	0.24389	N	0.994758	B	0.24186	0.099	B	0.17098	0.017	T	0.16041	-1.0416	9	.	.	.	.	8.9587	0.35834	0.0:0.8863:0.0:0.1137	.	47	Q8TE59	ATS19_HUMAN	T	47	ENSP00000274487:P47T	.	P	+	1	0	ADAMTS19	128824759	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.324000	0.33712	1.043000	0.40175	0.455000	0.32223	CCG	.	.	none		0.761	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
LRIT3	345193	hgsc.bcm.edu	37	4	110791273	110791273	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110791273G>T	ENST00000594814.1	+	4	1368	c.1368G>T	c.(1366-1368)aaG>aaT	p.K456N	LRIT3_ENST00000409621.2_Missense_Mutation_p.K273N|LRIT3_ENST00000327908.3_Missense_Mutation_p.K273N|LRIT3_ENST00000379920.3_Missense_Mutation_p.K411N	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	456					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGGTGGCAAAGAATGGAAGTA	0.463																																					p.K456N		Atlas-SNP	.											.	LRIT3	107	.	0			c.G1368T						PASS	.						69.0	71.0	70.0					4																	110791273		2203	4300	6503	SO:0001583	missense	345193	exon4			GGCAAAGAATGGA	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1368G>T	4.37:g.110791273G>T	ENSP00000469759:p.Lys456Asn	110.0	0.0	0		73.0	37.0	0.506849	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.351036	0.01256	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.58506	0.33;0.5;0.33	5.06	2.14	0.27477	.	0.790373	0.11066	N	0.603446	T	0.38639	0.1048	L	0.29908	0.895	0.09310	N	1	B;B	0.29805	0.097;0.257	B;B	0.26416	0.023;0.069	T	0.17592	-1.0364	10	0.18276	T	0.48	.	6.0052	0.19542	0.2318:0.2504:0.5178:0.0	.	411;273	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	N	273;411;273	ENSP00000328222:K273N;ENSP00000369252:K411N;ENSP00000386734:K273N	ENSP00000328222:K273N	K	+	3	2	LRIT3	111010722	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.171000	0.16685	1.118000	0.41863	0.655000	0.94253	AAG	.	.	none		0.463	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
CDON	50937	hgsc.bcm.edu	37	11	125871721	125871721	+	Missense_Mutation	SNP	G	G	C	rs145983470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125871721G>C	ENST00000392693.3	-	11	2178	c.2051C>G	c.(2050-2052)aCc>aGc	p.T684S	CDON_ENST00000263577.7_Missense_Mutation_p.T684S|CDON_ENST00000531738.1_Missense_Mutation_p.T61S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	684			T -> S (in HPE11; dbSNP:rs145983470). {ECO:0000269|PubMed:21802063}.		anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T684I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GGATGCCTGGGTGTTTTTTGA	0.393													G|||	9	0.00179712	0.0	0.0	5008	,	,		16120	0.0		0.008	False		,,,				2504	0.001				p.T684S		Atlas-SNP	.											CDON,right_lower_lobe,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	skin(1)	c.C2051G						PASS	.	G	SER/THR	12,4390	19.1+/-41.9	0,12,2189	121.0	121.0	121.0		2051	5.8	1.0	11	dbSNP_134	121	76,8522	44.9+/-103.4	0,76,4223	yes	missense	CDON	NM_016952.4	58	0,88,6412	CC,CG,GG		0.8839,0.2726,0.6769	benign	684/1265	125871721	88,12912	2201	4299	6500	SO:0001583	missense	50937	exon11			GCCTGGGTGTTTT	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.2051C>G	11.37:g.125871721G>C	ENSP00000376458:p.Thr684Ser	138.0	0.0	0		101.0	77.0	0.762376	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.73	2.323686	0.41096	0.002726	0.008839	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.69040	-0.36;0.25;-0.37	5.78	5.78	0.91487	.	0.231330	0.30383	N	0.009752	T	0.52158	0.1717	L	0.32530	0.975	0.41753	D	0.989675	B;P;B	0.36974	0.44;0.576;0.018	B;B;B	0.36845	0.118;0.234;0.016	T	0.56347	-0.7994	10	0.37606	T	0.19	-9.5924	20.3668	0.98882	0.0:0.0:1.0:0.0	.	684;684;61	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	S	684;61;684	ENSP00000376458:T684S;ENSP00000432901:T61S;ENSP00000263577:T684S	ENSP00000263577:T684S	T	-	2	0	CDON	125376931	1.000000	0.71417	0.971000	0.41717	0.478000	0.33099	4.745000	0.62125	2.894000	0.99253	0.655000	0.94253	ACC	G|0.994;C|0.006	0.006	strong		0.393	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
GJA8	2703	hgsc.bcm.edu	37	1	147380460	147380460	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:147380460G>A	ENST00000369235.1	+	1	378	c.378G>A	c.(376-378)caG>caA	p.Q126Q	GJA8_ENST00000240986.4_Silent_p.Q126Q			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	126					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCCCGGACCAGGGCAGCGTCA	0.647																																					p.Q126Q	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											GJA8,NS,carcinoma,+2,1	GJA8	108	1	0			c.G378A						PASS	.						46.0	55.0	52.0					1																	147380460		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			GGACCAGGGCAGC	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.378G>A	1.37:g.147380460G>A		63.0	0.0	0		42.0	11.0	0.261905	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																			.	.	none		0.647	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
CWF19L1	55280	hgsc.bcm.edu	37	10	101995477	101995477	+	Silent	SNP	T	T	G	rs139693285		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101995477T>G	ENST00000354105.4	-	13	1505	c.1419A>C	c.(1417-1419)acA>acC	p.T473T	CWF19L1_ENST00000370379.1_Silent_p.T188T|RP11-316M21.6_ENST00000444359.1_RNA|CWF19L1_ENST00000478047.1_5'UTR|SNORA12_ENST00000391162.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	473							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GCTTTTCTCCTGTGTCAAGTT	0.328													T|||	1	0.000199681	0.0	0.0	5008	,	,		20611	0.0		0.001	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											.	CWF19L1	39	.	0			c.A1419C						PASS	.	T		0,4406		0,0,2203	77.0	79.0	78.0		1419	1.6	1.0	10	dbSNP_134	78	24,8574	17.3+/-56.4	0,24,4275	no	coding-synonymous	CWF19L1	NM_018294.4		0,24,6478	GG,GT,TT		0.2791,0.0,0.1846		473/539	101995477	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	55280	exon13			TTCTCCTGTGTCA	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1419A>C	10.37:g.101995477T>G		51.0	0.0	0		38.0	16.0	0.421053	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Silent	SNP	ENST00000354105.4	37	CCDS7489.1																																																																																			T|0.999;G|0.001	0.001	strong		0.328	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
CDH1	999	hgsc.bcm.edu	37	16	68862165	68862165	+	Silent	SNP	C	C	T	rs33964119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:68862165C>T	ENST00000261769.5	+	14	2444	c.2253C>T	c.(2251-2253)aaC>aaT	p.N751N	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Silent_p.N690N	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	751		Cleavage; by caspase-3.			adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.N751N(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCCGGGACAACGTTTATTACT	0.507			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer				C|||	273	0.0545128	0.0582	0.0692	5008	,	,		19674	0.0694		0.0348	False		,,,				2504	0.044				p.N751N		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	CDH1,colon,carcinoma,0,3	CDH1	535	3	1	Substitution - coding silent(1)	stomach(1)	c.C2253T						PASS	.	C		215,4181	132.1+/-168.6	5,205,1988	98.0	94.0	95.0		2253	-12.1	0.0	16	dbSNP_126	95	273,8327	104.4+/-165.4	2,269,4029	no	coding-synonymous	CDH1	NM_004360.3		7,474,6017	TT,TC,CC		3.1744,4.8908,3.755		751/883	68862165	488,12508	2198	4300	6498	SO:0001819	synonymous_variant	999	exon14	Familial Cancer Database	HDGC	GGACAACGTTTAT	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2253C>T	16.37:g.68862165C>T		85.0	0.0	0		84.0	34.0	0.404762	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																			A|0.000;C|0.956;G|0.000;T|0.043	0.043	strong		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
RIF1	55183	hgsc.bcm.edu	37	2	152311612	152311612	+	Missense_Mutation	SNP	A	A	G	rs61750444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152311612A>G	ENST00000243326.5	+	21	3031	c.2548A>G	c.(2548-2550)Atg>Gtg	p.M850V	RIF1_ENST00000453091.2_Missense_Mutation_p.M850V|RIF1_ENST00000430328.2_Missense_Mutation_p.M850V|RIF1_ENST00000428287.2_Missense_Mutation_p.M850V|RIF1_ENST00000444746.2_Missense_Mutation_p.M850V			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTTGCCTTCTATGATCCGAAA	0.353													A|||	85	0.0169728	0.0371	0.0072	5008	,	,		17680	0.0		0.0268	False		,,,				2504	0.0041				p.M850V		Atlas-SNP	.											RIF1,NS,carcinoma,-2,1	RIF1	244	1	0			c.A2548G						scavenged	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	156,4250	106.0+/-144.5	5,146,2052	109.0	108.0	108.0		2548,2548,2548,2548	-1.1	1.0	2	dbSNP_129	108	167,8433	78.4+/-141.0	2,163,4135	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	21,21,21,21	7,309,6187	GG,GA,AA		1.9419,3.5406,2.4835	benign,benign,benign,benign	850/2447,850/2447,850/2447,850/2473	152311612	323,12683	2203	4300	6503	SO:0001583	missense	55183	exon22			CCTTCTATGATCC	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2548A>G	2.37:g.152311612A>G	ENSP00000243326:p.Met850Val	179.0	1.0	0.00558659		143.0	76.0	0.531469	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	48|48	0.02197802197802198|0.02197802197802198	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	24|24	0.0316622691292876|0.0316622691292876	A|A	1.477|1.477	-0.558248|-0.558248	0.03967|0.03967	0.035406|0.035406	0.019419|0.019419	ENSG00000080345|ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328|ENST00000414861	T;T;T;T;T|.	0.63744|.	-0.06;-0.06;-0.06;-0.06;-0.06|.	5.55|5.55	-1.09|-1.09	0.09904|0.09904	.|.	0.463720|.	0.26324|.	N|.	0.025028|.	T|T	0.19644|0.19644	0.0472|0.0472	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.16012|0.16012	-1.0417|-1.0417	10|5	0.11794|.	T|.	0.64|.	-3.1534|-3.1534	11.2086|11.2086	0.48784|0.48784	0.4305:0.0:0.5695:0.0|0.4305:0.0:0.5695:0.0	rs61750444|rs61750444	850;850|.	Q5UIP0;Q5UIP0-2|.	RIF1_HUMAN;.|.	V|C	850|841	ENSP00000390181:M850V;ENSP00000414615:M850V;ENSP00000415691:M850V;ENSP00000243326:M850V;ENSP00000416123:M850V|.	ENSP00000243326:M850V|.	M|Y	+|+	1|2	0|0	RIF1|RIF1	152019858|152019858	0.939000|0.939000	0.31865|0.31865	0.997000|0.997000	0.53966|0.53966	0.982000|0.982000	0.71751|0.71751	0.435000|0.435000	0.21510|0.21510	-0.136000|-0.136000	0.11475|0.11475	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.976;G|0.024	0.024	strong		0.353	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
TG	7038	hgsc.bcm.edu	37	8	133980076	133980076	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133980076G>A	ENST00000220616.4	+	31	5764	c.5724G>A	c.(5722-5724)gaG>gaA	p.E1908E	TG_ENST00000377869.1_Silent_p.E1851E|TG_ENST00000519543.1_Silent_p.E62E|TG_ENST00000542445.1_Silent_p.E278E	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1908					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.E1908E(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGCTCGCAGAGATAACAGAGA	0.498																																					p.E1908E		Atlas-SNP	.											TG,colon,carcinoma,0,1	TG	416	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G5724A						PASS	.						83.0	66.0	72.0					8																	133980076		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon31			CGCAGAGATAACA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5724G>A	8.37:g.133980076G>A		100.0	0.0	0		78.0	43.0	0.551282	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.014|0.014	-1.571920|-1.571920	0.00895|0.00895	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000518058	.|.	.|.	.|.	5.87|5.87	0.802|0.802	0.18686|0.18686	.|.	.|.	.|.	.|.	.|.	T|T	0.24470|0.24470	0.0593|0.0593	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24657|0.24657	-1.0154|-1.0154	4|4	.|.	.|.	.|.	.|.	4.5777|4.5777	0.12241|0.12241	0.1434:0.2262:0.5202:0.1102|0.1434:0.2262:0.5202:0.1102	.|.	.|.	.|.	.|.	N|K	364|40	.|.	.|.	D|R	+|+	1|2	0|0	TG|TG	134049258|134049258	0.111000|0.111000	0.22076|0.22076	0.038000|0.038000	0.18304|0.18304	0.021000|0.021000	0.10359|0.10359	0.030000|0.030000	0.13688|0.13688	-0.039000|-0.039000	0.13602|0.13602	-0.797000|-0.797000	0.03246|0.03246	GAT|AGA	.	.	none		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5.0	6.0	5.0					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	12.0	0.0	0		35.0	13.0	0.371429	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
EXOSC6	118460	hgsc.bcm.edu	37	16	70285780	70285780	+	Missense_Mutation	SNP	G	G	C	rs543954936		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70285780G>C	ENST00000435634.1	-	1	53	c.24C>G	c.(22-24)atC>atG	p.I8M		NM_058219.2	NP_478126.1	Q5RKV6	EXOS6_HUMAN	exosome component 6	8					DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CAGGGCCGCGGATGCGGCGGT	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		8098	0.0		0.0	False		,,,				2504	0.001				p.I8M		Atlas-SNP	.											.	EXOSC6	1	.	0			c.C24G						PASS	.						4.0	4.0	4.0					16																	70285780		1337	2762	4099	SO:0001583	missense	118460	exon1			GCCGCGGATGCGG	BC052252	CCDS10887.1	16q22.1	2008-02-05			ENSG00000223496	ENSG00000223496			19055	protein-coding gene	gene with protein product	"""Mtr3 (mRNA transport regulator 3)-homolog (yeast)"""	606490				11719186, 12419256	Standard	NM_058219		Approved	MTR3, hMtr3p, Mtr3p, EAP4, p11	uc002eym.1	Q5RKV6	OTTHUMG00000137578	ENST00000435634.1:c.24C>G	16.37:g.70285780G>C	ENSP00000398597:p.Ile8Met	5.0	0.0	0		18.0	9.0	0.5	NM_058219		Missense_Mutation	SNP	ENST00000435634.1	37	CCDS10887.1	.	.	.	.	.	.	.	.	.	.	N	10.08	1.251763	0.22880	.	.	ENSG00000223496	ENST00000435634	D	0.87412	-2.25	4.4	0.827	0.18835	.	0.086932	0.45126	U	0.000398	D	0.88518	0.6458	L	0.54323	1.7	0.29321	N	0.867386	D	0.61080	0.989	D	0.69654	0.965	T	0.80921	-0.1166	10	0.72032	D	0.01	-0.6466	5.5934	0.17313	0.0993:0.0:0.4371:0.4636	.	8	Q5RKV6	EXOS6_HUMAN	M	8	ENSP00000398597:I8M	ENSP00000398597:I8M	I	-	3	3	EXOSC6	68843281	0.895000	0.30542	1.000000	0.80357	0.026000	0.11368	-0.143000	0.10296	0.824000	0.34613	-0.823000	0.03104	ATC	.	.	none		0.697	EXOSC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268966.1	NM_058219	
NRXN1	9378	hgsc.bcm.edu	37	2	50779939	50779939	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50779939G>A	ENST00000406316.2	-	9	3021	c.1545C>T	c.(1543-1545)ggC>ggT	p.G515G	NRXN1_ENST00000406859.3_Silent_p.G515G|NRXN1_ENST00000401669.2_Silent_p.G515G|NRXN1_ENST00000402717.3_Silent_p.G507G|NRXN1_ENST00000405472.3_Silent_p.G507G|NRXN1_ENST00000404971.1_Silent_p.G555G|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	515	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATAAGATGAGGCCATTTGGCT	0.433																																					p.G555G		Atlas-SNP	.											NRXN1_ENST00000536085,rectum,carcinoma,0,6	NRXN1	1118	6	0			c.C1665T						PASS	.						162.0	151.0	154.0					2																	50779939		1904	4114	6018	SO:0001819	synonymous_variant	9378	exon10			GATGAGGCCATTT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1545C>T	2.37:g.50779939G>A		134.0	0.0	0		261.0	55.0	0.210728	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	none		0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
INO80	54617	hgsc.bcm.edu	37	15	41277551	41277551	+	Silent	SNP	T	T	C	rs61757083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41277551T>C	ENST00000361937.3	-	32	4330	c.3906A>G	c.(3904-3906)gaA>gaG	p.E1302E	INO80_ENST00000401393.3_Silent_p.E1302E|INO80_ENST00000561244.1_5'UTR			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1302	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTGCATACTTTTCCCGCTTCC	0.502													T|||	15	0.00299521	0.0008	0.0029	5008	,	,		19721	0.0		0.0089	False		,,,				2504	0.0031				p.E1302E		Atlas-SNP	.											.	INO80	122	.	0			c.A3906G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	229.0	179.0	196.0		3906	-0.1	1.0	15	dbSNP_129	196	94,8506	53.6+/-114.3	0,94,4206	no	coding-synonymous	INO80	NM_017553.1		0,98,6405	CC,CT,TT		1.093,0.0908,0.7535		1302/1557	41277551	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	54617	exon32			ATACTTTTCCCGC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3906A>G	15.37:g.41277551T>C		159.0	0.0	0		99.0	50.0	0.50505	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	37	CCDS10071.1																																																																																			T|0.992;C|0.008	0.008	strong		0.502	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
ZFP42	132625	hgsc.bcm.edu	37	4	188924523	188924523	+	Missense_Mutation	SNP	A	A	G	rs138176771		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924523A>G	ENST00000326866.4	+	4	970	c.562A>G	c.(562-564)Atc>Gtc	p.I188V	ZFP42_ENST00000509524.1_Missense_Mutation_p.I188V	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	188					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TCTGAGCGCAATCGCTTGTCC	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		17143	0.0		0.001	False		,,,				2504	0.0				p.I188V		Atlas-SNP	.											ZFP42,NS,carcinoma,-2,1	ZFP42	87	1	0			c.A562G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	107.0	113.0	111.0		562	-7.3	0.0	4	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ZFP42	NM_174900.3	29	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign	188/311	188924523	7,12999	2203	4300	6503	SO:0001583	missense	132625	exon4			AGCGCAATCGCTT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.562A>G	4.37:g.188924523A>G	ENSP00000317686:p.Ile188Val	89.0	0.0	0		87.0	46.0	0.528736	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	6.125	0.391354	0.11581	4.54E-4	5.81E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.61742	0.08;0.08	3.64	-7.28	0.01456	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.115814	0.53938	D	0.000048	T	0.24044	0.0582	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04427	-1.0952	10	0.35671	T	0.21	.	3.1416	0.06457	0.1935:0.4611:0.1484:0.197	.	188	Q96MM3	ZFP42_HUMAN	V	188	ENSP00000317686:I188V;ENSP00000424662:I188V	ENSP00000317686:I188V	I	+	1	0	ZFP42	189161517	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.764000	0.04735	-3.402000	0.00170	0.533000	0.62120	ATC	A|0.999;G|0.001	0.001	strong		0.488	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
PKHD1	5314	hgsc.bcm.edu	37	6	51768466	51768466	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51768466C>T	ENST00000371117.3	-	43	7200	c.6925G>A	c.(6925-6927)Gag>Aag	p.E2309K	PKHD1_ENST00000340994.4_Missense_Mutation_p.E2309K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2309					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E2309K(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAGAGTCCCTCGGCACCAGAA	0.428																																					p.E2309K		Atlas-SNP	.											PKHD1,colon,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	large_intestine(1)	c.G6925A						PASS	.						192.0	174.0	180.0					6																	51768466		2203	4300	6503	SO:0001583	missense	5314	exon43			GTCCCTCGGCACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.6925G>A	6.37:g.51768466C>T	ENSP00000360158:p.Glu2309Lys	114.0	0.0	0		98.0	34.0	0.346939	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822784	0.71028	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80304	-1.36;-1.36	5.87	5.87	0.94306	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.376162	0.25619	N	0.029438	D	0.85066	0.5612	M	0.71581	2.175	0.40270	D	0.978272	D;D;D	0.71674	0.998;0.992;0.998	P;P;P	0.60609	0.837;0.585;0.877	T	0.83066	-0.0145	10	0.35671	T	0.21	.	17.3804	0.87403	0.0:1.0:0.0:0.0	.	2309;2309;2309	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	K	2309	ENSP00000360158:E2309K;ENSP00000341097:E2309K	ENSP00000341097:E2309K	E	-	1	0	PKHD1	51876425	0.984000	0.35163	0.965000	0.40720	0.368000	0.29767	4.428000	0.59894	2.770000	0.95276	0.650000	0.86243	GAG	.	.	none		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
FCHSD1	89848	hgsc.bcm.edu	37	5	141030640	141030640	+	Silent	SNP	C	C	T	rs17287002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141030640C>T	ENST00000435817.2	-	2	116	c.66G>A	c.(64-66)ctG>ctA	p.L22L	ARAP3_ENST00000512390.1_5'Flank|FCHSD1_ENST00000522126.1_5'UTR|FCHSD1_ENST00000522783.1_Silent_p.L22L|FCHSD1_ENST00000519800.1_Silent_p.L22L	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	22	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.								FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGGATGCTCAGCTGTTCCA	0.582													C|||	132	0.0263578	0.003	0.0519	5008	,	,		12042	0.0		0.0805	False		,,,				2504	0.0112				p.L22L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.G66A						PASS	.	C		67,3993		0,67,1963	26.0	28.0	28.0		66	1.9	1.0	5	dbSNP_123	28	616,7746		21,574,3586	no	coding-synonymous	FCHSD1	NM_033449.2		21,641,5549	TT,TC,CC		7.3667,1.6502,5.4983		22/691	141030640	683,11739	2030	4181	6211	SO:0001819	synonymous_variant	89848	exon2			GATGCTCAGCTGT	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.66G>A	5.37:g.141030640C>T		70.0	0.0	0		74.0	32.0	0.432432	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	37	CCDS47295.1																																																																																			C|0.962;T|0.038	0.038	strong		0.582	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
ZNF536	9745	hgsc.bcm.edu	37	19	31039939	31039939	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:31039939A>G	ENST00000355537.3	+	4	3560	c.3413A>G	c.(3412-3414)aAg>aGg	p.K1138R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1138					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCTGATGGAAAGGCCCACTCT	0.532																																					p.K1138R		Atlas-SNP	.											.	ZNF536	424	.	0			c.A3413G						PASS	.						74.0	72.0	73.0					19																	31039939		2203	4300	6503	SO:0001583	missense	9745	exon4			ATGGAAAGGCCCA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3413A>G	19.37:g.31039939A>G	ENSP00000347730:p.Lys1138Arg	107.0	0.0	0		93.0	4.0	0.0430108	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	9.828	1.187633	0.21870	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.59	4.57	0.56435	.	0.454568	0.26428	N	0.024436	T	0.07863	0.0197	L	0.29908	0.895	0.28208	N	0.927077	B;P	0.44734	0.001;0.842	B;B	0.36922	0.001;0.236	T	0.13818	-1.0495	10	0.30078	T	0.28	-26.8781	11.4985	0.50424	0.9295:0.0:0.0705:0.0	.	1138;1138	A7E228;O15090	.;ZN536_HUMAN	R	1138	ENSP00000347730:K1138R	ENSP00000347730:K1138R	K	+	2	0	ZNF536	35731779	0.971000	0.33674	0.989000	0.46669	0.505000	0.33919	3.797000	0.55514	0.940000	0.37473	0.533000	0.62120	AAG	.	.	none		0.532	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
NEGR1	257194	hgsc.bcm.edu	37	1	72748169	72748169	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:72748169C>G	ENST00000357731.5	-	1	248	c.9G>C	c.(7-9)atG>atC	p.M3I	NEGR1_ENST00000434200.1_Start_Codon_SNP_p.M1I	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	3					feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		CCAACAGCATCATGTCCATCC	0.662																																					p.M3I		Atlas-SNP	.											.	NEGR1	60	.	0			c.G9C						PASS	.						89.0	68.0	76.0					1																	72748169		2203	4300	6503	SO:0001583	missense	257194	exon1			CAGCATCATGTCC	AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"""Immunoglobulin superfamily / I-set domain containing"""	17302	protein-coding gene	gene with protein product	"""a kindred of IgLON"", ""neurotractin"", ""IgLON family member 4"""	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.9G>C	1.37:g.72748169C>G	ENSP00000350364:p.Met3Ile	295.0	0.0	0		273.0	76.0	0.278388	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	C	7.644	0.681557	0.14907	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.69806	0.85;-0.43	5.14	4.17	0.49024	.	0.093449	0.64402	D	0.000001	T	0.23846	0.0577	N	0.04508	-0.205	0.29795	N	0.832905	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03887	-1.0995	10	0.15499	T	0.54	-14.4855	14.7993	0.69900	0.0:0.8412:0.1588:0.0	.	1;3	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	I	3;1	ENSP00000350364:M3I;ENSP00000413294:M1I	ENSP00000350364:M3I	M	-	3	0	NEGR1	72520757	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.185000	0.42584	2.385000	0.81259	0.561000	0.74099	ATG	.	.	none		0.662	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748148	8748148	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748148A>C	ENST00000276282.6	-	1	3007	c.2421T>G	c.(2419-2421)ctT>ctG	p.L807L		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	807										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CATGAGGCTTAAGCAGCAACC	0.572																																					p.L807L	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T2421G						PASS	.						67.0	66.0	66.0					8																	8748148		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGGCTTAAGCAGC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2421T>G	8.37:g.8748148A>C		82.0	0.0	0		61.0	35.0	0.57377	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.572	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
GLI3	2737	hgsc.bcm.edu	37	7	42007201	42007201	+	Missense_Mutation	SNP	T	T	C	rs62622373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:42007201T>C	ENST00000395925.3	-	14	2508	c.2424A>G	c.(2422-2424)atA>atG	p.I808M	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	808			I -> M (in GCPS; dbSNP:rs62622373). {ECO:0000269|PubMed:10441342}.		anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CACCATTTCCTATGAGAGGAG	0.443									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				T|||	3	0.000599042	0.0	0.0014	5008	,	,		18932	0.0		0.002	False		,,,				2504	0.0				p.I808M		Atlas-SNP	.											.	GLI3	312	.	0			c.A2424G	GRCh37	CM990707	GLI3	M	rs62622373	PASS	.	T	MET/ILE	3,4403	6.2+/-15.9	0,3,2200	197.0	214.0	208.0		2424	4.2	1.0	7	dbSNP_129	208	26,8574	16.6+/-54.9	0,26,4274	yes	missense	GLI3	NM_000168.5	10	0,29,6474	CC,CT,TT		0.3023,0.0681,0.223	possibly-damaging	808/1581	42007201	29,12977	2203	4300	6503	SO:0001583	missense	2737	exon14	Familial Cancer Database	;	ATTTCCTATGAGA		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2424A>G	7.37:g.42007201T>C	ENSP00000379258:p.Ile808Met	226.0	1.0	0.00442478		182.0	132.0	0.725275	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	15.74	2.921346	0.52653	6.81E-4	0.003023	ENSG00000106571	ENST00000395925	D	0.92545	-3.06	5.31	4.15	0.48705	.	0.203242	0.52532	D	0.000066	D	0.90428	0.7003	L	0.57536	1.79	0.80722	D	1	D	0.54397	0.966	P	0.48873	0.593	D	0.87818	0.2636	10	0.46703	T	0.11	.	6.3136	0.21178	0.1403:0.0746:0.0:0.7851	rs62622373	808	P10071	GLI3_HUMAN	M	808	ENSP00000379258:I808M	ENSP00000379258:I808M	I	-	3	3	GLI3	41973726	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.344000	0.44010	0.861000	0.35504	0.533000	0.62120	ATA	T|0.999;C|0.001	0.001	strong		0.443	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
OR52H1	390067	hgsc.bcm.edu	37	11	5566076	5566076	+	Silent	SNP	G	G	A	rs139835065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5566076G>A	ENST00000322653.4	-	1	703	c.678C>T	c.(676-678)taC>taT	p.Y226Y	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATGTGTGCGTAGGAAACAG	0.502													G|||	6	0.00119808	0.0	0.0	5008	,	,		23186	0.001		0.003	False		,,,				2504	0.002				p.Y226Y		Atlas-SNP	.											.	OR52H1	46	.	0			c.C678T						PASS	.	G		0,4402		0,0,2201	120.0	99.0	106.0		678	0.2	0.0	11	dbSNP_134	106	32,8562	22.8+/-68.1	0,32,4265	no	coding-synonymous	OR52H1	NM_001005289.1		0,32,6466	AA,AG,GG		0.3724,0.0,0.2462		226/321	5566076	32,12964	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GTGTGCGTAGGAA	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.678C>T	11.37:g.5566076G>A		108.0	0.0	0		123.0	108.0	0.878049	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.998;A|0.002	0.002	strong		0.502	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H|RFFL_ENST00000584655.1_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase											kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81.0	65.0	70.0		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871		"""RING-type (C3HC4) zinc fingers"""	24821	protein-coding gene	gene with protein product		609735	"""ring finger and FYVE-like domain containing"""			15229288	Standard	NR_037713		Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	109.0	0.0	0		91.0	4.0	0.043956	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178	
CFAP46	54777	hgsc.bcm.edu	37	10	134726272	134726272	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134726272T>C	ENST00000368586.5	-	19	2486	c.2386A>G	c.(2386-2388)Atc>Gtc	p.I796V	TTC40_ENST00000368582.2_Missense_Mutation_p.I796V	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ATCCAGCTGATGATCAGGCCT	0.607																																					p.I796V		Atlas-SNP	.											.	TTC40	100	.	0			c.A2386G						PASS	.																																			SO:0001583	missense	54777	exon19			AGCTGATGATCAG																												ENST00000368586.5:c.2386A>G	10.37:g.134726272T>C	ENSP00000357575:p.Ile796Val	76.0	0.0	0		63.0	34.0	0.539683	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	0.985	-0.695708	0.03279	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.41400	2.98;1.0	4.63	2.34	0.29019	.	.	.	.	.	T	0.27419	0.0673	.	.	.	0.09310	N	0.999994	B	0.29432	0.244	B	0.28638	0.092	T	0.17137	-1.0379	8	0.33141	T	0.24	.	5.6138	0.17420	0.1401:0.0:0.4971:0.3628	.	796	Q5SR76	CJ093_HUMAN	V	796	ENSP00000357575:I796V;ENSP00000357571:I796V	ENSP00000357571:I796V	I	-	1	0	C10orf93	134576262	0.003000	0.15002	0.157000	0.22605	0.022000	0.10575	0.082000	0.14847	0.631000	0.30412	0.443000	0.29094	ATC	.	.	none		0.607	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GRIA1	2890	hgsc.bcm.edu	37	5	153078582	153078582	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153078582A>C	ENST00000285900.5	+	10	1744	c.1401A>C	c.(1399-1401)cgA>cgC	p.R467R	GRIA1_ENST00000340592.5_Silent_p.R467R|GRIA1_ENST00000518142.1_Silent_p.R387R|GRIA1_ENST00000521843.2_Silent_p.R398R|GRIA1_ENST00000518783.1_Silent_p.R477R|GRIA1_ENST00000448073.4_Silent_p.R477R	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	467					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	ACGGAGCCCGAGACCCTGACA	0.562																																					p.R477R		Atlas-SNP	.											GRIA1_ENST00000544403,NS,carcinoma,+1,2	GRIA1	321	2	0			c.A1431C						PASS	.						66.0	63.0	64.0					5																	153078582		2203	4300	6503	SO:0001819	synonymous_variant	2890	exon10			AGCCCGAGACCCT		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1401A>C	5.37:g.153078582A>C		126.0	0.0	0		104.0	25.0	0.240385	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	37	CCDS4322.1																																																																																			.	.	none		0.562	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3		
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067194	46067194	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067194C>T	ENST00000334670.8	+	1	864	c.819C>T	c.(817-819)tgC>tgT	p.C273C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CGGCCTCCTGCGTGTCCCTCC	0.677																																					p.C273C		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,0,1	KRTAP10-11	36	1	0			c.C819T						scavenged	.						41.0	52.0	48.0					21																	46067194		2199	4293	6492	SO:0001819	synonymous_variant	386678	exon1			CTCCTGCGTGTCC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.819C>T	21.37:g.46067194C>T		88.0	1.0	0.0113636		108.0	5.0	0.0462963	NM_198692	A2RRF9	Silent	SNP	ENST00000334670.8	37	CCDS42962.1																																																																																			.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
ORM1	5004	hgsc.bcm.edu	37	9	117087412	117087412	+	Missense_Mutation	SNP	G	G	A	rs1126801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117087412G>A	ENST00000259396.8	+	5	598	c.520G>A	c.(520-522)Gtg>Atg	p.V174M	ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	174			V -> M (in allele ORM1*F2; dbSNP:rs1126801). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9050929}.		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GTCAGATGTCGTGTACACCGA	0.572													-|||	111	0.0221645	0.0408	0.0187	5008	,	,		23206	0.001		0.0328	False		,,,				2504	0.0102				p.V174M		Atlas-SNP	.											.	ORM1	20	.	0			c.G520A						PASS	.	A	MET/VAL	183,4223		0,183,2020	128.0	141.0	136.0		520	-8.5	0.0	9	dbSNP_86	136	191,8409		2,187,4111	no	missense	ORM1	NM_000607.2	21	2,370,6131	AA,AG,GG		2.2209,4.1534,2.8756	benign	174/202	117087412	374,12632	2203	4300	6503	SO:0001583	missense	5004	exon5			GATGTCGTGTACA		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.520G>A	9.37:g.117087412G>A	ENSP00000259396:p.Val174Met	150.0	0.0	0		128.0	67.0	0.523438	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	51	0.023351648351648352	18	0.036585365853658534	8	0.022099447513812154	1	0.0017482517482517483	24	0.0316622691292876	-	3.977	-0.007207	0.07773	0.041534	0.022209	ENSG00000229314	ENST00000259396	T	0.10099	2.91	4.23	-8.47	0.00939	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.390010	0.04077	N	0.308987	T	0.00524	0.0017	N	0.02916	-0.46	0.09310	N	0.999999	P	0.37525	0.598	B	0.18263	0.021	T	0.40905	-0.9538	10	0.12103	T	0.63	-0.9597	2.7473	0.05271	0.3979:0.2169:0.2939:0.0913	rs1126801;rs1803078;rs3182058;rs11552134;rs17412027	174	P02763	A1AG1_HUMAN	M	174	ENSP00000259396:V174M	ENSP00000259396:V174M	V	+	1	0	ORM1	116127233	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.459000	0.02370	-2.210000	0.00738	0.197000	0.17608	GTG	G|0.972;A|0.028	0.028	strong		0.572	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
KIF26A	26153	hgsc.bcm.edu	37	14	104643650	104643650	+	Missense_Mutation	SNP	C	C	T	rs372336742		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104643650C>T	ENST00000423312.2	+	12	4525	c.4525C>T	c.(4525-4527)Cgg>Tgg	p.R1509W	KIF26A_ENST00000315264.7_Missense_Mutation_p.R1370W	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1509					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)	p.R1509W(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		TGGTGGGTCGCGGGCTCTGGG	0.736																																					p.R1509W		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	1	Substitution - Missense(1)	endometrium(1)	c.C4525T						PASS	.	C	TRP/ARG	0,3588		0,0,1794	8.0	11.0	10.0		4525	-0.3	0.0	14		10	1,7821		0,1,3910	no	missense	KIF26A	NM_015656.1	101	0,1,5704	TT,TC,CC		0.0128,0.0,0.0088	probably-damaging	1509/1883	104643650	1,11409	1794	3911	5705	SO:0001583	missense	26153	exon12			GGGTCGCGGGCTC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.4525C>T	14.37:g.104643650C>T	ENSP00000388241:p.Arg1509Trp	62.0	0.0	0		97.0	58.0	0.597938	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	37	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828514	0.32329	0.0	1.28E-4	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.80824	-1.42;-1.42	4.09	-0.307	0.12777	.	.	.	.	.	D	0.82393	0.5027	L	0.47716	1.5	0.09310	N	1	D	0.76494	0.999	P	0.62014	0.897	T	0.71629	-0.4535	9	0.87932	D	0	.	8.6301	0.33915	0.5422:0.3597:0.098:0.0	.	1509	Q9ULI4	KI26A_HUMAN	W	1509;1370	ENSP00000388241:R1509W;ENSP00000325452:R1370W	ENSP00000325452:R1370W	R	+	1	2	KIF26A	103713403	0.964000	0.33143	0.001000	0.08648	0.002000	0.02628	2.357000	0.44125	0.113000	0.18004	0.462000	0.41574	CGG	.	.	weak		0.736	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CCDC33	80125	hgsc.bcm.edu	37	15	74625175	74625175	+	Missense_Mutation	SNP	C	C	A	rs200735867		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:74625175C>A	ENST00000398814.3	+	16	2358	c.1927C>A	c.(1927-1929)Cag>Aag	p.Q643K	CCDC33_ENST00000268082.4_Missense_Mutation_p.Q236K|CCDC33_ENST00000321288.5_Missense_Mutation_p.Q846K|CCDC33_ENST00000558821.1_Missense_Mutation_p.Q236K	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	846										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TCTGCAGCAACAGGCCCTGCC	0.592																																					p.Q643K		Atlas-SNP	.											.	CCDC33	160	.	0			c.C1927A						PASS	.	C	LYS/GLN,LYS/GLN	0,3826		0,0,1913	34.0	41.0	39.0		1927,706	5.0	1.0	15		39	3,8237		0,3,4117	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	53,53	0,3,6030	AA,AC,CC		0.0364,0.0,0.0249	probably-damaging,probably-damaging	643/756,236/368	74625175	3,12063	1913	4120	6033	SO:0001583	missense	80125	exon16			CAGCAACAGGCCC	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1927C>A	15.37:g.74625175C>A	ENSP00000381795:p.Gln643Lys	59.0	0.0	0		66.0	36.0	0.545455	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446257	0.63178	0.0	3.64E-4	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.34472	1.36;2.14;1.81;1.73	5.04	5.04	0.67666	.	0.277119	0.26126	N	0.026198	T	0.52996	0.1769	M	0.73962	2.25	0.30582	N	0.762407	P;B;P;D	0.64830	0.936;0.29;0.69;0.994	P;B;B;P	0.58013	0.554;0.081;0.292;0.831	T	0.55425	-0.8143	10	0.20046	T	0.44	.	15.3817	0.74661	0.0:1.0:0.0:0.0	.	236;236;846;643	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	K	846;643;236;236	ENSP00000325012:Q846K;ENSP00000381795:Q643K;ENSP00000325661:Q236K;ENSP00000268082:Q236K	ENSP00000268082:Q236K	Q	+	1	0	CCDC33	72412228	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.670000	0.61583	2.354000	0.79902	0.543000	0.68304	CAG	.	.	weak		0.592	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926536	88926536	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926536T>C	ENST00000303236.3	-	1	558	c.257A>G	c.(256-258)gAg>gGg	p.E86G	AC062029.1_ENST00000606164.1_RNA|AC062029.1_ENST00000453008.2_RNA|EIF2AK3_ENST00000419748.1_5'Flank	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	86					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						ACCCCGAGGCTCCTGCTCTCc	0.731																																					p.E86G	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A257G						PASS	.						11.0	14.0	13.0					2																	88926536		1978	4004	5982	SO:0001583	missense	9451	exon1			CGAGGCTCCTGCT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.257A>G	2.37:g.88926536T>C	ENSP00000307235:p.Glu86Gly	44.0	0.0	0		55.0	19.0	0.345455	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185631	0.21870	.	.	ENSG00000172071	ENST00000303236	T	0.73258	-0.73	3.67	3.67	0.42095	.	0.229807	0.30011	N	0.010633	T	0.57932	0.2087	L	0.44542	1.39	0.20074	N	0.999937	B	0.31318	0.319	B	0.29440	0.102	T	0.48163	-0.9059	10	0.29301	T	0.29	-6.3314	8.8508	0.35199	0.0:0.0:0.0:1.0	.	86	Q9NZJ5	E2AK3_HUMAN	G	86	ENSP00000307235:E86G	ENSP00000307235:E86G	E	-	2	0	EIF2AK3	88707651	0.289000	0.24334	0.051000	0.19133	0.018000	0.09664	3.014000	0.49590	1.651000	0.50673	0.459000	0.35465	GAG	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
EPHA3	2042	hgsc.bcm.edu	37	3	89391215	89391215	+	Silent	SNP	G	G	A	rs56112995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:89391215G>A	ENST00000336596.2	+	5	1506	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	EPHA3_ENST00000494014.1_Silent_p.A427A|EPHA3_ENST00000452448.2_Silent_p.A427A	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	427	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AGTTTGCTGCGGTCAGCATCA	0.458										TSP Lung(6;0.00050)			G|||	16	0.00319489	0.0	0.0	5008	,	,		18214	0.0		0.008	False		,,,				2504	0.0082				p.A427A		Atlas-SNP	.											EPHA3_ENST00000452448,caecum,carcinoma,0,4	EPHA3	501	4	0			c.G1281A						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	65.0	54.0	57.0		1281,1281	-11.1	0.5	3	dbSNP_129	57	55,8545	33.8+/-87.4	1,53,4246	no	coding-synonymous,coding-synonymous	EPHA3	NM_005233.5,NM_182644.2	,	1,56,6446	AA,AG,GG		0.6395,0.0681,0.4459	,	427/984,427/540	89391215	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon5			TGCTGCGGTCAGC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1281G>A	3.37:g.89391215G>A		81.0	0.0	0		72.0	31.0	0.430556	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230348	23230348	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230348C>G	ENST00000526893.1	+	1	389	c.115C>G	c.(115-117)Ctg>Gtg	p.L39V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L39V|IGLL5_ENST00000532223.2_Missense_Mutation_p.L39V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115G						PASS	.																																			SO:0001583	missense	100423062	exon1			GGCCTGCTGCGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.115C>G	22.37:g.23230348C>G	ENSP00000431254:p.Leu39Val	149.0	0.0	0		143.0	28.0	0.195804	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410199	0.25465	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00717	5.79;5.8	3.92	-2.91	0.05631	.	.	.	.	.	T	0.00608	0.0020	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.13407	0.009	T	0.47509	-0.9112	9	0.51188	T	0.08	.	0.7315	0.00958	0.1663:0.3182:0.1632:0.3524	.	39	B9A064	IGLL5_HUMAN	V	39	ENSP00000436353:L39V;ENSP00000431254:L39V	ENSP00000431254:L39V	L	+	1	2	IGLL5	21560348	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.230000	0.09083	-0.436000	0.07254	0.643000	0.83706	CTG	.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
COL28A1	340267	hgsc.bcm.edu	37	7	7514293	7514293	+	Missense_Mutation	SNP	T	T	C	rs199518824		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7514293T>C	ENST00000399429.3	-	15	1381	c.1241A>G	c.(1240-1242)aAa>aGa	p.K414R		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	414					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTCAGAACCTTTTTCACCCTG	0.393																																					p.K414R		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1241G						PASS	.	T	ARG/LYS	0,3672		0,0,1836	121.0	117.0	118.0		1241	4.7	1.0	7		118	4,8194		0,4,4095	yes	missense	COL28A1	NM_001037763.2	26	0,4,5931	CC,CT,TT		0.0488,0.0,0.0337	possibly-damaging	414/1126	7514293	4,11866	1836	4099	5935	SO:0001583	missense	340267	exon15			GAACCTTTTTCAC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1241A>G	7.37:g.7514293T>C	ENSP00000382356:p.Lys414Arg	81.0	0.0	0		81.0	63.0	0.777778	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022978	0.35701	0.0	4.88E-4	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.90004	-2.6	4.7	4.7	0.59300	.	0.106321	0.35805	U	0.002969	D	0.88100	0.6346	N	0.25332	0.735	0.32928	D	0.516805	D;D	0.64830	0.994;0.993	D;D	0.72982	0.979;0.968	D	0.84976	0.0885	10	0.10902	T	0.67	-7.2148	10.7486	0.46196	0.0:0.0:0.0:1.0	.	414;414	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	R	414	ENSP00000382356:K414R	ENSP00000382347:K414R	K	-	2	0	COL28A1	7480818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.768000	0.47645	2.108000	0.64289	0.528000	0.53228	AAA	.	.	weak		0.393	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
MED24	9862	hgsc.bcm.edu	37	17	38189328	38189328	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38189328G>A	ENST00000394128.2	-	8	884	c.803C>T	c.(802-804)aCg>aTg	p.T268M	MED24_ENST00000394126.1_Missense_Mutation_p.T293M|MED24_ENST00000501516.3_Missense_Mutation_p.T287M|MED24_ENST00000479829.1_5'Flank|MED24_ENST00000394127.2_Missense_Mutation_p.T255M|MED24_ENST00000356271.3_Missense_Mutation_p.T255M	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	268					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CTTCACCATCGTCAGCTGCTC	0.637																																					p.T268M		Atlas-SNP	.											.	MED24	89	.	0			c.C803T						PASS	.						51.0	43.0	46.0					17																	38189328		2203	4300	6503	SO:0001583	missense	9862	exon8			ACCATCGTCAGCT	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.803C>T	17.37:g.38189328G>A	ENSP00000377686:p.Thr268Met	75.0	0.0	0		48.0	10.0	0.208333	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	9.996	1.232071	0.22626	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000431269;ENST00000428757	T;T;T;T	0.48836	0.8;1.02;1.02;1.02	5.58	3.38	0.38709	Mediator complex, subunit Med24, N-terminal (1);	0.164448	0.64402	N	0.000003	T	0.14098	0.0341	N	0.00436	-1.5	0.25784	N	0.984692	B;B;B;B;B;B;B;B	0.13594	0.0;0.001;0.0;0.001;0.0;0.0;0.0;0.008	B;B;B;B;B;B;B;B	0.08055	0.001;0.003;0.0;0.001;0.001;0.0;0.001;0.001	T	0.22487	-1.0215	10	0.22109	T	0.4	-22.9865	8.1246	0.30990	0.8066:0.0:0.0711:0.1223	.	255;218;197;218;178;255;268;210	B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;MED24_HUMAN;.	M	268;268;268;218;255;210;242;178;287	ENSP00000377684:T268M;ENSP00000377686:T268M;ENSP00000443344:T218M;ENSP00000377685:T255M	ENSP00000348610:T268M	T	-	2	0	MED24	35442854	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	5.178000	0.65037	0.416000	0.25844	-1.099000	0.02127	ACG	.	.	none		0.637	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
PXDNL	137902	hgsc.bcm.edu	37	8	52321238	52321238	+	Silent	SNP	G	G	A	rs141024159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52321238G>A	ENST00000356297.4	-	17	3046	c.2946C>T	c.(2944-2946)gcC>gcT	p.A982A	PXDNL_ENST00000543296.1_Silent_p.A982A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	982					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				ACAGCTCCGTGGCCATCCTGT	0.647													G|||	29	0.00579073	0.0008	0.0058	5008	,	,		16344	0.0		0.0219	False		,,,				2504	0.002				p.A982A		Atlas-SNP	.											.	PXDNL	414	.	0			c.C2946T						PASS	.	G		9,4085		0,9,2038	17.0	20.0	19.0		2946	-2.5	0.0	8	dbSNP_134	19	127,8265		1,125,4070	no	coding-synonymous	PXDNL	NM_144651.4		1,134,6108	AA,AG,GG		1.5133,0.2198,1.0892		982/1464	52321238	136,12350	2047	4196	6243	SO:0001819	synonymous_variant	137902	exon17			CTCCGTGGCCATC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2946C>T	8.37:g.52321238G>A		75.0	0.0	0		67.0	46.0	0.686567	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	0.093	-1.164305	0.01673	0.002198	0.015133	ENSG00000147485	ENST00000522933	.	.	.	4.47	-2.51	0.06365	.	.	.	.	.	T	0.16085	0.0387	.	.	.	0.52501	D	0.99995	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	.	0.455	0.00507	0.3332:0.127:0.2814:0.2584	.	.	.	.	L	101	.	.	P	-	2	0	PXDNL	52483791	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.056000	0.03489	-1.110000	0.02992	-0.175000	0.13238	CCA	G|0.989;A|0.011	0.011	strong		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
NPHS1	4868	hgsc.bcm.edu	37	19	36340009	36340009	+	Missense_Mutation	SNP	G	G	A	rs113825926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36340009G>A	ENST00000378910.5	-	8	880	c.881C>T	c.(880-882)aCc>aTc	p.T294I	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Missense_Mutation_p.T294I	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	294	Ig-like C2-type 3.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CACCGCCTGGGTGTGCTCTGT	0.677													G|||	18	0.00359425	0.0008	0.0029	5008	,	,		18085	0.0		0.0109	False		,,,				2504	0.0041				p.T294I		Atlas-SNP	.											.	NPHS1	165	.	0			c.C881T	GRCh37	CM044680	NPHS1	M	rs113825926	PASS	.	G	ILE/THR	17,4389	23.3+/-48.9	0,17,2186	45.0	42.0	43.0		881	-1.0	0.0	19	dbSNP_132	43	102,8496	56.4+/-117.6	1,100,4198	yes	missense	NPHS1	NM_004646.3	89	1,117,6384	AA,AG,GG		1.1863,0.3858,0.9151	benign	294/1242	36340009	119,12885	2203	4299	6502	SO:0001583	missense	4868	exon8			GCCTGGGTGTGCT		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.881C>T	19.37:g.36340009G>A	ENSP00000368190:p.Thr294Ile	58.0	0.0	0		48.0	19.0	0.395833	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	11.76	1.734293	0.30774	0.003858	0.011863	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.76578	-1.03;-1.03	5.17	-1.04	0.10068	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.458410	0.04145	N	0.320188	T	0.54191	0.1843	N	0.21583	0.68	0.09310	N	1	B	0.24092	0.097	B	0.27076	0.076	T	0.43702	-0.9375	10	0.24483	T	0.36	-0.2874	3.5633	0.07890	0.373:0.0:0.4437:0.1832	.	294	O60500	NPHN_HUMAN	I	294	ENSP00000368190:T294I;ENSP00000343634:T294I	ENSP00000343634:T294I	T	-	2	0	NPHS1	41031849	0.000000	0.05858	0.011000	0.14972	0.862000	0.49288	0.089000	0.15002	0.224000	0.20940	0.467000	0.42956	ACC	G|0.992;A|0.008	0.008	strong		0.677	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769334	140769334	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140769334G>C	ENST00000519479.1	+	1	1883	c.1883G>C	c.(1882-1884)cGt>cCt	p.R628P	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	628	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCACAGCGCGTGCCTTAGGC	0.692																																					p.R628P		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G1883C						PASS	.						36.0	41.0	39.0					5																	140769334		2128	4243	6371	SO:0001583	missense	8641	exon1			CAGCGCGTGCCTT	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1883G>C	5.37:g.140769334G>C	ENSP00000428288:p.Arg628Pro	38.0	0.0	0		36.0	11.0	0.305556	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	15.68	2.906359	0.52333	.	.	ENSG00000253953	ENST00000519479	T	0.54279	0.58	5.05	5.05	0.67936	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.78528	0.4297	H	0.94345	3.525	0.28002	N	0.935256	D;D	0.56521	0.97;0.976	P;P	0.57911	0.793;0.829	T	0.76838	-0.2811	9	0.87932	D	0	.	18.4161	0.90571	0.0:0.0:1.0:0.0	.	628;628	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	P	628	ENSP00000428288:R628P	ENSP00000428288:R628P	R	+	2	0	PCDHGB4	140749518	0.784000	0.28713	0.057000	0.19452	0.031000	0.12232	4.360000	0.59455	2.503000	0.84419	0.563000	0.77884	CGT	.	.	none		0.692	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
MAP3K6	9064	hgsc.bcm.edu	37	1	27686373	27686373	+	Silent	SNP	G	G	A	rs138787990		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:27686373G>A	ENST00000493901.1	-	18	2534	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	MAP3K6_ENST00000357582.2_Silent_p.N765N|MAP3K6_ENST00000374040.3_Silent_p.N757N	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCACGATGTGGTTGTCGTGCA	0.612																																					p.N765N		Atlas-SNP	.											.	MAP3K6	134	.	0			c.C2295T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115.0	105.0	108.0		2295	2.2	1.0	1	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K6	NM_004672.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		765/1289	27686373	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9064	exon17			GATGTGGTTGTCG	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2295C>T	1.37:g.27686373G>A		176.0	0.0	0		183.0	89.0	0.486339	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Silent	SNP	ENST00000493901.1	37	CCDS299.1	.	.	.	.	.	.	.	.	.	.	G	3.628	-0.076203	0.07184	2.27E-4	1.16E-4	ENSG00000142733	ENST00000472410	.	.	.	5.03	2.16	0.27623	.	.	.	.	.	T	0.58004	0.2092	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50625	-0.8806	4	.	.	.	.	9.1199	0.36780	0.243:0.0:0.757:0.0	.	.	.	.	I	489	.	.	T	-	2	0	MAP3K6	27558960	1.000000	0.71417	0.989000	0.46669	0.380000	0.30137	1.262000	0.32992	0.309000	0.22966	0.561000	0.74099	ACC	G|1.000;A|0.000	0.000	weak		0.612	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
CACNA1S	779	hgsc.bcm.edu	37	1	201058530	201058530	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201058530G>A	ENST00000362061.3	-	6	982	c.756C>T	c.(754-756)cgC>cgT	p.R252R	CACNA1S_ENST00000367338.3_Silent_p.R252R	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	252					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGTGCACCGGCGCCCTGAGC	0.617																																					p.R252R		Atlas-SNP	.											CACNA1S,colon,carcinoma,-2,1	CACNA1S	249	1	0			c.C756T						PASS	.						50.0	45.0	47.0					1																	201058530		2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACCGGCGCCCT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.756C>T	1.37:g.201058530G>A		133.0	0.0	0		117.0	72.0	0.615385	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			.	.	none		0.617	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410417	105410417	+	Silent	SNP	G	G	A	rs200284292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105410417G>A	ENST00000333244.5	-	7	11490	c.11371C>T	c.(11371-11373)Ctg>Ttg	p.L3791L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3791						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTGTCGGCCAGGGACAGGTCC	0.582													.|||	177	0.0353435	0.053	0.0231	5008	,	,		20409	0.0417		0.004	False		,,,				2504	0.046				p.L3791L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C11371T						PASS	.						216.0	217.0	217.0					14																	105410417		1998	4162	6160	SO:0001819	synonymous_variant	113146	exon7			CGGCCAGGGACAG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.11371C>T	14.37:g.105410417G>A		140.0	0.0	0		117.0	9.0	0.0769231	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
EAF1	85403	hgsc.bcm.edu	37	3	15477861	15477861	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477861A>G	ENST00000396842.2	+	5	964	c.539A>G	c.(538-540)gAa>gGa	p.E180G	EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000595975.1_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000593876.1_RNA|EAF1_ENST00000432764.2_Missense_Mutation_p.E79G	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						CTGAGGGCTGAAGTTGACATT	0.473																																					p.E180G		Atlas-SNP	.											.	EAF1	16	.	0			c.A539G						PASS	.						45.0	46.0	45.0					3																	15477861		2203	4300	6503	SO:0001583	missense	85403	exon5			GGGCTGAAGTTGA	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.539A>G	3.37:g.15477861A>G	ENSP00000380054:p.Glu180Gly	151.0	0.0	0		161.0	32.0	0.198758	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.523059	0.85600	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.78848	0.4348	M	0.78637	2.42	0.80722	D	1	D;D	0.71674	0.989;0.998	D;D	0.70487	0.969;0.968	T	0.81678	-0.0824	9	0.72032	D	0.01	-27.7472	14.8502	0.70292	1.0:0.0:0.0:0.0	.	79;180	B4E3F5;Q96JC9	.;EAF1_HUMAN	G	180;79	.	ENSP00000380054:E180G	E	+	2	0	EAF1	15452865	1.000000	0.71417	0.898000	0.35279	0.924000	0.55760	8.962000	0.93254	2.150000	0.67090	0.397000	0.26171	GAA	.	.	none		0.473	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
MUC5B	727897	hgsc.bcm.edu	37	11	1270691	1270691	+	Missense_Mutation	SNP	G	G	C	rs201822010		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270691G>C	ENST00000529681.1	+	31	12639	c.12581G>C	c.(12580-12582)aGc>aCc	p.S4194T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S4197T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4194	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GTGGAATGCAGCCTGGACTTT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		18430	0.0		0.001	False		,,,				2504	0.0				p.S4194T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12581C						PASS	.	G	THR/SER	1,3771		0,1,1885	35.0	44.0	41.0		12581	-0.3	0.0	11		41	14,8120		0,14,4053	no	missense	MUC5B	NM_002458.2	58	0,15,5938	CC,CG,GG		0.1721,0.0265,0.126	possibly-damaging	4194/5763	1270691	15,11891	1886	4067	5953	SO:0001583	missense	727897	exon31			AATGCAGCCTGGA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.12581G>C	11.37:g.1270691G>C	ENSP00000436812:p.Ser4194Thr	882.0	1.0	0.00113379		1023.0	155.0	0.151515	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	5.081	0.200521	0.09652	2.65E-4	0.001721	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.18810	2.19;2.19	3.69	-0.352	0.12598	.	.	.	.	.	T	0.23330	0.0564	M	0.74467	2.265	0.09310	N	1	P;P	0.42123	0.771;0.771	B;B	0.38562	0.216;0.276	T	0.12268	-1.0554	9	0.87932	D	0	.	8.4625	0.32936	0.6517:0.0:0.3483:0.0	.	4667;4197	A7Y9J9;E9PBJ0	.;.	T	4194;4197;4138;4044	ENSP00000436812:S4194T;ENSP00000415793:S4197T	ENSP00000343037:S4138T	S	+	2	0	MUC5B	1227267	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.695000	0.01913	-0.269000	0.09298	-0.515000	0.04445	AGC	G|0.996;C|0.004	0.004	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
DNAH5	1767	hgsc.bcm.edu	37	5	13716796	13716796	+	Missense_Mutation	SNP	C	C	T	rs138045391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716796C>T	ENST00000265104.4	-	74	12813	c.12709G>A	c.(12709-12711)Gtc>Atc	p.V4237I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4237					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTCCAGGAGACACCCTGGGAA	0.403									Kartagener syndrome				C|||	2	0.000399361	0.0015	0.0	5008	,	,		16991	0.0		0.0	False		,,,				2504	0.0				p.V4237I		Atlas-SNP	.											.	DNAH5	868	.	0			c.G12709A						PASS	.																																			SO:0001583	missense	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGAGACACCCTG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12709G>A	5.37:g.13716796C>T	ENSP00000265104:p.Val4237Ile	88.0	0.0	0		103.0	43.0	0.417476	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	7.699	0.692759	0.15039	.	.	ENSG00000039139	ENST00000265104	T	0.09538	2.97	5.53	4.67	0.58626	Dynein heavy chain (1);	0.128288	0.51477	N	0.000093	T	0.08537	0.0212	N	0.25426	0.745	0.58432	D	0.999996	B	0.09022	0.002	B	0.23574	0.047	T	0.23619	-1.0183	10	0.20046	T	0.44	.	11.2865	0.49224	0.0:0.8422:0.0:0.1578	.	4237	Q8TE73	DYH5_HUMAN	I	4237	ENSP00000265104:V4237I	ENSP00000265104:V4237I	V	-	1	0	DNAH5	13769796	0.996000	0.38824	0.686000	0.30086	0.589000	0.36550	3.359000	0.52292	1.348000	0.45733	-0.157000	0.13467	GTC	A|0.001;C|0.999	.	weak		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89.0	89.0	89.0		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.1122T>C	19.37:g.20044886T>C		56.0	0.0	0		36.0	36.0	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
VCX3A	51481	hgsc.bcm.edu	37	X	6451834	6451834	+	Silent	SNP	C	C	T	rs146638597		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:6451834C>T	ENST00000381089.3	-	3	819	c.513G>A	c.(511-513)gaG>gaA	p.E171E	VCX3A_ENST00000398729.1_Silent_p.E151E	NM_016379.3	NP_057463.2	Q9NNX9	VCX3_HUMAN	variable charge, X-linked 3A	171	8 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				brain development (GO:0007420)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|lung(2)|pancreas(1)	4						TCAGTGGTTCCTCCACCTGGC	0.587																																					p.E171E		Atlas-SNP	.											.	VCX3A	17	.	0			c.G513A						PASS	.						230.0	203.0	212.0					X																	6451834		2203	4296	6499	SO:0001819	synonymous_variant	51481	exon3			TGGTTCCTCCACC	AF159128	CCDS35199.1	Xp22.31	2008-02-05	2005-01-11	2005-01-12	ENSG00000169059	ENSG00000169059			18159	protein-coding gene	gene with protein product		300533	"""variable charge, X-linked 3"""	VCX3		10607842	Standard	NM_016379		Approved	VCX-8r, VCX-8R, VCX-A	uc004crs.3	Q9NNX9	OTTHUMG00000021097	ENST00000381089.3:c.513G>A	X.37:g.6451834C>T		1050.0	0.0	0		927.0	82.0	0.0884574	NM_016379	Q9P0H4	Silent	SNP	ENST00000381089.3	37	CCDS35199.1																																																																																			.	.	weak		0.587	VCX3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055679.1	NM_016379	
NUP210	23225	hgsc.bcm.edu	37	3	13364836	13364836	+	Missense_Mutation	SNP	C	C	T	rs199752879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:13364836C>T	ENST00000254508.5	-	34	4823	c.4741G>A	c.(4741-4743)Gtg>Atg	p.V1581M		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1581					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)		p.V1581M(1)		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)					CTGTCTCCCACGGCAACAATC	0.582																																					p.V1581M		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	1	1	Substitution - Missense(1)	liver(1)	c.G4741A						PASS	.	C	MET/VAL	0,4406		0,0,2203	138.0	139.0	139.0		4741	-4.2	0.0	3		139	5,8595	4.3+/-15.6	0,5,4295	yes	missense	NUP210	NM_024923.2	21	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	possibly-damaging	1581/1888	13364836	5,13001	2203	4300	6503	SO:0001583	missense	23225	exon34			CTCCCACGGCAAC	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.4741G>A	3.37:g.13364836C>T	ENSP00000254508:p.Val1581Met	78.0	0.0	0		64.0	23.0	0.359375	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674605	0.29693	0.0	5.81E-4	ENSG00000132182	ENST00000254508	T	0.04970	3.52	5.54	-4.17	0.03857	.	0.660669	0.15319	N	0.268660	T	0.04182	0.0116	L	0.46157	1.445	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.36212	-0.9757	10	0.48119	T	0.1	-10.586	0.6247	0.00784	0.3136:0.1703:0.125:0.3911	.	1581	Q8TEM1	PO210_HUMAN	M	1581	ENSP00000254508:V1581M	ENSP00000254508:V1581M	V	-	1	0	NUP210	13339836	0.028000	0.19301	0.020000	0.16555	0.749000	0.42624	-0.160000	0.10041	-0.685000	0.05177	-0.137000	0.14449	GTG	.	.	weak		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
SCFD2	152579	hgsc.bcm.edu	37	4	54218834	54218834	+	Missense_Mutation	SNP	G	G	A	rs147606542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:54218834G>A	ENST00000401642.3	-	2	1071	c.938C>T	c.(937-939)gCg>gTg	p.A313V	SCFD2_ENST00000388940.4_Missense_Mutation_p.A313V	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	313					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.A313V(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TGCAGTGAGCGCTATCATGTT	0.428													G|||	64	0.0127796	0.0008	0.0	5008	,	,		19473	0.0		0.001	False		,,,				2504	0.0634				p.A313V		Atlas-SNP	.											SCFD2,NS,NS,0,1	SCFD2	78	1	1	Substitution - Missense(1)	pancreas(1)	c.C938T						scavenged	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	182.0	157.0	166.0		938	4.2	0.9	4	dbSNP_134	166	21,8579	16.0+/-53.3	0,21,4279	yes	missense	SCFD2	NM_152540.3	64	0,23,6480	AA,AG,GG		0.2442,0.0454,0.1768	benign	313/685	54218834	23,12983	2203	4300	6503	SO:0001583	missense	152579	exon2			GTGAGCGCTATCA	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.938C>T	4.37:g.54218834G>A	ENSP00000384182:p.Ala313Val	207.0	1.0	0.00483092		196.0	90.0	0.459184	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	9.740	1.164726	0.21538	4.54E-4	0.002442	ENSG00000184178	ENST00000401642;ENST00000388940;ENST00000503450	D;D	0.85629	-2.01;-2.01	5.33	4.15	0.48705	.	0.060828	0.64402	D	0.000005	T	0.70081	0.3183	N	0.08118	0	0.21553	N	0.999646	B;B	0.13594	0.008;0.005	B;B	0.12837	0.008;0.003	T	0.56890	-0.7904	10	0.30078	T	0.28	.	11.6001	0.50997	0.0:0.0:0.1497:0.8503	.	313;313	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	V	313;313;6	ENSP00000384182:A313V;ENSP00000373592:A313V	ENSP00000373592:A313V	A	-	2	0	SCFD2	53913591	0.999000	0.42202	0.921000	0.36526	0.006000	0.05464	3.548000	0.53670	0.849000	0.35215	-0.357000	0.07601	GCG	G|0.998;A|0.002	0.002	strong		0.428	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
DNAH14	127602	hgsc.bcm.edu	37	1	225237950	225237950	+	Missense_Mutation	SNP	A	A	G	rs78320839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:225237950A>G	ENST00000445597.2	+	12	1864	c.1864A>G	c.(1864-1866)Atc>Gtc	p.I622V	DNAH14_ENST00000439375.2_Missense_Mutation_p.I651V|DNAH14_ENST00000430092.1_Missense_Mutation_p.I651V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	622					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CCAGCTGTCTATCTTCATTGA	0.343													A|||	43	0.00858626	0.0008	0.0101	5008	,	,		16907	0.0129		0.007	False		,,,				2504	0.0153				p.I651V		Atlas-SNP	.											.	DNAH14	300	.	0			c.A1951G						PASS	.	A	VAL/ILE	2,1382		0,2,690	169.0	139.0	148.0		1951	-4.1	0.0	1	dbSNP_131	148	58,3124		1,56,1534	yes	missense	DNAH14	NM_001373.1	29	1,58,2224	GG,GA,AA		1.8228,0.1445,1.3141	benign	651/4516	225237950	60,4506	692	1591	2283	SO:0001583	missense	127602	exon16			CTGTCTATCTTCA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.1864A>G	1.37:g.225237950A>G	ENSP00000409472:p.Ile622Val	172.0	0.0	0		181.0	80.0	0.441989	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		20	0.009157509157509158	1	0.0020325203252032522	6	0.016574585635359115	9	0.015734265734265736	4	0.005277044854881266	A	14.53	2.563703	0.45694	0.001445	0.018228	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.27890	2.61;1.64;1.64	5.49	-4.13	0.03904	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.09310	N	0.999998	B	0.10296	0.003	B	0.12156	0.007	T	0.32134	-0.9918	9	0.21014	T	0.42	.	7.8316	0.29347	0.4385:0.1253:0.4362:0.0	.	651	Q0VDD8-4	.	V	622;651;651	ENSP00000409472:I622V;ENSP00000414402:I651V;ENSP00000392061:I651V	ENSP00000414402:I651V	I	+	1	0	DNAH14	223304573	0.000000	0.05858	0.005000	0.12908	0.439000	0.31926	-1.628000	0.02031	-0.704000	0.05042	0.338000	0.21704	ATC	A|0.991;G|0.009	0.009	strong		0.343	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PAPPA	5069	hgsc.bcm.edu	37	9	119028233	119028233	+	Missense_Mutation	SNP	A	A	C	rs117124330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:119028233A>C	ENST00000328252.3	+	8	3199	c.2830A>C	c.(2830-2832)Agt>Cgt	p.S944R	PAPPA_ENST00000534838.1_5'UTR	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	944			S -> R (in dbSNP:rs117124330). {ECO:0000269|PubMed:7508748, ECO:0000269|PubMed:8620868}.		cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CATCCATGGAAGTGGGTACTG	0.438													A|||	48	0.00958466	0.0	0.0159	5008	,	,		19890	0.0		0.0169	False		,,,				2504	0.0204				p.S944R		Atlas-SNP	.											.	PAPPA	243	.	0			c.A2830C						PASS	.	A	ARG/SER	17,4389	25.3+/-52.1	0,17,2186	103.0	94.0	97.0		2830	2.9	1.0	9	dbSNP_132	97	154,8446	73.8+/-136.5	1,152,4147	yes	missense	PAPPA	NM_002581.3	110	1,169,6333	CC,CA,AA		1.7907,0.3858,1.3148	possibly-damaging	944/1628	119028233	171,12835	2203	4300	6503	SO:0001583	missense	5069	exon8			CATGGAAGTGGGT		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2830A>C	9.37:g.119028233A>C	ENSP00000330658:p.Ser944Arg	81.0	0.0	0		68.0	39.0	0.573529	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	A	12.44	1.939319	0.34189	0.003858	0.017907	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.42513	0.97	5.28	2.88	0.33553	.	0.277336	0.47093	D	0.000259	T	0.29882	0.0747	L	0.45698	1.435	0.80722	D	1	D;P	0.59357	0.985;0.918	P;P	0.56916	0.809;0.475	T	0.06127	-1.0844	10	0.30078	T	0.28	-1.3511	8.9684	0.35890	0.8425:0.0:0.1575:0.0	.	388;944	E7EMD3;Q13219	.;PAPP1_HUMAN	R	944;388	ENSP00000330658:S944R	ENSP00000330658:S944R	S	+	1	0	PAPPA	118068054	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	1.669000	0.37492	0.306000	0.22856	0.455000	0.32223	AGT	A|0.988;C|0.012	0.012	strong		0.438	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
MUC4	4585	hgsc.bcm.edu	37	3	195510073	195510073	+	Missense_Mutation	SNP	G	G	A	rs200663432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510073G>A	ENST00000463781.3	-	2	8837	c.8378C>T	c.(8377-8379)gCa>gTa	p.A2793V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2793V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGG	0.587													.|||	15	0.00299521	0.0113	0.0	5008	,	,		6295	0.0		0.0	False		,,,				2504	0.0				p.A2793V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C8378T						PASS	.						57.0	33.0	41.0					3																	195510073		689	1521	2210	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8378C>T	3.37:g.195510073G>A	ENSP00000417498:p.Ala2793Val	55.0	0.0	0		92.0	14.0	0.152174	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	2.540	-0.306588	0.05458	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.54	0.918	-0.419	0.12340	.	.	.	.	.	T	0.12689	0.0308	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30090	-0.9990	8	.	.	.	.	5.3055	0.15801	0.579:0.0:0.421:0.0	.	2665	E7ESK3	.	V	2793	ENSP00000417498:A2793V;ENSP00000420243:A2793V	.	A	-	2	0	MUC4	196994852	0.000000	0.05858	0.034000	0.17996	0.015000	0.08874	0.293000	0.19029	-1.755000	0.01320	-1.973000	0.00462	GCA	G|0.756;A|0.244	0.244	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NAGLU	4669	hgsc.bcm.edu	37	17	40696122	40696122	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696122A>C	ENST00000225927.2	+	6	2199	c.2098A>C	c.(2098-2100)Aat>Cat	p.N700H	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	700					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GTTTGACAAAAATGTCTTCCA	0.577																																					p.N700H		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2098C						PASS	.						50.0	47.0	48.0					17																	40696122		2203	4300	6503	SO:0001583	missense	4669	exon6			GACAAAAATGTCT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.2098A>C	17.37:g.40696122A>C	ENSP00000225927:p.Asn700His	58.0	0.0	0		54.0	18.0	0.333333	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720488	0.30503	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98649	-5.05	5.03	1.08	0.20341	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.878057	0.10023	N	0.725727	D	0.95868	0.8655	L	0.42245	1.32	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	D	0.90986	0.4831	10	0.52906	T	0.07	0.2904	3.5341	0.07788	0.3663:0.2592:0.3745:0.0	.	700	P54802	ANAG_HUMAN	H	700;376	ENSP00000225927:N700H	ENSP00000225927:N700H	N	+	1	0	NAGLU	37949648	0.991000	0.36638	0.010000	0.14722	0.865000	0.49528	3.225000	0.51246	0.354000	0.24105	0.454000	0.30748	AAT	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
GABRB3	2562	hgsc.bcm.edu	37	15	26825545	26825545	+	Silent	SNP	G	G	A	rs75965657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26825545G>A	ENST00000311550.5	-	6	714	c.603C>T	c.(601-603)acC>acT	p.T201T	GABRB3_ENST00000545868.1_Silent_p.T116T|GABRB3_ENST00000299267.4_Silent_p.T201T|GABRB3_ENST00000541819.2_Silent_p.T257T|GABRB3_ENST00000400188.3_Silent_p.T130T	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	201					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTCCACTCCGGTAACAGCCT	0.537													G|||	90	0.0179712	0.0643	0.0058	5008	,	,		18278	0.0		0.001	False		,,,				2504	0.0				p.T201T		Atlas-SNP	.											.	GABRB3	338	.	0			c.C603T						PASS	.	G	,,,	275,4131	154.8+/-188.1	7,261,1935	122.0	105.0	111.0		603,348,390,603	-10.2	0.0	15	dbSNP_131	111	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	7,279,6217	AA,AG,GG		0.2093,6.2415,2.2528	,,,	201/474,116/389,130/403,201/474	26825545	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon6			CACTCCGGTAACA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.603C>T	15.37:g.26825545G>A		92.0	0.0	0		90.0	43.0	0.477778	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.982;A|0.018	0.018	strong		0.537	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
ZNF461	92283	hgsc.bcm.edu	37	19	37130419	37130419	+	Silent	SNP	G	G	A	rs61746298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37130419G>A	ENST00000588268.1	-	6	1055	c.828C>T	c.(826-828)aaC>aaT	p.N276N	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Silent_p.N253N	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TCCCACATTCGTTACATTCAT	0.368													G|||	73	0.0145767	0.0	0.0317	5008	,	,		20302	0.001		0.0398	False		,,,				2504	0.0102				p.N276N		Atlas-SNP	.											.	ZNF461	73	.	0			c.C828T						PASS	.	G		18,4354	22.3+/-47.3	1,16,2169	56.0	60.0	59.0		828	1.0	1.0	19	dbSNP_129	59	265,8305	97.5+/-159.1	5,255,4025	no	coding-synonymous	ZNF461	NM_153257.2		6,271,6194	AA,AG,GG		3.0922,0.4117,2.1867		276/564	37130419	283,12659	2186	4285	6471	SO:0001819	synonymous_variant	92283	exon6			ACATTCGTTACAT	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.828C>T	19.37:g.37130419G>A		99.0	0.0	0		81.0	39.0	0.481481	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	37	CCDS54257.1																																																																																			G|0.980;A|0.020	0.020	strong		0.368	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
SLC37A2	219855	hgsc.bcm.edu	37	11	124953735	124953735	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124953735G>A	ENST00000403796.2	+	11	1302	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E	SLC37A2_ENST00000298280.5_Missense_Mutation_p.G334E|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G334E|SLC37A2_ENST00000525837.1_3'UTR|SLC37A2_ENST00000407458.1_Missense_Mutation_p.G334E	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	334					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AAGGAGGCTGGGGACCTGTCT	0.557																																					p.G334E	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G1001A						PASS	.						150.0	116.0	127.0					11																	124953735		2201	4299	6500	SO:0001583	missense	219855	exon11			AGGCTGGGGACCT	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.1001G>A	11.37:g.124953735G>A	ENSP00000384407:p.Gly334Glu	127.0	0.0	0		98.0	4.0	0.0408163	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818168	0.90790	.	.	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.66099	0.02;0.02;-0.19;0.02	4.97	4.97	0.65823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.92970	3.365	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.83275	0.996;0.979	D	0.88033	0.2776	10	0.72032	D	0.01	-19.5454	18.0204	0.89253	0.0:0.0:1.0:0.0	.	334;334	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	E	334	ENSP00000384407:G334E;ENSP00000385126:G334E;ENSP00000298280:G334E;ENSP00000311833:G334E	ENSP00000298280:G334E	G	+	2	0	SLC37A2	124458945	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.214000	0.95140	2.583000	0.87209	0.655000	0.94253	GGG	.	.	none		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
PTCHD3	374308	hgsc.bcm.edu	37	10	27687437	27687437	+	Missense_Mutation	SNP	C	C	A	rs139600575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:27687437C>A	ENST00000438700.3	-	4	2207	c.2090G>T	c.(2089-2091)tGg>tTg	p.W697L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	697					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TGCATCTAACCAAAACTCTGT	0.284																																					p.W697L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G2090T						PASS	.	C	LEU/TRP	0,4404		0,0,2202	39.0	41.0	41.0		2090	4.2	1.0	10	dbSNP_134	41	5,8569	3.7+/-12.6	0,5,4282	yes	missense	PTCHD3	NM_001034842.3	61	0,5,6484	AA,AC,CC		0.0583,0.0,0.0385	probably-damaging	697/768	27687437	5,12973	2202	4287	6489	SO:0001583	missense	374308	exon4			TCTAACCAAAACT	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.2090G>T	10.37:g.27687437C>A	ENSP00000417658:p.Trp697Leu	133.0	0.0	0		76.0	35.0	0.460526	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895630	0.52121	0.0	5.83E-4	ENSG00000182077	ENST00000438700	D	0.89746	-2.56	4.18	4.18	0.49190	.	0.183449	0.51477	D	0.000085	D	0.94548	0.8244	M	0.84326	2.69	0.49130	D	0.999753	D	0.89917	1.0	D	0.87578	0.998	D	0.95493	0.8571	10	0.87932	D	0	-7.4899	16.2851	0.82714	0.0:1.0:0.0:0.0	.	697	Q3KNS1	PTHD3_HUMAN	L	697	ENSP00000417658:W697L	ENSP00000417658:W697L	W	-	2	0	PTCHD3	27727443	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	3.467000	0.53078	2.169000	0.68431	0.542000	0.68232	TGG	C|0.999;A|0.001	0.001	strong		0.284	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
CYFIP2	26999	hgsc.bcm.edu	37	5	156741411	156741411	+	Silent	SNP	C	C	T	rs139943836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156741411C>T	ENST00000521420.1	+	11	1183	c.1092C>T	c.(1090-1092)ttC>ttT	p.F364F	CYFIP2_ENST00000435847.2_Silent_p.F64F|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000541131.1_Silent_p.F315F|CYFIP2_ENST00000318218.6_Silent_p.F390F|CYFIP2_ENST00000347377.6_Silent_p.F390F|CYFIP2_ENST00000522463.1_Silent_p.F194F|CYFIP2_ENST00000377576.3_Silent_p.F390F					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCGAGCTCTTCGACCTAGCCC	0.597													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16212	0.0		0.003	False		,,,				2504	0.0				p.F390F		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1170T						PASS	.	C	,,	1,4071		0,1,2035	100.0	104.0	103.0		1170,1170,1170	-0.7	1.0	5	dbSNP_134	103	27,8355		0,27,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,28,6199	TT,TC,CC		0.3221,0.0246,0.2248	,,	390/1254,390/1254,390/1254	156741411	28,12426	2036	4191	6227	SO:0001819	synonymous_variant	26999	exon12			GCTCTTCGACCTA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1092C>T	5.37:g.156741411C>T		103.0	0.0	0		71.0	38.0	0.535211	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.597	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
TOR3A	64222	hgsc.bcm.edu	37	1	179064145	179064145	+	Missense_Mutation	SNP	T	T	C	rs138598531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179064145T>C	ENST00000367627.3	+	6	1738	c.986T>C	c.(985-987)aTt>aCt	p.I329T	TOR3A_ENST00000352445.6_Intron	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	329					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						GAAAACCTGATTGACTACTTC	0.502													T|||	3	0.000599042	0.0	0.0	5008	,	,		20059	0.0		0.003	False		,,,				2504	0.0				p.I329T		Atlas-SNP	.											.	TOR3A	28	.	0			c.T986C						PASS	.	T	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	207.0	183.0	191.0		986	5.6	1.0	1	dbSNP_134	191	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TOR3A	NM_022371.3	89	0,9,6494	CC,CT,TT		0.093,0.0227,0.0692	possibly-damaging	329/398	179064145	9,12997	2203	4300	6503	SO:0001583	missense	64222	exon6			ACCTGATTGACTA	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.986T>C	1.37:g.179064145T>C	ENSP00000356599:p.Ile329Thr	213.0	0.0	0		192.0	98.0	0.510417	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	23.6	4.433498	0.83776	2.27E-4	9.3E-4	ENSG00000186283	ENST00000367627	T	0.60797	0.16	5.62	5.62	0.85841	.	0.102990	0.64402	D	0.000005	T	0.67998	0.2953	M	0.90650	3.135	0.80722	D	1	P	0.46706	0.883	B	0.42827	0.399	T	0.76567	-0.2912	10	0.62326	D	0.03	-9.8442	15.0006	0.71469	0.0:0.0:0.0:1.0	.	329	Q9H497	TOR3A_HUMAN	T	329	ENSP00000356599:I329T	ENSP00000356599:I329T	I	+	2	0	TOR3A	177330768	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.662000	0.83803	2.134000	0.65973	0.496000	0.49642	ATT	T|0.999;C|0.001	0.001	strong		0.502	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
KPTN	11133	hgsc.bcm.edu	37	19	47978739	47978739	+	Silent	SNP	C	C	T	rs1046273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47978739C>T	ENST00000338134.3	-	12	1352	c.1245G>A	c.(1243-1245)agG>agA	p.R415R	KPTN_ENST00000536339.1_Silent_p.R175R	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	415					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GCCGACGTCTCCTCTGCTCCA	0.612													C|||	92	0.0183706	0.0008	0.062	5008	,	,		19204	0.0		0.0249	False		,,,				2504	0.0235				p.R415R		Atlas-SNP	.											.	KPTN	34	.	0			c.G1245A						PASS	.	C		13,4085		0,13,2036	35.0	37.0	36.0		1245	2.5	0.9	19	dbSNP_86	36	166,8212		3,160,4026	no	coding-synonymous	KPTN	NM_007059.2		3,173,6062	TT,TC,CC		1.9814,0.3172,1.4348		415/437	47978739	179,12297	2049	4189	6238	SO:0001819	synonymous_variant	11133	exon12			ACGTCTCCTCTGC	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.1245G>A	19.37:g.47978739C>T		82.0	0.0	0		95.0	31.0	0.326316	NM_007059	B3KN86|B4DQ76|Q96GT1	Silent	SNP	ENST00000338134.3	37	CCDS42583.1																																																																																			C|0.982;T|0.018	0.018	strong		0.612	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
HDAC7	51564	hgsc.bcm.edu	37	12	48189061	48189061	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48189061G>A	ENST00000427332.2	-	11	1229	c.1073C>T	c.(1072-1074)tCa>tTa	p.S358L	HDAC7_ENST00000080059.7_Missense_Mutation_p.S397L|HDAC7_ENST00000354334.3_Missense_Mutation_p.S360L|HDAC7_ENST00000552960.1_Missense_Mutation_p.S380L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S414L			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	358	Transcription repression 2. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		CAGGGGCTCTGAGCGAGTCCG	0.677																																					p.S397L		Atlas-SNP	.											HDAC7,NS,carcinoma,+1,1	HDAC7	71	1	0			c.C1190T						scavenged	.						28.0	33.0	31.0					12																	48189061		2195	4297	6492	SO:0001583	missense	51564	exon11			GGCTCTGAGCGAG	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.1073C>T	12.37:g.48189061G>A	ENSP00000404394:p.Ser358Leu	42.0	1.0	0.0238095		46.0	16.0	0.347826	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	G	32	5.178706	0.94846	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.74632	-0.66;-0.86;-0.63;-0.78;-0.57	4.37	4.37	0.52481	.	0.000000	0.64402	D	0.000001	D	0.84570	0.5501	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	D	0.86580	0.1853	10	0.87932	D	0	.	16.0096	0.80391	0.0:0.0:1.0:0.0	.	397;380;360	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	L	397;360;380;414;358	ENSP00000080059:S397L;ENSP00000351326:S360L;ENSP00000448532:S380L;ENSP00000369984:S414L;ENSP00000404394:S358L	ENSP00000080059:S397L	S	-	2	0	HDAC7	46475328	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.065000	0.93941	2.418000	0.82041	0.561000	0.74099	TCA	.	.	none		0.677	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
CDH9	1007	hgsc.bcm.edu	37	5	26902724	26902724	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:26902724T>G	ENST00000231021.4	-	7	1286	c.1114A>C	c.(1114-1116)Ata>Cta	p.I372L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	372	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCCACAGATATTTTGACCACA	0.403																																					p.I372L	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1114C						PASS	.						124.0	121.0	122.0					5																	26902724		2203	4300	6503	SO:0001583	missense	1007	exon7			CAGATATTTTGAC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1114A>C	5.37:g.26902724T>G	ENSP00000231021:p.Ile372Leu	120.0	0.0	0		147.0	35.0	0.238095	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.102931	0.56183	.	.	ENSG00000113100	ENST00000231021	T	0.68181	-0.31	5.62	3.25	0.37280	Cadherin (3);Cadherin-like (1);	0.179874	0.51477	D	0.000089	T	0.70055	0.3180	M	0.83223	2.63	0.36617	D	0.875535	B	0.09022	0.002	B	0.36134	0.218	T	0.66244	-0.5972	9	.	.	.	.	7.5723	0.27915	0.0:0.2391:0.0:0.7609	.	372	Q9ULB4	CADH9_HUMAN	L	372	ENSP00000231021:I372L	.	I	-	1	0	CDH9	26938481	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	1.231000	0.32624	0.426000	0.26116	0.528000	0.53228	ATA	.	.	none		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
KIF7	374654	hgsc.bcm.edu	37	15	90195948	90195948	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90195948G>C	ENST00000394412.3	-	2	290	c.214C>G	c.(214-216)Cag>Gag	p.Q72E		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	72	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			ACGCAGGCCTGGTACACGGCC	0.637																																					p.Q72E		Atlas-SNP	.											.	KIF7	130	.	0			c.C214G						PASS	.						74.0	79.0	78.0					15																	90195948		689	1590	2279	SO:0001583	missense	374654	exon2			AGGCCTGGTACAC	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.214C>G	15.37:g.90195948G>C	ENSP00000377934:p.Gln72Glu	100.0	0.0	0		120.0	71.0	0.591667	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.957591	0.02267	.	.	ENSG00000166813	ENST00000394412	T	0.70869	-0.52	4.75	3.77	0.43336	Kinesin, motor domain (4);	.	.	.	.	T	0.36082	0.0954	N	0.00864	-1.135	0.24841	N	0.99247	B	0.09022	0.002	B	0.12156	0.007	T	0.24333	-1.0163	9	0.16420	T	0.52	.	7.1539	0.25626	0.0:0.2579:0.4681:0.274	.	72	Q2M1P5	KIF7_HUMAN	E	72	ENSP00000377934:Q72E	ENSP00000377934:Q72E	Q	-	1	0	KIF7	87996952	0.015000	0.18098	1.000000	0.80357	0.464000	0.32679	0.295000	0.19065	2.183000	0.69458	0.655000	0.94253	CAG	.	.	none		0.637	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
MUC4	4585	hgsc.bcm.edu	37	3	195508490	195508490	+	Missense_Mutation	SNP	C	C	A	rs200820395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508490C>A	ENST00000463781.3	-	2	10420	c.9961G>T	c.(9961-9963)Gca>Tca	p.A3321S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3321S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGCG	0.572													.|||	42	0.00838658	0.0015	0.0173	5008	,	,		10309	0.001		0.0268	False		,,,				2504	0.0				p.A3321S		Atlas-SNP	.											.	MUC4	1505	.	2	Deletion - In frame(2)	stomach(2)	c.G9961T						PASS	.						13.0	14.0	14.0					3																	195508490		671	1560	2231	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9961G>T	3.37:g.195508490C>A	ENSP00000417498:p.Ala3321Ser	112.0	0.0	0		37.0	8.0	0.216216	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	7.260	0.605089	0.14002	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.3;1.26	1.03	1.03	0.20045	.	.	.	.	.	T	0.14657	0.0354	N	0.14661	0.345	0.09310	N	1	P	0.38110	0.618	B	0.25884	0.064	T	0.11941	-1.0567	8	.	.	.	.	5.3938	0.16259	0.0:1.0:0.0:0.0	.	3193	E7ESK3	.	S	3321	ENSP00000417498:A3321S;ENSP00000420243:A3321S	.	A	-	1	0	MUC4	196993269	0.000000	0.05858	0.007000	0.13788	0.019000	0.09904	-3.950000	0.00327	0.494000	0.27859	0.089000	0.15464	GCA	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR8J1	219477	hgsc.bcm.edu	37	11	56128031	56128031	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56128031G>C	ENST00000303039.3	+	1	341	c.309G>C	c.(307-309)ggG>ggC	p.G103G		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AACTGGGAGGGTTCTTGTTCT	0.423																																					p.G103G		Atlas-SNP	.											.	OR8J1	87	.	0			c.G309C						PASS	.						150.0	140.0	143.0					11																	56128031		2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GGGAGGGTTCTTG	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.309G>C	11.37:g.56128031G>C		216.0	0.0	0		187.0	49.0	0.262032	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			.	.	none		0.423	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ZNF180	7733	hgsc.bcm.edu	37	19	44981009	44981009	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44981009G>T	ENST00000221327.4	-	5	1970	c.1689C>A	c.(1687-1689)caC>caA	p.H563Q	ZNF180_ENST00000391956.4_Missense_Mutation_p.H538Q|ZNF180_ENST00000592529.1_Missense_Mutation_p.H536Q|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	563					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(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GCATAACAAGGTGAGAACTGC	0.418																																					p.H563Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C1689A						PASS	.						103.0	104.0	104.0					19																	44981009		2203	4300	6503	SO:0001583	missense	7733	exon5			AACAAGGTGAGAA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1689C>A	19.37:g.44981009G>T	ENSP00000221327:p.His563Gln	90.0	0.0	0		81.0	15.0	0.185185	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105656	0.37145	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07216	3.21;3.21	5.23	2.97	0.34412	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000440	T	0.04272	0.0118	N	0.12961	0.28	0.80722	D	1	P;P;P	0.47545	0.874;0.897;0.897	B;B;B	0.39068	0.191;0.289;0.289	T	0.37430	-0.9706	10	0.51188	T	0.08	-7.8305	6.5992	0.22691	0.1566:0.0:0.6887:0.1546	.	538;562;563	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	Q	563;538	ENSP00000221327:H563Q;ENSP00000375818:H538Q	ENSP00000221327:H563Q	H	-	3	2	ZNF180	49672849	0.000000	0.05858	1.000000	0.80357	0.872000	0.50106	-1.418000	0.02462	2.437000	0.82529	0.467000	0.42956	CAC	.	.	none		0.418	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
NUP188	23511	hgsc.bcm.edu	37	9	131752487	131752487	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131752487G>A	ENST00000372577.2	+	25	2643	c.2622G>A	c.(2620-2622)ctG>ctA	p.L874L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	874					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)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CCATTCAGCTGCTGAAACGTC	0.473																																					p.L874L		Atlas-SNP	.											.	NUP188	140	.	0			c.G2622A						PASS	.						371.0	316.0	334.0					9																	131752487		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon25			TCAGCTGCTGAAA	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2622G>A	9.37:g.131752487G>A		202.0	0.0	0		187.0	38.0	0.203209	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			.	.	none		0.473	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
NAGLU	4669	hgsc.bcm.edu	37	17	40696120	40696120	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696120A>T	ENST00000225927.2	+	6	2197	c.2096A>T	c.(2095-2097)aAa>aTa	p.K699I	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	699					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CAGTTTGACAAAAATGTCTTC	0.577																																					p.K699I		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2096T						PASS	.						48.0	46.0	47.0					17																	40696120		2203	4300	6503	SO:0001583	missense	4669	exon6			TTGACAAAAATGT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.2096A>T	17.37:g.40696120A>T	ENSP00000225927:p.Lys699Ile	59.0	0.0	0		53.0	17.0	0.320755	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.590453	0.46214	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98777	-5.13	5.03	2.8	0.32819	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.606411	0.18227	N	0.147694	D	0.96059	0.8716	L	0.31526	0.94	0.09310	N	0.99999	P	0.38395	0.629	B	0.41619	0.361	D	0.92173	0.5745	10	0.46703	T	0.11	-5.9234	8.3135	0.32086	0.833:0.0:0.167:0.0	.	699	P54802	ANAG_HUMAN	I	699;375	ENSP00000225927:K699I	ENSP00000225927:K699I	K	+	2	0	NAGLU	37949646	0.903000	0.30736	0.023000	0.16930	0.900000	0.52787	2.106000	0.41835	0.879000	0.35944	0.454000	0.30748	AAA	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
NPHP4	261734	hgsc.bcm.edu	37	1	5940243	5940243	+	Missense_Mutation	SNP	G	G	A	rs17472401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:5940243G>A	ENST00000378156.4	-	19	2807	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	848			R -> W (does not affect interaction with RPGRIP1L; dbSNP:rs17472401). {ECO:0000269|PubMed:12205563, ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GAGATGACCCGAGATCTGGAC	0.527													G|||	38	0.00758786	0.0015	0.0086	5008	,	,		21450	0.0		0.0278	False		,,,				2504	0.002				p.R848W		Atlas-SNP	.											.	NPHP4	119	.	0			c.C2542T	GRCh37	CM022976	NPHP4	M	rs17472401	PASS	.	G	TRP/ARG	15,4117		0,15,2051	82.0	89.0	87.0		2542	0.8	0.2	1	dbSNP_123	87	184,8206		2,180,4013	yes	missense	NPHP4	NM_015102.3	101	2,195,6064	AA,AG,GG		2.1931,0.363,1.5892	probably-damaging	848/1427	5940243	199,12323	2066	4195	6261	SO:0001583	missense	261734	exon19			TGACCCGAGATCT	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2542C>T	1.37:g.5940243G>A	ENSP00000367398:p.Arg848Trp	111.0	0.0	0		72.0	26.0	0.361111	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	26	0.011904761904761904	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	12.26	1.883773	0.33255	0.00363	0.021931	ENSG00000131697	ENST00000378156	D	0.88124	-2.34	5.21	0.782	0.18567	.	0.153997	0.41500	D	0.000868	T	0.81059	0.4744	M	0.66939	2.045	0.23070	N	0.99835	D	0.89917	1.0	D	0.74674	0.984	T	0.79652	-0.1714	10	0.72032	D	0.01	.	12.097	0.53761	0.0:0.0:0.4162:0.5838	rs17472401;rs52814007;rs17472401	848	O75161	NPHP4_HUMAN	W	848	ENSP00000367398:R848W	ENSP00000367398:R848W	R	-	1	2	NPHP4	5862830	0.900000	0.30661	0.234000	0.24042	0.013000	0.08279	1.160000	0.31761	0.154000	0.19237	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.527	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742413C>T	ENST00000373095.1	-	1	379	c.4G>A	c.(4-6)Gct>Act	p.A2T		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	2										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						ATCAAGAAAGCCATGAGCGAG	0.517																																					p.A2T		Atlas-SNP	.											.	FAM102A	32	.	0			c.G4A						PASS	.						89.0	103.0	98.0					9																	130742413		2203	4300	6503	SO:0001583	missense	399665	exon1			AGAAAGCCATGAG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.4G>A	9.37:g.130742413C>T	ENSP00000362187:p.Ala2Thr	75.0	0.0	0		68.0	27.0	0.397059	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141355	0.57044	.	.	ENSG00000167106	ENST00000373095	.	.	.	4.76	4.76	0.60689	.	0.117104	0.56097	D	0.000025	T	0.54013	0.1832	L	0.43152	1.355	0.80722	D	1	B	0.29162	0.235	B	0.17098	0.017	T	0.55023	-0.8205	9	0.42905	T	0.14	-9.6451	16.7632	0.85517	0.0:1.0:0.0:0.0	.	2	Q5T9C2	F102A_HUMAN	T	2	.	ENSP00000362187:A2T	A	-	1	0	FAM102A	129782234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.711000	0.54868	2.185000	0.69588	0.462000	0.41574	GCT	.	.	none		0.517	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230428	23230428	+	Missense_Mutation	SNP	C	C	G	rs151173231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230428C>G	ENST00000526893.1	+	1	469	c.195C>G	c.(193-195)agC>agG	p.S65R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S65R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S65R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	65						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCTGCGGAGCCTGTGGGGCA	0.647																																					p.S65R		Atlas-SNP	.											IGLL5,caecum,carcinoma,+1,1	IGLL5	26	1	0			c.C195G						PASS	.																																			SO:0001583	missense	100423062	exon1			GCGGAGCCTGTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.195C>G	22.37:g.23230428C>G	ENSP00000431254:p.Ser65Arg	107.0	0.0	0		86.0	22.0	0.255814	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558610	0.45590	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00576	6.45;6.54	3.92	1.8	0.24995	.	.	.	.	.	T	0.00468	0.0015	N	0.19112	0.55	0.09310	N	1	B	0.15930	0.015	B	0.12837	0.008	T	0.46775	-0.9167	9	0.56958	D	0.05	.	4.9248	0.13887	0.2081:0.6824:0.0:0.1095	.	65	B9A064	IGLL5_HUMAN	R	65	ENSP00000436353:S65R;ENSP00000431254:S65R	ENSP00000431254:S65R	S	+	3	2	IGLL5	21560428	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.510000	0.06328	0.610000	0.30035	0.643000	0.83706	AGC	C|1.000;T|0.000	.	alt		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
GIGYF2	26058	hgsc.bcm.edu	37	2	233697708	233697708	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233697708C>T	ENST00000409547.1	+	24	2982	c.2671C>T	c.(2671-2673)Cgg>Tgg	p.R891W	GIGYF2_ENST00000409451.3_Missense_Mutation_p.R912W|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R722W|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R913W|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R891W|GIGYF2_ENST00000409196.3_Missense_Mutation_p.R885W|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R913W	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	891	Gln-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)		GGAGGTCCAGCGGCAGAAGGA	0.587																																					p.R912W		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C2734T						PASS	.						21.0	21.0	21.0					2																	233697708		2188	4277	6465	SO:0001583	missense	26058	exon24			GTCCAGCGGCAGA	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.2671C>T	2.37:g.233697708C>T	ENSP00000386537:p.Arg891Trp	68.0	0.0	0		77.0	29.0	0.376623	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812568	0.50527	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000452341	T;T;T;T;T;T;T	0.77098	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-1.07	5.36	3.43	0.39272	.	0.054543	0.64402	D	0.000001	D	0.83589	0.5287	L	0.50333	1.59	0.46609	D	0.999126	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;P;P	0.76071	0.987;0.908;0.908;0.908	D	0.84996	0.0897	10	0.87932	D	0	-21.7548	12.8794	0.58008	0.4371:0.5629:0.0:0.0	.	722;912;891;885	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	W	913;891;913;891;885;912;722	ENSP00000362667:R913W;ENSP00000362664:R891W;ENSP00000386765:R913W;ENSP00000386537:R891W;ENSP00000387070:R885W;ENSP00000387170:R912W;ENSP00000411505:R722W	ENSP00000362664:R891W	R	+	1	2	GIGYF2	233405952	0.993000	0.37304	1.000000	0.80357	0.815000	0.46073	1.280000	0.33202	1.188000	0.43014	0.655000	0.94253	CGG	.	.	none		0.587	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
DEF8	54849	hgsc.bcm.edu	37	16	90028509	90028509	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90028509C>T	ENST00000268676.7	+	9	1169	c.1080C>T	c.(1078-1080)taC>taT	p.Y360Y	DEF8_ENST00000563795.1_Silent_p.Y299Y|DEF8_ENST00000563594.1_Silent_p.Y299Y|DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.Y289Y|DEF8_ENST00000569453.1_Silent_p.Y299Y|DEF8_ENST00000567874.1_Silent_p.Y239Y	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	360					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		TGTTCAGCTACGTGGAGGAGC	0.662																																					p.Y360Y		Atlas-SNP	.											.	DEF8	28	.	0			c.C1080T						PASS	.						44.0	36.0	39.0					16																	90028509		2198	4300	6498	SO:0001819	synonymous_variant	54849	exon9			CAGCTACGTGGAG	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1080C>T	16.37:g.90028509C>T		78.0	0.0	0		107.0	74.0	0.691589	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			.	.	none		0.662	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
PARVA	55742	hgsc.bcm.edu	37	11	12540037	12540037	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:12540037T>C	ENST00000550549.1	+	12	1064	c.1015T>C	c.(1015-1017)Ttg>Ctg	p.L339L	PARVA_ENST00000539723.1_Silent_p.L339L|PARVA_ENST00000334956.8_Silent_p.L379L			Q9NVD7	PARVA_HUMAN	parvin, alpha	339	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|actin-mediated cell contraction (GO:0070252)|cell junction assembly (GO:0034329)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|heterotypic cell-cell adhesion (GO:0034113)|outflow tract septum morphogenesis (GO:0003148)|regulation of cell shape (GO:0008360)|smooth muscle cell chemotaxis (GO:0071670)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)	11				Epithelial(150;0.00624)		AGATGGAGGGTTGGAAAAGCC	0.512																																					p.L379L		Atlas-SNP	.											.	PARVA	27	.	0			c.T1135C						PASS	.						89.0	87.0	87.0					11																	12540037		1969	4145	6114	SO:0001819	synonymous_variant	55742	exon12			GGAGGGTTGGAAA	AF237771	CCDS44541.1, CCDS44541.2	11p15.3	2014-06-13	2005-05-26		ENSG00000197702	ENSG00000197702		"""Parvins"""	14652	protein-coding gene	gene with protein product		608120	"""matrix-remodelling associated 2"""	MXRA2		11171322	Standard	NM_018222		Approved	FLJ12254, FLJ10793	uc001mki.4	Q9NVD7	OTTHUMG00000165778	ENST00000550549.1:c.1015T>C	11.37:g.12540037T>C		221.0	0.0	0		189.0	33.0	0.174603	NM_018222	Q96C85|Q9HA48	Silent	SNP	ENST00000550549.1	37																																																																																				.	.	none		0.512	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222	
WWP2	11060	hgsc.bcm.edu	37	16	69922079	69922079	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69922079G>A	ENST00000359154.2	+	8	942	c.841G>A	c.(841-843)Gga>Aga	p.G281R	WWP2_ENST00000569174.1_Missense_Mutation_p.G281R|WWP2_ENST00000448661.1_Missense_Mutation_p.G281R|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Missense_Mutation_p.G281R|WWP2_ENST00000542271.1_Missense_Mutation_p.G165R	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	281					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACCGGCTGAAGGAGAGGAACC	0.622																																					p.G281R		Atlas-SNP	.											.	WWP2	88	.	0			c.G841A						PASS	.						68.0	67.0	67.0					16																	69922079		2198	4300	6498	SO:0001583	missense	11060	exon8			GCTGAAGGAGAGG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.841G>A	16.37:g.69922079G>A	ENSP00000352069:p.Gly281Arg	95.0	0.0	0		127.0	51.0	0.401575	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627292	0.66901	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.32515	1.45;1.45;1.45;1.48	6.07	6.07	0.98685	.	3.592490	0.00447	N	0.000099	T	0.29556	0.0737	N	0.24115	0.695	0.47737	D	0.9995	P	0.34780	0.468	B	0.31191	0.125	T	0.17623	-1.0363	9	.	.	.	.	17.7999	0.88584	0.0:0.0:1.0:0.0	.	281	O00308	WWP2_HUMAN	R	281;281;281;168;165	ENSP00000352069:G281R;ENSP00000396871:G281R;ENSP00000348283:G281R;ENSP00000445616:G165R	.	G	+	1	0	WWP2	68479580	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.845000	0.55880	2.884000	0.98904	0.655000	0.94253	GGA	.	.	none		0.622	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
KRT37	8688	hgsc.bcm.edu	37	17	39580310	39580310	+	Missense_Mutation	SNP	G	G	A	rs142829376		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580310G>A	ENST00000225550.3	-	1	465	c.466C>T	c.(466-468)Cgt>Tgt	p.R156C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	156	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R156C(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				TCGATTGTACGGAAGTAGGAC	0.597																																					p.R156C		Atlas-SNP	.											KRT37,hand,carcinoma,0,1	KRT37	61	1	1	Substitution - Missense(1)	skin(1)	c.C466T						scavenged	.	G	CYS/ARG	0,4406		0,0,2203	87.0	77.0	81.0		466	3.6	0.7	17	dbSNP_134	81	1,8599		0,1,4299	no	missense	KRT37	NM_003770.4	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	156/450	39580310	1,13005	2203	4300	6503	SO:0001583	missense	8688	exon1			TTGTACGGAAGTA	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.466C>T	17.37:g.39580310G>A	ENSP00000225550:p.Arg156Cys	91.0	1.0	0.010989		73.0	47.0	0.643836	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	12.99	2.103923	0.37145	0.0	1.16E-4	ENSG00000108417	ENST00000225550	D	0.89415	-2.51	4.69	3.62	0.41486	Filament (1);	0.297247	0.23563	N	0.046837	D	0.85885	0.5801	M	0.68593	2.085	0.09310	N	0.999993	B	0.18863	0.031	B	0.12156	0.007	T	0.76075	-0.3092	10	0.38643	T	0.18	.	10.3203	0.43762	0.0:0.1176:0.6892:0.1932	.	156	O76014	KRT37_HUMAN	C	156	ENSP00000225550:R156C	ENSP00000225550:R156C	R	-	1	0	KRT37	36833836	0.000000	0.05858	0.749000	0.31150	0.958000	0.62258	0.157000	0.16402	2.169000	0.68431	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	weak		0.597	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
LAMA5	3911	hgsc.bcm.edu	37	20	60898654	60898654	+	Silent	SNP	G	G	A	rs11696243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60898654G>A	ENST00000252999.3	-	45	5988	c.5922C>T	c.(5920-5922)aaC>aaT	p.N1974N		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1974	Laminin EGF-like 19. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGGGGTCACCGTTGCCGCTGC	0.697													.|||	60	0.0119808	0.0015	0.0216	5008	,	,		13277	0.0		0.0388	False		,,,				2504	0.0041				p.N1974N		Atlas-SNP	.											.	LAMA5	268	.	0			c.C5922T						PASS	.	G		32,4354		0,32,2161	21.0	29.0	26.0		5922	-2.2	0.2	20	dbSNP_120	26	256,8322		4,248,4037	no	coding-synonymous	LAMA5	NM_005560.3		4,280,6198	AA,AG,GG		2.9844,0.7296,2.2215		1974/3696	60898654	288,12676	2193	4289	6482	SO:0001819	synonymous_variant	3911	exon45			GTCACCGTTGCCG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5922C>T	20.37:g.60898654G>A		58.0	0.0	0		97.0	47.0	0.484536	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.980;A|0.020	0.020	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
GAR1	54433	hgsc.bcm.edu	37	4	110739212	110739212	+	Missense_Mutation	SNP	A	A	G	rs143266987		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110739212A>G	ENST00000226796.6	+	3	599	c.335A>G	c.(334-336)aAa>aGa	p.K112R	RP11-602N24.3_ENST00000609440.1_lincRNA|GAR1_ENST00000394631.3_Missense_Mutation_p.K112R	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein	112					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA snoRNP complex (GO:0031429)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cation channel activity (GO:0005261)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	9						CAAATTGGAAAAGTGGATGAA	0.348													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19750	0.0		0.0	False		,,,				2504	0.0				p.K112R		Atlas-SNP	.											.	GAR1	16	.	0			c.A335G						PASS	.	A	ARG/LYS,ARG/LYS	0,4406		0,0,2203	83.0	86.0	85.0		335,335	4.8	1.0	4	dbSNP_134	85	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense	GAR1	NM_018983.3,NM_032993.2	26,26	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	probably-damaging,probably-damaging	112/218,112/218	110739212	6,13000	2203	4300	6503	SO:0001583	missense	54433	exon3			TTGGAAAAGTGGA	AJ276003	CCDS34050.1	4q	2013-07-31	2013-07-31	2008-10-13	ENSG00000109534	ENSG00000109534			14264	protein-coding gene	gene with protein product		606468	"""nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs)"", ""GAR1 ribonucleoprotein homolog (yeast)"""	NOLA1		10757788	Standard	XM_005263069		Approved		uc003hzu.3	Q9NY12	OTTHUMG00000161108	ENST00000226796.6:c.335A>G	4.37:g.110739212A>G	ENSP00000226796:p.Lys112Arg	81.0	0.0	0		60.0	30.0	0.5	NM_018983	Q5MJQ2	Missense_Mutation	SNP	ENST00000226796.6	37	CCDS34050.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564745	0.86439	0.0	6.98E-4	ENSG00000109534	ENST00000394631;ENST00000226796	.	.	.	4.78	4.78	0.61160	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.81341	2.54	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82928	-0.0214	9	0.72032	D	0.01	.	14.6205	0.68582	1.0:0.0:0.0:0.0	.	112;112	Q9NY12-2;Q9NY12	.;GAR1_HUMAN	R	112	.	ENSP00000226796:K112R	K	+	2	0	GAR1	110958661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	1.913000	0.55393	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	weak		0.348	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2		
RYR3	6263	hgsc.bcm.edu	37	15	33954552	33954552	+	Silent	SNP	T	T	C	rs200740143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33954552T>C	ENST00000389232.4	+	35	4891	c.4821T>C	c.(4819-4821)taT>taC	p.Y1607Y	RYR3_ENST00000415757.3_Silent_p.Y1607Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1607	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGGTTTCTATGACCTGCTCA	0.567													T|||	2	0.000399361	0.0	0.0	5008	,	,		20622	0.0		0.002	False		,,,				2504	0.0				p.Y1607Y		Atlas-SNP	.											.	RYR3	760	.	0			c.T4821C						PASS	.	T		6,4026		0,6,2010	72.0	71.0	71.0		4821	3.7	1.0	15		71	36,8294		0,36,4129	no	coding-synonymous	RYR3	NM_001036.3		0,42,6139	CC,CT,TT		0.4322,0.1488,0.3398		1607/4871	33954552	42,12320	2016	4165	6181	SO:0001819	synonymous_variant	6263	exon35			TTTCTATGACCTG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.4821T>C	15.37:g.33954552T>C		91.0	0.0	0		122.0	56.0	0.459016	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
CCDC89	220388	hgsc.bcm.edu	37	11	85396746	85396746	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:85396746T>C	ENST00000316398.3	-	1	574	c.428A>G	c.(427-429)tAc>tGc	p.Y143C	CREBZF_ENST00000531515.1_5'Flank|CREBZF_ENST00000534224.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	143						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CTCACTCTTGTATTCATCCTT	0.517																																					p.Y143C		Atlas-SNP	.											.	CCDC89	45	.	0			c.A428G						PASS	.						100.0	90.0	93.0					11																	85396746		2203	4299	6502	SO:0001583	missense	220388	exon1			CTCTTGTATTCAT	AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.428A>G	11.37:g.85396746T>C	ENSP00000320649:p.Tyr143Cys	119.0	0.0	0		102.0	85.0	0.833333	NM_152723		Missense_Mutation	SNP	ENST00000316398.3	37	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	t	13.79	2.340823	0.41498	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.53	5.53	0.82687	.	0.343021	0.33110	N	0.005272	T	0.49779	0.1577	L	0.29908	0.895	0.37455	D	0.914985	D	0.54964	0.969	P	0.49528	0.614	T	0.54077	-0.8347	8	.	.	.	-8.5222	15.664	0.77213	0.0:0.0:0.0:1.0	.	143	Q8N998	CCD89_HUMAN	C	143	.	.	Y	-	2	0	CCDC89	85074394	1.000000	0.71417	0.950000	0.38849	0.578000	0.36192	5.298000	0.65710	2.104000	0.64026	0.529000	0.55759	TAC	.	.	none		0.517	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723	
H2AFY	9555	hgsc.bcm.edu	37	5	134670756	134670756	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:134670756G>C	ENST00000511689.1	-	9	1622	c.1029C>G	c.(1027-1029)tcC>tcG	p.S343S	H2AFY_ENST00000510038.1_Silent_p.S343S|H2AFY_ENST00000423969.2_Silent_p.S171S|CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000312469.4_Silent_p.S340S|H2AFY_ENST00000304332.4_Silent_p.S342S|H2AFY_ENST00000512507.1_5'UTR	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	343	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGATGGAAGAGGACATTGTAG	0.478																																					p.S343S		Atlas-SNP	.											.	H2AFY	61	.	0			c.C1029G						PASS	.						142.0	129.0	133.0					5																	134670756		2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			GGAAGAGGACATT	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1029C>G	5.37:g.134670756G>C		250.0	0.0	0		236.0	70.0	0.29661	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			.	.	none		0.478	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
ESPN	83715	hgsc.bcm.edu	37	1	6500712	6500712	+	Silent	SNP	C	C	G	rs367944375		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500712C>G	ENST00000377828.1	+	4	870	c.702C>G	c.(700-702)tcC>tcG	p.S234S	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	234					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TGAGCCTGTCCGAGCAGGACA	0.741																																					p.S234S		Atlas-SNP	.											.	ESPN	32	.	0			c.C702G						PASS	.						3.0	5.0	4.0					1																	6500712		1942	3924	5866	SO:0001819	synonymous_variant	83715	exon4			CCTGTCCGAGCAG	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.702C>G	1.37:g.6500712C>G		9.0	0.0	0		12.0	10.0	0.833333	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	37	CCDS70.1																																																																																			.	.	none		0.741	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121995A>T	ENST00000271588.4	+	96	15239	c.15010A>T	c.(15010-15012)Act>Tct	p.T5004S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGCTGAAGTCACTGTAAAGGT	0.438													A|||	9	0.00179712	0.0	0.0	5008	,	,		18499	0.0		0.008	False		,,,				2504	0.001				p.T5004S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A15010T						PASS	.	A	SER/THR	3,4403	4.2+/-10.8	0,3,2200	196.0	170.0	179.0		15010	0.8	0.1	1	dbSNP_133	179	28,8572	9.1+/-34.3	1,26,4273	yes	missense	HMCN1	NM_031935.2	58	1,29,6473	TT,TA,AA		0.3256,0.0681,0.2384	benign	5004/5636	186121995	31,12975	2203	4300	6503	SO:0001583	missense	83872	exon96			GAAGTCACTGTAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15010A>T	1.37:g.186121995A>T	ENSP00000271588:p.Thr5004Ser	215.0	0.0	0		170.0	87.0	0.511765	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	2.871	-0.233991	0.05983	6.81E-4	0.003256	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32988	1.43;1.43	5.9	0.836	0.18891	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32161	-0.9917	10	0.05833	T	0.94	.	6.2405	0.20787	0.6238:0.1195:0.2567:0.0	.	5004	Q96RW7	HMCN1_HUMAN	S	5004	ENSP00000271588:T5004S;ENSP00000356462:T5004S	ENSP00000271588:T5004S	T	+	1	0	HMCN1	184388618	0.001000	0.12720	0.065000	0.19835	0.779000	0.44077	0.806000	0.27126	-0.101000	0.12219	-0.263000	0.10527	ACT	A|0.996;T|0.004	0.004	strong		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CADM2	253559	hgsc.bcm.edu	37	3	85935455	85935455	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:85935455C>A	ENST00000407528.2	+	4	542	c.480C>A	c.(478-480)ttC>ttA	p.F160L	CADM2_ENST00000405615.2_Missense_Mutation_p.F162L|CADM2_ENST00000383699.3_Missense_Mutation_p.F169L	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	160	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TAAGATGGTTCAAAAATGACA	0.343																																					p.F169L		Atlas-SNP	.											.	CADM2	195	.	0			c.C507A						PASS	.						56.0	54.0	55.0					3																	85935455		2203	4300	6503	SO:0001583	missense	253559	exon5			ATGGTTCAAAAAT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.480C>A	3.37:g.85935455C>A	ENSP00000384575:p.Phe160Leu	188.0	0.0	0		124.0	31.0	0.25	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378550	0.42207	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.73575	-0.76;-0.76;-0.76	5.3	3.04	0.35103	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.60196	0.2250	L	0.36672	1.1	0.58432	D	0.99999	B;B;B	0.25272	0.009;0.122;0.031	B;B;B	0.24848	0.02;0.056;0.047	T	0.51371	-0.8714	10	0.16896	T	0.51	.	9.3638	0.38212	0.0:0.7276:0.0:0.2724	.	162;169;160	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	L	169;160;162	ENSP00000373200:F169L;ENSP00000384575:F160L;ENSP00000384193:F162L	ENSP00000373200:F169L	F	+	3	2	CADM2	86018145	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.963000	0.40452	1.137000	0.42214	0.557000	0.71058	TTC	.	.	none		0.343	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
SREBF2	6721	hgsc.bcm.edu	37	22	42290890	42290890	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42290890T>C	ENST00000361204.4	+	13	2610	c.2444T>C	c.(2443-2445)tTg>tCg	p.L815S	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	815					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						ATAGAGTCCTTGGTGAAACCT	0.572																																					p.L815S		Atlas-SNP	.											.	SREBF2	99	.	0			c.T2444C						PASS	.						82.0	83.0	83.0					22																	42290890		2203	4300	6503	SO:0001583	missense	6721	exon13			AGTCCTTGGTGAA	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2444T>C	22.37:g.42290890T>C	ENSP00000354476:p.Leu815Ser	60.0	0.0	0		73.0	21.0	0.287671	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	T	29.4	4.999699	0.93227	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.27104	1.69	5.96	5.96	0.96718	.	0.063149	0.64402	D	0.000005	T	0.47655	0.1457	M	0.69358	2.11	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.47812	-0.9088	10	0.87932	D	0	-12.0099	16.4484	0.83959	0.0:0.0:0.0:1.0	.	815	Q12772	SRBP2_HUMAN	S	815	ENSP00000354476:L815S	ENSP00000354476:L815S	L	+	2	0	SREBF2	40620836	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.049000	0.76613	2.285000	0.76669	0.533000	0.62120	TTG	.	.	none		0.572	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
IRF8	3394	hgsc.bcm.edu	37	16	85942659	85942659	+	Missense_Mutation	SNP	A	A	G	rs397514711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:85942659A>G	ENST00000268638.5	+	3	660	c.238A>G	c.(238-240)Acg>Gcg	p.T80A	IRF8_ENST00000563180.1_Missense_Mutation_p.T80A	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	80			T -> A (in IMD32A; impairs transcriptional activity by disrupting the interaction between IRF8 and DNA). {ECO:0000269|PubMed:21524210}.		cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CACTTGGAAGACGAGGTTACG	0.458																																					p.T80A		Atlas-SNP	.											IRF8,NS,neuroblastoma,-1,1	IRF8	65	1	0			c.A238G						PASS	.						74.0	76.0	75.0					16																	85942659		2198	4300	6498	SO:0001583	missense	3394	exon3			TGGAAGACGAGGT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.238A>G	16.37:g.85942659A>G	ENSP00000268638:p.Thr80Ala	87.0	0.0	0		107.0	24.0	0.224299	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763543	0.69878	.	.	ENSG00000140968	ENST00000268638	D	0.97688	-4.49	4.88	4.88	0.63580	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.046894	0.85682	D	0.000000	D	0.97791	0.9275	L	0.45470	1.425	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.91635	0.999;0.996	D	0.97383	0.9984	10	0.30854	T	0.27	-15.9347	14.7789	0.69751	1.0:0.0:0.0:0.0	.	80;80	B2R8V7;Q02556	.;IRF8_HUMAN	A	80	ENSP00000268638:T80A	ENSP00000268638:T80A	T	+	1	0	IRF8	84500160	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.780000	0.91799	1.973000	0.57446	0.397000	0.26171	ACG	.	.	none		0.458	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
LRRC15	131578	hgsc.bcm.edu	37	3	194080174	194080174	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194080174G>A	ENST00000347624.3	-	2	1684	c.1599C>T	c.(1597-1599)acC>acT	p.T533T	LRRC15_ENST00000428839.1_Silent_p.T539T|LRRC15_ENST00000439944.2_Silent_p.T539T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	533					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TCTGGGCCTGGGTCATGCCCC	0.587																																					p.T539T		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1617T						PASS	.						89.0	88.0	88.0					3																	194080174		2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GGCCTGGGTCATG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1599C>T	3.37:g.194080174G>A		133.0	0.0	0		142.0	45.0	0.316901	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			.	.	none		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
KRT84	3890	hgsc.bcm.edu	37	12	52777466	52777466	+	Silent	SNP	C	C	A	rs138204915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52777466C>A	ENST00000257951.3	-	2	729	c.663G>T	c.(661-663)ctG>ctT	p.L221L	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	221	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ACTGCCTCCGCAGGTTGGTGA	0.542													C|||	7	0.00139776	0.0	0.0	5008	,	,		20929	0.0		0.006	False		,,,				2504	0.001				p.L221L		Atlas-SNP	.											.	KRT84	61	.	0			c.G663T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	71.0	68.0	69.0		663	1.4	1.0	12	dbSNP_134	69	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	KRT84	NM_033045.3		0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922		221/601	52777466	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CCTCCGCAGGTTG	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.663G>T	12.37:g.52777466C>A		144.0	0.0	0		129.0	69.0	0.534884	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			C|0.998;A|0.002	0.002	strong		0.542	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
CMYA5	202333	hgsc.bcm.edu	37	5	79027030	79027030	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79027030A>T	ENST00000446378.2	+	2	2473	c.2442A>T	c.(2440-2442)aaA>aaT	p.K814N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	814					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CTCAAAAGAAAATAATCAATG	0.443																																					p.K814N		Atlas-SNP	.											.	CMYA5	643	.	0			c.A2442T						PASS	.						85.0	81.0	83.0					5																	79027030		1922	4130	6052	SO:0001583	missense	202333	exon2			AAAGAAAATAATC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.2442A>T	5.37:g.79027030A>T	ENSP00000394770:p.Lys814Asn	139.0	0.0	0		100.0	20.0	0.2	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018125	0.35606	.	.	ENSG00000164309	ENST00000446378	T	0.39229	1.09	5.41	-3.18	0.05186	.	0.937011	0.08936	N	0.872269	T	0.24431	0.0592	L	0.41236	1.265	0.09310	N	1	B	0.25441	0.126	B	0.22753	0.041	T	0.27331	-1.0077	10	0.29301	T	0.29	.	0.3705	0.00378	0.2947:0.1275:0.2331:0.3446	.	814	Q8N3K9	CMYA5_HUMAN	N	814	ENSP00000394770:K814N	ENSP00000394770:K814N	K	+	3	2	CMYA5	79062786	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.107000	0.15375	-0.130000	0.11599	0.528000	0.53228	AAA	.	.	none		0.443	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000438717.2_Silent_p.D354D|FER_ENST00000536402.1_3'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138.0	131.0	133.0		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1587T>C	5.37:g.108294979T>C		138.0	0.0	0		108.0	64.0	0.592593	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
SAMD8	142891	hgsc.bcm.edu	37	10	76910705	76910705	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:76910705A>T	ENST00000542569.1	+	2	522	c.419A>T	c.(418-420)cAt>cTt	p.H140L	SAMD8_ENST00000372690.3_Missense_Mutation_p.H203L|SAMD8_ENST00000372687.4_Missense_Mutation_p.H140L	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	140					ceramide biosynthetic process (GO:0046513)|regulation of ceramide biosynthetic process (GO:2000303)|sphingomyelin biosynthetic process (GO:0006686)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	12	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					AAAAACAAACATTCTGTTCGA	0.373																																					p.H140L		Atlas-SNP	.											.	SAMD8	57	.	0			c.A419T						PASS	.						73.0	68.0	69.0					10																	76910705		2203	4300	6503	SO:0001583	missense	142891	exon2			ACAAACATTCTGT	AK057811	CCDS7347.1, CCDS53543.1	10q22.3	2013-01-10			ENSG00000156671	ENSG00000156671		"""Sterile alpha motif (SAM) domain containing"""	26320	protein-coding gene	gene with protein product		611575					Standard	NM_144660		Approved	FLJ25082	uc001jwx.2	Q96LT4	OTTHUMG00000018515	ENST00000542569.1:c.419A>T	10.37:g.76910705A>T	ENSP00000438042:p.His140Leu	115.0	0.0	0		88.0	20.0	0.227273	NM_144660	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	37	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881147	0.33255	.	.	ENSG00000156671	ENST00000447533;ENST00000372690;ENST00000542569;ENST00000372687	.	.	.	5.7	5.7	0.88788	.	0.046754	0.85682	D	0.000000	T	0.45276	0.1334	L	0.29908	0.895	0.43141	D	0.994895	P;B	0.36535	0.557;0.007	B;B	0.33620	0.167;0.009	T	0.40117	-0.9580	9	0.23302	T	0.38	-17.3105	15.9627	0.79941	1.0:0.0:0.0:0.0	.	140;140	Q96LT4-2;Q96LT4	.;SAMD8_HUMAN	L	140;203;140;140	.	ENSP00000361772:H140L	H	+	2	0	SAMD8	76580711	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.750000	0.74888	2.179000	0.69175	0.402000	0.26972	CAT	.	.	none		0.373	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660	
TUT1	64852	hgsc.bcm.edu	37	11	62343141	62343141	+	Missense_Mutation	SNP	C	C	T	rs369889181		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62343141C>T	ENST00000476907.1	-	9	2741	c.2050G>A	c.(2050-2052)Ggt>Agt	p.G684S	MIR3654_ENST00000496634.2_Intron|TUT1_ENST00000308436.7_Missense_Mutation_p.G722S|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	684					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TCTTCCCCACCGTCCCCTGCA	0.577																																					p.G722S		Atlas-SNP	.											.	TUT1	122	.	0			c.G2164A						PASS	.						455.0	441.0	446.0					11																	62343141		2202	4299	6501	SO:0001583	missense	64852	exon9			CCCCACCGTCCCC	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.2050G>A	11.37:g.62343141C>T	ENSP00000419607:p.Gly684Ser	152.0	0.0	0		133.0	111.0	0.834586	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	37		.	.	.	.	.	.	.	.	.	.	C	2.734	-0.263855	0.05754	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	T;T	0.34859	1.34;1.35	5.63	2.54	0.30619	.	1.415740	0.03776	N	0.260632	T	0.24314	0.0589	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.18745	-1.0327	10	0.17369	T	0.5	-2.5756	10.007	0.41964	0.0:0.2926:0.5678:0.1396	.	684;722	Q9H6E5;F5H0R1	STPAP_HUMAN;.	S	722;684	ENSP00000308000:G722S;ENSP00000419607:G684S	ENSP00000308000:G722S	G	-	1	0	TUT1	62099717	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.233000	0.32648	0.723000	0.32274	-0.165000	0.13383	GGT	.	.	none		0.577	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37442545	37442545	+	Missense_Mutation	SNP	G	G	T	rs200557667		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37442545G>T	ENST00000602533.1	+	13	1684	c.1585G>T	c.(1585-1587)Gct>Tct	p.A529S	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.A529S|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A529S			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	585					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TTTACCCAAGGCTACACATCA	0.294																																					p.A529S		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G1585T						scavenged	.	G	SER/ALA	2,3602		0,2,1800	149.0	148.0	149.0		1585	1.5	0.0	10		149	7,8129		0,7,4061	no	missense	ANKRD30A	NM_052997.2	99	0,9,5861	TT,TG,GG		0.086,0.0555,0.0767	possibly-damaging	529/1342	37442545	9,11731	1802	4068	5870	SO:0001583	missense	91074	exon13			CCCAAGGCTACAC	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1585G>T	10.37:g.37442545G>T	ENSP00000473551:p.Ala529Ser	779.0	0.0	0		714.0	132.0	0.184874	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	10.35	1.325943	0.24080	5.55E-4	8.6E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.08458	3.09;3.09	1.47	1.47	0.22746	.	.	.	.	.	T	0.13841	0.0335	L	0.34521	1.04	0.09310	N	1	D	0.58970	0.984	D	0.65443	0.935	T	0.18429	-1.0337	9	0.39692	T	0.17	.	6.4351	0.21819	0.0:0.0:1.0:0.0	.	585	Q9BXX3	AN30A_HUMAN	S	529	ENSP00000354432:A529S;ENSP00000363792:A529S	ENSP00000354432:A529S	A	+	1	0	ANKRD30A	37482551	0.001000	0.12720	0.015000	0.15790	0.022000	0.10575	0.229000	0.17833	1.140000	0.42260	0.384000	0.25694	GCT	G|0.999;T|0.001	0.001	weak		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
TEKT5	146279	hgsc.bcm.edu	37	16	10788624	10788624	+	Missense_Mutation	SNP	T	T	C	rs145995713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:10788624T>C	ENST00000283025.2	-	1	178	c.107A>G	c.(106-108)tAt>tGt	p.Y36C	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	36						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						GTAGGGCTGATAGCATTCCTG	0.562													T|||	19	0.00379393	0.0	0.0043	5008	,	,		17761	0.0		0.0119	False		,,,				2504	0.0041				p.Y36C		Atlas-SNP	.											.	TEKT5	66	.	0			c.A107G						PASS	.	T	CYS/TYR	3,4391		0,3,2194	79.0	74.0	75.0		107	5.3	1.0	16	dbSNP_134	75	73,8527		0,73,4227	yes	missense	TEKT5	NM_144674.1	194	0,76,6421	CC,CT,TT		0.8488,0.0683,0.5849	probably-damaging	36/486	10788624	76,12918	2197	4300	6497	SO:0001583	missense	146279	exon1			GGCTGATAGCATT		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.107A>G	16.37:g.10788624T>C	ENSP00000283025:p.Tyr36Cys	73.0	0.0	0		69.0	56.0	0.811594	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	.	11.16	1.557014	0.27827	6.83E-4	0.008488	ENSG00000153060	ENST00000283025	T	0.03212	4.01	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000032	T	0.08846	0.0219	M	0.72894	2.215	0.49483	D	0.999795	D	0.69078	0.997	D	0.63192	0.912	T	0.01356	-1.1376	10	0.39692	T	0.17	-39.6857	8.7187	0.34428	0.0:0.0854:0.0:0.9146	.	36	Q96M29	TEKT5_HUMAN	C	36	ENSP00000283025:Y36C	ENSP00000283025:Y36C	Y	-	2	0	TEKT5	10696125	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.922000	0.40045	1.992000	0.58205	0.533000	0.62120	TAT	T|0.994;C|0.006	0.006	strong		0.562	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748686	8748686	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748686C>G	ENST00000276282.6	-	1	2469	c.1883G>C	c.(1882-1884)aGc>aCc	p.S628T		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	628	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GTCCCTGCAGCTAACAGGCAA	0.567																																					p.S628T	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G1883C						PASS	.						75.0	63.0	67.0					8																	8748686		2203	4300	6503	SO:0001583	missense	9258	exon1			CTGCAGCTAACAG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1883G>C	8.37:g.8748686C>G	ENSP00000276282:p.Ser628Thr	55.0	0.0	0		39.0	15.0	0.384615	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789423	0.49997	.	.	ENSG00000147324	ENST00000276282	D	0.91295	-2.82	5.28	5.28	0.74379	ROC GTPase (1);	0.051489	0.85682	N	0.000000	D	0.90728	0.7090	M	0.71036	2.16	0.58432	D	0.999998	B	0.27791	0.189	B	0.30179	0.112	D	0.89321	0.3640	10	0.66056	D	0.02	.	18.0901	0.89472	0.0:1.0:0.0:0.0	.	628	Q9Y4C4	MFHA1_HUMAN	T	628	ENSP00000276282:S628T	ENSP00000276282:S628T	S	-	2	0	MFHAS1	8786096	1.000000	0.71417	0.992000	0.48379	0.715000	0.41141	7.591000	0.82666	2.736000	0.93811	0.655000	0.94253	AGC	.	.	none		0.567	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
ALPK2	115701	hgsc.bcm.edu	37	18	56202470	56202470	+	Missense_Mutation	SNP	G	G	A	rs55656447	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202470G>A	ENST00000361673.3	-	5	5162	c.4949C>T	c.(4948-4950)gCg>gTg	p.A1650V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1650						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CAAGGTCTTCGCTGAGGAGCT	0.453													G|||	26	0.00519169	0.0015	0.0187	5008	,	,		20727	0.0		0.0089	False		,,,				2504	0.002				p.A1650V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C4949T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	75.0	79.0	77.0		4949	-1.1	0.0	18	dbSNP_129	77	112,8488	57.9+/-119.4	1,110,4189	yes	missense	ALPK2	NM_052947.3	64	1,129,6373	AA,AG,GG		1.3023,0.4312,1.0072	benign	1650/2171	56202470	131,12875	2203	4300	6503	SO:0001583	missense	115701	exon5			GTCTTCGCTGAGG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4949C>T	18.37:g.56202470G>A	ENSP00000354991:p.Ala1650Val	62.0	0.0	0		40.0	21.0	0.525	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	16	0.007326007326007326	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	8	0.010554089709762533	G	16.95	3.264457	0.59431	0.004312	0.013023	ENSG00000198796	ENST00000361673	T	0.43688	0.94	5.74	-1.14	0.09741	.	2.962290	0.00633	N	0.000494	T	0.11623	0.0283	L	0.48642	1.525	0.09310	N	1	P;P	0.46952	0.887;0.482	B;B	0.32211	0.142;0.04	T	0.28586	-1.0039	10	0.02654	T	1	-0.4975	0.6684	0.00854	0.2374:0.1259:0.2499:0.3868	rs55656447	1645;1650	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1650	ENSP00000354991:A1650V	ENSP00000354991:A1650V	A	-	2	0	ALPK2	54353450	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.250000	0.18235	0.060000	0.16281	0.655000	0.94253	GCG	G|0.987;A|0.013	0.013	strong		0.453	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
MFSD3	113655	hgsc.bcm.edu	37	8	145735120	145735120	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145735120G>C	ENST00000301327.4	+	1	664	c.404G>C	c.(403-405)gGc>gCc	p.G135A	RECQL4_ENST00000532237.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	135	Leu-rich.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTGGGGCCGGGCAATACCGTG	0.692											OREG0019059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G135A		Atlas-SNP	.											.	MFSD3	17	.	0			c.G404C						PASS	.						8.0	8.0	8.0					8																	145735120		2127	4210	6337	SO:0001583	missense	113655	exon1			GGCCGGGCAATAC		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177	ENST00000301327.4:c.404G>C	8.37:g.145735120G>C	ENSP00000301327:p.Gly135Ala	29.0	0.0	0	1696	32.0	18.0	0.5625	NM_138431		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053076	0.75960	.	.	ENSG00000167700	ENST00000301327	T	0.47869	0.83	5.02	5.02	0.67125	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.67002	0.2847	M	0.66506	2.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68322	-0.5439	10	0.52906	T	0.07	-7.8332	16.1659	0.81754	0.0:0.0:1.0:0.0	.	135	Q96ES6	MFSD3_HUMAN	A	135	ENSP00000301327:G135A	ENSP00000301327:G135A	G	+	2	0	MFSD3	145705928	1.000000	0.71417	0.980000	0.43619	0.068000	0.16541	4.514000	0.60482	2.484000	0.83849	0.561000	0.74099	GGC	.	.	none		0.692	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
SWAP70	23075	hgsc.bcm.edu	37	11	9685781	9685781	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:9685781C>G	ENST00000318950.6	+	1	158	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	SWAP70_ENST00000447399.2_Missense_Mutation_p.L19V	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	19					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		CTTCACCGCACTCGACCAGGA	0.701																																					p.L19V		Atlas-SNP	.											.	SWAP70	40	.	0			c.C55G						PASS	.						32.0	26.0	28.0					11																	9685781		2187	4288	6475	SO:0001583	missense	23075	exon1			ACCGCACTCGACC	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.55C>G	11.37:g.9685781C>G	ENSP00000315630:p.Leu19Val	161.0	0.0	0		251.0	57.0	0.227092	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950471	0.73787	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86956	-2.19;2.8	5.5	5.5	0.81552	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93874	0.8040	M	0.81497	2.545	0.53005	D	0.999966	D;P;D	0.69078	0.993;0.748;0.997	D;B;D	0.78314	0.987;0.351;0.991	D	0.94329	0.7560	10	0.87932	D	0	-7.6476	19.0354	0.92974	0.0:1.0:0.0:0.0	.	19;19;19	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	V	19	ENSP00000399056:L19V;ENSP00000315630:L19V	ENSP00000315630:L19V	L	+	1	0	SWAP70	9642357	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	3.715000	0.54897	2.584000	0.87258	0.563000	0.77884	CTC	.	.	none		0.701	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
DCLK3	85443	hgsc.bcm.edu	37	3	36759599	36759599	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:36759599G>C	ENST00000416516.2	-	4	2145	c.1655C>G	c.(1654-1656)cCa>cGa	p.P552R	DCLK3_ENST00000498047.1_5'UTR	NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	552	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						GCTGCGGAATGGGGGAAAGCC	0.552																																					p.P552R		Atlas-SNP	.											.	DCLK3	95	.	0			c.C1655G						PASS	.						157.0	171.0	167.0					3																	36759599		2085	4248	6333	SO:0001583	missense	85443	exon4			CGGAATGGGGGAA	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.1655C>G	3.37:g.36759599G>C	ENSP00000394484:p.Pro552Arg	67.0	0.0	0		89.0	28.0	0.314607	NM_033403		Missense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.913710	0.72983	.	.	ENSG00000163673	ENST00000416516	T	0.58652	0.32	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.32518	N	0.005993	D	0.86464	0.5939	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91296	0.5063	10	0.87932	D	0	.	19.7913	0.96458	0.0:0.0:1.0:0.0	.	552	Q9C098	DCLK3_HUMAN	R	552	ENSP00000394484:P552R	ENSP00000394484:P552R	P	-	2	0	DCLK3	36734603	1.000000	0.71417	0.754000	0.31244	0.213000	0.24496	9.869000	0.99810	2.765000	0.95021	0.555000	0.69702	CCA	.	.	none		0.552	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389046	1389046	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1389046C>T	ENST00000324803.4	+	1	3707	c.747C>T	c.(745-747)gcC>gcT	p.A249A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	249					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGTGGAGTGCCCGCCTGCTCA	0.692																																					p.A249A		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,1	CRIPAK	185	1	0			c.C747T						PASS	.						148.0	130.0	136.0					4																	1389046		2202	4299	6501	SO:0001819	synonymous_variant	285464	exon1			GAGTGCCCGCCTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.747C>T	4.37:g.1389046C>T		82.0	0.0	0		59.0	9.0	0.152542	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.692	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
WDR66	144406	hgsc.bcm.edu	37	12	122413481	122413481	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122413481C>T	ENST00000288912.4	+	19	3750	c.2896C>T	c.(2896-2898)Cgc>Tgc	p.R966C		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	966							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TTCTCAGCTCCGCAGTCAAGG	0.438																																					p.R966C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C2896T						PASS	.						107.0	97.0	101.0					12																	122413481		1935	4131	6066	SO:0001583	missense	144406	exon19			CAGCTCCGCAGTC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2896C>T	12.37:g.122413481C>T	ENSP00000288912:p.Arg966Cys	150.0	0.0	0		132.0	59.0	0.44697	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417308	0.42918	.	.	ENSG00000158023	ENST00000288912	T	0.08546	3.08	5.26	5.26	0.73747	.	0.400698	0.27096	N	0.020942	T	0.12092	0.0294	M	0.84326	2.69	0.80722	D	1	P	0.44429	0.835	B	0.35278	0.199	T	0.01702	-1.1292	10	0.54805	T	0.06	.	9.8744	0.41194	0.1397:0.7858:0.0:0.0745	.	966	Q8TBY9	WDR66_HUMAN	C	966	ENSP00000288912:R966C	ENSP00000288912:R966C	R	+	1	0	WDR66	120897864	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	1.700000	0.37815	2.452000	0.82932	0.561000	0.74099	CGC	.	.	none		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
SYNE1	23345	hgsc.bcm.edu	37	6	152763258	152763258	+	Silent	SNP	T	T	C	rs138705766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152763258T>C	ENST00000367255.5	-	31	4561	c.3960A>G	c.(3958-3960)acA>acG	p.T1320T	SYNE1_ENST00000265368.4_Silent_p.T1320T|SYNE1_ENST00000423061.1_Silent_p.T1327T|SYNE1_ENST00000448038.1_Silent_p.T1327T|SYNE1_ENST00000367253.4_Silent_p.T1320T|SYNE1_ENST00000367248.3_Silent_p.T1310T|SYNE1_ENST00000413186.2_Silent_p.T1320T|SYNE1_ENST00000341594.5_Silent_p.T1386T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1320					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCCATCCAGTGTGCTCTCCA	0.632										HNSCC(10;0.0054)			G|||	64	0.0127796	0.0106	0.0159	5008	,	,		16360	0.001		0.0209	False		,,,				2504	0.0174				p.T1327T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A3981G						PASS	.	G	,	51,4355		0,51,2152	72.0	70.0	71.0		3981,3960	-1.4	0.7	6	dbSNP_134	71	158,8442		2,154,4144	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	2,205,6296	CC,CT,TT		1.8372,1.1575,1.607	,	1327/8750,1320/8798	152763258	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon31			ATCCAGTGTGCTC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3960A>G	6.37:g.152763258T>C		66.0	0.0	0		43.0	33.0	0.767442	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			T|0.983;C|0.017	0.017	strong		0.632	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SNAPC4	6621	hgsc.bcm.edu	37	9	139276448	139276448	+	Silent	SNP	A	A	G	rs150900916	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139276448A>G	ENST00000298532.2	-	17	2513	c.2145T>C	c.(2143-2145)caT>caC	p.H715H		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GCCACTGCACATGGGATCGGG	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		17692	0.0		0.002	False		,,,				2504	0.0				p.H715H		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T2145C						PASS	.	A		2,4396		0,2,2197	19.0	20.0	20.0		2145	-8.2	0.0	9	dbSNP_134	20	11,8579		0,11,4284	no	coding-synonymous	SNAPC4	NM_003086.2		0,13,6481	GG,GA,AA		0.1281,0.0455,0.1001		715/1470	139276448	13,12975	2199	4295	6494	SO:0001819	synonymous_variant	6621	exon17			CTGCACATGGGAT	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2145T>C	9.37:g.139276448A>G		157.0	0.0	0		112.0	62.0	0.553571	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.999;G|0.001	0.001	strong		0.657	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
IGFN1	91156	hgsc.bcm.edu	37	1	201163306	201163306	+	Missense_Mutation	SNP	C	C	G	rs41313898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163306C>G	ENST00000335211.4	+	3	162	c.32C>G	c.(31-33)cCt>cGt	p.P11R	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Missense_Mutation_p.P11R	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	11						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TCCCACATCCCTGGAGTGAGC	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18751	0.0		0.004	False		,,,				2504	0.0				p.P11R		Atlas-SNP	.											.	IGFN1	220	.	0			c.C32G						PASS	.						30.0	36.0	34.0					1																	201163306		692	1591	2283	SO:0001583	missense	91156	exon3			ACATCCCTGGAGT	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.32C>G	1.37:g.201163306C>G	ENSP00000334714:p.Pro11Arg	122.0	0.0	0		116.0	116.0	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	11.13	1.547817	0.27652	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.62788	0.24;0.0	4.55	3.61	0.41365	.	.	.	.	.	T	0.66723	0.2818	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.68146	-0.5486	7	0.87932	D	0	.	10.9911	0.47549	0.1992:0.8008:0.0:0.0	rs41313898	.	.	.	R	11	ENSP00000334714:P11R;ENSP00000398386:P11R	ENSP00000334714:P11R	P	+	2	0	IGFN1	199429929	0.281000	0.24258	0.781000	0.31783	0.577000	0.36160	2.171000	0.42453	0.840000	0.34995	0.637000	0.83480	CCT	C|0.999;G|0.001	0.001	strong		0.607	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
PCNXL3	399909	hgsc.bcm.edu	37	11	65386029	65386029	+	Missense_Mutation	SNP	G	G	A	rs538665832		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65386029G>A	ENST00000355703.3	+	6	1735	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	399						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCACCCCTGCGAAGACACTCT	0.657													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14826	0.0		0.0	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	PCNXL3	140	.	0			c.G1196A						PASS	.						17.0	19.0	18.0					11																	65386029		1990	4164	6154	SO:0001583	missense	399909	exon6			CCCTGCGAAGACA	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.1196G>A	11.37:g.65386029G>A	ENSP00000347931:p.Arg399Gln	47.0	0.0	0		53.0	16.0	0.301887	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802379	0.31869	.	.	ENSG00000197136	ENST00000355703	T	0.01051	5.4	4.47	3.55	0.40652	.	0.000000	0.31381	N	0.007758	T	0.00967	0.0032	L	0.27053	0.805	0.30274	N	0.791956	B	0.13594	0.008	B	0.04013	0.001	T	0.32851	-0.9891	10	0.15499	T	0.54	.	8.6129	0.33813	0.1056:0.0:0.8944:0.0	.	399	Q9H6A9	PCX3_HUMAN	Q	399	ENSP00000347931:R399Q	ENSP00000347931:R399Q	R	+	2	0	PCNXL3	65142605	0.853000	0.29707	0.917000	0.36280	0.882000	0.50991	2.024000	0.41049	1.098000	0.41479	0.462000	0.41574	CGA	.	.	none		0.657	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
ZNF345	25850	hgsc.bcm.edu	37	19	37368492	37368492	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37368492G>C	ENST00000529555.1	+	2	1548	c.760G>C	c.(760-762)Ggt>Cgt	p.G254R	ZNF345_ENST00000589046.1_Missense_Mutation_p.G254R|ZNF345_ENST00000420450.1_Missense_Mutation_p.G254R|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	254					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATTCATACCGGTGAGAAACC	0.423																																					p.G254R		Atlas-SNP	.											.	ZNF345	68	.	0			c.G760C						PASS	.						73.0	74.0	74.0					19																	37368492		2203	4300	6503	SO:0001583	missense	25850	exon4			CATACCGGTGAGA	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.760G>C	19.37:g.37368492G>C	ENSP00000431202:p.Gly254Arg	64.0	0.0	0		41.0	13.0	0.317073	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369349	0.61624	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.01629	4.72;4.72	3.96	3.96	0.45880	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07007	0.0178	L	0.55743	1.74	0.32084	N	0.592773	D	0.76494	0.999	D	0.63877	0.919	T	0.02156	-1.1204	9	0.87932	D	0	.	13.8686	0.63603	0.0:0.0:1.0:0.0	.	254	Q14585	ZN345_HUMAN	R	254;254;18	ENSP00000431216:G254R;ENSP00000431202:G254R	ENSP00000442320:G18R	G	+	1	0	ZNF345	42060332	0.974000	0.33945	0.999000	0.59377	0.975000	0.68041	3.047000	0.49854	2.176000	0.68965	0.561000	0.74099	GGT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
SPAG9	9043	hgsc.bcm.edu	37	17	49067870	49067870	+	Missense_Mutation	SNP	G	G	A	rs534277665		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:49067870G>A	ENST00000262013.7	-	20	2766	c.2558C>T	c.(2557-2559)aCg>aTg	p.T853M	SPAG9_ENST00000510283.1_Missense_Mutation_p.T696M|SPAG9_ENST00000357122.4_Missense_Mutation_p.T839M|SPAG9_ENST00000505279.1_Missense_Mutation_p.T843M	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	853					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GGCAGCTCCCGTCACACCTTC	0.468																																					p.T853M		Atlas-SNP	.											.	SPAG9	151	.	0			c.C2558T						PASS	.						112.0	84.0	93.0					17																	49067870		2203	4300	6503	SO:0001583	missense	9043	exon20			GCTCCCGTCACAC	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2558C>T	17.37:g.49067870G>A	ENSP00000262013:p.Thr853Met	192.0	0.0	0		146.0	75.0	0.513699	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.61|14.61	2.587305|2.587305	0.46110|0.46110	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000513906|ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.|T;T;T;T	.|0.24723	.|1.84;1.85;1.84;1.84	5.9|5.9	3.59|3.59	0.41128|0.41128	.|WD40 repeat-like-containing domain (1);	.|0.377306	.|0.31648	.|N	.|0.007293	T|T	0.23410|0.23410	0.0566|0.0566	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|P;P;P;P;P;P	.|0.44659	.|0.84;0.72;0.597;0.646;0.592;0.742	.|B;P;B;B;B;B	.|0.44732	.|0.438;0.459;0.336;0.12;0.277;0.191	T|T	0.07158|0.07158	-1.0787|-1.0787	5|10	.|0.51188	.|T	.|0.08	-3.8257|-3.8257	11.9883|11.9883	0.53161|0.53161	0.1577:0.0:0.8423:0.0|0.1577:0.0:0.8423:0.0	.|.	.|839;853;843;853;839;696	.|O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.|.;.;.;JIP4_HUMAN;.;.	W|M	112|853;610;600;390;696;843;839;451	.|ENSP00000262013:T853M;ENSP00000423165:T696M;ENSP00000426900:T843M;ENSP00000349636:T839M	.|ENSP00000262013:T853M	R|T	-|-	1|2	2|0	SPAG9|SPAG9	46422869|46422869	0.997000|0.997000	0.39634|0.39634	0.969000|0.969000	0.41365|0.41365	0.983000|0.983000	0.72400|0.72400	4.424000|4.424000	0.59868|0.59868	1.512000|1.512000	0.48834|0.48834	0.650000|0.650000	0.86243|0.86243	CGG|ACG	.	.	none		0.468	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
C19orf45	374877	hgsc.bcm.edu	37	19	7569245	7569245	+	Missense_Mutation	SNP	A	A	G	rs145077335		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7569245A>G	ENST00000361664.2	+	4	871	c.730A>G	c.(730-732)Acg>Gcg	p.T244A	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	244										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CTATGGATCAACGTGTTCGGA	0.592													a|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.T244A		Atlas-SNP	.											.	C19orf45	36	.	0			c.A730G						PASS	.	A	ALA/THR	2,4404	6.2+/-15.9	0,2,2201	63.0	65.0	64.0		730	-6.4	0.0	19	dbSNP_134	64	10,8590	7.1+/-27.0	0,10,4290	yes	missense	C19orf45	NM_198534.2	58	0,12,6491	GG,GA,AA		0.1163,0.0454,0.0923	benign	244/506	7569245	12,12994	2203	4300	6503	SO:0001583	missense	374877	exon4			GGATCAACGTGTT	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.730A>G	19.37:g.7569245A>G	ENSP00000355241:p.Thr244Ala	111.0	0.0	0		116.0	70.0	0.603448	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	a	5.651	0.304727	0.10678	4.54E-4	0.001163	ENSG00000198723	ENST00000361664	T	0.13420	2.59	4.37	-6.39	0.01951	.	2.395820	0.01247	N	0.008772	T	0.07593	0.0191	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21759	-1.0236	10	0.27785	T	0.31	-0.997	2.6616	0.05028	0.2167:0.4136:0.2533:0.1164	.	244	Q8NA69	CS045_HUMAN	A	244	ENSP00000355241:T244A	ENSP00000355241:T244A	T	+	1	0	C19orf45	7475245	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.028000	0.03589	-1.595000	0.01613	-0.549000	0.04216	ACG	A|0.999;G|0.001	0.001	strong		0.592	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
TMCO4	255104	hgsc.bcm.edu	37	1	20072082	20072082	+	Missense_Mutation	SNP	C	C	T	rs35760408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20072082C>T	ENST00000294543.6	-	10	1061	c.820G>A	c.(820-822)Ggc>Agc	p.G274S	TMCO4_ENST00000375122.2_Intron|TMCO4_ENST00000375127.1_Missense_Mutation_p.G274S	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	274						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGCTGCCTGCCCTCCGTCAGA	0.572													C|||	157	0.0313498	0.0	0.0677	5008	,	,		14564	0.0605		0.0159	False		,,,				2504	0.0337				p.G274S		Atlas-SNP	.											.	TMCO4	46	.	0			c.G820A						PASS	.	C	SER/GLY	16,4390	24.3+/-50.5	0,16,2187	124.0	122.0	123.0		820	5.0	1.0	1	dbSNP_126	123	152,8448	73.8+/-136.5	1,150,4149	yes	missense	TMCO4	NM_181719.4	56	1,166,6336	TT,TC,CC		1.7674,0.3631,1.2917	possibly-damaging	274/635	20072082	168,12838	2203	4300	6503	SO:0001583	missense	255104	exon10			GCCTGCCCTCCGT		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.820G>A	1.37:g.20072082C>T	ENSP00000294543:p.Gly274Ser	160.0	0.0	0		130.0	54.0	0.415385	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	59	0.027014652014652016	0	0.0	14	0.03867403314917127	34	0.05944055944055944	11	0.014511873350923483	C	33	5.193426	0.94960	0.003631	0.017674	ENSG00000162542	ENST00000294543;ENST00000375127	T;T	0.39997	1.05;1.05	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.39467	1.215	0.80722	D	1	D	0.54397	0.966	P	0.62885	0.908	T	0.03863	-1.0997	10	0.41790	T	0.15	-17.103	16.2009	0.82078	0.0:1.0:0.0:0.0	rs35760408	274	Q5TGY1	TMCO4_HUMAN	S	274	ENSP00000294543:G274S;ENSP00000364269:G274S	ENSP00000294543:G274S	G	-	1	0	TMCO4	19944669	1.000000	0.71417	0.988000	0.46212	0.950000	0.60333	7.072000	0.76777	2.492000	0.84095	0.455000	0.32223	GGC	C|0.981;T|0.019	0.019	strong		0.572	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
PCNX	22990	hgsc.bcm.edu	37	14	71502824	71502824	+	Missense_Mutation	SNP	G	G	T	rs117405927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71502824G>T	ENST00000304743.2	+	19	4263	c.3817G>T	c.(3817-3819)Ggt>Tgt	p.G1273C	PCNX_ENST00000238570.5_Missense_Mutation_p.G1273C|PCNX_ENST00000439984.3_Missense_Mutation_p.G1162C	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1273						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CATTGTAATTGGTGTGCTGTA	0.328													G|||	2	0.000399361	0.0	0.0	5008	,	,		18875	0.0		0.002	False		,,,				2504	0.0				p.G1273C		Atlas-SNP	.											.	PCNX	198	.	0			c.G3817T						PASS	.	G	CYS/GLY	3,4403	6.2+/-15.9	0,3,2200	280.0	246.0	257.0		3817	5.5	1.0	14	dbSNP_133	257	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PCNX	NM_014982.2	159	0,12,6491	TT,TG,GG		0.1047,0.0681,0.0923	probably-damaging	1273/2342	71502824	12,12994	2203	4300	6503	SO:0001583	missense	22990	exon19			GTAATTGGTGTGC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3817G>T	14.37:g.71502824G>T	ENSP00000304192:p.Gly1273Cys	242.0	0.0	0		191.0	98.0	0.513089	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	17.74|17.74	3.464833|3.464833	0.63513|0.63513	6.81E-4|6.81E-4	0.001047|0.001047	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.09911|.	3.37;3.37;2.93|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.60025|0.60025	0.2237|0.2237	L|L	0.31926|0.31926	0.97|0.97	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D|.	0.64830|.	0.975;0.994;0.983|.	P;D;P|.	0.65987|.	0.742;0.94;0.754|.	T|T	0.54050|0.54050	-0.8351|-0.8351	10|5	0.62326|.	D|.	0.03|.	.|.	19.329|19.329	0.94278|0.94278	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1273;1162;1273|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	C|F	1273;1273;1162|331	ENSP00000304192:G1273C;ENSP00000238570:G1273C;ENSP00000396617:G1162C|.	ENSP00000238570:G1273C|.	G|L	+|+	1|3	0|2	PCNX|PCNX	70572577|70572577	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.991000|0.991000	0.79684|0.79684	9.289000|9.289000	0.96061|0.96061	2.565000|2.565000	0.86533|0.86533	0.467000|0.467000	0.42956|0.42956	GGT|TTG	G|0.999;T|0.001	0.001	strong		0.328	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
ASB17	127247	hgsc.bcm.edu	37	1	76397871	76397871	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:76397871C>T	ENST00000284142.6	-	1	245	c.106G>A	c.(106-108)Ggt>Agt	p.G36S		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	36					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						CCCCACTGACCCAAAAACTGT	0.388																																					p.G36S		Atlas-SNP	.											.	ASB17	53	.	0			c.G106A						PASS	.						106.0	106.0	106.0					1																	76397871		2203	4300	6503	SO:0001583	missense	127247	exon1			ACTGACCCAAAAA	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.106G>A	1.37:g.76397871C>T	ENSP00000284142:p.Gly36Ser	172.0	0.0	0		147.0	42.0	0.285714	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	37	CCDS671.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929346	0.73327	.	.	ENSG00000154007	ENST00000284142	T	0.36340	1.26	6.08	3.06	0.35304	.	0.328218	0.26525	N	0.023882	T	0.09512	0.0234	N	0.19112	0.55	0.32637	N	0.521267	B	0.13594	0.008	B	0.08055	0.003	T	0.08617	-1.0713	10	0.52906	T	0.07	.	7.9022	0.29742	0.0:0.6092:0.3092:0.0817	.	36	Q8WXJ9	ASB17_HUMAN	S	36	ENSP00000284142:G36S	ENSP00000284142:G36S	G	-	1	0	ASB17	76170459	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.786000	0.38694	0.901000	0.36495	-0.136000	0.14681	GGT	.	.	none		0.388	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
SEMA3A	10371	hgsc.bcm.edu	37	7	83764113	83764113	+	Silent	SNP	T	T	C	rs74349534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:83764113T>C	ENST00000265362.4	-	2	581	c.267A>G	c.(265-267)caA>caG	p.Q89Q	SEMA3A_ENST00000436949.1_Silent_p.Q89Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	89	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTGATACCTTTTGAAAATCCT	0.328													t|||	14	0.00279553	0.0008	0.0043	5008	,	,		18311	0.0		0.0099	False		,,,				2504	0.0				p.Q89Q		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A267G						PASS	.	T		12,4394	17.9+/-39.9	0,12,2191	73.0	73.0	73.0		267	3.6	1.0	7	dbSNP_132	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	SEMA3A	NM_006080.2		1,111,6391	CC,CT,TT		1.1744,0.2724,0.8688		89/772	83764113	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon2			TACCTTTTGAAAA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.267A>G	7.37:g.83764113T>C		56.0	0.0	0		72.0	38.0	0.527778	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
PANK4	55229	hgsc.bcm.edu	37	1	2449631	2449631	+	Missense_Mutation	SNP	C	C	G	rs144881953		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:2449631C>G	ENST00000378466.3	-	9	1202	c.1190G>C	c.(1189-1191)gGc>gCc	p.G397A	PANK4_ENST00000435556.3_Missense_Mutation_p.G358A	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	397					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CTGCGCCGGGCCGAGCTCGGG	0.657																																					p.G397A		Atlas-SNP	.											.	PANK4	64	.	0			c.G1190C						PASS	.						34.0	37.0	36.0					1																	2449631		2198	4297	6495	SO:0001583	missense	55229	exon9			GCCGGGCCGAGCT	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1190G>C	1.37:g.2449631C>G	ENSP00000367727:p.Gly397Ala	47.0	0.0	0		26.0	8.0	0.307692	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	C	1.513	-0.548845	0.04024	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.96491	-4.03;-3.75	4.81	2.37	0.29283	.	0.356706	0.32106	N	0.006574	D	0.85296	0.5664	N	0.11560	0.145	0.23023	N	0.99841	B;B	0.13145	0.007;0.0	B;B	0.14023	0.01;0.001	T	0.72354	-0.4319	10	0.02654	T	1	-16.9416	1.8614	0.03189	0.2961:0.4266:0.0:0.2773	.	358;397	E9PHT6;Q9NVE7	.;PANK4_HUMAN	A	397;358	ENSP00000367727:G397A;ENSP00000421433:G358A	ENSP00000367727:G397A	G	-	2	0	PANK4	2439491	1.000000	0.71417	0.974000	0.42286	0.034000	0.12701	2.218000	0.42889	2.226000	0.72624	0.561000	0.74099	GGC	C|1.000;T|0.000	.	alt		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
LILRA6	79168	hgsc.bcm.edu	37	19	54744711	54744711	+	Missense_Mutation	SNP	C	C	G	rs1132599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744711C>G	ENST00000396365.2	-	5	990	c.951G>C	c.(949-951)atG>atC	p.M317I	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000245621.5_Missense_Mutation_p.M317I|LILRA6_ENST00000419410.2_Missense_Mutation_p.M317I|LILRA6_ENST00000440558.2_Missense_Mutation_p.M317I	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	317					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCTCACCTGCCATCAGGATGT	0.692													.|||	119	0.023762	0.0424	0.0202	5008	,	,		19749	0.001		0.0129	False		,,,				2504	0.0358				p.M317I		Atlas-SNP	.											.	LILRA6	75	.	0			c.G951C						PASS	.						17.0	26.0	23.0					19																	54744711		2084	4143	6227	SO:0001583	missense	79168	exon5			ACCTGCCATCAGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.951G>C	19.37:g.54744711C>G	ENSP00000379651:p.Met317Ile	202.0	0.0	0		147.0	16.0	0.108844	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.376427	0.00015	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.00648	5.99;5.99;5.99;5.99	2.16	-4.31	0.03698	.	0.839827	0.09740	N	0.762011	T	0.00144	0.0004	N	0.00029	-2.625	0.09310	N	0.999999	B;B;B;B	0.17852	0.001;0.024;0.0;0.0	B;B;B;B	0.09377	0.0;0.004;0.0;0.0	T	0.37174	-0.9717	10	0.02654	T	1	.	7.4079	0.27001	0.3138:0.5245:0.1617:0.0	.	317;317;317;317	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	I	317	ENSP00000390120:M317I;ENSP00000411227:M317I;ENSP00000379651:M317I;ENSP00000245621:M317I	ENSP00000245621:M317I	M	-	3	0	LILRA6	59436523	0.010000	0.17322	0.000000	0.03702	0.010000	0.07245	-0.018000	0.12568	-2.030000	0.00929	-1.042000	0.02369	ATG	C|0.976;G|0.024	0.024	strong		0.692	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
SPATA31C2	645961	hgsc.bcm.edu	37	9	90746159	90746159	+	IGR	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90746159C>T								U6 (132909 upstream) : U3 (243024 downstream)																							AAGCCAGGATCGACGCACACT	0.527																																					p.R598Q		Atlas-SNP	.											.	.	.	.	0			c.G1793A						PASS	.						45.0	38.0	40.0					9																	90746159		692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CAGGATCGACGCA																													9.37:g.90746159C>T		106.0	0.0	0		78.0	20.0	0.25641	NM_001166137		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.527								
DIRAS3	9077	hgsc.bcm.edu	37	1	68512893	68512893	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:68512893T>G	ENST00000370981.1	-	4	724	c.88A>C	c.(88-90)Aag>Cag	p.K30Q	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Missense_Mutation_p.K30Q			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	30					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CTGTGGGGCTTGAAGGCGCGG	0.607																																					p.K30Q		Atlas-SNP	.											DIRAS3,NS,carcinoma,+2,1	DIRAS3	31	1	0			c.A88C						scavenged	.						45.0	50.0	49.0					1																	68512893		2203	4300	6503	SO:0001583	missense	9077	exon2			GGGGCTTGAAGGC	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"""ras homolog gene family, member I"""	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.88A>C	1.37:g.68512893T>G	ENSP00000360020:p.Lys30Gln	100.0	2.0	0.02		86.0	23.0	0.267442	NM_004675	B3KMP3	Missense_Mutation	SNP	ENST00000370981.1	37	CCDS641.1	.	.	.	.	.	.	.	.	.	.	T	9.916	1.210778	0.22289	.	.	ENSG00000162595	ENST00000370981;ENST00000395201	T;T	0.73258	-0.73;-0.73	3.98	-5.83	0.02325	.	.	.	.	.	T	0.21103	0.0508	N	0.19112	0.55	0.09310	N	1	B	0.26775	0.159	B	0.18263	0.021	T	0.06552	-1.0820	9	0.27082	T	0.32	.	2.268	0.04084	0.1192:0.3611:0.1562:0.3635	.	30	O95661	DIRA3_HUMAN	Q	30	ENSP00000360020:K30Q;ENSP00000378627:K30Q	ENSP00000360020:K30Q	K	-	1	0	DIRAS3	68285481	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.537000	0.06128	-1.117000	0.02965	-0.468000	0.05107	AAG	.	.	none		0.607	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675	
GPR88	54112	hgsc.bcm.edu	37	1	101005554	101005554	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:101005554C>A	ENST00000315033.4	+	2	1471	c.1032C>A	c.(1030-1032)cgC>cgA	p.R344R		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	344					G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		AGGAGTTCCGCCGCTCCGTGC	0.736																																					p.R344R		Atlas-SNP	.											.	GPR88	17	.	0			c.C1032A						PASS	.						5.0	6.0	6.0					1																	101005554		2049	4046	6095	SO:0001819	synonymous_variant	54112	exon2			GTTCCGCCGCTCC	AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656		"""GPCR / Class A : Orphans"""	4539	protein-coding gene	gene with protein product		607468	"""G-protein coupled receptor 88"", ""G protein coupled receptor 88"""				Standard	NM_022049		Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.1032C>A	1.37:g.101005554C>A		5.0	0.0	0		16.0	5.0	0.3125	NM_022049	Q29S24|Q6VN48	Silent	SNP	ENST00000315033.4	37	CCDS772.1																																																																																			.	.	none		0.736	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049	
ADRM1	11047	hgsc.bcm.edu	37	20	60883192	60883192	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60883192G>A	ENST00000253003.2	+	8	1018	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	324					positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			CGCAGACCGCGGATGAGATCC	0.652																																					p.A324A		Atlas-SNP	.											.	ADRM1	28	.	0			c.G972A						PASS	.						39.0	39.0	39.0					20																	60883192		2199	4295	6494	SO:0001819	synonymous_variant	11047	exon8			GACCGCGGATGAG	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.972G>A	20.37:g.60883192G>A		72.0	0.0	0		48.0	12.0	0.25	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Silent	SNP	ENST00000253003.2	37	CCDS13496.1																																																																																			.	.	none		0.652	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
ABCB5	340273	hgsc.bcm.edu	37	7	20767981	20767981	+	Missense_Mutation	SNP	T	T	C	rs117749018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:20767981T>C	ENST00000404938.2	+	23	3422	c.2770T>C	c.(2770-2772)Ttc>Ctc	p.F924L	ABCB5_ENST00000258738.6_Missense_Mutation_p.F479L	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	924	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CTGTTATGCATTCAGCCATGC	0.393													T|||	23	0.00459265	0.0	0.0072	5008	,	,		18255	0.0		0.0109	False		,,,				2504	0.0072				p.F924L		Atlas-SNP	.											.	ABCB5	357	.	0			c.T2770C						PASS	.	T	LEU/PHE,LEU/PHE	13,4393	20.2+/-43.8	0,13,2190	150.0	154.0	153.0		2770,1435	2.7	1.0	7	dbSNP_132	153	103,8497	56.8+/-118.0	0,103,4197	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	22,22	0,116,6387	CC,CT,TT		1.1977,0.2951,0.8919	benign,benign	924/1258,479/813	20767981	116,12890	2203	4300	6503	SO:0001583	missense	340273	exon23			TATGCATTCAGCC	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2770T>C	7.37:g.20767981T>C	ENSP00000384881:p.Phe924Leu	160.0	0.0	0		134.0	31.0	0.231343	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	11.75	1.732023	0.30684	0.002951	0.011977	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90133	-2.62;-2.62	3.91	2.73	0.32206	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.220353	0.30464	N	0.009574	T	0.73345	0.3575	N	0.17474	0.49	0.29103	N	0.881356	B;B;B	0.16802	0.019;0.0;0.004	B;B;B	0.23150	0.044;0.005;0.02	T	0.64141	-0.6477	10	0.25751	T	0.34	.	4.4745	0.11729	0.1917:0.0:0.2168:0.5914	.	924;102;479	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	L	924;479	ENSP00000384881:F924L;ENSP00000258738:F479L	ENSP00000258738:F479L	F	+	1	0	ABCB5	20734506	0.810000	0.29049	0.998000	0.56505	0.990000	0.78478	1.014000	0.29950	0.827000	0.34685	0.533000	0.62120	TTC	T|0.992;C|0.008	0.008	strong		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
SLC4A4	8671	hgsc.bcm.edu	37	4	72363294	72363294	+	Missense_Mutation	SNP	A	A	T	rs35891845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:72363294A>T	ENST00000264485.5	+	16	2168	c.2051A>T	c.(2050-2052)aAc>aTc	p.N684I	SLC4A4_ENST00000351898.6_Missense_Mutation_p.N684I|SLC4A4_ENST00000340595.3_Missense_Mutation_p.N640I|SLC4A4_ENST00000425175.1_Missense_Mutation_p.N684I	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	684					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	CTCGTCGGGAACAACTGTAAT	0.378													A|||	2	0.000399361	0.0	0.0	5008	,	,		18419	0.0		0.002	False		,,,				2504	0.0				p.N684I		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A2051T						PASS	.	A	ILE/ASN,ILE/ASN,ILE/ASN	1,4405	2.1+/-5.4	0,1,2202	115.0	117.0	116.0		2051,2051,1919	3.0	1.0	4	dbSNP_126	116	24,8576	17.9+/-57.8	0,24,4276	yes	missense,missense,missense	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	149,149,149	0,25,6478	TT,TA,AA		0.2791,0.0227,0.1922	benign,benign,benign	684/1080,684/1095,640/1036	72363294	25,12981	2203	4300	6503	SO:0001583	missense	8671	exon16			TCGGGAACAACTG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2051A>T	4.37:g.72363294A>T	ENSP00000264485:p.Asn684Ile	126.0	0.0	0		140.0	66.0	0.471429	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.64	1.999658	0.35320	2.27E-4	0.002791	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000340595	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.44	3.02	0.34903	Bicarbonate transporter, C-terminal (1);	0.219123	0.53938	D	0.000044	T	0.73544	0.3600	N	0.14661	0.345	0.48087	D	0.999585	P;D;B;B	0.69078	0.592;0.997;0.313;0.136	P;D;B;B	0.64042	0.477;0.921;0.346;0.353	T	0.72364	-0.4316	10	0.41790	T	0.15	.	9.4956	0.38986	0.8562:0.0:0.1438:0.0	rs35891845	684;684;640;684	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;.;S4A4_HUMAN	I	684;684;684;640	ENSP00000264485:N684I;ENSP00000393557:N684I;ENSP00000307349:N684I;ENSP00000344272:N640I	ENSP00000264485:N684I	N	+	2	0	SLC4A4	72582158	1.000000	0.71417	1.000000	0.80357	0.241000	0.25554	3.803000	0.55560	1.002000	0.39104	0.533000	0.62120	AAC	A|0.998;T|0.002	0.002	strong		0.378	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
IFT140	9742	hgsc.bcm.edu	37	16	1652418	1652418	+	Missense_Mutation	SNP	C	C	T	rs146128830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1652418C>T	ENST00000426508.2	-	4	685	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	108					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CAACGGAGCACGGTGATGTCG	0.582													C|||	14	0.00279553	0.0023	0.0029	5008	,	,		17970	0.0		0.007	False		,,,				2504	0.002				p.V108M		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	0			c.G322A						PASS	.	C	MET/VAL	12,4386	19.1+/-41.9	0,12,2187	110.0	80.0	90.0		322	-1.2	0.0	16	dbSNP_134	90	81,8519	47.6+/-106.9	0,81,4219	yes	missense	IFT140	NM_014714.3	21	0,93,6406	TT,TC,CC		0.9419,0.2729,0.7155	possibly-damaging	108/1463	1652418	93,12905	2199	4300	6499	SO:0001583	missense	9742	exon4			GGAGCACGGTGAT	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.322G>A	16.37:g.1652418C>T	ENSP00000406012:p.Val108Met	79.0	0.0	0		85.0	15.0	0.176471	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.51	1.660137	0.29515	0.002729	0.009419	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T;T	0.60299	0.7;0.2	4.83	-1.19	0.09585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.456706	0.22233	N	0.062786	T	0.56790	0.2009	M	0.78801	2.425	0.24640	N	0.993577	D	0.59357	0.985	P	0.56042	0.79	T	0.58126	-0.7691	10	0.32370	T	0.25	.	9.8005	0.40761	0.0:0.4051:0.0:0.5949	.	108	Q96RY7	IF140_HUMAN	M	108	ENSP00000380562:V108M;ENSP00000406012:V108M	ENSP00000380562:V108M	V	-	1	0	IFT140	1592419	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	-0.032000	0.12266	-0.555000	0.06142	0.561000	0.74099	GTG	C|0.993;T|0.007	0.007	strong		0.582	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230394	23230394	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230394C>T	ENST00000526893.1	+	1	435	c.161C>T	c.(160-162)gCc>gTc	p.A54V	IGLL5_ENST00000531372.1_Missense_Mutation_p.A54V|IGLL5_ENST00000532223.2_Missense_Mutation_p.A54V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	54						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GACCCTGGAGCCTCAGTTGGA	0.667																																					p.A54V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C161T						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGGAGCCTCAGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.161C>T	22.37:g.23230394C>T	ENSP00000431254:p.Ala54Val	135.0	0.0	0		114.0	24.0	0.210526	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975826	0.53720	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00617	6.19;6.19	3.92	-1.07	0.09968	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.11329	0.006	T	0.47071	-0.9145	9	0.87932	D	0	.	2.5676	0.04787	0.1918:0.3543:0.3485:0.1053	.	54	B9A064	IGLL5_HUMAN	V	54	ENSP00000436353:A54V;ENSP00000431254:A54V	ENSP00000431254:A54V	A	+	2	0	IGLL5	21560394	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.197000	0.17197	-0.079000	0.12707	-0.152000	0.13540	GCC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
OBSCN	84033	hgsc.bcm.edu	37	1	228464303	228464303	+	Missense_Mutation	SNP	G	G	T	rs75280352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228464303G>T	ENST00000422127.1	+	22	6417	c.6373G>T	c.(6373-6375)Gct>Tct	p.A2125S	RP5-1139B12.3_ENST00000602947.1_RNA|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.A972S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A2125S|OBSCN_ENST00000570156.2_Missense_Mutation_p.A2500S|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2125	Ig-like 21.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGCCACCTGGCTGTGCGGGG	0.672													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		15176	0.0		0.0139	False		,,,				2504	0.001				p.A2500S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G7498T						PASS	.	G	SER/ALA,SER/ALA	19,4145		0,19,2063	16.0	21.0	20.0		6373,6373	1.9	0.1	1	dbSNP_131	20	234,8182		4,226,3978	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	99,99	4,245,6041	TT,TG,GG		2.7804,0.4563,2.0111	benign,benign	2125/7969,2125/6621	228464303	253,12327	2082	4208	6290	SO:0001583	missense	84033	exon26			CACCTGGCTGTGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.6373G>T	1.37:g.228464303G>T	ENSP00000409493:p.Ala2125Ser	234.0	0.0	0		232.0	134.0	0.577586	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	10.48	1.363003	0.24684	0.004563	0.027804	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04234	3.67;3.67;3.67	5.23	1.86	0.25419	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.356983	0.26203	N	0.025723	T	0.00724	0.0024	N	0.13168	0.305	0.20403	N	0.999906	P;P	0.44816	0.844;0.499	B;B	0.39152	0.292;0.069	T	0.39901	-0.9591	10	0.08599	T	0.76	.	4.5827	0.12266	0.298:0.0:0.5441:0.1578	.	2125;2125	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	2125;2125;972	ENSP00000284548:A2125S;ENSP00000409493:A2125S;ENSP00000352613:A972S	ENSP00000284548:A2125S	A	+	1	0	OBSCN	226530926	0.038000	0.19896	0.075000	0.20258	0.026000	0.11368	1.268000	0.33062	1.193000	0.43086	0.549000	0.68633	GCT	G|0.993;T|0.007	0.007	strong		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GGCX	2677	hgsc.bcm.edu	37	2	85788528	85788528	+	Silent	SNP	C	C	T	rs371622780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85788528C>T	ENST00000233838.4	-	1	104	c.24G>A	c.(22-24)gcG>gcA	p.A8A	VAMP8_ENST00000432071.1_5'Flank|GGCX_ENST00000430215.3_Silent_p.A8A	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	8					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GCGAGGTCCGCGCGGACCCGG	0.697																																					p.A8A		Atlas-SNP	.											.	GGCX	44	.	0			c.G24A						PASS	.	C	,	0,4272		0,0,2136	6.0	8.0	8.0		24,24	1.2	0.1	2		8	5,8413		0,5,4204	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,5,6340	TT,TC,CC		0.0594,0.0,0.0394	,	8/759,8/702	85788528	5,12685	2136	4209	6345	SO:0001819	synonymous_variant	2677	exon1			GGTCCGCGCGGAC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.24G>A	2.37:g.85788528C>T		126.0	0.0	0		137.0	67.0	0.489051	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			.	.	weak		0.697	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28213527	28213527	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28213527C>T	ENST00000377294.2	-	5	1248	c.1005G>A	c.(1003-1005)ctG>ctA	p.L335L	ZKSCAN4_ENST00000423974.2_Silent_p.L180L	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	335					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TGTGTTTAGTCAGGCCTGAAC	0.453																																					p.L335L		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.G1005A						PASS	.						130.0	114.0	119.0					6																	28213527		2203	4300	6503	SO:0001819	synonymous_variant	387032	exon5			TTTAGTCAGGCCT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.1005G>A	6.37:g.28213527C>T		152.0	0.0	0		138.0	54.0	0.391304	NM_019110	B2RE32|Q5U7L4	Silent	SNP	ENST00000377294.2	37	CCDS4647.1																																																																																			.	.	none		0.453	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
CLDND2	125875	hgsc.bcm.edu	37	19	51871194	51871194	+	Missense_Mutation	SNP	C	C	T	rs61736500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51871194C>T	ENST00000291715.1	-	2	681	c.256G>A	c.(256-258)Gac>Aac	p.D86N	CTD-2616J11.10_ENST00000595500.1_RNA|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.D21N|CLDND2_ENST00000601435.1_Missense_Mutation_p.D86N|ETFB_ENST00000309244.4_5'Flank	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	86						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCGCCCTCGTCGCACCGAATC	0.726													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		11998	0.0		0.0089	False		,,,				2504	0.002				p.D86N		Atlas-SNP	.											.	CLDND2	11	.	0			c.G256A						PASS	.	C	ASN/ASP	2,4398		0,2,2198	29.0	29.0	29.0		256	-0.3	0.0	19	dbSNP_129	29	54,8540		0,54,4243	yes	missense	CLDND2	NM_152353.2	23	0,56,6441	TT,TC,CC		0.6283,0.0455,0.431	benign	86/168	51871194	56,12938	2200	4297	6497	SO:0001583	missense	125875	exon2			CCTCGTCGCACCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.256G>A	19.37:g.51871194C>T	ENSP00000291715:p.Asp86Asn	133.0	0.0	0		118.0	68.0	0.576271	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	7.665	0.685760	0.14973	4.55E-4	0.006283	ENSG00000160318	ENST00000291715	D	0.88509	-2.39	4.69	-0.277	0.12898	.	1.778600	0.02886	N	0.133517	T	0.67859	0.2938	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.62388	-0.6865	10	0.12766	T	0.61	-0.1713	3.1085	0.06350	0.097:0.3345:0.3983:0.1702	.	86	Q8NHS1	CLDN2_HUMAN	N	86	ENSP00000291715:D86N	ENSP00000291715:D86N	D	-	1	0	CLDND2	56563006	0.000000	0.05858	0.010000	0.14722	0.379000	0.30106	0.451000	0.21779	0.081000	0.16988	-0.228000	0.12330	GAC	C|0.995;T|0.005	0.005	strong		0.726	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
MTRR	4552	hgsc.bcm.edu	37	5	7900056	7900056	+	Missense_Mutation	SNP	A	A	G	rs148909799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:7900056A>G	ENST00000264668.2	+	15	2093	c.2063A>G	c.(2062-2064)cAt>cGt	p.H688R	MTRR_ENST00000440940.2_Missense_Mutation_p.H661R	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	688					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AAGGATGTACATGATGCCCTT	0.358													A|||	3	0.000599042	0.0	0.0	5008	,	,		17957	0.0		0.002	False		,,,				2504	0.001				p.H688R		Atlas-SNP	.											.	MTRR	74	.	0			c.A2063G						PASS	.	A	ARG/HIS,ARG/HIS	3,4403	4.2+/-10.8	0,3,2200	100.0	105.0	103.0		1982,2063	3.3	0.0	5	dbSNP_134	103	24,8576	17.3+/-56.4	1,22,4277	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	29,29	1,25,6477	GG,GA,AA		0.2791,0.0681,0.2076	benign,benign	661/699,688/726	7900056	27,12979	2203	4300	6503	SO:0001583	missense	4552	exon15			ATGTACATGATGC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.2063A>G	5.37:g.7900056A>G	ENSP00000264668:p.His688Arg	153.0	0.0	0		129.0	67.0	0.51938	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.273	1.046111	0.19748	6.81E-4	0.002791	ENSG00000124275	ENST00000264668;ENST00000440940	D;D	0.85629	-2.01;-2.01	5.71	3.29	0.37713	Oxidoreductase FAD/NAD(P)-binding (1);	0.266108	0.46758	D	0.000276	T	0.72399	0.3455	N	0.16862	0.45	0.44316	D	0.997191	B	0.21821	0.061	B	0.24974	0.057	T	0.64228	-0.6457	10	0.27785	T	0.31	-16.3277	9.6534	0.39910	0.7885:0.0:0.2115:0.0	.	688	Q9UBK8	MTRR_HUMAN	R	688;661	ENSP00000264668:H688R;ENSP00000402510:H661R	ENSP00000264668:H688R	H	+	2	0	MTRR	7953056	1.000000	0.71417	0.013000	0.15412	0.988000	0.76386	2.540000	0.45727	0.999000	0.39023	0.533000	0.62120	CAT	A|0.998;G|0.002	0.002	strong		0.358	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
ATP10B	23120	hgsc.bcm.edu	37	5	160115007	160115007	+	Silent	SNP	C	C	T	rs201071012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:160115007C>T	ENST00000327245.5	-	5	921	c.75G>A	c.(73-75)tcG>tcA	p.S25S	CTC-529G1.1_ENST00000524198.1_RNA|ATP10B_ENST00000518411.1_5'UTR	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	25					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGTGGTTTCCGATGGACAAT	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		18673	0.0		0.001	False		,,,				2504	0.0				p.S25S		Atlas-SNP	.											.	ATP10B	201	.	0			c.G75A						PASS	.	T		3,4129		0,3,2063	96.0	98.0	97.0		75	1.4	0.9	5		97	20,8428		0,20,4204	no	coding-synonymous	ATP10B	NM_025153.2		0,23,6267	TT,TC,CC		0.2367,0.0726,0.1828		25/1462	160115007	23,12557	2066	4224	6290	SO:0001819	synonymous_variant	23120	exon5			GGTTTCCGATGGA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.75G>A	5.37:g.160115007C>T		177.0	1.0	0.00564972		146.0	86.0	0.589041	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			C|0.996;T|0.005	0.005	strong		0.537	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
CHDH	55349	hgsc.bcm.edu	37	3	53855738	53855738	+	Silent	SNP	G	G	C	rs35064726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142.0	126.0	131.0		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.921C>G	3.37:g.53855738G>C		96.0	0.0	0		71.0	38.0	0.535211	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
HAS1	3036	hgsc.bcm.edu	37	19	52217174	52217174	+	Missense_Mutation	SNP	C	C	T	rs45625331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52217174C>T	ENST00000222115.1	-	5	1277	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M	HAS1_ENST00000540069.2_Missense_Mutation_p.V414M|HAS1_ENST00000601714.1_Missense_Mutation_p.V422M|HAS1_ENST00000594621.1_3'UTR	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	415					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GTGGCCGCCACGAAGAAGGGG	0.672													c|||	5	0.000998403	0.0	0.0029	5008	,	,		16422	0.0		0.002	False		,,,				2504	0.001				p.V415M	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G1243A						PASS	.		MET/VAL	5,4393	8.1+/-20.4	0,5,2194	48.0	42.0	44.0		1243	3.2	1.0	19	dbSNP_127	44	58,8542	32.8+/-85.7	0,58,4242	yes	missense	HAS1	NM_001523.2	21	0,63,6436	TT,TC,CC		0.6744,0.1137,0.4847	probably-damaging	415/579	52217174	63,12935	2199	4300	6499	SO:0001583	missense	3036	exon5			CCGCCACGAAGAA	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1243G>A	19.37:g.52217174C>T	ENSP00000222115:p.Val415Met	21.0	0.0	0		17.0	8.0	0.470588	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	16.44	3.122752	0.56613	0.001137	0.006744	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59638	0.25;0.25	3.19	3.19	0.36642	.	0.000000	0.64402	U	0.000002	T	0.56093	0.1962	L	0.49778	1.585	0.58432	D	0.999992	D;D;D	0.67145	0.992;0.996;0.996	P;P;P	0.58013	0.63;0.831;0.831	T	0.65919	-0.6051	10	0.72032	D	0.01	-12.5318	12.2755	0.54733	0.0:1.0:0.0:0.0	rs45625331	414;415;414	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	M	414;415	ENSP00000445021:V414M;ENSP00000222115:V415M	ENSP00000222115:V415M	V	-	1	0	HAS1	56908986	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	3.956000	0.56722	1.812000	0.52913	0.165000	0.16767	GTG	C|0.997;T|0.003	0.003	strong		0.672	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274266	39274266	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39274266C>T	ENST00000391413.2	-	1	340	c.302G>A	c.(301-303)cGc>cAc	p.R101H		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	101	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcatctggggcggcagcaAGT	0.647																																					p.R101H		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G302A						PASS	.						5.0	9.0	8.0					17																	39274266		655	1560	2215	SO:0001583	missense	653240	exon1			CTGGGGCGGCAGC	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.302G>A	17.37:g.39274266C>T	ENSP00000375232:p.Arg101His	37.0	0.0	0		32.0	8.0	0.25	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249110	0.22880	.	.	ENSG00000212721	ENST00000391413	T	0.00638	6.04	3.99	1.96	0.26148	.	1.399950	0.05646	U	0.584357	T	0.01189	0.0039	M	0.78456	2.415	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.50550	-0.8815	10	0.42905	T	0.14	.	3.6707	0.08273	0.1929:0.5877:0.0:0.2193	.	101	Q9BYQ6	KR411_HUMAN	H	101	ENSP00000375232:R101H	ENSP00000375232:R101H	R	-	2	0	KRTAP4-11	36527792	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.701000	0.05075	0.180000	0.19960	-0.192000	0.12808	CGC	.	.	none		0.647	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
DAPK1	1612	hgsc.bcm.edu	37	9	90252966	90252966	+	Silent	SNP	C	C	T	rs55800264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90252966C>T	ENST00000408954.3	+	4	728	c.393C>T	c.(391-393)caC>caT	p.H131H	DAPK1_ENST00000472284.1_Silent_p.H131H|DAPK1_ENST00000469640.2_Silent_p.H131H|DAPK1_ENST00000358077.5_Silent_p.H131H|DAPK1_ENST00000491893.1_Silent_p.H131H	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						ACTACCTGCACTCCCTTCAAA	0.408									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	19	0.00379393	0.0	0.0101	5008	,	,		20103	0.0		0.0089	False		,,,				2504	0.0031				p.H131H		Atlas-SNP	.											.	DAPK1	329	.	0			c.C393T						PASS	.	C		13,3843		0,13,1915	101.0	94.0	96.0		393	0.3	1.0	9	dbSNP_129	96	140,8146		1,138,4004	no	coding-synonymous	DAPK1	NM_004938.2		1,151,5919	TT,TC,CC		1.6896,0.3371,1.2601		131/1431	90252966	153,11989	1928	4143	6071	SO:0001819	synonymous_variant	1612	exon4	Familial Cancer Database	Familial CLL	CCTGCACTCCCTT	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.393C>T	9.37:g.90252966C>T		110.0	0.0	0		75.0	32.0	0.426667	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
OR13C3	138803	hgsc.bcm.edu	37	9	107298270	107298270	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:107298270C>A	ENST00000374781.2	-	1	867	c.825G>T	c.(823-825)ctG>ctT	p.L275L		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						TCACCACAGTCAGGTGAGCTG	0.423																																					p.L275L	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.G825T						PASS	.						134.0	126.0	129.0					9																	107298270		2203	4300	6503	SO:0001819	synonymous_variant	138803	exon1			CACAGTCAGGTGA		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.825G>T	9.37:g.107298270C>A		141.0	0.0	0		108.0	22.0	0.203704	NM_001001961	Q5VVG1|Q6IF52	Silent	SNP	ENST00000374781.2	37	CCDS35089.1																																																																																			.	.	none		0.423	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
PTHLH	5744	hgsc.bcm.edu	37	12	28116465	28116465	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:28116465A>G	ENST00000545234.1	-	5	880	c.340T>C	c.(340-342)Tac>Cac	p.Y114H	PTHLH_ENST00000535992.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000539239.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000201015.4_Missense_Mutation_p.Y114H|PTHLH_ENST00000395868.3_Missense_Mutation_p.Y114H|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000354417.3_Missense_Mutation_p.Y114H|PTHLH_ENST00000395872.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000538310.1_Missense_Mutation_p.Y114H			P12272	PTHR_HUMAN	parathyroid hormone-like hormone	114					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|endochondral ossification (GO:0001958)|endoderm development (GO:0007492)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|lung alveolus development (GO:0048286)|mammary gland bud elongation (GO:0060649)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|nipple sheath formation (GO:0060659)|osteoblast development (GO:0002076)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|protein processing (GO:0016485)|regulation of gene expression (GO:0010468)|skeletal system development (GO:0001501)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	10	Lung SC(9;0.184)					TGCTCTTTGTACGTCTCCACC	0.517																																					p.Y114H		Atlas-SNP	.											.	PTHLH	36	.	0			c.T340C						PASS	.						160.0	151.0	154.0					12																	28116465		2203	4300	6503	SO:0001583	missense	5744	exon3			CTTTGTACGTCTC		CCDS8715.1, CCDS44853.1	12p12.1-p11.2	2014-01-07			ENSG00000087494	ENSG00000087494		"""Endogenous ligands"""	9607	protein-coding gene	gene with protein product	"""osteostatin"", ""parathyroid hormone-like hormone preproprotein"", ""parathyroid hormone-related protein preproprotein"""	168470				2708388	Standard	NM_002820		Approved	PTHRP, HHM, PLP, PTHR	uc001ril.3	P12272	OTTHUMG00000169221	ENST00000545234.1:c.340T>C	12.37:g.28116465A>G	ENSP00000441765:p.Tyr114His	214.0	0.0	0		169.0	38.0	0.224852	NM_198964	Q15251|Q6FH74	Missense_Mutation	SNP	ENST00000545234.1	37	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241957	0.79912	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963	D;D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.56	5.56	0.83823	.	0.054525	0.85682	D	0.000000	D	0.88808	0.6537	L	0.39245	1.2	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.88398	0.3013	10	0.41790	T	0.15	-16.5447	14.8854	0.70564	1.0:0.0:0.0:0.0	.	114	P12272	PTHR_HUMAN	H	114	ENSP00000379213:Y114H;ENSP00000441571:Y114H;ENSP00000441765:Y114H;ENSP00000441890:Y114H;ENSP00000346398:Y114H;ENSP00000201015:Y114H;ENSP00000440613:Y114H;ENSP00000379209:Y114H;ENSP00000444519:Y114H	ENSP00000201015:Y114H	Y	-	1	0	PTHLH	28007732	1.000000	0.71417	0.891000	0.34965	0.917000	0.54804	7.859000	0.86982	2.111000	0.64477	0.477000	0.44152	TAC	.	.	none		0.517	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	NM_198965	
C1orf110	339512	hgsc.bcm.edu	37	1	162824960	162824960	+	Silent	SNP	G	G	A	rs190249067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162824960G>A	ENST00000367910.1	-	4	624	c.504C>T	c.(502-504)gaC>gaT	p.D168D	C1orf110_ENST00000367912.2_Silent_p.D167D|C1orf110_ENST00000367911.2_Silent_p.D163D|C1orf110_ENST00000524691.1_Intron	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	168										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						TGGGGTCTACGTCCTTAGATG	0.463													G|||	3	0.000599042	0.0	0.0	5008	,	,		20117	0.002		0.001	False		,,,				2504	0.0				p.D168D		Atlas-SNP	.											.	C1orf110	22	.	0			c.C504T						PASS	.	G		2,3840		0,2,1919	274.0	261.0	265.0		504	-0.1	0.0	1		265	33,8235		0,33,4101	no	coding-synonymous	C1orf110	NM_178550.4		0,35,6020	AA,AG,GG		0.3991,0.0521,0.289		168/303	162824960	35,12075	1921	4134	6055	SO:0001819	synonymous_variant	339512	exon4			GTCTACGTCCTTA	BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860			28736	protein-coding gene	gene with protein product						12477932	Standard	NM_178550		Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000367910.1:c.504C>T	1.37:g.162824960G>A		242.0	0.0	0		215.0	103.0	0.47907	NM_178550	Q5JSG1|Q6ZW57	Silent	SNP	ENST00000367910.1	37	CCDS44269.1																																																																																			G|0.999;A|0.001	0.001	strong		0.463	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550	
PHPT1	29085	hgsc.bcm.edu	37	9	139744578	139744578	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139744578G>A	ENST00000247665.10	+	2	611	c.274G>A	c.(274-276)Ggc>Agc	p.G92S	MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000371661.1_Missense_Mutation_p.G92S|PHPT1_ENST00000545326.1_Missense_Mutation_p.G92S|MAMDC4_ENST00000445819.1_5'Flank	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	92					negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		TCACGTGTACGGCTATTCCAT	0.657																																					p.G92S		Atlas-SNP	.											.	PHPT1	14	.	0			c.G274A						PASS	.						97.0	90.0	92.0					9																	139744578		2202	4300	6502	SO:0001583	missense	29085	exon2			GTGTACGGCTATT	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.274G>A	9.37:g.139744578G>A	ENSP00000247665:p.Gly92Ser	111.0	0.0	0		146.0	39.0	0.267123	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	35	5.458139	0.96240	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	D	0.85270	0.5658	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88984	0.3410	8	0.66056	D	0.02	-0.5277	16.4133	0.83726	0.0:0.0:1.0:0.0	.	92;92	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	S	92	.	ENSP00000247665:G92S	G	+	1	0	PHPT1	138864399	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.076000	0.57591	2.098000	0.63641	0.455000	0.32223	GGC	.	.	none		0.657	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.V598M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5.0	6.0	6.0		2512	-3.5	0.0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	89.0	0.0	0		119.0	22.0	0.184874	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721208	135721208	+	Missense_Mutation	SNP	A	A	G	rs146596318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:135721208A>G	ENST00000264977.3	+	2	1485	c.868A>G	c.(868-870)Aaa>Gaa	p.K290E	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	290					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATCCTATCTGAAAAAGTTACC	0.378																																					p.K290E		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A868G						PASS	.	A	,GLU/LYS	0,4406		0,0,2203	93.0	91.0	91.0		,868	5.3	1.0	3	dbSNP_134	91	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	,possibly-damaging	,290/1151	135721208	4,13002	2203	4300	6503	SO:0001583	missense	5523	exon2			TATCTGAAAAAGT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.868A>G	3.37:g.135721208A>G	ENSP00000264977:p.Lys290Glu	51.0	0.0	0		44.0	22.0	0.5	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.463519	0.63513	0.0	4.65E-4	ENSG00000073711	ENST00000264977	T	0.16897	2.31	5.34	5.34	0.76211	.	0.102401	0.64402	D	0.000004	T	0.23611	0.0571	L	0.58101	1.795	0.80722	D	1	P	0.45348	0.856	B	0.43754	0.43	T	0.01894	-1.1252	10	0.87932	D	0	.	14.5059	0.67752	1.0:0.0:0.0:0.0	.	290	Q06190	P2R3A_HUMAN	E	290	ENSP00000264977:K290E	ENSP00000264977:K290E	K	+	1	0	PPP2R3A	137203898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.957000	0.93082	2.010000	0.58986	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	strong		0.378	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
RC3H2	54542	hgsc.bcm.edu	37	9	125639808	125639808	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125639808C>T	ENST00000373670.1	-	8	1867	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	RC3H2_ENST00000423239.2_Missense_Mutation_p.G423R|RC3H2_ENST00000335387.5_Missense_Mutation_p.G423R|SNORD90_ENST00000391145.1_RNA|RC3H2_ENST00000357244.2_Missense_Mutation_p.G423R|RC3H2_ENST00000373665.2_Missense_Mutation_p.G423R			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	423					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						GGACAACCCCCTTGCTGTCGC	0.418																																					p.G423R		Atlas-SNP	.											.	RC3H2	150	.	0			c.G1267A						PASS	.						276.0	270.0	272.0					9																	125639808		1898	4121	6019	SO:0001583	missense	54542	exon9			AACCCCCTTGCTG	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.1267G>A	9.37:g.125639808C>T	ENSP00000362774:p.Gly423Arg	73.0	0.0	0		60.0	37.0	0.616667	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810872	0.90707	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000373663;ENST00000423239;ENST00000373665;ENST00000335387	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	5.54	5.54	0.83059	Zinc finger, CCCH-type (3);	0.109140	0.64402	N	0.000006	D	0.84660	0.5521	M	0.69463	2.115	0.54753	D	0.999985	B;D;D;D	0.76494	0.329;0.988;0.999;0.998	B;D;D;D	0.70487	0.327;0.954;0.969;0.948	T	0.82774	-0.0291	10	0.35671	T	0.21	-10.2029	18.4783	0.90800	0.0:1.0:0.0:0.0	.	423;294;423;423	A6NHN2;Q4VXB0;Q9HBD1;Q9HBD1-4	.;.;RC3H2_HUMAN;.	R	423;423;294;423;423;423	ENSP00000362774:G423R;ENSP00000349783:G423R;ENSP00000411767:G423R;ENSP00000362769:G423R;ENSP00000335150:G423R	ENSP00000335150:G423R	G	-	1	0	RC3H2	124679629	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.043000	0.71004	2.627000	0.88993	0.637000	0.83480	GGG	.	.	none		0.418	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
PIPOX	51268	hgsc.bcm.edu	37	17	27371919	27371919	+	Missense_Mutation	SNP	C	C	T	rs543013733		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27371919C>T	ENST00000323372.4	+	2	483	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	53					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	TGGACAAAGCCGGATAATCCG	0.517																																					p.R53W		Atlas-SNP	.											PIPOX,NS,carcinoma,-1,1	PIPOX	42	1	0			c.C157T						PASS	.						123.0	108.0	113.0					17																	27371919		2203	4300	6503	SO:0001583	missense	51268	exon2			CAAAGCCGGATAA	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"""L-pipecolic acid oxidase"""					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.157C>T	17.37:g.27371919C>T	ENSP00000317721:p.Arg53Trp	109.0	0.0	0		108.0	18.0	0.166667	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	37	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.484929	0.84854	.	.	ENSG00000179761	ENST00000323372	D	0.81908	-1.55	5.8	4.82	0.62117	FAD dependent oxidoreductase (1);	0.167524	0.51477	D	0.000093	D	0.90556	0.7040	M	0.90542	3.125	0.80722	D	1	D	0.67145	0.996	P	0.58520	0.84	D	0.91764	0.5422	10	0.66056	D	0.02	-12.3601	13.0057	0.58703	0.0:0.9201:0.0:0.0798	.	53	Q9P0Z9	SOX_HUMAN	W	53	ENSP00000317721:R53W	ENSP00000317721:R53W	R	+	1	2	PIPOX	24396045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.408000	0.44574	2.740000	0.93945	0.650000	0.86243	CGG	.	.	none		0.517	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518	
MUC4	4585	hgsc.bcm.edu	37	3	195506676	195506676	+	Silent	SNP	G	G	A	rs147667126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506676G>A	ENST00000463781.3	-	2	12234	c.11775C>T	c.(11773-11775)gaC>gaT	p.D3925D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3925D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCGAGGAAACGTCGGTGACAG	0.587													.|||	605	0.120807	0.3185	0.0994	5008	,	,		11176	0.0208		0.0885	False		,,,				2504	0.0051				p.D3925D		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11775T						PASS	.						24.0	25.0	24.0					3																	195506676		539	1108	1647	SO:0001819	synonymous_variant	4585	exon2			GGAAACGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11775C>T	3.37:g.195506676G>A		205.0	0.0	0		117.0	112.0	0.957265	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.740;A|0.260	0.260	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1.0	1.0	1.0					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	128.0	0.0	0		126.0	22.0	0.174603	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
KIF13A	63971	hgsc.bcm.edu	37	6	17764896	17764896	+	Missense_Mutation	SNP	G	G	C	rs41267712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:17764896G>C	ENST00000259711.6	-	39	4968	c.4863C>G	c.(4861-4863)gaC>gaG	p.D1621E	KIF13A_ENST00000378816.5_Missense_Mutation_p.D1586E|KIF13A_ENST00000378814.5_Missense_Mutation_p.D1573E|KIF13A_ENST00000378826.2_Missense_Mutation_p.D1586E|KIF13A_ENST00000378843.2_Missense_Mutation_p.D1573E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1621					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TGGCCAGCTGGTCTGAGCTGT	0.537													G|||	17	0.00339457	0.0008	0.0029	5008	,	,		18971	0.0		0.0119	False		,,,				2504	0.002				p.D1621E		Atlas-SNP	.											.	KIF13A	276	.	0			c.C4863G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	7,4099		0,7,2046	76.0	76.0	76.0		4758,4719,4719,4863	-10.1	0.3	6	dbSNP_127	76	89,8313		0,89,4112	yes	missense,missense,missense,missense	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	45,45,45,45	0,96,6158	CC,CG,GG		1.0593,0.1705,0.7675	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1586/1771,1573/1758,1573/1750,1621/1806	17764896	96,12412	2053	4201	6254	SO:0001583	missense	63971	exon39			CAGCTGGTCTGAG	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.4863C>G	6.37:g.17764896G>C	ENSP00000259711:p.Asp1621Glu	83.0	0.0	0		67.0	37.0	0.552239	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	22.2	4.253429	0.80135	0.001705	0.010593	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	-10.1	0.00402	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	L	0.34521	1.04	0.33165	D	0.54753	D;D;D;D	0.67145	0.996;0.996;0.988;0.996	D;D;P;D	0.77557	0.99;0.99;0.675;0.99	T	0.76876	-0.2797	10	0.05721	T	0.95	.	21.8125	0.99961	0.3087:0.0:0.6913:0.0	rs41267712	1573;1586;1621;1573	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	E	1573;625;1621;1586;1573;1586	ENSP00000368091:D1573E;ENSP00000425616:D625E;ENSP00000259711:D1621E;ENSP00000368103:D1586E;ENSP00000368120:D1573E;ENSP00000368093:D1586E	ENSP00000259711:D1621E	D	-	3	2	KIF13A	17872875	0.992000	0.36948	0.342000	0.25602	0.975000	0.68041	0.249000	0.18216	-1.853000	0.01165	-0.423000	0.05987	GAC	G|0.995;C|0.005	0.005	strong		0.537	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
PPP1R32	220004	hgsc.bcm.edu	37	11	61252200	61252200	+	Missense_Mutation	SNP	A	A	G	rs146231065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61252200A>G	ENST00000338608.2	+	5	547	c.422A>G	c.(421-423)cAg>cGg	p.Q141R	RP11-286N22.8_ENST00000544880.1_3'UTR|PPP1R32_ENST00000432063.2_Missense_Mutation_p.Q141R	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	141							phosphatase binding (GO:0019902)										CACGGGCCTCAGGCCATCACG	0.642													A|||	25	0.00499201	0.0	0.0	5008	,	,		17677	0.001		0.0089	False		,,,				2504	0.0153				p.Q141R		Atlas-SNP	.											.	.	.	.	0			c.A422G						PASS	.	A	ARG/GLN,ARG/GLN	11,4393	19.1+/-41.9	1,9,2192	32.0	29.0	30.0		422,422	5.3	0.5	11	dbSNP_134	30	63,8535	37.4+/-92.8	0,63,4236	yes	missense,missense	C11orf66	NM_001170753.1,NM_145017.2	43,43	1,72,6428	GG,GA,AA		0.7327,0.2498,0.5691	possibly-damaging,possibly-damaging	141/406,141/426	61252200	74,12928	2202	4299	6501	SO:0001583	missense	220004	exon5			GGCCTCAGGCCAT	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.422A>G	11.37:g.61252200A>G	ENSP00000344140:p.Gln141Arg	106.0	0.0	0		84.0	48.0	0.571429	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	13.34	2.208254	0.39003	0.002498	0.007327	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.45276	0.9;1.49	5.33	5.33	0.75918	.	0.548000	0.17786	N	0.162044	T	0.29491	0.0735	M	0.63428	1.95	0.29499	N	0.855042	B;B	0.32829	0.386;0.386	B;B	0.31101	0.124;0.124	T	0.35251	-0.9796	9	.	.	.	-12.7669	7.9832	0.30196	0.9082:0.0:0.0918:0.0	.	141;141	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	R	141	ENSP00000391560:Q141R;ENSP00000344140:Q141R	.	Q	+	2	0	C11orf66	61008776	0.092000	0.21681	0.540000	0.28089	0.816000	0.46133	1.745000	0.38278	2.028000	0.59812	0.379000	0.24179	CAG	A|0.995;G|0.005	0.005	strong		0.642	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
TRIM63	84676	hgsc.bcm.edu	37	1	26384973	26384973	+	Nonsense_Mutation	SNP	G	G	A	rs148395034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26384973G>A	ENST00000374272.3	-	5	877	c.739C>T	c.(739-741)Cag>Tag	p.Q247*	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	247					cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTACTGCTGGATGAGGGCC	0.557													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19266	0.0		0.0	False		,,,				2504	0.0				p.Q247X		Atlas-SNP	.											.	TRIM63	33	.	0			c.C739T						PASS	.	G	stop/GLN	0,4406		0,0,2203	142.0	129.0	133.0		739	5.5	1.0	1	dbSNP_134	133	6,8594	5.0+/-18.6	0,6,4294	yes	stop-gained	TRIM63	NM_032588.2		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		247/354	26384973	6,13000	2203	4300	6503	SO:0001587	stop_gained	84676	exon5			ACTGCTGGATGAG	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	16007	protein-coding gene	gene with protein product	"""muscle-specific RING finger protein 1"", ""iris ring finger protein"", ""striated muscle RING zinc finger protein"""	606131	"""ring finger protein 28"", ""tripartite motif-containing 63"", ""tripartite motif containing 63"""	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.739C>T	1.37:g.26384973G>A	ENSP00000363390:p.Gln247*	153.0	0.0	0		160.0	73.0	0.45625	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Nonsense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	.	.	.	.	.	.	.	.	.	.	G	36	5.623049	0.96660	0.0	6.98E-4	ENSG00000158022	ENST00000374272	.	.	.	5.5	5.5	0.81552	.	0.425067	0.28436	N	0.015350	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	9.3577	0.38177	0.0778:0.1466:0.7756:0.0	.	.	.	.	X	247	.	ENSP00000363390:Q247X	Q	-	1	0	TRIM63	26257560	0.561000	0.26578	1.000000	0.80357	0.968000	0.65278	0.572000	0.23684	2.581000	0.87130	0.561000	0.74099	CAG	G|0.999;A|0.001	0.001	strong		0.557	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588	
MUC17	140453	hgsc.bcm.edu	37	7	100683796	100683796	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100683796T>C	ENST00000306151.4	+	3	9163	c.9099T>C	c.(9097-9099)ggT>ggC	p.G3033G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3033	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGCTGAAGGTACCGGCATAC	0.512																																					p.G3033G		Atlas-SNP	.											MUC17,caecum,carcinoma,+2,2	MUC17	804	2	0			c.T9099C						scavenged	.						265.0	278.0	274.0					7																	100683796		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAAGGTACCGGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9099T>C	7.37:g.100683796T>C		24.0	0.0	0		35.0	2.0	0.0571429	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SCAPER	49855	hgsc.bcm.edu	37	15	77025687	77025687	+	Silent	SNP	C	C	T	rs144694379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77025687C>T	ENST00000563290.1	-	16	2000	c.1905G>A	c.(1903-1905)caG>caA	p.Q635Q	SCAPER_ENST00000538941.2_Silent_p.Q389Q|SCAPER_ENST00000324767.7_Silent_p.Q635Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	635	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GACGTTTATTCTGGGCTTCAA	0.348													C|||	38	0.00758786	0.0015	0.0187	5008	,	,		19249	0.0		0.0129	False		,,,				2504	0.0102				p.Q635Q		Atlas-SNP	.											SCAPER_ENST00000538941,NS,carcinoma,-2,2	SCAPER	160	2	0			c.G1905A						PASS	.	C	,	22,3630		0,22,1804	106.0	93.0	97.0		1167,1905	4.6	1.0	15	dbSNP_134	97	207,7951		2,203,3874	no	coding-synonymous,coding-synonymous	SCAPER	NM_001145923.1,NM_020843.2	,	2,225,5678	TT,TC,CC		2.5374,0.6024,1.939	,	389/1155,635/1401	77025687	229,11581	1826	4079	5905	SO:0001819	synonymous_variant	49855	exon15			TTTATTCTGGGCT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1905G>A	15.37:g.77025687C>T		180.0	0.0	0		189.0	103.0	0.544974	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																			C|0.988;T|0.012	0.012	strong		0.348	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	
TMEM44	93109	hgsc.bcm.edu	37	3	194346704	194346704	+	Missense_Mutation	SNP	A	A	G	rs140271606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194346704A>G	ENST00000392432.2	-	3	485	c.280T>C	c.(280-282)Tac>Cac	p.Y94H	TMEM44_ENST00000347147.4_Missense_Mutation_p.Y94H|TMEM44_ENST00000381975.3_Missense_Mutation_p.Y94H|TMEM44_ENST00000473092.1_Missense_Mutation_p.Y94H|TMEM44_ENST00000330115.3_5'UTR|TMEM44_ENST00000273580.7_Missense_Mutation_p.Y94H	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	94						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		GCTGCTAGGTAGGCACCAGTG	0.468													A|||	6	0.00119808	0.0	0.0014	5008	,	,		20623	0.0		0.003	False		,,,				2504	0.002				p.Y94H		Atlas-SNP	.											.	TMEM44	42	.	0			c.T280C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR	1,4405		0,1,2202	149.0	129.0	135.0		280,280,280,280	4.9	1.0	3	dbSNP_134	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense,missense,missense	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	83,83,83,83	0,18,6485	GG,GA,AA		0.1977,0.0227,0.1384	probably-damaging,probably-damaging,probably-damaging,probably-damaging	94/429,94/476,94/397,94/439	194346704	18,12988	2203	4300	6503	SO:0001583	missense	93109	exon3			CTAGGTAGGCACC	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.280T>C	3.37:g.194346704A>G	ENSP00000376227:p.Tyr94His	218.0	0.0	0		195.0	90.0	0.461538	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	14.86	2.662149	0.47572	2.27E-4	0.001977	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28	4.94	4.94	0.65067	.	0.104825	0.38837	N	0.001559	T	0.54191	0.1843	L	0.60455	1.87	0.42318	D	0.992247	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.998;0.996;0.998	T	0.58081	-0.7699	10	0.87932	D	0	-18.408	11.2784	0.49180	1.0:0.0:0.0:0.0	.	94;94;94;94;94	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	H	94	ENSP00000376227:Y94H;ENSP00000273580:Y94H;ENSP00000333355:Y94H;ENSP00000371402:Y94H;ENSP00000418674:Y94H	ENSP00000273580:Y94H	Y	-	1	0	TMEM44	195827993	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.194000	0.58393	1.980000	0.57719	0.459000	0.35465	TAC	A|0.998;G|0.002	0.002	strong		0.468	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
HSPA6	3310	hgsc.bcm.edu	37	1	161495344	161495344	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161495344T>C	ENST00000309758.4	+	1	1309	c.896T>C	c.(895-897)aTc>aCc	p.I299T	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	299					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TACACGTCCATCACTCGTGCC	0.647																																					p.I299T		Atlas-SNP	.											.	HSPA6	53	.	0			c.T896C						PASS	.						29.0	32.0	31.0					1																	161495344		2203	4300	6503	SO:0001583	missense	3310	exon1			CGTCCATCACTCG		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.896T>C	1.37:g.161495344T>C	ENSP00000310219:p.Ile299Thr	101.0	0.0	0		75.0	17.0	0.226667	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	15.17	2.755454	0.49362	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01165	5.24	3.12	3.12	0.35913	.	0.000000	0.39475	U	0.001354	T	0.09774	0.0240	H	0.99806	4.795	0.43953	D	0.996624	P	0.43885	0.82	D	0.74023	0.982	T	0.00206	-1.1920	10	0.87932	D	0	.	9.3095	0.37895	0.0:0.0:0.0:1.0	.	299	P17066	HSP76_HUMAN	T	299;275	ENSP00000310219:I299T	ENSP00000310219:I299T	I	+	2	0	HSPA6	159761968	1.000000	0.71417	0.972000	0.41901	0.619000	0.37552	5.244000	0.65400	1.264000	0.44198	0.443000	0.29094	ATC	.	.	none		0.647	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
SLIT2	9353	hgsc.bcm.edu	37	4	20487867	20487867	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20487867T>C	ENST00000504154.1	+	7	836	c.584T>C	c.(583-585)tTc>tCc	p.F195S	SLIT2_ENST00000503823.1_Missense_Mutation_p.F195S|SLIT2_ENST00000503837.1_Missense_Mutation_p.F195S|SLIT2_ENST00000273739.5_Missense_Mutation_p.F195S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	195					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GTGGCAAGTTTCAACCATATG	0.289																																					p.F195S		Atlas-SNP	.											.	SLIT2	290	.	0			c.T584C						PASS	.						76.0	77.0	77.0					4																	20487867		2202	4299	6501	SO:0001583	missense	9353	exon7			CAAGTTTCAACCA	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.584T>C	4.37:g.20487867T>C	ENSP00000422591:p.Phe195Ser	269.0	0.0	0		163.0	45.0	0.276074	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.867172	0.91511	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.3	5.3	0.74995	.	0.090982	0.85682	D	0.000000	D	0.88175	0.6366	H	0.94620	3.56	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.75484	0.986;0.978	D	0.91139	0.4944	10	0.59425	D	0.04	.	15.5307	0.75960	0.0:0.0:0.0:1.0	.	195;195	O94813-3;O94813	.;SLIT2_HUMAN	S	195	ENSP00000427548:F195S;ENSP00000422591:F195S;ENSP00000273739:F195S;ENSP00000422261:F195S	ENSP00000273739:F195S	F	+	2	0	SLIT2	20096965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.120000	0.65058	0.459000	0.35465	TTC	.	.	none		0.289	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417683	105417683	+	Missense_Mutation	SNP	C	C	T	rs367930189		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417683C>T	ENST00000333244.5	-	7	4224	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1369						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTGAGGTCCCCCTGCATGGAG	0.647																																					p.G1369R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+2,1	AHNAK2	719	1	0			c.G4105A						PASS	.	C	ARG/GLY	0,3684		0,0,1842	99.0	74.0	83.0		4105	2.3	0.0	14		83	2,6232		1,0,3116	no	missense	AHNAK2	NM_138420.2	125	1,0,4958	TT,TC,CC		0.0321,0.0,0.0202	probably-damaging	1369/5796	105417683	2,9916	1842	3117	4959	SO:0001583	missense	113146	exon7			GGTCCCCCTGCAT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4105G>A	14.37:g.105417683C>T	ENSP00000353114:p.Gly1369Arg	0.0	0.0	.		88.0	4.0	0.0454545	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	15.55	2.867501	0.51588	0.0	3.21E-4	ENSG00000185567	ENST00000333244	T	0.01584	4.75	4.18	2.29	0.28610	.	.	.	.	.	T	0.06188	0.0160	M	0.75264	2.295	0.09310	N	1	D	0.62365	0.991	P	0.61592	0.891	T	0.32745	-0.9895	9	0.25106	T	0.35	.	6.5072	0.22202	0.1794:0.7206:0.0:0.1001	.	1369	Q8IVF2	AHNK2_HUMAN	R	1369	ENSP00000353114:G1369R	ENSP00000353114:G1369R	G	-	1	0	AHNAK2	104488728	0.006000	0.16342	0.000000	0.03702	0.087000	0.18053	1.114000	0.31196	0.237000	0.21200	0.485000	0.47835	GGG	.	.	weak		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
LGALS14	56891	hgsc.bcm.edu	37	19	40196548	40196548	+	Intron	SNP	A	A	G	rs140242272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40196548A>G	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Start_Codon_SNP_p.M1V	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14						apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			CCCTCCAGTTATGTCCCTGAC	0.478													a|||	2	0.000399361	0.0	0.0014	5008	,	,		21476	0.0		0.001	False		,,,				2504	0.0				p.M1V		Atlas-SNP	.											.	LGALS14	38	.	0			c.A1G						PASS	.	A	,VAL/MET	0,4406		0,0,2203	184.0	141.0	156.0		,1	-0.4	0.0	19	dbSNP_134	156	7,8593		0,7,4293	no	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,21	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	,1/169	40196548	7,12999	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			CCAGTTATGTCCC	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.16-689A>G	19.37:g.40196548A>G		157.0	0.0	0		156.0	72.0	0.461538	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	6.163	0.398345	0.11696	0.0	8.14E-4	ENSG00000006659	ENST00000360675	T	0.06933	3.24	0.906	-0.363	0.12556	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.80722	D	1	B	0.26041	0.14	B	0.26202	0.067	T	0.29119	-1.0022	8	0.62326	D	0.03	.	3.5978	0.08013	0.5843:0.4157:0.0:0.0	.	1	A8MPV8	.	V	1	ENSP00000353893:M1V	ENSP00000353893:M1V	M	+	1	0	LGALS14	44888388	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-0.385000	0.07379	-0.203000	0.10251	0.260000	0.18958	ATG	A|0.999;G|0.001	0.001	strong		0.478	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
ENGASE	64772	hgsc.bcm.edu	37	17	77082174	77082174	+	Missense_Mutation	SNP	C	C	T	rs117014247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77082174C>T	ENST00000579016.1	+	14	1975	c.1975C>T	c.(1975-1977)Cgt>Tgt	p.R659C		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	659						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CTCACAAGTCCGTTGCTTCCG	0.637													C|||	34	0.00678914	0.0015	0.013	5008	,	,		17023	0.0		0.0199	False		,,,				2504	0.0031				p.R659C		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1975T						PASS	.	C	CYS/ARG	17,4281		0,17,2132	58.0	68.0	64.0		1975	2.0	0.1	17	dbSNP_132	64	185,8325		1,183,4071	yes	missense	ENGASE	NM_001042573.1	180	1,200,6203	TT,TC,CC		2.1739,0.3955,1.5771	benign	659/744	77082174	202,12606	2149	4255	6404	SO:0001583	missense	64772	exon14			CAAGTCCGTTGCT	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1975C>T	17.37:g.77082174C>T	ENSP00000462333:p.Arg659Cys	70.0	0.0	0		63.0	42.0	0.666667	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	22	0.010073260073260074	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	6.060	0.379407	0.11466	0.003955	0.021739	ENSG00000167280	ENST00000545583	.	.	.	4.26	2.01	0.26516	.	0.333614	0.31797	N	0.007049	T	0.16642	0.0400	L	0.56769	1.78	0.09310	N	0.999999	B	0.27594	0.182	B	0.17979	0.02	T	0.20107	-1.0285	9	0.54805	T	0.06	-3.595	2.1577	0.03816	0.4416:0.2981:0.1551:0.1052	.	659	Q8NFI3	ENASE_HUMAN	C	659	.	ENSP00000438577:R659C	R	+	1	0	ENGASE	74593769	0.000000	0.05858	0.093000	0.20910	0.199000	0.23934	-0.105000	0.10907	0.939000	0.37446	0.467000	0.42956	CGT	C|0.982;T|0.018	0.018	strong		0.637	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
UTRN	7402	hgsc.bcm.edu	37	6	144774982	144774982	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:144774982T>G	ENST00000367545.3	+	18	2261	c.2261T>G	c.(2260-2262)aTc>aGc	p.I754S		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	754	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACTGGACAAATCCTTGTGGAG	0.358																																					p.I754S		Atlas-SNP	.											.	UTRN	327	.	0			c.T2261G						PASS	.						90.0	95.0	93.0					6																	144774982		2203	4300	6503	SO:0001583	missense	7402	exon18			GACAAATCCTTGT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2261T>G	6.37:g.144774982T>G	ENSP00000356515:p.Ile754Ser	87.0	0.0	0		58.0	30.0	0.517241	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	T	0.223	-1.027393	0.02045	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.32988	1.43	5.87	-1.66	0.08265	.	0.697165	0.12797	N	0.438319	T	0.04588	0.0125	N	0.24115	0.695	0.32854	D	0.507058	B	0.21309	0.054	B	0.15484	0.013	T	0.39014	-0.9634	10	0.09084	T	0.74	.	5.6165	0.17434	0.1604:0.2957:0.0:0.5439	.	754	P46939	UTRO_HUMAN	S	754	ENSP00000356515:I754S	ENSP00000356499:I754S	I	+	2	0	UTRN	144816675	0.915000	0.31059	0.238000	0.24106	0.304000	0.27724	0.951000	0.29135	-0.106000	0.12110	-0.290000	0.09829	ATC	.	.	none		0.358	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	IGLL5_ENST00000531372.1_Silent_p.L27L|IGLL5_ENST00000532223.2_Silent_p.L27L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>T	22.37:g.23230312C>T		152.0	0.0	0		159.0	41.0	0.257862	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
WNK1	65125	hgsc.bcm.edu	37	12	939268	939268	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:939268C>A	ENST00000315939.6	+	4	1896	c.1253C>A	c.(1252-1254)tCt>tAt	p.S418Y	WNK1_ENST00000530271.2_Missense_Mutation_p.S418Y|WNK1_ENST00000537687.1_Missense_Mutation_p.S418Y|WNK1_ENST00000535572.1_Missense_Mutation_p.S418Y|WNK1_ENST00000540360.1_3'UTR	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ATGGCTACATCTGAATATCCT	0.468																																					p.S418Y	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C1253A						PASS	.						241.0	202.0	215.0					12																	939268		2203	4300	6503	SO:0001583	missense	65125	exon4			CTACATCTGAATA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1253C>A	12.37:g.939268C>A	ENSP00000313059:p.Ser418Tyr	280.0	0.0	0		293.0	72.0	0.245734	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037262	0.93630	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000530271	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000006	T	0.43700	0.1259	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.36890	-0.9729	10	0.87932	D	0	-15.3704	19.3708	0.94484	0.0:1.0:0.0:0.0	.	418;418	F5GWT4;Q9H4A3	.;WNK1_HUMAN	Y	418	ENSP00000441972:S418Y;ENSP00000313059:S418Y;ENSP00000444465:S418Y;ENSP00000433548:S418Y	ENSP00000313059:S418Y	S	+	2	0	WNK1	809529	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.818000	0.86416	2.571000	0.86741	0.467000	0.42956	TCT	.	.	none		0.468	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
HCN4	10021	hgsc.bcm.edu	37	15	73615097	73615097	+	Missense_Mutation	SNP	T	T	C	rs142735148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:73615097T>C	ENST00000261917.3	-	8	4330	c.3337A>G	c.(3337-3339)Atg>Gtg	p.M1113V		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	1113					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AAGGCAGCCATGGACTCCCCT	0.716													T|||	41	0.0081869	0.0068	0.0086	5008	,	,		11518	0.0		0.0129	False		,,,				2504	0.0133				p.M1113V		Atlas-SNP	.											.	HCN4	150	.	0			c.A3337G						PASS	.	T	VAL/MET	29,4303		0,29,2137	8.0	10.0	9.0		3337	-5.1	0.3	15	dbSNP_134	9	107,8365		2,103,4131	no	missense	HCN4	NM_005477.2	21	2,132,6268	CC,CT,TT		1.263,0.6694,1.0622	benign	1113/1204	73615097	136,12668	2166	4236	6402	SO:0001583	missense	10021	exon8			CAGCCATGGACTC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.3337A>G	15.37:g.73615097T>C	ENSP00000261917:p.Met1113Val	24.0	0.0	0		33.0	19.0	0.575758	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	18	0.008241758241758242	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.004	-2.366028	0.00212	0.006694	0.01263	ENSG00000138622	ENST00000261917	D	0.96651	-4.08	3.32	-5.11	0.02901	.	.	.	.	.	T	0.77698	0.4169	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76063	-0.3096	9	0.02654	T	1	.	10.5547	0.45110	0.0:0.421:0.0:0.579	.	1113	Q9Y3Q4	HCN4_HUMAN	V	1113	ENSP00000261917:M1113V	ENSP00000261917:M1113V	M	-	1	0	HCN4	71402150	0.000000	0.05858	0.260000	0.24451	0.142000	0.21351	-1.800000	0.01744	-1.006000	0.03412	-0.659000	0.03860	ATG	T|0.992;C|0.008	0.008	strong		0.716	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
CNST	163882	hgsc.bcm.edu	37	1	246829147	246829147	+	Missense_Mutation	SNP	C	C	G	rs138848173		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:246829147C>G	ENST00000366513.4	+	11	2387	c.2118C>G	c.(2116-2118)ttC>ttG	p.F706L		NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	706					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						ACATGGACTTCTATTACACTA	0.463																																					p.F706L		Atlas-SNP	.											.	CNST	73	.	0			c.C2118G						PASS	.						143.0	126.0	132.0					1																	246829147		2203	4300	6503	SO:0001583	missense	163882	exon11			GGACTTCTATTAC	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.2118C>G	1.37:g.246829147C>G	ENSP00000355470:p.Phe706Leu	137.0	0.0	0		128.0	54.0	0.421875	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592013	0.66219	.	.	ENSG00000162852	ENST00000366513	T	0.28255	1.62	5.61	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.51084	-0.8750	10	0.66056	D	0.02	-20.4305	5.088	0.14693	0.1498:0.5976:0.0:0.2526	.	706	Q6PJW8	CNST_HUMAN	L	706	ENSP00000355470:F706L	ENSP00000355470:F706L	F	+	3	2	CNST	244895770	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.581000	0.23819	1.366000	0.46076	0.655000	0.94253	TTC	C|1.000;T|0.000	.	alt		0.463	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
MAP4K4	9448	hgsc.bcm.edu	37	2	102314984	102314984	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102314984A>T	ENST00000347699.4	+	2	107	c.107A>T	c.(106-108)tAt>tTt	p.Y36F	MAP4K4_ENST00000456652.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000413150.2_Missense_Mutation_p.Y36F|MAP4K4_ENST00000425019.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000324219.4_Missense_Mutation_p.Y36F|MAP4K4_ENST00000302217.5_Missense_Mutation_p.Y36F|MAP4K4_ENST00000350198.4_Missense_Mutation_p.Y36F	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	36	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AATGGCACCTATGGACAAGTC	0.488																																					p.Y36F		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A107T						PASS	.						247.0	242.0	244.0					2																	102314984		1880	4108	5988	SO:0001583	missense	9448	exon2			GCACCTATGGACA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.107A>T	2.37:g.102314984A>T	ENSP00000314363:p.Tyr36Phe	402.0	1.0	0.00248756		312.0	90.0	0.288462	NM_004834	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645786	0.67358	.	.	ENSG00000071054	ENST00000427603;ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699	T;T;T;T;T;T;T;T	0.17691	3.68;2.26;2.26;2.26;2.26;2.26;2.26;2.26	4.26	4.26	0.50523	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49305	U	0.000157	T	0.17023	0.0409	N	0.02345	-0.59	0.80722	D	1	D;P;P;P;P;P;P;P	0.64830	0.994;0.939;0.809;0.939;0.939;0.475;0.925;0.925	D;D;P;D;D;P;D;D	0.67548	0.942;0.952;0.739;0.952;0.952;0.634;0.92;0.92	T	0.43360	-0.9396	10	0.72032	D	0.01	.	13.0603	0.59003	1.0:0.0:0.0:0.0	.	36;36;36;36;36;36;36;36	B7Z3V5;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;M4K4_HUMAN;.;.;.;.	F	36	ENSP00000403016:Y36F;ENSP00000392830:Y36F;ENSP00000313644:Y36F;ENSP00000281111:Y36F;ENSP00000303600:Y36F;ENSP00000389752:Y36F;ENSP00000387370:Y36F;ENSP00000314363:Y36F	ENSP00000303600:Y36F	Y	+	2	0	MAP4K4	101681416	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.623000	0.90957	1.544000	0.49359	0.482000	0.46254	TAT	.	.	none		0.488	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
TEAD4	7004	hgsc.bcm.edu	37	12	3120180	3120180	+	De_novo_Start_InFrame	SNP	G	G	A	rs147476820		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:3120180G>A	ENST00000397122.2	+	0	135				TEAD4_ENST00000358409.2_Silent_p.E79E|TEAD4_ENST00000359864.2_Silent_p.E79E	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4						gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GTCGGAACGAGCTGATTGCCC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16156	0.0		0.001	False		,,,				2504	0.0				p.E79E		Atlas-SNP	.											.	TEAD4	45	.	0			c.G237A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	74.0	71.0	72.0		237,237,	3.3	1.0	12	dbSNP_134	72	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,utr-5	TEAD4	NM_003213.3,NM_201441.2,NM_201443.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	79/435,79/392,	3120180	6,13000	2203	4300	6503			7004	exon4			GAACGAGCTGATT	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561			12.37:g.3120180G>A		127.0	0.0	0		139.0	78.0	0.561151	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Silent	SNP	ENST00000397122.2	37	CCDS41737.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
OR2M3	127062	hgsc.bcm.edu	37	1	248366632	248366632	+	Missense_Mutation	SNP	G	G	T	rs139107079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248366632G>T	ENST00000456743.1	+	1	301	c.263G>T	c.(262-264)gGc>gTc	p.G88V		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TACCTGTCTGGCAGCAAGTCC	0.502													G|||	2	0.000399361	0.0	0.0	5008	,	,		20388	0.0		0.002	False		,,,				2504	0.0				p.G88V		Atlas-SNP	.											.	OR2M3	116	.	0			c.G263T						PASS	.	G	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	267.0	265.0	265.0		263	0.3	0.0	1	dbSNP_134	265	2,8598	3.0+/-9.4	0,2,4298	no	missense	OR2M3	NM_001004689.1	109	0,4,6499	TT,TG,GG		0.0233,0.0454,0.0308	probably-damaging	88/313	248366632	4,13002	2203	4300	6503	SO:0001583	missense	127062	exon1			TGTCTGGCAGCAA		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.263G>T	1.37:g.248366632G>T	ENSP00000389625:p.Gly88Val	207.0	0.0	0		142.0	68.0	0.478873	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.552	0.875710	0.17395	4.54E-4	2.33E-4	ENSG00000228198	ENST00000456743	T	0.02656	4.21	2.44	0.325	0.15903	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32640	U	0.005825	T	0.05777	0.0151	M	0.81239	2.535	0.09310	N	1	P	0.49783	0.928	P	0.47705	0.555	T	0.21415	-1.0246	10	0.87932	D	0	.	2.9467	0.05848	0.2618:0.0:0.4954:0.2428	.	88	Q8NG83	OR2M3_HUMAN	V	88	ENSP00000389625:G88V	ENSP00000389625:G88V	G	+	2	0	OR2M3	246433255	0.000000	0.05858	0.006000	0.13384	0.038000	0.13279	-0.139000	0.10358	0.312000	0.23038	0.405000	0.27470	GGC	G|0.999;T|0.001	0.001	strong		0.502	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
MINA	84864	hgsc.bcm.edu	37	3	97686159	97686159	+	Silent	SNP	C	C	T	rs34097037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97686159C>T	ENST00000333396.7	-	2	861	c.279G>A	c.(277-279)ggG>ggA	p.G93G	MINA_ENST00000330299.2_Silent_p.G93G|MINA_ENST00000394198.2_Silent_p.G93G|MINA_ENST00000360258.4_Silent_p.G93G	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						CATAGTACATCCCCCGGCTGC	0.473													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18523	0.0		0.007	False		,,,				2504	0.0				p.G93G		Atlas-SNP	.											.	MINA	39	.	0			c.G279A						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	215.0	231.0	226.0		279,279,279	-6.5	0.0	3	dbSNP_126	226	52,8548	33.3+/-86.6	0,52,4248	no	coding-synonymous,coding-synonymous,coding-synonymous	MINA	NM_001042533.1,NM_032778.4,NM_153182.2	,,	0,58,6445	TT,TC,CC		0.6047,0.1362,0.4459	,,	93/466,93/465,93/466	97686159	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84864	exon2			GTACATCCCCCGG	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.279G>A	3.37:g.97686159C>T		103.0	0.0	0		107.0	51.0	0.476636	NM_001261829		Silent	SNP	ENST00000333396.7	37	CCDS43114.1																																																																																			C|0.996;T|0.004	0.004	strong		0.473	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778	
LAMA3	3909	hgsc.bcm.edu	37	18	21453038	21453038	+	Intron	SNP	C	C	T	rs145044428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21453038C>T	ENST00000313654.9	+	38	5239				LAMA3_ENST00000399516.3_Intron|LAMA3_ENST00000269217.6_Silent_p.C10C|LAMA3_ENST00000587184.1_Silent_p.C10C	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3						cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGTCAGCCTGCAGCATGGGAT	0.612													C|||	5	0.000998403	0.0	0.0014	5008	,	,		19022	0.0		0.003	False		,,,				2504	0.001				p.C10C		Atlas-SNP	.											.	LAMA3	397	.	0			c.C30T						PASS	.	C	,,,	0,4406		0,0,2203	84.0	81.0	82.0		30,,30,	0.3	0.0	18	dbSNP_134	82	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,intron,coding-synonymous,intron	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,9,6494	TT,TC,CC		0.1047,0.0,0.0692	,,,	10/1725,,10/1669,	21453038	9,12997	2203	4300	6503	SO:0001627	intron_variant	3909	exon1			AGCCTGCAGCATG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4998+1413C>T	18.37:g.21453038C>T		97.0	0.0	0		86.0	41.0	0.476744	NM_001127718	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
MCM10	55388	hgsc.bcm.edu	37	10	13230915	13230915	+	Missense_Mutation	SNP	C	C	T	rs35114749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:13230915C>T	ENST00000484800.2	+	10	1356	c.1253C>T	c.(1252-1254)gCt>gTt	p.A418V	MCM10_ENST00000378694.1_Missense_Mutation_p.A417V|MCM10_ENST00000378714.3_Missense_Mutation_p.A417V			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	418			A -> V (in dbSNP:rs35114749).		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						CATGTCCAGGCTCAGTACAAG	0.547													C|||	49	0.00978435	0.0	0.0086	5008	,	,		18533	0.001		0.0179	False		,,,				2504	0.0245				p.A418V		Atlas-SNP	.											.	MCM10	76	.	0			c.C1253T						PASS	.	C	VAL/ALA,VAL/ALA	8,4398	12.9+/-30.5	0,8,2195	142.0	131.0	134.0		1250,1253	5.9	1.0	10	dbSNP_126	134	110,8490	58.3+/-119.8	0,110,4190	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	64,64	0,118,6385	TT,TC,CC		1.2791,0.1816,0.9073	possibly-damaging,possibly-damaging	417/875,418/876	13230915	118,12888	2203	4300	6503	SO:0001583	missense	55388	exon10			TCCAGGCTCAGTA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1253C>T	10.37:g.13230915C>T	ENSP00000418268:p.Ala418Val	106.0	0.0	0		88.0	38.0	0.431818	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	13	0.005952380952380952	0	0.0	0	0.0	1	0.0017482517482517483	12	0.0158311345646438	C	33	5.250184	0.95305	0.001816	0.012791	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.45668	0.89;0.89;0.89	5.87	5.87	0.94306	Zinc finger, Mcm10/DnaG-type (1);	0.191044	0.56097	D	0.000036	T	0.30008	0.0751	L	0.54323	1.7	0.80722	D	1	D;P;P	0.55385	0.971;0.827;0.857	P;B;B	0.44696	0.458;0.26;0.378	T	0.09271	-1.0682	10	0.31617	T	0.26	-15.6206	20.5827	0.99408	0.0:1.0:0.0:0.0	rs35114749	417;417;418	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	V	417;418;418;417	ENSP00000367986:A417V;ENSP00000418268:A418V;ENSP00000367966:A417V	ENSP00000354945:A418V	A	+	2	0	MCM10	13270921	1.000000	0.71417	0.990000	0.47175	0.646000	0.38490	6.030000	0.70903	2.941000	0.99782	0.655000	0.94253	GCT	C|0.991;T|0.009	0.009	strong		0.547	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
CMKLR1	1240	hgsc.bcm.edu	37	12	108686572	108686572	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:108686572C>T	ENST00000312143.7	-	3	531	c.168G>A	c.(166-168)ctG>ctA	p.L56L	CMKLR1_ENST00000397688.2_Silent_p.L54L|CMKLR1_ENST00000550402.1_Silent_p.L56L|CMKLR1_ENST00000552995.1_Silent_p.L54L|CMKLR1_ENST00000412676.1_Silent_p.L56L	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	56					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GACCATTGCCCAGAATCCCGA	0.517																																					p.L56L		Atlas-SNP	.											CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	0			c.G168A						PASS	.						101.0	100.0	100.0					12																	108686572		2010	4173	6183	SO:0001819	synonymous_variant	1240	exon3			ATTGCCCAGAATC	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.168G>A	12.37:g.108686572C>T		169.0	0.0	0		117.0	28.0	0.239316	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																			.	.	none		0.517	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
KLHL13	90293	hgsc.bcm.edu	37	X	117035896	117035896	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:117035896A>G	ENST00000262820.3	-	6	2289	c.1380T>C	c.(1378-1380)tgT>tgC	p.C460C	KLHL13_ENST00000469946.1_Silent_p.C409C|KLHL13_ENST00000539496.1_Silent_p.C463C|KLHL13_ENST00000541812.1_Silent_p.C444C|KLHL13_ENST00000545703.1_Silent_p.C418C|KLHL13_ENST00000540167.1_Silent_p.C444C|KLHL13_ENST00000371882.1_Silent_p.C409C|KLHL13_ENST00000371876.1_Silent_p.C409C|KLHL13_ENST00000371878.1_Silent_p.C409C	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	460					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TTGGATTGTAACATTCTACTG	0.318																																					p.C463C		Atlas-SNP	.											.	KLHL13	87	.	0			c.T1389C						PASS	.						133.0	112.0	119.0					X																	117035896		2203	4300	6503	SO:0001819	synonymous_variant	90293	exon7			ATTGTAACATTCT	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.1380T>C	X.37:g.117035896A>G		157.0	0.0	0		112.0	34.0	0.303571	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			.	.	none		0.318	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
STOX2	56977	hgsc.bcm.edu	37	4	184930961	184930961	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184930961G>A	ENST00000308497.4	+	3	2405	c.970G>A	c.(970-972)Gtg>Atg	p.V324M	STOX2_ENST00000438269.1_Missense_Mutation_p.V324M	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	324					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AGACCTGACCGTGGAAAATGT	0.562																																					p.V324M		Atlas-SNP	.											.	STOX2	142	.	0			c.G970A						PASS	.						24.0	24.0	24.0					4																	184930961		1943	4139	6082	SO:0001583	missense	56977	exon3			CTGACCGTGGAAA	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.970G>A	4.37:g.184930961G>A	ENSP00000311257:p.Val324Met	64.0	0.0	0		51.0	11.0	0.215686	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	37	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.612462	0.66672	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;D	0.88741	-1.49;-2.42	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.94922	0.8358	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.987	D	0.94499	0.7708	10	0.87932	D	0	-21.6529	20.6634	0.99662	0.0:0.0:1.0:0.0	.	324;324	Q9P2F5-2;Q9P2F5	.;STOX2_HUMAN	M	324	ENSP00000311257:V324M;ENSP00000390127:V324M	ENSP00000311257:V324M	V	+	1	0	STOX2	185167955	1.000000	0.71417	0.988000	0.46212	0.374000	0.29953	9.869000	0.99810	2.894000	0.99253	0.655000	0.94253	GTG	.	.	none		0.562	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
BTBD6	90135	hgsc.bcm.edu	37	14	105716854	105716854	+	Missense_Mutation	SNP	G	G	A	rs146426875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105716854G>A	ENST00000392554.3	+	4	1600	c.1303G>A	c.(1303-1305)Gtc>Atc	p.V435I	BRF1_ENST00000379937.2_Intron|BTBD6_ENST00000463376.2_Missense_Mutation_p.V360I|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000536364.1_Missense_Mutation_p.V435I|BRF1_ENST00000446501.2_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.V360I|BRF1_ENST00000440513.3_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	435						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GGCCAGTGCCGTCCTGGACGG	0.572													G|||	8	0.00159744	0.0	0.0	5008	,	,		19762	0.0		0.002	False		,,,				2504	0.0061				p.V435I		Atlas-SNP	.											.	BTBD6	24	.	0			c.G1303A						PASS	.	G	,,,,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	95.0	83.0	87.0		,,,,1303	3.1	0.6	14	dbSNP_134	87	25,8575	17.9+/-57.8	0,25,4275	yes	intron,intron,intron,intron,missense	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,29	0,28,6475	AA,AG,GG		0.2907,0.0681,0.2153	,,,,benign	,,,,435/486	105716854	28,12978	2203	4300	6503	SO:0001583	missense	90135	exon5			AGTGCCGTCCTGG	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.1303G>A	14.37:g.105716854G>A	ENSP00000376337:p.Val435Ile	70.0	0.0	0		56.0	29.0	0.517857	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	37	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	G	2.830	-0.242885	0.05906	6.81E-4	0.002907	ENSG00000184887	ENST00000536364;ENST00000392554;ENST00000327471	T;T;T	0.73789	-0.78;-0.78;-0.69	5.16	3.06	0.35304	PHR (1);	0.122234	0.53938	D	0.000047	T	0.43188	0.1236	N	0.02802	-0.49	0.80722	D	1	B	0.16603	0.018	B	0.17979	0.02	T	0.16571	-1.0398	9	.	.	.	-41.9028	4.7344	0.12981	0.3872:0.0:0.6128:0.0	.	435	Q96KE9	BTBD6_HUMAN	I	435;435;360	ENSP00000443091:V435I;ENSP00000376337:V435I;ENSP00000329361:V360I	.	V	+	1	0	BTBD6	104787899	1.000000	0.71417	0.641000	0.29422	0.440000	0.31957	4.545000	0.60698	1.161000	0.42604	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.572	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
ZFAT	57623	hgsc.bcm.edu	37	8	135622851	135622851	+	Missense_Mutation	SNP	G	G	A	rs75596750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135622851G>A	ENST00000377838.3	-	4	670	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W	ZFAT_ENST00000429442.2_Missense_Mutation_p.R154W|ZFAT_ENST00000520214.1_Missense_Mutation_p.R154W|ZFAT_ENST00000520356.1_Missense_Mutation_p.R154W|ZFAT_ENST00000523399.1_Intron|ZFAT_ENST00000520727.1_Missense_Mutation_p.R154W	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	166					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GCTTTTTCCCGATCATCTTCC	0.448													G|||	2	0.000399361	0.0	0.0	5008	,	,		23535	0.0		0.002	False		,,,				2504	0.0				p.R166W		Atlas-SNP	.											.	ZFAT	265	.	0			c.C496T						PASS	.	G	TRP/ARG,TRP/ARG,,TRP/ARG,TRP/ARG	1,3813		0,1,1906	179.0	166.0	170.0		460,460,,460,496	4.4	1.0	8	dbSNP_132	170	7,8231		0,7,4112	yes	missense,missense,intron,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	101,101,,101,101	0,8,6018	AA,AG,GG		0.085,0.0262,0.0664	probably-damaging,probably-damaging,,probably-damaging,probably-damaging	154/1232,154/1232,,154/1146,166/1244	135622851	8,12044	1907	4119	6026	SO:0001583	missense	57623	exon4			TTTCCCGATCATC	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.496C>T	8.37:g.135622851G>A	ENSP00000367069:p.Arg166Trp	309.0	0.0	0		286.0	62.0	0.216783	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.3	3.967099	0.74131	2.62E-4	8.5E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000398946;ENST00000522257	T;T;T;T;T;T	0.54279	2.82;2.75;2.76;2.74;2.75;0.58	5.36	4.43	0.53597	.	0.087086	0.48286	D	0.000185	T	0.60392	0.2265	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.965;0.999;0.998	T	0.62478	-0.6846	10	0.66056	D	0.02	-7.6436	12.0426	0.53462	0.0:0.0:0.7035:0.2965	.	154;154;166	E9PBN4;Q9P243-3;Q9P243	.;.;ZFAT_HUMAN	W	154;154;154;166;154;154;154;104	ENSP00000427879:R154W;ENSP00000427831:R154W;ENSP00000394501:R154W;ENSP00000367069:R166W;ENSP00000428483:R154W;ENSP00000429983:R104W	ENSP00000326997:R154W	R	-	1	2	ZFAT	135692033	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.592000	0.53993	2.498000	0.84270	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.448	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
UNC13A	23025	hgsc.bcm.edu	37	19	17749893	17749893	+	Splice_Site	SNP	G	G	A	rs200328448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17749893G>A	ENST00000519716.2	-	25	3079	c.3080C>T	c.(3079-3081)cCg>cTg	p.P1027L	UNC13A_ENST00000252773.7_Splice_Site_p.P1027L|UNC13A_ENST00000551649.1_Splice_Site_p.P1027L|UNC13A_ENST00000428389.2_Splice_Site_p.P1115L|UNC13A_ENST00000552293.1_Splice_Site_p.P1027L|UNC13A_ENST00000550896.1_Splice_Site_p.P1025L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1027					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GAGTCTCACCGGGTCTGTCTG	0.517													G|||	3	0.000599042	0.0	0.0029	5008	,	,		16830	0.0		0.001	False		,,,				2504	0.0				p.P1027L		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	2	0			c.C3080T						PASS	.	G	LEU/PRO	7,3979		0,7,1986	27.0	28.0	28.0		3080	1.0	0.0	19		28	54,8314		0,54,4130	yes	missense-near-splice	UNC13A	NM_001080421.2	98	0,61,6116	AA,AG,GG		0.6453,0.1756,0.4938	possibly-damaging	1027/1704	17749893	61,12293	1993	4184	6177	SO:0001630	splice_region_variant	23025	exon24			CTCACCGGGTCTG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3081+1C>T	19.37:g.17749893G>A		86.0	0.0	0		67.0	39.0	0.58209	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	11.97	1.796712	0.31777	0.001756	0.006453	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.81247	-1.45;-1.47;-1.45;-1.32;-1.33;-1.46	3.39	1.0	0.19881	Calcium-dependent secretion activator (1);	0.182504	0.35262	U	0.003331	T	0.57873	0.2083	L	0.34521	1.04	0.58432	D	0.999999	P	0.48089	0.905	B	0.36808	0.233	T	0.60525	-0.7246	10	0.66056	D	0.02	.	9.4402	0.38664	0.0:0.0:0.6171:0.3828	.	1027	Q9UPW8	UN13A_HUMAN	L	1027;1115;1027;1027;1027;1025	ENSP00000429562:P1027L;ENSP00000400409:P1115L;ENSP00000252773:P1027L;ENSP00000447236:P1027L;ENSP00000447572:P1027L;ENSP00000446831:P1025L	ENSP00000252773:P1027L	P	-	2	0	UNC13A	17610893	1.000000	0.71417	0.020000	0.16555	0.803000	0.45373	7.588000	0.82629	0.066000	0.16515	0.478000	0.44815	CCG	G|0.996;A|0.004	0.004	strong		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	Missense_Mutation
SH3BP4	23677	hgsc.bcm.edu	37	2	235951183	235951183	+	Silent	SNP	G	G	A	rs140262787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235951183G>A	ENST00000409212.1	+	4	2277	c.1770G>A	c.(1768-1770)cgG>cgA	p.R590R	SH3BP4_ENST00000392011.2_Silent_p.R590R|SH3BP4_ENST00000344528.4_Silent_p.R590R			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	590					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		TCACGCTGCGGGTTCAGGTGA	0.587													G|||	39	0.00778754	0.0	0.0029	5008	,	,		16535	0.0		0.0149	False		,,,				2504	0.0225				p.R590R		Atlas-SNP	.											SH3BP4,NS,carcinoma,+2,1	SH3BP4	109	1	0			c.G1770A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	60.0	64.0	63.0		1770	5.1	1.0	2	dbSNP_134	63	92,8508	51.5+/-111.7	1,90,4209	no	coding-synonymous	SH3BP4	NM_014521.2		1,98,6404	AA,AG,GG		1.0698,0.1816,0.7689		590/964	235951183	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			GCTGCGGGTTCAG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1770G>A	2.37:g.235951183G>A		104.0	0.0	0		73.0	38.0	0.520548	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			G|0.992;A|0.008	0.008	strong		0.587	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
PIGS	94005	hgsc.bcm.edu	37	17	26881923	26881923	+	Silent	SNP	C	C	T	rs146249165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26881923C>T	ENST00000308360.7	-	11	1713	c.1338G>A	c.(1336-1338)gcG>gcA	p.A446A	PIGS_ENST00000395346.2_Silent_p.A438A|PIGS_ENST00000543734.1_Silent_p.A385A|UNC119_ENST00000301032.4_5'Flank|UNC119_ENST00000335765.4_5'Flank	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	446					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					CCAGAAGCTGCGCCAGGGAGG	0.587																																					p.A446A		Atlas-SNP	.											.	PIGS	42	.	0			c.G1338A						PASS	.	C		0,4406		0,0,2203	123.0	101.0	109.0		1338	-2.2	1.0	17	dbSNP_134	109	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PIGS	NM_033198.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		446/556	26881923	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	94005	exon11			AAGCTGCGCCAGG		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.1338G>A	17.37:g.26881923C>T		134.0	0.0	0		111.0	53.0	0.477477	NM_033198	Q6UVX6	Silent	SNP	ENST00000308360.7	37	CCDS11235.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198	
SF3B1	23451	hgsc.bcm.edu	37	2	198257075	198257075	+	Silent	SNP	G	G	A	rs78516934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198257075G>A	ENST00000335508.6	-	25	3958	c.3867C>T	c.(3865-3867)aaC>aaT	p.N1289N		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1289					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TCTTATCATCGTTGTAGATTC	0.358			Mis		myelodysplastic syndrome								G|||	16	0.00319489	0.0008	0.0014	5008	,	,		17476	0.0		0.0139	False		,,,				2504	0.0				p.N1289N		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.C3867T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122.0	121.0	121.0		3867	0.9	1.0	2	dbSNP_132	121	86,8514	49.8+/-109.6	0,86,4214	no	coding-synonymous	SF3B1	NM_012433.2		0,91,6412	AA,AG,GG		1.0,0.1135,0.6997		1289/1305	198257075	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	23451	exon25			ATCATCGTTGTAG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.3867C>T	2.37:g.198257075G>A		111.0	0.0	0		106.0	40.0	0.377358	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			G|0.993;A|0.007	0.007	strong		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
CAV1	857	hgsc.bcm.edu	37	7	116165140	116165140	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116165140C>A	ENST00000341049.2	+	1	302	c.24C>A	c.(22-24)gaC>gaA	p.D8E	CAV1_ENST00000393470.1_Missense_Mutation_p.D8E|CAV1_ENST00000405348.1_5'Flank|CAV1_ENST00000393468.1_5'Flank|CAV1_ENST00000393467.1_5'Flank	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	8					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			AATACGTAGACTCGGAGGTAG	0.612																																					p.D8E		Atlas-SNP	.											.	CAV1	13	.	0			c.C24A						PASS	.						87.0	100.0	96.0					7																	116165140		2203	4300	6503	SO:0001583	missense	857	exon1			CGTAGACTCGGAG	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"""caveolin 1, caveolae protein, 22kD"""	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.24C>A	7.37:g.116165140C>A	ENSP00000339191:p.Asp8Glu	122.0	0.0	0		92.0	37.0	0.402174	NM_001753	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	37	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184175	0.57800	.	.	ENSG00000105974	ENST00000341049;ENST00000393470	D;D	0.93189	-3.18;-3.06	4.71	2.91	0.33838	.	0.683428	0.14907	N	0.291489	D	0.90307	0.6968	L	0.56769	1.78	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	D	0.86138	0.1579	10	0.66056	D	0.02	-15.711	8.0118	0.30357	0.0:0.7413:0.0:0.2587	.	8	Q03135	CAV1_HUMAN	E	8	ENSP00000339191:D8E;ENSP00000377113:D8E	ENSP00000339191:D8E	D	+	3	2	CAV1	115952376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.667000	0.25112	0.696000	0.31696	0.650000	0.86243	GAC	.	.	none		0.612	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753	
RAVER1	125950	hgsc.bcm.edu	37	19	10439501	10439501	+	Silent	SNP	C	C	T	rs3745263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439501C>T	ENST00000293677.6	-	3	705	c.624G>A	c.(622-624)tcG>tcA	p.S208S		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	191	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			CCAGCAGGTCCGACTTGGCAC	0.632													C|||	108	0.0215655	0.0015	0.0058	5008	,	,		13773	0.0407		0.0338	False		,,,				2504	0.0276				p.S208S		Atlas-SNP	.											.	RAVER1	67	.	0			c.G624A						PASS	.	C		40,4254		0,40,2107	24.0	30.0	28.0		624	-6.7	0.9	19	dbSNP_107	28	275,8223		6,263,3980	no	coding-synonymous	RAVER1	NM_133452.2		6,303,6087	TT,TC,CC		3.2361,0.9315,2.4625		208/757	10439501	315,12477	2147	4249	6396	SO:0001819	synonymous_variant	125950	exon3			CAGGTCCGACTTG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.624G>A	19.37:g.10439501C>T		249.0	0.0	0		187.0	86.0	0.459893	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			C|0.971;T|0.029	0.029	strong		0.632	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26245986A>T	ENST00000337620.4	+	3	452		c.e3-1		CBX3_ENST00000396386.2_Splice_Site|CBX3_ENST00000409747.1_Splice_Site|CBX3_ENST00000497498.1_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GTTTTATTTTAGCAAAAAATG	0.308																																					.		Atlas-SNP	.											CBX3,colon,adenoma,0,1	CBX3	25	1	0			c.25-2A>T						scavenged	.						32.0	33.0	32.0					7																	26245986		2200	4300	6500	SO:0001630	splice_region_variant	11335	exon3			TATTTTAGCAAAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.25-1A>T	7.37:g.26245986A>T		37.0	1.0	0.027027		26.0	6.0	0.230769	NM_007276	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999549	0.54147	.	.	ENSG00000122565	ENST00000337620;ENST00000396386;ENST00000456948;ENST00000409747	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2344	0.54508	0.8582:0.1418:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26212511	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.092000	0.50207	2.323000	0.78572	0.533000	0.62120	.	.	.	none		0.308	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	Intron
PCNXL4	64430	hgsc.bcm.edu	37	14	60592491	60592491	+	Missense_Mutation	SNP	A	A	G	rs145320435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60592491A>G	ENST00000406854.1	+	10	3771	c.3217A>G	c.(3217-3219)Att>Gtt	p.I1073V	PCNXL4_ENST00000317623.4_Missense_Mutation_p.I839V|PCNXL4_ENST00000406949.1_Missense_Mutation_p.I839V|PCNXL4_ENST00000535349.1_Missense_Mutation_p.I280V|PCNXL4_ENST00000404681.2_Missense_Mutation_p.I1073V			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1073						integral component of membrane (GO:0016021)											GAAGGAAGCAATTTTACAAGA	0.323													A|||	10	0.00199681	0.0	0.0029	5008	,	,		17125	0.0		0.005	False		,,,				2504	0.0031				p.I839V		Atlas-SNP	.											.	.	.	.	0			c.A2515G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	67.0	70.0	69.0		2515	-1.6	0.9	14	dbSNP_134	69	38,8562	24.0+/-70.4	0,38,4262	yes	missense	C14orf135	NM_022495.5	29	0,40,6463	GG,GA,AA		0.4419,0.0454,0.3076	benign	839/939	60592491	40,12966	2203	4300	6503	SO:0001583	missense	64430	exon9			GAAGCAATTTTAC	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.3217A>G	14.37:g.60592491A>G	ENSP00000384801:p.Ile1073Val	99.0	0.0	0		101.0	48.0	0.475248	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	2.385	-0.341295	0.05243	4.54E-4	0.004419	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.26	-1.63	0.08345	.	0.323849	0.32120	N	0.006555	T	0.11537	0.0281	N	0.02266	-0.62	0.32445	N	0.546244	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.43261	-0.9402	10	0.02654	T	1	.	13.3605	0.60652	0.2688:0.0:0.7312:0.0	.	1073;839	Q63HM2;B5MC47	CN135_HUMAN;.	V	839;1073;839;1073;280	ENSP00000317396:I839V;ENSP00000384801:I1073V;ENSP00000385201:I839V;ENSP00000385713:I1073V;ENSP00000445644:I280V	ENSP00000317396:I839V	I	+	1	0	C14orf135	59662244	0.998000	0.40836	0.917000	0.36280	0.928000	0.56348	1.437000	0.34991	-0.407000	0.07576	-0.410000	0.06199	ATT	A|0.998;G|0.002	0.002	strong		0.323	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
HSD17B3	3293	hgsc.bcm.edu	37	9	99064378	99064378	+	Silent	SNP	G	G	A	rs139582148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:99064378G>A	ENST00000375263.3	-	1	56	c.9C>T	c.(7-9)gaC>gaT	p.D3D	HSD17B3_ENST00000375262.2_Silent_p.D3D	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	3					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				GTTCCAGGACGTCCCCCATGG	0.567													G|||	8	0.00159744	0.0038	0.0014	5008	,	,		17045	0.0		0.002	False		,,,				2504	0.0				p.D3D		Atlas-SNP	.											.	HSD17B3	32	.	0			c.C9T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	82.0	72.0	75.0		9	-6.7	0.0	9	dbSNP_134	75	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	HSD17B3	NM_000197.1		0,12,6491	AA,AG,GG		0.0698,0.1362,0.0923		3/311	99064378	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	3293	exon1			CAGGACGTCCCCC		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5212	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 2"""	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.9C>T	9.37:g.99064378G>A		97.0	0.0	0		109.0	56.0	0.513761	NM_000197	Q5U0Q6	Silent	SNP	ENST00000375263.3	37	CCDS6716.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197	
SSPO	23145	hgsc.bcm.edu	37	7	149520553	149520553	+	RNA	SNP	G	G	A	rs141884347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149520553G>A	ENST00000378016.2	+	0	13371							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCTGCCAGCCGGGCTGCTACT	0.627													G|||	48	0.00958466	0.0008	0.013	5008	,	,		17506	0.002		0.0129	False		,,,				2504	0.0235				p.P4457P		Atlas-SNP	.											.	.	.	.	0			c.G13371A						PASS	.	G		5,4069		0,5,2032	34.0	41.0	39.0		13385	-9.9	0.6	7	dbSNP_134	39	118,8248		1,116,4066	yes	coding-notMod3	SSPO	NM_198455.2		1,121,6098	AA,AG,GG		1.4105,0.1227,0.9887			149520553	123,12317	2037	4183	6220			23145	exon92			CCAGCCGGGCTGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149520553G>A		37.0	0.0	0		45.0	18.0	0.4	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124563	26124563	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124563C>G	ENST00000602637.1	+	1	133	c.103C>G	c.(103-105)Ctc>Gtc	p.L35V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Missense_Mutation_p.L35V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	35						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						GCACCGCCTGCTCCGTAAAGG	0.657																																					p.L35V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.C103G						PASS	.						42.0	44.0	44.0					6																	26124563		2203	4300	6503	SO:0001583	missense	8334	exon1			CGCCTGCTCCGTA	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.103C>G	6.37:g.26124563C>G	ENSP00000473534:p.Leu35Val	99.0	0.0	0		100.0	32.0	0.32	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Missense_Mutation	SNP	ENST00000602637.1	37	CCDS4585.1	.	.	.	.	.	.	.	.	.	.	.	14.39	2.522457	0.44866	.	.	ENSG00000180573	ENST00000377791;ENST00000314088	T;T	0.59224	0.28;0.28	5.6	5.6	0.85130	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.38897	N	0.001536	T	0.80199	0.4579	H	0.97564	4.03	0.40025	D	0.975457	D	0.64830	0.994	D	0.66351	0.943	D	0.85943	0.1459	10	0.87932	D	0	.	12.3103	0.54925	0.0:0.9229:0.0:0.0771	.	35	Q93077	H2A1C_HUMAN	V	35	ENSP00000367022:L35V;ENSP00000321389:L35V	ENSP00000321389:L35V	L	+	1	0	HIST1H2AC	26232542	1.000000	0.71417	0.810000	0.32431	0.125000	0.20455	3.848000	0.55903	2.793000	0.96121	0.591000	0.81541	CTC	.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
PSPH	5723	hgsc.bcm.edu	37	7	56084977	56084977	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56084977T>C	ENST00000395471.3	-	6	1176	c.371A>G	c.(370-372)aAt>aGt	p.N124S	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.N124S			P78330	SERB_HUMAN	phosphoserine phosphatase	124					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TGCTGGGATATTGAGCTTTGA	0.413																																					p.N124S		Atlas-SNP	.											.	PSPH	23	.	0			c.A371G						PASS	.						95.0	79.0	84.0					7																	56084977		2203	4300	6503	SO:0001583	missense	5723	exon6			GGGATATTGAGCT	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.371A>G	7.37:g.56084977T>C	ENSP00000378854:p.Asn124Ser	548.0	1.0	0.00182482		508.0	130.0	0.255906	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.891711	0.33442	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.84442	-1.85;-1.85;-1.85	4.85	2.45	0.29901	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.459751	0.25414	N	0.030855	T	0.74928	0.3781	L	0.33668	1.02	0.23700	N	0.997076	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.64106	-0.6485	10	0.46703	T	0.11	-8.4835	7.6611	0.28404	0.0:0.1848:0.0:0.8152	.	124;124	Q53EY1;P78330	.;SERB_HUMAN	S	124	ENSP00000275605:N124S;ENSP00000378854:N124S;ENSP00000398653:N124S	ENSP00000275605:N124S	N	-	2	0	PSPH	56052471	0.897000	0.30589	0.689000	0.30133	0.972000	0.66771	1.222000	0.32515	0.742000	0.32697	0.472000	0.43445	AAT	.	.	none		0.413	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
MKS1	54903	hgsc.bcm.edu	37	17	56294075	56294075	+	Missense_Mutation	SNP	G	G	C	rs142813109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56294075G>C	ENST00000393119.2	-	3	287	c.213C>G	c.(211-213)gaC>gaG	p.D71E	LPO_ENST00000582328.1_5'Flank|MKS1_ENST00000313863.6_Missense_Mutation_p.D71E|MKS1_ENST00000546108.1_5'UTR|MKS1_ENST00000537529.2_Missense_Mutation_p.D61E|MKS1_ENST00000337050.7_Missense_Mutation_p.D71E	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	71					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)		p.D71V(1)		endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCTCCTCTTCGTCTTCCTCTG	0.483													G|||	8	0.00159744	0.0	0.0029	5008	,	,		18460	0.0		0.006	False		,,,				2504	0.0				p.D71E		Atlas-SNP	.											MKS1_ENST00000337050,NS,carcinoma,0,2	MKS1	100	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C213G						PASS	.	G	GLU/ASP,GLU/ASP	8,3946		0,8,1969	135.0	140.0	138.0		183,213	-3.3	1.0	17	dbSNP_134	138	48,8250		0,48,4101	yes	missense,missense	MKS1	NM_001165927.1,NM_017777.3	45,45	0,56,6070	CC,CG,GG		0.5785,0.2023,0.4571	benign,benign	61/550,71/560	56294075	56,12196	1977	4149	6126	SO:0001583	missense	54903	exon3			CTCTTCGTCTTCC	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"""POC12 centriolar protein homolog (Chlamydomonas)"""	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.213C>G	17.37:g.56294075G>C	ENSP00000376827:p.Asp71Glu	158.0	0.0	0		151.0	71.0	0.470199	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Missense_Mutation	SNP	ENST00000393119.2	37	CCDS11603.2	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	11.11|11.11	1.542037|1.542037	0.27563|0.27563	0.002023|0.002023	0.005785|0.005785	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050|ENST00000313863	T;T;T;T|.	0.68331|.	-0.32;1.5;-0.27;-0.04|.	5.41|5.41	-3.29|-3.29	0.05017|0.05017	.|.	0.246500|.	0.23866|.	N|.	0.043797|.	T|T	0.10294|0.10294	0.0252|0.0252	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.19877|0.19877	-1.0292|-1.0292	10|5	0.06891|.	T|.	0.86|.	-13.0566|-13.0566	1.4484|1.4484	0.02369|0.02369	0.2305:0.3965:0.1768:0.1963|0.2305:0.3965:0.1768:0.1963	.|.	71;71|.	A8MPP8;Q9NXB0|.	.;MKS1_HUMAN|.	E|R	61;71;71;71|72	ENSP00000442096:D61E;ENSP00000376828:D71E;ENSP00000376827:D71E;ENSP00000338407:D71E|.	ENSP00000338407:D71E|.	D|T	-|-	3|2	2|0	MKS1|MKS1	53649074|53649074	0.123000|0.123000	0.22298|0.22298	0.997000|0.997000	0.53966|0.53966	0.988000|0.988000	0.76386|0.76386	-0.681000|-0.681000	0.05191|0.05191	-0.194000|-0.194000	0.10399|0.10399	-0.323000|-0.323000	0.08544|0.08544	GAC|ACG	G|0.996;C|0.004	0.004	strong		0.483	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777	
PRCC	5546	hgsc.bcm.edu	37	1	156756948	156756948	+	Silent	SNP	C	C	T	rs201827573		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156756948C>T	ENST00000271526.4	+	3	1337	c.1065C>T	c.(1063-1065)gcC>gcT	p.A355A	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Silent_p.A355A	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	355					mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATGCCAATGCCGCTGGTGCTT	0.532			T	TFE3	papillary renal								C|||	1	0.000199681	0.0	0.0	5008	,	,		14844	0.0		0.001	False		,,,				2504	0.0				p.A355A		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1065T						PASS	.	C		0,4406		0,0,2203	116.0	121.0	119.0		1065	-2.6	1.0	1		119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PRCC	NM_005973.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		355/492	156756948	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5546	exon3			CAATGCCGCTGGT	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.1065C>T	1.37:g.156756948C>T		405.0	0.0	0		327.0	157.0	0.480122	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Silent	SNP	ENST00000271526.4	37	CCDS1157.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.757	0.704598	0.15172	0.0	2.33E-4	ENSG00000143294	ENST00000454659	.	.	.	5.15	-2.57	0.06248	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.52501	D	0.999954	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	-9.8382	4.9292	0.13909	0.0964:0.5476:0.0971:0.2588	.	.	.	.	L	89	.	.	P	+	2	0	PRCC	155023572	0.271000	0.24162	0.973000	0.42090	0.986000	0.74619	-0.613000	0.05610	-0.687000	0.05162	-1.094000	0.02160	CCG	C|0.999;T|0.001	0.001	strong		0.532	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973	
NCOA2	10499	hgsc.bcm.edu	37	8	71126255	71126255	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:71126255C>T	ENST00000452400.2	-	4	323	c.142G>A	c.(142-144)Gaa>Aaa	p.E48K		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	48	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TCTGCAAGTTCTTCTATATAT	0.299			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.E48K		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	NCOA2,NS,carcinoma,0,1	NCOA2	147	1	0			c.G142A						PASS	.						111.0	101.0	104.0					8																	71126255		1783	4058	5841	SO:0001583	missense	10499	exon4			CAAGTTCTTCTAT	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.142G>A	8.37:g.71126255C>T	ENSP00000399968:p.Glu48Lys	108.0	0.0	0		77.0	4.0	0.0519481	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	34	5.304743	0.95601	.	.	ENSG00000140396	ENST00000452400	T	0.02446	4.29	5.53	5.53	0.82687	Helix-loop-helix DNA-binding (4);	0.000000	0.85682	D	0.000000	T	0.19046	0.0457	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00191	-1.1936	10	0.87932	D	0	.	19.466	0.94939	0.0:1.0:0.0:0.0	.	48	Q15596	NCOA2_HUMAN	K	48	ENSP00000399968:E48K	ENSP00000399968:E48K	E	-	1	0	NCOA2	71288809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.607000	0.88179	0.655000	0.94253	GAA	.	.	none		0.299	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230419	23230419	+	Silent	SNP	C	C	T	rs554734650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230419C>T	ENST00000526893.1	+	1	460	c.186C>T	c.(184-186)agC>agT	p.S62S	IGLL5_ENST00000531372.1_Silent_p.S62S|IGLL5_ENST00000532223.2_Silent_p.S62S|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	62						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCGATCCAGCCTGCGGAGCC	0.647													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11441	0.001		0.001	False		,,,				2504	0.0				p.A27V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C80T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			ATCCAGCCTGCGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.186C>T	22.37:g.23230419C>T		113.0	0.0	0		97.0	25.0	0.257732	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
GGT1	2678	hgsc.bcm.edu	37	22	25023881	25023881	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25023881T>G	ENST00000400382.1	+	13	2026	c.1271T>G	c.(1270-1272)tTc>tGc	p.F424C	GGT1_ENST00000248923.4_Missense_Mutation_p.F424C|GGT1_ENST00000404223.1_Missense_Mutation_p.F80C|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400380.1_Missense_Mutation_p.F424C|GGT1_ENST00000404920.1_Missense_Mutation_p.F80C|GGT1_ENST00000403838.1_Missense_Mutation_p.F80C|GGT1_ENST00000401885.1_Missense_Mutation_p.F80C|GGT1_ENST00000400383.1_Missense_Mutation_p.F424C|GGT1_ENST00000406383.2_Missense_Mutation_p.F424C|GGT1_ENST00000404532.1_Missense_Mutation_p.F80C			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	424					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|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(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ATGGACGACTTCAGCTCTCCC	0.617																																					p.F424C		Atlas-SNP	.											.	GGT1	68	.	0			c.T1271G						PASS	.						75.0	82.0	79.0					22																	25023881		2203	4300	6503	SO:0001583	missense	2678	exon13			ACGACTTCAGCTC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1271T>G	22.37:g.25023881T>G	ENSP00000383232:p.Phe424Cys	538.0	0.0	0		431.0	104.0	0.241299	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	13.74	2.326429	0.41197	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	H	0.99357	4.53	0.48511	D	0.999661	D	0.89917	1.0	D	0.81914	0.995	T	0.72001	-0.4422	10	0.87932	D	0	-41.2004	11.6793	0.51448	0.0:0.0:0.0:1.0	.	424	P19440	GGT1_HUMAN	C	424;424;424;424;424;424;80;80;80;80;80	ENSP00000248923:F424C;ENSP00000393537:F424C;ENSP00000383232:F424C;ENSP00000383233:F424C;ENSP00000383231:F424C;ENSP00000385975:F424C;ENSP00000384381:F80C;ENSP00000385445:F80C;ENSP00000384820:F80C;ENSP00000385016:F80C;ENSP00000385001:F80C	ENSP00000248923:F424C	F	+	2	0	GGT1	23353881	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	3.722000	0.54948	1.593000	0.50029	0.373000	0.22412	TTC	.	.	none		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
DARS2	55157	hgsc.bcm.edu	37	1	173822936	173822936	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:173822936C>T	ENST00000361951.4	+	15	2294	c.1567C>T	c.(1567-1569)Cgt>Tgt	p.R523C	DARS2_ENST00000471476.1_Intron|DARS2_ENST00000239457.5_Intron	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	523					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.R523S(1)		breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	CTTCTAGGCCCGTAGCCAACA	0.388																																					p.R523C		Atlas-SNP	.											.	DARS2	61	.	1	Substitution - Missense(1)	lung(1)	c.C1567T						PASS	.						101.0	105.0	103.0					1																	173822936		2203	4300	6503	SO:0001583	missense	55157	exon15			TAGGCCCGTAGCC	AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	25538	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 2, mitochondrial"""	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.1567C>T	1.37:g.173822936C>T	ENSP00000355086:p.Arg523Cys	93.0	0.0	0		63.0	15.0	0.238095	NM_018122		Missense_Mutation	SNP	ENST00000361951.4	37	CCDS1311.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.384482	0.82792	.	.	ENSG00000117593	ENST00000361951	T	0.80123	-1.34	4.65	4.65	0.58169	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.055932	0.64402	D	0.000001	D	0.92492	0.7616	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94831	0.7996	10	0.72032	D	0.01	-15.4489	16.6683	0.85259	0.0:1.0:0.0:0.0	.	523	Q6PI48	SYDM_HUMAN	C	523	ENSP00000355086:R523C	ENSP00000355086:R523C	R	+	1	0	DARS2	172089559	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.614000	0.67695	2.304000	0.77564	0.591000	0.81541	CGT	.	.	none		0.388	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122	
GH1	2688	hgsc.bcm.edu	37	17	61995189	61995189	+	Silent	SNP	G	G	A	rs370785603		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61995189G>A	ENST00000323322.5	-	4	429	c.387C>T	c.(385-387)taC>taT	p.Y129Y	GH1_ENST00000342364.4_Intron|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Silent_p.Y89Y|GH1_ENST00000458650.2_Silent_p.Y114Y	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	129					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						CAGAGGCGCCGTACACCAGGC	0.607																																					p.Y129Y		Atlas-SNP	.											GH1,caecum,carcinoma,0,1	GH1	39	1	0			c.C387T						scavenged	.	A	,,,,	1,4405	826.1+/-416.6	0,1,2202	67.0	66.0	66.0		387,342,267,,	-4.1	0.6	17		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	GH1	NM_000515.3,NM_022559.2,NM_022560.2,NM_022561.2,NM_022562.2	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	129/218,114/203,89/178,,	61995189	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GGCGCCGTACACC	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"""Endogenous ligands"""	4261	protein-coding gene	gene with protein product	"""pituitary growth hormone"", ""somatotropin"""	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.387C>T	17.37:g.61995189G>A		131.0	1.0	0.00763359		101.0	30.0	0.29703	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	37	CCDS11653.1																																																																																			.	.	weak		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515	
TLN2	83660	hgsc.bcm.edu	37	15	62994208	62994208	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62994208G>A	ENST00000561311.1	+	17	1944	c.1714G>A	c.(1714-1716)Gac>Aac	p.D572N	TLN2_ENST00000306829.6_Missense_Mutation_p.D572N			Q9Y4G6	TLN2_HUMAN	talin 2	572					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TGCAGACACTGACTACACAGC	0.517																																					p.D572N		Atlas-SNP	.											.	TLN2	253	.	0			c.G1714A						PASS	.						97.0	77.0	83.0					15																	62994208		2203	4300	6503	SO:0001583	missense	83660	exon15			GACACTGACTACA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.1714G>A	15.37:g.62994208G>A	ENSP00000453508:p.Asp572Asn	104.0	0.0	0		129.0	65.0	0.503876	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822336	0.71028	.	.	ENSG00000171914	ENST00000306829	T	0.70282	-0.47	5.1	5.1	0.69264	Talin, central (3);	0.000000	0.85682	D	0.000000	T	0.70141	0.3190	L	0.61387	1.9	0.80722	D	1	B	0.21905	0.062	B	0.23419	0.046	T	0.66006	-0.6030	10	0.30854	T	0.27	-28.968	18.8833	0.92365	0.0:0.0:1.0:0.0	.	572	Q9Y4G6	TLN2_HUMAN	N	572	ENSP00000303476:D572N	ENSP00000303476:D572N	D	+	1	0	TLN2	60781500	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.813000	0.99286	2.532000	0.85374	0.561000	0.74099	GAC	.	.	none		0.517	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
TMF1	7110	hgsc.bcm.edu	37	3	69073223	69073223	+	Missense_Mutation	SNP	G	G	A	rs185749329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69073223G>A	ENST00000398559.2	-	16	3337	c.3121C>T	c.(3121-3123)Ctt>Ttt	p.L1041F	CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|TMF1_ENST00000489370.1_5'Flank|CTD-2013N24.2_ENST00000597366.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.L1044F|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	1041					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		TGAGTTCTAAGTTTGGGTATC	0.303													G|||	4	0.000798722	0.0	0.0043	5008	,	,		15654	0.0		0.001	False		,,,				2504	0.0				p.L1041F		Atlas-SNP	.											.	TMF1	77	.	0			c.C3121T						PASS	.	G	PHE/LEU	2,3652		0,2,1825	158.0	144.0	149.0		3121	5.6	1.0	3		149	12,8158		0,12,4073	yes	missense	TMF1	NM_007114.2	22	0,14,5898	AA,AG,GG		0.1469,0.0547,0.1184	probably-damaging	1041/1094	69073223	14,11810	1827	4085	5912	SO:0001583	missense	7110	exon16			TTCTAAGTTTGGG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.3121C>T	3.37:g.69073223G>A	ENSP00000381567:p.Leu1041Phe	132.0	0.0	0		138.0	70.0	0.507246	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.43	3.621363	0.66787	5.47E-4	0.001469	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000001	D	0.91771	0.7397	M	0.88512	2.96	0.58432	D	0.999993	D;D	0.89917	1.0;0.981	D;D	0.91635	0.999;0.91	D	0.92645	0.6128	10	0.72032	D	0.01	-10.3062	12.4791	0.55831	0.1197:0.0:0.8803:0.0	.	1044;1041	P82094-2;P82094	.;TMF1_HUMAN	F	1041;1044;957	ENSP00000381567:L1041F;ENSP00000438706:L1044F	ENSP00000348582:L957F	L	-	1	0	TMF1	69155913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.905000	0.56333	2.620000	0.88729	0.557000	0.71058	CTT	G|0.999;A|0.001	0.001	strong		0.303	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114	
PHTF2	57157	hgsc.bcm.edu	37	7	77567051	77567051	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77567051T>C	ENST00000248550.7	+	12	1439	c.1363T>C	c.(1363-1365)Tcc>Ccc	p.S455P	PHTF2_ENST00000422959.2_Missense_Mutation_p.S421P|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000424760.1_Missense_Mutation_p.S417P|PHTF2_ENST00000307305.8_Missense_Mutation_p.S417P|PHTF2_ENST00000416283.2_Missense_Mutation_p.S421P|PHTF2_ENST00000275575.7_Missense_Mutation_p.S417P			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						GCTCCATAGTTCCCACCCAGG	0.289																																					p.S421P		Atlas-SNP	.											.	PHTF2	104	.	0			c.T1261C						PASS	.						53.0	47.0	49.0					7																	77567051		1795	4059	5854	SO:0001583	missense	57157	exon11			CATAGTTCCCACC	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1363T>C	7.37:g.77567051T>C	ENSP00000248550:p.Ser455Pro	94.0	0.0	0		83.0	5.0	0.060241	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	T	15.62	2.887106	0.52014	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.19	2.81	0.32909	.	0.292942	0.33553	N	0.004795	T	0.38241	0.1033	L	0.38175	1.15	0.39118	D	0.961615	P;P;B;P;P;P	0.50156	0.731;0.918;0.437;0.736;0.49;0.932	B;P;B;B;B;P	0.48571	0.347;0.556;0.244;0.232;0.315;0.582	T	0.18967	-1.0320	9	0.27082	T	0.32	-0.7834	4.84	0.13485	0.1369:0.1486:0.0:0.7145	.	417;280;421;455;417;417	Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;PHTF2_HUMAN;.;.	P	421;421;417;417;417;421;455	.	ENSP00000248550:S455P	S	+	1	0	PHTF2	77404987	1.000000	0.71417	0.979000	0.43373	0.994000	0.84299	1.931000	0.40134	0.391000	0.25143	0.482000	0.46254	TCC	.	.	none		0.289	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
MET	4233	hgsc.bcm.edu	37	7	116339282	116339282	+	Silent	SNP	G	G	A	rs11762213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000436117.2_Silent_p.A48A|MET_ENST00000397752.3_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100.0	99.0	99.0		144,144	-11.8	0.0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.144G>A	7.37:g.116339282G>A		126.0	0.0	0		136.0	69.0	0.507353	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28898778C>G	ENST00000357084.3	+	8	930	c.663C>G	c.(661-663)ggC>ggG	p.G221G	ATP2A1_ENST00000536376.1_Silent_p.G96G|ATP2A1_ENST00000395503.4_Silent_p.G221G	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	221					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGCCTTGGGCATCGTGGCCA	0.607													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18988	0.0		0.008	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C663G						PASS	.	C	,	7,4387	12.9+/-30.5	0,7,2190	85.0	82.0	83.0		663,663	3.4	1.0	16	dbSNP_132	83	72,8528	43.6+/-101.6	1,70,4229	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1,77,6419	GG,GC,CC		0.8372,0.1593,0.608	,	221/995,221/1002	28898778	79,12915	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CTTGGGCATCGTG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.663C>G	16.37:g.28898778C>G		61.0	0.0	0		74.0	43.0	0.581081	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			C|0.995;G|0.005	0.005	strong		0.607	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
SLC19A3	80704	hgsc.bcm.edu	37	2	228563835	228563835	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228563835A>C	ENST00000258403.3	-	3	667	c.596T>G	c.(595-597)tTt>tGt	p.F199C	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.F195C	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	199					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TTTTGCATGAAAAAACATGCT	0.433																																					p.F199C		Atlas-SNP	.											.	SLC19A3	62	.	0			c.T596G						PASS	.						91.0	83.0	86.0					2																	228563835		2203	4300	6503	SO:0001583	missense	80704	exon3			GCATGAAAAAACA	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.596T>G	2.37:g.228563835A>C	ENSP00000258403:p.Phe199Cys	117.0	0.0	0		90.0	23.0	0.255556	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308304	0.81247	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.91295	-2.82;-2.82	5.77	5.77	0.91146	Major facilitator superfamily domain, general substrate transporter (1);	0.044924	0.85682	D	0.000000	D	0.95996	0.8696	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.96405	0.9300	10	0.59425	D	0.04	-19.6375	16.0872	0.81065	1.0:0.0:0.0:0.0	.	195;199	F5H2M8;Q9BZV2	.;S19A3_HUMAN	C	199;195	ENSP00000258403:F199C;ENSP00000445519:F195C	ENSP00000258403:F199C	F	-	2	0	SLC19A3	228272079	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.160000	0.77495	2.202000	0.70862	0.533000	0.62120	TTT	.	.	none		0.433	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
PRKD1	5587	hgsc.bcm.edu	37	14	30066914	30066914	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:30066914G>T	ENST00000331968.5	-	16	2446	c.2217C>A	c.(2215-2217)ttC>ttA	p.F739L	PRKD1_ENST00000415220.2_Missense_Mutation_p.F747L	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	739	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CTGACCTCCGGAAAGACTTCT	0.488																																					p.F739L		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2217A						PASS	.						68.0	70.0	70.0					14																	30066914		2203	4300	6503	SO:0001583	missense	5587	exon16			CCTCCGGAAAGAC		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2217C>A	14.37:g.30066914G>T	ENSP00000333568:p.Phe739Leu	60.0	0.0	0		38.0	9.0	0.236842	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600019	0.66332	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.64438	-0.1;-0.1	5.72	4.82	0.62117	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.34483	0.0899	N	0.01668	-0.77	0.80722	D	1	P	0.37207	0.587	B	0.37091	0.241	T	0.46498	-0.9187	10	0.56958	D	0.05	-19.8775	10.6337	0.45551	0.2039:0.0:0.7961:0.0	.	739	Q15139	KPCD1_HUMAN	L	739;747	ENSP00000333568:F739L;ENSP00000390535:F747L	ENSP00000333568:F739L	F	-	3	2	PRKD1	29136665	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.672000	0.46850	1.517000	0.48917	0.650000	0.86243	TTC	.	.	none		0.488	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
C3orf67	200844	hgsc.bcm.edu	37	3	58870321	58870321	+	Missense_Mutation	SNP	C	C	T	rs116534917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:58870321C>T	ENST00000482387.1	-	3	386	c.290G>A	c.(289-291)cGc>cAc	p.R97H	RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000492031.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.R97H|C3orf67_ENST00000472469.1_Missense_Mutation_p.R17H|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	97										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		TTCAGTTTGGCGAAGTTTAGT	0.413													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18406	0.0		0.005	False		,,,				2504	0.002				p.R97H		Atlas-SNP	.											C3orf67,NS,carcinoma,-1,1	C3orf67	45	1	0			c.G290A						PASS	.	C	HIS/ARG	10,4396	16.8+/-37.8	0,10,2193	204.0	196.0	199.0		290	1.8	1.0	3	dbSNP_132	199	93,8507	52.7+/-113.3	1,91,4208	yes	missense	C3orf67	NM_198463.2	29	1,101,6401	TT,TC,CC		1.0814,0.227,0.7919	benign	97/564	58870321	103,12903	2203	4300	6503	SO:0001583	missense	200844	exon7			GTTTGGCGAAGTT	AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.290G>A	3.37:g.58870321C>T	ENSP00000417122:p.Arg97His	188.0	0.0	0		170.0	78.0	0.458824	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	14.64	2.594771	0.46318	0.00227	0.010814	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000472469	T;T;T	0.50277	0.75;0.75;0.75	5.61	1.83	0.25207	.	0.410282	0.27906	N	0.017375	T	0.23886	0.0578	L	0.41824	1.3	0.80722	D	1	B;B	0.22983	0.078;0.045	B;B	0.20384	0.029;0.019	T	0.04607	-1.0939	9	.	.	.	-1.7255	4.7606	0.13106	0.1522:0.6058:0.0:0.242	.	17;97	C9J3M8;Q6ZVT6-2	.;.	H	97;97;17	ENSP00000295966:R97H;ENSP00000417122:R97H;ENSP00000417271:R17H	.	R	-	2	0	C3orf67	58845361	0.994000	0.37717	0.992000	0.48379	0.517000	0.34286	0.505000	0.22642	0.318000	0.23185	-0.140000	0.14226	CGC	C|0.994;T|0.006	0.006	strong		0.413	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463	
SAFB2	9667	hgsc.bcm.edu	37	19	5622579	5622579	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5622579C>T	ENST00000252542.4	-	1	412	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	SAFB_ENST00000454510.1_5'Flank|SAFB_ENST00000588852.1_5'Flank|SAFB_ENST00000433404.1_5'Flank|SAFB_ENST00000292123.5_5'Flank|SAFB_ENST00000538656.1_5'Flank|SAFB_ENST00000592224.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	50	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TTGTTGCCGCCCGTGTCCAGG	0.716																																					p.G50S	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.G148A						PASS	.						26.0	25.0	25.0					19																	5622579		2203	4300	6503	SO:0001583	missense	9667	exon1			TGCCGCCCGTGTC	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.148G>A	19.37:g.5622579C>T	ENSP00000252542:p.Gly50Ser	93.0	0.0	0		105.0	37.0	0.352381	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932295	0.34096	.	.	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542;ENST00000536849	T	0.06528	3.29	3.87	1.73	0.24493	DNA-binding SAP (4);	0.285141	0.24671	N	0.036545	T	0.03520	0.0101	N	0.00621	-1.32	0.41073	D	0.985466	P;D	0.89917	0.529;1.0	P;D	0.87578	0.536;0.998	T	0.50767	-0.8789	10	0.05436	T	0.98	-16.0604	6.3775	0.21515	0.0:0.6753:0.151:0.1737	.	50;50	A0PJ47;Q14151	.;SAFB2_HUMAN	S	50;50;50;50;29	ENSP00000252542:G50S	ENSP00000252542:G50S	G	-	1	0	SAFB2	5573579	0.881000	0.30235	0.979000	0.43373	0.956000	0.61745	0.882000	0.28186	0.420000	0.25954	0.561000	0.74099	GGC	.	.	none		0.716	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529595	80529595	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:80529595C>T	ENST00000295057.3	-	2	2006	c.1350G>A	c.(1348-1350)tgG>tgA	p.W450*	LRRTM1_ENST00000409148.1_Nonsense_Mutation_p.W450*|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	450					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						GGAAACACTTCCAGGACACGT	0.577										HNSCC(69;0.2)																											p.W450X		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1350A						PASS	.						100.0	89.0	93.0					2																	80529595		2203	4300	6503	SO:0001587	stop_gained	347730	exon2			ACACTTCCAGGAC	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1350G>A	2.37:g.80529595C>T	ENSP00000295057:p.Trp450*	83.0	0.0	0		91.0	22.0	0.241758	NM_178839	A8K397|D6W5K1|Q96DN1	Nonsense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	38	7.112766	0.98070	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	.	.	.	5.18	5.18	0.71444	.	0.077796	0.56097	U	0.000031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6948	0.91596	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	.	W	-	3	0	LRRTM1	80383106	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.803000	0.62546	2.383000	0.81215	0.561000	0.74099	TGG	.	.	none		0.577	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
PHACTR3	116154	hgsc.bcm.edu	37	20	58342349	58342349	+	Missense_Mutation	SNP	C	C	T	rs73598372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58342349C>T	ENST00000371015.1	+	5	1117	c.650C>T	c.(649-651)cCt>cTt	p.P217L	PHACTR3_ENST00000395636.2_Missense_Mutation_p.P176L|PHACTR3_ENST00000355648.4_Missense_Mutation_p.P176L|PHACTR3_ENST00000395639.4_Intron|PHACTR3_ENST00000361300.4_Intron|PHACTR3_ENST00000359926.3_Missense_Mutation_p.P214L|PHACTR3_ENST00000541461.1_Missense_Mutation_p.P176L	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	217	Pro-rich.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			CTGGACAGTCCTCCCAGACCT	0.612													C|||	102	0.0203674	0.0	0.0043	5008	,	,		16709	0.0377		0.0129	False		,,,				2504	0.0491				p.P217L		Atlas-SNP	.											.	PHACTR3	104	.	0			c.C650T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	12,4394	19.1+/-41.9	0,12,2191	42.0	41.0	41.0		641,527,650,527,	3.7	1.0	20	dbSNP_130	41	104,8496	55.6+/-116.7	0,104,4196	yes	missense,missense,missense,missense,intron	PHACTR3	NM_001199505.1,NM_001199506.1,NM_080672.3,NM_183244.1,NM_183246.1	98,98,98,98,	0,116,6387	TT,TC,CC		1.2093,0.2724,0.8919	benign,benign,benign,benign,	214/557,176/519,217/560,176/519,	58342349	116,12890	2203	4300	6503	SO:0001583	missense	116154	exon5			ACAGTCCTCCCAG	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"""Phosphatase and actin regulators"""	15833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 123"""	608725	"""chromosome 20 open reading frame 101"""	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.650C>T	20.37:g.58342349C>T	ENSP00000360054:p.Pro217Leu	128.0	0.0	0		109.0	58.0	0.53211	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	37	CCDS13480.1	34	0.015567765567765568	0	0.0	2	0.0055248618784530384	23	0.04020979020979021	9	0.011873350923482849	C	15.45	2.838151	0.50951	0.002724	0.012093	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000541461;ENST00000355648;ENST00000395636	T;T;T;T;T	0.26518	1.73;1.77;1.79;1.79;1.79	4.7	3.74	0.42951	.	0.297029	0.25714	N	0.028791	T	0.04634	0.0126	L	0.33485	1.01	0.80722	D	1	B;B	0.18461	0.028;0.006	B;B	0.13407	0.009;0.004	T	0.03651	-1.1016	10	0.52906	T	0.07	-9.1105	12.1901	0.54266	0.0:0.9151:0.0:0.0849	.	217;214	Q96KR7;B1AKX0	PHAR3_HUMAN;.	L	214;217;176;176;176	ENSP00000353002:P214L;ENSP00000360054:P217L;ENSP00000442483:P176L;ENSP00000347866:P176L;ENSP00000378998:P176L	ENSP00000347866:P176L	P	+	2	0	PHACTR3	57775744	0.991000	0.36638	1.000000	0.80357	0.991000	0.79684	3.791000	0.55469	2.166000	0.68216	0.460000	0.39030	CCT	C|0.989;T|0.011	0.011	strong		0.612	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672	
BCL7A	605	hgsc.bcm.edu	37	12	122460048	122460048	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122460048T>G	ENST00000261822.4	+	1	257	c.51T>G	c.(49-51)gaT>gaG	p.D17E	BCL7A_ENST00000538010.1_Missense_Mutation_p.D17E|RP11-87C12.5_ENST00000538710.1_lincRNA	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	17					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CCAAAGATGATATCAAGAGGG	0.716			T	MYC	BNHL																																p.D17E	GBM(17;197 467 16477 23242 44349)	Atlas-SNP	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	BCL7A	31	.	0			c.T51G						PASS	.						23.0	23.0	23.0					12																	122460048		2201	4297	6498	SO:0001583	missense	605	exon1			AGATGATATCAAG	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.51T>G	12.37:g.122460048T>G	ENSP00000261822:p.Asp17Glu	32.0	0.0	0		47.0	8.0	0.170213	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	t	12.37	1.916812	0.33815	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.62788	0.0;0.06	4.22	0.427	0.16489	.	0.000000	0.85682	U	0.000000	T	0.63248	0.2495	L	0.42245	1.32	0.46078	D	0.998856	D;P	0.63046	0.992;0.537	D;B	0.76071	0.987;0.391	T	0.58261	-0.7667	10	0.35671	T	0.21	.	3.1649	0.06533	0.1787:0.3071:0.0:0.5142	.	17;17	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	E	17	ENSP00000445868:D17E;ENSP00000261822:D17E	ENSP00000261822:D17E	D	+	3	2	BCL7A	120944431	1.000000	0.71417	0.996000	0.52242	0.059000	0.15707	1.804000	0.38873	-0.181000	0.10619	-0.570000	0.04155	GAT	.	.	none		0.716	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		
FAM188B	84182	hgsc.bcm.edu	37	7	30818128	30818128	+	Silent	SNP	A	A	G	rs200053449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818128A>G	ENST00000265299.6	+	2	221	c.144A>G	c.(142-144)cgA>cgG	p.R48R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	48										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATGATCTTCGAAAGGTTTTGC	0.453													A|||	5	0.000998403	0.0	0.0014	5008	,	,		21808	0.0		0.004	False		,,,				2504	0.0				p.R48R		Atlas-SNP	.											FAM188B,colon,carcinoma,+2,4	FAM188B	62	4	0			c.A144G						PASS	.	A		4,3884		0,4,1940	123.0	120.0	121.0		144	-3.1	1.0	7		121	62,8220		0,62,4079	no	coding-synonymous	FAM188B	NM_032222.2		0,66,6019	GG,GA,AA		0.7486,0.1029,0.5423		48/758	30818128	66,12104	1944	4141	6085	SO:0001819	synonymous_variant	84182	exon2			TCTTCGAAAGGTT	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.144A>G	7.37:g.30818128A>G		224.0	0.0	0		205.0	47.0	0.229268	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			A|0.998;G|0.002	0.002	strong		0.453	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
LRPPRC	10128	hgsc.bcm.edu	37	2	44201317	44201317	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201317A>C	ENST00000260665.7	-	9	1184	c.1127T>G	c.(1126-1128)tTt>tGt	p.F376C	LRPPRC_ENST00000409659.1_Missense_Mutation_p.F376C|LRPPRC_ENST00000409946.1_Missense_Mutation_p.F376C	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	376					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GTGTTGTAAAAAGAAACTGCC	0.358																																					p.F376C		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1127G						PASS	.						98.0	97.0	97.0					2																	44201317		2203	4300	6503	SO:0001583	missense	10128	exon9			TGTAAAAAGAAAC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1127T>G	2.37:g.44201317A>C	ENSP00000260665:p.Phe376Cys	347.0	0.0	0		555.0	64.0	0.115315	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.396960	0.83120	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70516	0.2;0.21;0.22;-0.49	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.83704	0.5312	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.987;0.998	D	0.84275	0.0491	10	0.42905	T	0.14	-11.3834	11.417	0.49958	0.8652:0.0:0.0:0.1348	.	276;350;376	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	C	276;376;376;376;350	ENSP00000260665:F376C;ENSP00000386234:F376C;ENSP00000386562:F376C;ENSP00000403637:F350C	ENSP00000260665:F376C	F	-	2	0	LRPPRC	44054821	1.000000	0.71417	0.969000	0.41365	0.952000	0.60782	7.100000	0.76989	2.333000	0.79357	0.482000	0.46254	TTT	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
SLC16A3	9123	hgsc.bcm.edu	37	17	80195163	80195163	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80195163C>T	ENST00000581287.1	+	3	2839	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	SLC16A3_ENST00000392341.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000582743.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000392339.1_Missense_Mutation_p.R173C	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 3	173					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|leukocyte migration (GO:0050900)|monocarboxylic acid transport (GO:0015718)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|poly(A) RNA binding (GO:0044822)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(20;0.00285)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0149)		Gamma Hydroxybutyric Acid(DB01440)|Niacin(DB00627)|Pyruvic acid(DB00119)	GCTGCAGGACCGCTACGGCTG	0.701																																					p.R173C	Pancreas(52;652 1135 19190 37282 52456)	Atlas-SNP	.											.	SLC16A3	19	.	0			c.C517T						PASS	.						6.0	6.0	6.0					17																	80195163		2142	4199	6341	SO:0001583	missense	9123	exon4			CAGGACCGCTACG	U81800	CCDS11804.1	17q25.3	2013-07-18	2013-07-18		ENSG00000141526	ENSG00000141526		"""Solute carriers"""	10924	protein-coding gene	gene with protein product		603877	"""solute carrier family 16 (monocarboxylic acid transporters), member 3"", ""solute carrier family 16, member 3 (monocarboxylic acid transporter 4)"""			9425115	Standard	NM_004207		Approved	MCT3, MCT4	uc021ufm.1	O15427	OTTHUMG00000178832	ENST00000581287.1:c.517C>T	17.37:g.80195163C>T	ENSP00000463978:p.Arg173Cys	93.0	0.0	0		108.0	34.0	0.314815	NM_001206950	B3KXG8|Q2M1P8	Missense_Mutation	SNP	ENST00000581287.1	37	CCDS11804.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735148	0.30774	.	.	ENSG00000141526	ENST00000392341;ENST00000392339	T;T	0.37584	1.19;1.19	5.69	4.71	0.59529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.834666	0.11530	N	0.554741	T	0.41419	0.1158	L	0.40543	1.245	0.33977	D	0.647467	P;D	0.53462	0.919;0.96	P;P	0.53062	0.717;0.657	T	0.49293	-0.8955	10	0.56958	D	0.05	.	9.2009	0.37258	0.0:0.6825:0.2372:0.0802	.	173;173	Q53G91;O15427	.;MOT4_HUMAN	C	173	ENSP00000376152:R173C;ENSP00000376150:R173C	ENSP00000376150:R173C	R	+	1	0	SLC16A3	77788452	0.010000	0.17322	0.980000	0.43619	0.812000	0.45895	0.633000	0.24598	2.696000	0.92011	0.655000	0.94253	CGC	.	.	none		0.701	SLC16A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443498.1	NM_004207	
DHRS2	10202	hgsc.bcm.edu	37	14	24114437	24114437	+	Missense_Mutation	SNP	T	T	A	rs146187363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24114437T>A	ENST00000250383.6	+	9	1294	c.818T>A	c.(817-819)gTg>gAg	p.V273E	DHRS2_ENST00000344777.7_Missense_Mutation_p.W277R	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	273					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		AACATTGCGGTGGCAGGCTAC	0.597													t|||	14	0.00279553	0.0	0.0	5008	,	,		18947	0.0		0.0	False		,,,				2504	0.0143				p.W277R		Atlas-SNP	.											.	DHRS2	78	.	0			c.T829A						PASS	.		GLU/VAL,ARG/TRP	0,4406		0,0,2203	109.0	93.0	99.0		818,829	4.4	0.7	14	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	DHRS2	NM_005794.3,NM_182908.4	121,101	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging,probably-damaging	273/281,277/301	24114437	2,13004	2203	4300	6503	SO:0001583	missense	10202	exon9			TTGCGGTGGCAGG		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.818T>A	14.37:g.24114437T>A	ENSP00000250383:p.Val273Glu	108.0	0.0	0		84.0	38.0	0.452381	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.18|15.18	2.758232|2.758232	0.49468|0.49468	0.0|0.0	2.33E-4|2.33E-4	ENSG00000100867|ENSG00000100867	ENST00000250383|ENST00000344777	T|D	0.39056|0.82526	1.1|-1.62	4.42|4.42	4.42|4.42	0.53409|0.53409	.|.	.|0.473111	.|0.23616	.|N	.|0.046297	D|D	0.88919|0.88919	0.6568|0.6568	.|.	.|.	.|.	0.30039|0.30039	N|N	0.812755|0.812755	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.69479	0.999|0.964	D|D	0.85869|0.85869	0.1415|0.1415	8|9	0.87932|0.56958	D|D	0|0.05	.|.	11.9261|11.9261	0.52820|0.52820	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273|255	D3DS54|Q13268-2	.|.	E|R	273|277	ENSP00000250383:V273E|ENSP00000344674:W277R	ENSP00000250383:V273E|ENSP00000344674:W277R	V|W	+|+	2|1	0|0	DHRS2|DHRS2	23184277|23184277	1.000000|1.000000	0.71417|0.71417	0.707000|0.707000	0.30419|0.30419	0.018000|0.018000	0.09664|0.09664	6.595000|6.595000	0.74109|0.74109	1.981000|1.981000	0.57761|0.57761	0.455000|0.455000	0.32223|0.32223	GTG|TGG	T|1.000;A|0.000	0.000	weak		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
GIT1	28964	hgsc.bcm.edu	37	17	27903998	27903998	+	Silent	SNP	A	A	C	rs144787773		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27903998A>C	ENST00000225394.3	-	12	1358	c.1110T>G	c.(1108-1110)tcT>tcG	p.S370S	GIT1_ENST00000394869.3_Silent_p.S379S|GIT1_ENST00000579937.1_Silent_p.S370S|GIT1_ENST00000581348.1_Silent_p.S379S|RP11-68I3.2_ENST00000581474.1_RNA	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	370	PTK2/FAK1-binding. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		GGCTCCGCAGAGACAGCTCGA	0.627																																					p.S379S	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.T1137G						PASS	.						48.0	49.0	49.0					17																	27903998		2203	4300	6503	SO:0001819	synonymous_variant	28964	exon13			CCGCAGAGACAGC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4272	protein-coding gene	gene with protein product		608434	"""G protein-coupled receptor kinase interactor 1"""			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.1110T>G	17.37:g.27903998A>C		36.0	0.0	0		31.0	19.0	0.612903	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Silent	SNP	ENST00000225394.3	37	CCDS11250.1																																																																																			A|0.998;C|0.002	0.002	weak		0.627	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030	
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_5'Flank|CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S|CHRD_ENST00000482805.1_3'UTR	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21.0	26.0	24.0		280	4.3	1.0	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	267.0	0.0	0		250.0	144.0	0.576	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695445	45695445	+	Missense_Mutation	SNP	C	C	G	rs143453038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45695445C>G	ENST00000305560.6	+	1	917	c.818C>G	c.(817-819)tCc>tGc	p.S273C	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.S273C|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	273						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CTGCAGGGTTCCCGGCCTGGG	0.761													C|||	50	0.00998403	0.0023	0.0202	5008	,	,		12129	0.0		0.0298	False		,,,				2504	0.0031				p.S273C		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C818G						PASS	.	C	CYS/SER	17,3375		0,17,1679	3.0	4.0	4.0		818	4.9	0.3	15	dbSNP_134	4	149,7059		1,147,3456	no	missense	SPATA5L1	NM_024063.2	112	1,164,5135	GG,GC,CC		2.0671,0.5012,1.566	possibly-damaging	273/754	45695445	166,10434	1696	3604	5300	SO:0001583	missense	79029	exon1			AGGGTTCCCGGCC	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.818C>G	15.37:g.45695445C>G	ENSP00000305494:p.Ser273Cys	5.0	0.0	0		22.0	6.0	0.272727	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	37	CCDS10123.1	40	0.018315018315018316	8	0.016260162601626018	9	0.024861878453038673	0	0.0	23	0.030343007915567283	C	20.5	3.999282	0.74818	0.005012	0.020671	ENSG00000171763	ENST00000305560	D	0.93426	-3.22	4.9	4.9	0.64082	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.367137	0.28560	N	0.014910	D	0.89111	0.6622	M	0.68728	2.09	0.20307	N	0.999919	D	0.56035	0.974	P	0.57057	0.812	D	0.85330	0.1089	10	0.87932	D	0	-22.4119	16.8259	0.85931	0.0:1.0:0.0:0.0	.	273	Q9BVQ7	SPA5L_HUMAN	C	273	ENSP00000305494:S273C	ENSP00000305494:S273C	S	+	2	0	SPATA5L1	43482737	0.758000	0.28405	0.314000	0.25224	0.281000	0.26958	7.247000	0.78257	2.536000	0.85505	0.585000	0.79938	TCC	C|0.982;G|0.018	0.018	strong		0.761	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
LAMA5	3911	hgsc.bcm.edu	37	20	60887028	60887028	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60887028C>T	ENST00000252999.3	-	70	9649	c.9583G>A	c.(9583-9585)Ggc>Agc	p.G3195S	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3195	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCGGCGAAGCCCGCTTGAGTT	0.647																																					p.G3195S		Atlas-SNP	.											.	LAMA5	268	.	0			c.G9583A						PASS	.						64.0	69.0	67.0					20																	60887028		2203	4298	6501	SO:0001583	missense	3911	exon70			CGAAGCCCGCTTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9583G>A	20.37:g.60887028C>T	ENSP00000252999:p.Gly3195Ser	80.0	0.0	0		51.0	5.0	0.0980392	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	c	4.219	0.039521	0.08148	.	.	ENSG00000130702	ENST00000252999	T	0.76709	-1.04	4.62	1.51	0.23008	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.886282	0.09702	N	0.766863	T	0.45538	0.1347	N	0.01352	-0.895	0.09310	N	1	B	0.10296	0.003	B	0.17098	0.017	T	0.35574	-0.9783	10	0.06757	T	0.87	.	7.2199	0.25981	0.0:0.4457:0.3986:0.1557	.	3195	O15230	LAMA5_HUMAN	S	3195	ENSP00000252999:G3195S	ENSP00000252999:G3195S	G	-	1	0	LAMA5	60320423	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.515000	0.06290	0.049000	0.15920	0.556000	0.70494	GGC	.	.	none		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SPTBN2	6712	hgsc.bcm.edu	37	11	66476403	66476403	+	Silent	SNP	G	G	A	rs74909073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66476403G>A	ENST00000533211.1	-	11	1492	c.1161C>T	c.(1159-1161)cgC>cgT	p.R387R	SPTBN2_ENST00000529997.1_Silent_p.R387R|SPTBN2_ENST00000309996.2_Silent_p.R387R			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	387					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCCGGCCCTCGCGGGGCGTGT	0.622													G|||	6	0.00119808	0.0	0.0	5008	,	,		15517	0.0		0.006	False		,,,				2504	0.0				p.R387R		Atlas-SNP	.											SPTBN2,colon,carcinoma,-2,3	SPTBN2	188	3	0			c.C1161T						PASS	.	G		3,4397	6.2+/-15.9	0,3,2197	66.0	66.0	66.0		1161	-10.3	0.6	11	dbSNP_134	66	36,8554	25.1+/-72.6	1,34,4260	no	coding-synonymous	SPTBN2	NM_006946.2		1,37,6457	AA,AG,GG		0.4191,0.0682,0.3002		387/2391	66476403	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon10			GCCCTCGCGGGGC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.1161C>T	11.37:g.66476403G>A		96.0	0.0	0		95.0	28.0	0.294737	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			G|0.996;A|0.004	0.004	strong		0.622	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
KRT82	3888	hgsc.bcm.edu	37	12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	rs61730587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						PASS	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48.0	48.0	48.0		1487	-0.4	0.0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	150.0	0.0	0		114.0	56.0	0.491228	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
SRGN	5552	hgsc.bcm.edu	37	10	70856963	70856963	+	Missense_Mutation	SNP	C	C	G	rs67852477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70856963C>G	ENST00000242465.3	+	2	243	c.203C>G	c.(202-204)cCc>cGc	p.P68R	SRGN_ENST00000462445.1_Intron	NM_002727.2	NP_002718.2	P10124	SRGN_HUMAN	serglycin	68					biomineral tissue development (GO:0031214)|blood coagulation (GO:0007596)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|maintenance of granzyme B location in T cell secretory granule (GO:0033382)|maintenance of protease location in mast cell secretory granule (GO:0033373)|mast cell secretory granule organization (GO:0033364)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine secretion (GO:0050710)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein processing (GO:0016485)|T cell secretory granule organization (GO:0033371)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|platelet alpha granule lumen (GO:0031093)|zymogen granule (GO:0042588)				large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(3)	7						AACAAGATCCCCCGTCTGAGG	0.413													C|||	22	0.00439297	0.0008	0.0029	5008	,	,		16334	0.001		0.0149	False		,,,				2504	0.0031				p.P68R		Atlas-SNP	.											SRGN,NS,carcinoid-endocrine_tumour,0,1	SRGN	15	1	0			c.C203G						PASS	.	C	ARG/PRO	12,4394	19.1+/-41.9	0,12,2191	96.0	87.0	90.0		203	0.2	0.0	10	dbSNP_130	90	107,8493	57.2+/-118.5	1,105,4194	yes	missense	SRGN	NM_002727.2	103	1,117,6385	GG,GC,CC		1.2442,0.2724,0.915	possibly-damaging	68/159	70856963	119,12887	2203	4300	6503	SO:0001583	missense	5552	exon2			AGATCCCCCGTCT	BC015516	CCDS7285.1	10q22.1	2007-02-16	2007-02-15	2007-02-15	ENSG00000122862	ENSG00000122862		"""Proteoglycans / Extracellular Matrix : Other"""	9361	protein-coding gene	gene with protein product	"""serglycin proteoglycan"""	177040	"""proteoglycan 1, secretory granule"""	PRG, PRG1			Standard	NR_036430		Approved	PPG	uc001joz.3	P10124	OTTHUMG00000018369	ENST00000242465.3:c.203C>G	10.37:g.70856963C>G	ENSP00000242465:p.Pro68Arg	160.0	0.0	0		122.0	62.0	0.508197	NM_002727	B2R4L7|Q5VW06	Missense_Mutation	SNP	ENST00000242465.3	37	CCDS7285.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	12	0.0158311345646438	C	4.802	0.149123	0.09185	0.002724	0.012442	ENSG00000122862	ENST00000242465	T	0.50548	0.74	5.26	0.242	0.15498	.	1.444430	0.04231	N	0.335288	T	0.22704	0.0548	L	0.29908	0.895	0.09310	N	1	B	0.25955	0.138	B	0.32677	0.15	T	0.33292	-0.9874	10	0.59425	D	0.04	-14.8937	4.3284	0.11051	0.0:0.2911:0.1779:0.531	.	68	P10124	SRGN_HUMAN	R	68	ENSP00000242465:P68R	ENSP00000242465:P68R	P	+	2	0	SRGN	70526969	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.360000	0.20250	-0.129000	0.11620	-0.367000	0.07326	CCC	C|0.991;G|0.009	0.009	strong		0.413	SRGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048379.1	NM_002727	
TIAM2	26230	hgsc.bcm.edu	37	6	155500242	155500242	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:155500242T>C	ENST00000461783.3	+	13	3866	c.2593T>C	c.(2593-2595)Tgc>Cgc	p.C865R	TIAM2_ENST00000360366.4_Missense_Mutation_p.C889R|TIAM2_ENST00000367174.2_Missense_Mutation_p.C241R|TIAM2_ENST00000528391.2_Missense_Mutation_p.C201R|TIAM2_ENST00000456144.1_Missense_Mutation_p.C865R|TIAM2_ENST00000318981.5_Missense_Mutation_p.C865R|TIAM2_ENST00000529824.2_Missense_Mutation_p.C865R|TIAM2_ENST00000456877.2_Missense_Mutation_p.C177R			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	865	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TGTTGAGTATTGCATCCCTGC	0.383																																					p.C865R		Atlas-SNP	.											.	TIAM2	161	.	0			c.T2593C						PASS	.						118.0	107.0	111.0					6																	155500242		2203	4300	6503	SO:0001583	missense	26230	exon10			GAGTATTGCATCC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2593T>C	6.37:g.155500242T>C	ENSP00000437188:p.Cys865Arg	210.0	0.0	0		146.0	46.0	0.315068	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	T	6.692	0.496320	0.12762	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2	5.18	1.17	0.20885	Raf-like Ras-binding (2);PDZ/DHR/GLGF (1);	0.495104	0.22584	N	0.058171	T	0.09730	0.0239	L	0.44542	1.39	0.09310	N	0.999997	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.09377	0.001;0.003;0.004;0.001	T	0.27773	-1.0064	10	0.28530	T	0.3	.	5.0741	0.14622	0.2795:0.0759:0.0:0.6446	.	201;865;889;865	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	R	865;1111;865;865;865;241;889;865;177;201	ENSP00000437188:C865R;ENSP00000434901:C865R;ENSP00000407746:C865R;ENSP00000327315:C865R;ENSP00000356142:C241R;ENSP00000353528:C889R;ENSP00000433348:C865R;ENSP00000407183:C177R;ENSP00000435335:C201R	ENSP00000327315:C865R	C	+	1	0	TIAM2	155541934	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.639000	0.24690	0.379000	0.24794	0.533000	0.62120	TGC	.	.	none		0.383	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
WNK1	65125	hgsc.bcm.edu	37	12	994030	994030	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:994030G>A	ENST00000315939.6	+	19	4703	c.4060G>A	c.(4060-4062)Gca>Aca	p.A1354T	WNK1_ENST00000530271.2_Missense_Mutation_p.A1852T|WNK1_ENST00000537687.1_Missense_Mutation_p.A1614T|WNK1_ENST00000535572.1_Missense_Mutation_p.A1107T|WNK1_ENST00000340908.4_Missense_Mutation_p.A947T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1354					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AGCAGCCACAGCACCAGTCCC	0.498																																					p.A1614T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G4840A						PASS	.						92.0	88.0	89.0					12																	994030		2203	4300	6503	SO:0001583	missense	65125	exon19			GCCACAGCACCAG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.4060G>A	12.37:g.994030G>A	ENSP00000313059:p.Ala1354Thr	190.0	0.0	0		180.0	62.0	0.344444	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	7.571	0.666826	0.14710	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.63	2.65	0.31530	.	0.499734	0.20150	N	0.098164	T	0.22704	0.0548	N	0.14661	0.345	0.18873	N	0.999989	B;B;B	0.19200	0.01;0.034;0.02	B;B;B	0.21708	0.022;0.036;0.016	T	0.14227	-1.0480	10	0.29301	T	0.29	-1.4729	6.408	0.21676	0.2705:0.1226:0.6068:0.0	.	1107;1107;1354	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1107;1354;1614;527;1852;947	ENSP00000441972:A1107T;ENSP00000313059:A1354T;ENSP00000444465:A1614T;ENSP00000433548:A1852T;ENSP00000341292:A947T	ENSP00000252477:A527T	A	+	1	0	WNK1	864291	0.191000	0.23288	0.918000	0.36340	0.051000	0.14879	0.566000	0.23593	0.850000	0.35239	0.655000	0.94253	GCA	.	.	none		0.498	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1676			Q -> E (in dbSNP:rs12187098).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130.0	127.0	128.0		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	183.0	0.0	0		197.0	67.0	0.340102	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
PPP1R16A	84988	hgsc.bcm.edu	37	8	145722726	145722726	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145722726C>A	ENST00000292539.4	+	2	1066	c.149C>A	c.(148-150)cCt>cAt	p.P50H	PPP1R16A_ENST00000529009.1_3'UTR|CTD-2517M14.5_ENST00000569326.1_RNA|CTD-2517M22.14_ENST00000532766.1_RNA|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.P50H			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	50				Missing (in Ref. 1; BAC03452). {ECO:0000305}.		plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AAGAAGGGTCCTGGGGAGCGT	0.652																																					p.P50H		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.C149A						PASS	.						48.0	43.0	45.0					8																	145722726		2203	4299	6502	SO:0001583	missense	84988	exon1			AGGGTCCTGGGGA		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14941	protein-coding gene	gene with protein product		609172	"""protein phosphatase 1, regulatory (inhibitor) subunit 16A"""			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.149C>A	8.37:g.145722726C>A	ENSP00000292539:p.Pro50His	116.0	0.0	0		145.0	80.0	0.551724	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.245088	0.22796	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.70986	-0.53;-0.53	4.49	-8.98	0.00754	.	0.960193	0.08687	N	0.908585	T	0.34106	0.0886	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41698	-0.9494	10	0.42905	T	0.14	.	10.2052	0.43109	0.1214:0.5237:0.3549:0.0	.	50	Q96I34	PP16A_HUMAN	H	50	ENSP00000292539:P50H;ENSP00000391126:P50H	ENSP00000292539:P50H	P	+	2	0	PPP1R16A	145693534	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.717000	0.01876	-1.769000	0.01297	-0.521000	0.04368	CCT	.	.	none		0.652	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902	
GABRA5	2558	hgsc.bcm.edu	37	15	27182422	27182422	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27182422A>T	ENST00000335625.5	+	8	1559	c.671A>T	c.(670-672)cAg>cTg	p.Q224L	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Missense_Mutation_p.Q224L|GABRA5_ENST00000400081.3_Missense_Mutation_p.Q224L	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	224					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	AGACTGAACCAGTACCACCTG	0.597																																					p.Q224L		Atlas-SNP	.											GABRA5,colon,carcinoma,-1,1	GABRA5	127	1	0			c.A671T						PASS	.						80.0	84.0	83.0					15																	27182422		2112	4220	6332	SO:0001583	missense	2558	exon8			TGAACCAGTACCA		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.671A>T	15.37:g.27182422A>T	ENSP00000335592:p.Gln224Leu	79.0	0.0	0		77.0	32.0	0.415584	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	A	32	5.143883	0.94603	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	T;T;T	0.79141	-1.24;-1.24;-1.24	5.28	5.28	0.74379	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.88966	0.6581	M	0.88704	2.975	0.80722	D	1	D	0.63046	0.992	D	0.66351	0.943	D	0.91133	0.4939	10	0.87932	D	0	.	14.6925	0.69096	1.0:0.0:0.0:0.0	.	224	P31644	GBRA5_HUMAN	L	224	ENSP00000335592:Q224L;ENSP00000347557:Q224L;ENSP00000382953:Q224L	ENSP00000335592:Q224L	Q	+	2	0	GABRA5	24765168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.114000	0.64651	0.379000	0.24179	CAG	.	.	none		0.597	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
C2orf16	84226	hgsc.bcm.edu	37	2	27799712	27799712	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27799712G>A	ENST00000408964.2	+	1	324	c.273G>A	c.(271-273)gtG>gtA	p.V91V		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	91						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TAAAATCTGTGGAATTAGCAC	0.393																																					p.V91V		Atlas-SNP	.											.	C2orf16	357	.	0			c.G273A						PASS	.						65.0	60.0	61.0					2																	27799712		1873	4107	5980	SO:0001819	synonymous_variant	84226	exon1			ATCTGTGGAATTA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.273G>A	2.37:g.27799712G>A		147.0	0.0	0		185.0	89.0	0.481081	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			.	.	none		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
DUSP2	1844	hgsc.bcm.edu	37	2	96810085	96810085	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810085G>C	ENST00000288943.4	-	3	623	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	180					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				CCCAGGAACAGGTAGGGCAAG	0.662																																					p.L180V		Atlas-SNP	.											.	DUSP2	20	.	0			c.C538G						PASS	.						39.0	42.0	41.0					2																	96810085		2203	4300	6503	SO:0001583	missense	1844	exon3			GGAACAGGTAGGG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.538C>G	2.37:g.96810085G>C	ENSP00000288943:p.Leu180Val	76.0	0.0	0		61.0	10.0	0.163934	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	18.49	3.636287	0.67130	.	.	ENSG00000158050	ENST00000288943	D	0.86627	-2.15	4.56	1.77	0.24775	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.64402	D	0.000013	D	0.91998	0.7465	M	0.83953	2.67	0.49687	D	0.999815	D	0.56035	0.974	D	0.80764	0.994	D	0.90547	0.4506	10	0.66056	D	0.02	.	7.8982	0.29719	0.2871:0.0:0.7129:0.0	.	180	Q05923	DUS2_HUMAN	V	180	ENSP00000288943:L180V	ENSP00000288943:L180V	L	-	1	2	DUSP2	96173812	1.000000	0.71417	0.980000	0.43619	0.696000	0.40369	2.783000	0.47766	0.680000	0.31366	0.550000	0.68814	CTG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
MYCBP2	23077	hgsc.bcm.edu	37	13	77740577	77740577	+	Missense_Mutation	SNP	T	T	C	rs111642157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77740577T>C	ENST00000544440.2	-	41	6130	c.6113A>G	c.(6112-6114)aAt>aGt	p.N2038S	MYCBP2_ENST00000407578.2_Missense_Mutation_p.N2076S|MYCBP2_ENST00000357337.6_Missense_Mutation_p.N2038S|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATATCCTGAATTCTGAACAGT	0.398													T|||	16	0.00319489	0.0068	0.0072	5008	,	,		17955	0.0		0.002	False		,,,				2504	0.0				p.N2076S		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A6227G						PASS	.	T	SER/ASN	24,4382	30.8+/-60.4	0,24,2179	109.0	107.0	108.0		6227	3.3	1.0	13	dbSNP_132	108	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MYCBP2	NM_015057.4	46	0,33,6470	CC,CT,TT		0.1047,0.5447,0.2537	benign	2076/4679	77740577	33,12973	2203	4300	6503	SO:0001583	missense	23077	exon41			CCTGAATTCTGAA	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6113A>G	13.37:g.77740577T>C	ENSP00000444596:p.Asn2038Ser	193.0	0.0	0		131.0	73.0	0.557252	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		7	0.003205128205128205	3	0.006097560975609756	4	0.011049723756906077	0	0.0	0	0.0	T	8.715	0.913023	0.17907	0.005447	0.001047	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28069	1.63;1.63;1.63	5.79	3.27	0.37495	.	0.264107	0.38326	N	0.001731	T	0.05868	0.0153	N	0.01874	-0.695	0.23030	N	0.998406	B	0.02656	0.0	B	0.01281	0.0	T	0.30822	-0.9965	10	0.08599	T	0.76	.	3.9352	0.09302	0.3857:0.1334:0.0:0.4809	.	2038	O75592	MYCB2_HUMAN	S	2038;2076;2038	ENSP00000349892:N2038S;ENSP00000384288:N2076S;ENSP00000444596:N2038S	ENSP00000349892:N2038S	N	-	2	0	MYCBP2	76638578	1.000000	0.71417	0.993000	0.49108	0.943000	0.58893	1.627000	0.37050	0.978000	0.38470	0.528000	0.53228	AAT	T|0.997;C|0.003	0.003	strong		0.398	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
WWC3	55841	hgsc.bcm.edu	37	X	10085582	10085582	+	Missense_Mutation	SNP	G	G	A	rs5934750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:10085582G>A	ENST00000380861.4	+	11	1874	c.1483G>A	c.(1483-1485)Gcc>Acc	p.A495T	WWC3_ENST00000454666.1_Missense_Mutation_p.A495T	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	495			A -> T (in dbSNP:rs5934750).		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						AGGCCTGGGCGCCCTAGACAG	0.716													G|||	103	0.0272848	0.0015	0.1153	3775	,	,		11338	0.0		0.0179	False		,,,				2504	0.0031				p.A495T		Atlas-SNP	.											.	WWC3	142	.	0			c.G1483A						PASS	.	G	THR/ALA	17,3724		0,15,2,1590,529	6.0	7.0	7.0		1483	-1.5	0.0	X	dbSNP_114	7	117,6434		1,87,28,2309,1729	yes	missense	WWC3	NM_015691.3	58	1,102,30,3899,2258	AA,AG,A,GG,G		1.786,0.4544,1.302	benign	495/1093	10085582	134,10158	2136	4154	6290	SO:0001583	missense	55841	exon11			CTGGGCGCCCTAG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1483G>A	X.37:g.10085582G>A	ENSP00000370242:p.Ala495Thr	40.0	0.0	0		61.0	60.0	0.983607	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	43	0.02591922845087402	2	0.0040650406504065045	20	0.057803468208092484	0	0.0	10	0.013333333333333334	G	6.680	0.494023	0.12702	0.004544	0.01786	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.04970	3.52;3.52	5.43	-1.5	0.08691	.	0.930558	0.09241	N	0.829226	T	0.00328	0.0010	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.48525	-0.9028	9	0.13108	T	0.6	-0.0979	4.8631	0.13594	0.3152:0.0:0.4536:0.2312	rs5934750	495	Q9ULE0	WWC3_HUMAN	T	495;495;159;495	ENSP00000370242:A495T;ENSP00000399584:A495T	ENSP00000370242:A495T	A	+	1	0	WWC3	10045582	0.000000	0.05858	0.000000	0.03702	0.567000	0.35839	0.043000	0.13971	-0.495000	0.06659	-0.382000	0.06688	GCC	G|0.973;A|0.027	0.027	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
PCDHA11	56138	hgsc.bcm.edu	37	5	140249884	140249884	+	Missense_Mutation	SNP	C	C	T	rs62622798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140249884C>T	ENST00000398640.2	+	1	1196	c.1196C>T	c.(1195-1197)aCc>aTc	p.T399I	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	399	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGTCCACCTTCAAGAAT	0.602													.|||	62	0.0123802	0.0008	0.0461	5008	,	,		21105	0.0		0.0149	False		,,,				2504	0.0143				p.T399I		Atlas-SNP	.											.	PCDHA11	209	.	0			c.C1196T						PASS	.	C	,,ILE/THR,,,,,,,,,,,,ILE/THR	34,4372	40.0+/-72.8	0,34,2169	146.0	134.0	138.0		,,1196,,,,,,,,,,,,1196	4.8	1.0	5	dbSNP_129	138	234,8366	95.6+/-157.4	1,232,4067	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,89,,,,,,,,,,,,89	1,266,6236	TT,TC,CC		2.7209,0.7717,2.0606	,,,,,,,,,,,,,,	,,399/950,,,,,,,,,,,,399/811	140249884	268,12738	2203	4300	6503	SO:0001583	missense	56138	exon1			TGTCCACCTTCAA	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1196C>T	5.37:g.140249884C>T	ENSP00000381636:p.Thr399Ile	239.0	0.0	0		178.0	80.0	0.449438	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	26	0.011904761904761904	0	0.0	13	0.03591160220994475	0	0.0	13	0.017150395778364115	C	13.18	2.161051	0.38119	0.007717	0.027209	ENSG00000249158	ENST00000398640	T	0.29142	1.58	5.7	4.81	0.61882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.15522	0.0374	L	0.29908	0.895	0.24765	N	0.992905	D;D	0.76494	0.998;0.999	D;D	0.76575	0.986;0.988	T	0.17410	-1.0370	9	0.87932	D	0	.	15.4515	0.75277	0.14:0.86:0.0:0.0	rs62622798	399;399	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	I	399	ENSP00000381636:T399I	ENSP00000381636:T399I	T	+	2	0	PCDHA11	140230068	0.030000	0.19436	0.997000	0.53966	0.560000	0.35617	3.034000	0.49751	1.338000	0.45544	0.563000	0.77884	ACC	C|0.989;T|0.011	0.011	strong		0.602	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
VSX2	338917	hgsc.bcm.edu	37	14	74707911	74707911	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74707911C>T	ENST00000261980.2	+	2	487	c.397C>T	c.(397-399)Cga>Tga	p.R133*		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	133	Ser/Thr-rich.				cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		CTCCAGCGATCGAAAAATGTC	0.597																																					p.R133X		Atlas-SNP	.											VSX2,right_upper_lobe,carcinoma,-1,1	VSX2	32	1	0			c.C397T						PASS	.						83.0	85.0	84.0					14																	74707911		2203	4300	6503	SO:0001587	stop_gained	338917	exon2			AGCGATCGAAAAA	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"""Homeoboxes / PRD class"""	1975	protein-coding gene	gene with protein product		142993	"""C elegans ceh-10 homeo domain-containing homolog"", ""ceh-10 homeo domain containing homolog (C. elegans)"", ""ceh-10 homeodomain containing homolog (C. elegans)"""	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.397C>T	14.37:g.74707911C>T	ENSP00000261980:p.Arg133*	36.0	0.0	0		49.0	10.0	0.204082	NM_182894	A1A4X6	Nonsense_Mutation	SNP	ENST00000261980.2	37	CCDS9827.1	.	.	.	.	.	.	.	.	.	.	C	37	6.112200	0.97296	.	.	ENSG00000119614	ENST00000261980	.	.	.	4.56	2.52	0.30459	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2645	0.60125	0.3715:0.6285:0.0:0.0	.	.	.	.	X	133	.	ENSP00000261980:R133X	R	+	1	2	VSX2	73777664	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.035000	0.41155	1.126000	0.42016	0.462000	0.41574	CGA	.	.	none		0.597	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894	
SLC37A2	219855	hgsc.bcm.edu	37	11	124951767	124951767	+	Missense_Mutation	SNP	G	G	A	rs143239155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124951767G>A	ENST00000403796.2	+	9	1151	c.850G>A	c.(850-852)Gct>Act	p.A284T	SLC37A2_ENST00000298280.5_Missense_Mutation_p.A284T|SLC37A2_ENST00000308074.4_Missense_Mutation_p.A284T|SLC37A2_ENST00000407458.1_Missense_Mutation_p.A284T	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	284					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		CGAAGAGCCTGCTGCCATCAG	0.557													G|||	2	0.000399361	0.0	0.0	5008	,	,		18767	0.0		0.002	False		,,,				2504	0.0				p.A284T	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G850A						PASS	.	G	THR/ALA,THR/ALA	0,4402		0,0,2201	54.0	54.0	54.0		850,850	1.5	0.3	11	dbSNP_134	54	19,8579	14.0+/-48.4	0,19,4280	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	58,58	0,19,6481	AA,AG,GG		0.221,0.0,0.1462	benign,benign	284/502,284/506	124951767	19,12981	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGCCTGCTGCCA	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.850G>A	11.37:g.124951767G>A	ENSP00000384407:p.Ala284Thr	68.0	0.0	0		68.0	53.0	0.779412	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	2.657	-0.280533	0.05642	0.0	0.00221	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.54	1.53	0.23141	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.642521	0.15596	N	0.254169	T	0.42653	0.1212	L	0.35341	1.055	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.16722	0.016;0.016	T	0.33548	-0.9864	10	0.51188	T	0.08	0.1127	6.8982	0.24267	0.0824:0.0:0.6082:0.3094	.	284;284	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	T	284	ENSP00000384407:A284T;ENSP00000385126:A284T;ENSP00000298280:A284T;ENSP00000311833:A284T	ENSP00000298280:A284T	A	+	1	0	SLC37A2	124456977	0.002000	0.14202	0.349000	0.25694	0.102000	0.19082	1.264000	0.33015	0.236000	0.21180	-0.182000	0.12963	GCT	G|0.999;A|0.001	0.001	strong		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
NEK3	4752	hgsc.bcm.edu	37	13	52726772	52726772	+	Missense_Mutation	SNP	C	C	T	rs56190615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52726772C>T	ENST00000400357.2	-	4	1658	c.365G>A	c.(364-366)cGt>cAt	p.R122H	NEK3_ENST00000452082.2_Missense_Mutation_p.R143H|NEK3_ENST00000339406.3_Missense_Mutation_p.R122H|NEK3_ENST00000378101.2_Missense_Mutation_p.R122H			P51956	NEK3_HUMAN	NIMA-related kinase 3	122	Interaction with VAV2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs56190615). {ECO:0000269|PubMed:17344846}.		mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		GTGTAGCACACGTTTCTTGTG	0.353													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18153	0.0		0.0089	False		,,,				2504	0.0041				p.R122H		Atlas-SNP	.											.	NEK3	41	.	0			c.G365A						PASS	.	C	HIS/ARG,HIS/ARG	3,3687		0,3,1842	165.0	150.0	154.0		365,365	4.1	1.0	13	dbSNP_129	154	55,8141		1,53,4044	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	29,29	1,56,5886	TT,TC,CC		0.6711,0.0813,0.488	probably-damaging,probably-damaging	122/490,122/507	52726772	58,11828	1845	4098	5943	SO:0001583	missense	4752	exon5			AGCACACGTTTCT	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.365G>A	13.37:g.52726772C>T	ENSP00000383210:p.Arg122His	123.0	0.0	0		105.0	51.0	0.485714	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	15.21	2.765809	0.49574	8.13E-4	0.006711	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.50277	1.82;1.82;1.82;1.82;0.75	5.92	4.1	0.47936	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.106321	0.64402	N	0.000020	T	0.27098	0.0664	.	.	.	0.41280	D	0.986903	B;P;P	0.45348	0.174;0.856;0.727	B;B;B	0.39562	0.12;0.303;0.201	T	0.03268	-1.1054	9	0.19590	T	0.45	.	11.7317	0.51741	0.0:0.849:0.0:0.151	rs56190615	122;143;116	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	H	122;122;122;143;116	ENSP00000339429:R122H;ENSP00000367341:R122H;ENSP00000383210:R122H;ENSP00000404197:R143H;ENSP00000448716:R116H	ENSP00000448782:R122H	R	-	2	0	NEK3	51624773	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.816000	0.48026	0.741000	0.32674	-0.136000	0.14681	CGT	C|0.995;T|0.005	0.005	strong		0.353	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
CD22	933	hgsc.bcm.edu	37	19	35835739	35835739	+	Silent	SNP	G	G	A	rs7259477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35835739G>A	ENST00000085219.5	+	10	2109	c.2043G>A	c.(2041-2043)ccG>ccA	p.P681P	CD22_ENST00000341773.6_Silent_p.P504P|CD22_ENST00000544992.2_Silent_p.P681P|CD22_ENST00000536635.2_Silent_p.P593P|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000270311.6_Silent_p.P561P|CD22_ENST00000419549.2_Silent_p.P509P|CD22_ENST00000594250.1_Silent_p.P504P	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	681					cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGATAGCCCGGAGACCATCG	0.617													G|||	14	0.00279553	0.0	0.0072	5008	,	,		18790	0.0		0.0089	False		,,,				2504	0.0				p.P681P	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.G2043A						PASS	.	G	,,,	10,4396	16.8+/-37.8	0,10,2193	116.0	121.0	120.0		1779,2043,1512,2043	-9.6	0.0	19	dbSNP_116	120	81,8519	46.7+/-105.8	0,81,4219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	0,91,6412	AA,AG,GG		0.9419,0.227,0.6997	,,,	593/760,681/752,504/671,681/848	35835739	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	933	exon10			TAGCCCGGAGACC	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2043G>A	19.37:g.35835739G>A		76.0	0.0	0		62.0	35.0	0.564516	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	rs587702923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65.0	63.0	63.0					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	153.0	0.0	0		153.0	11.0	0.0718954	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
HEPH	9843	hgsc.bcm.edu	37	X	65390579	65390579	+	Splice_Site	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:65390579T>C	ENST00000343002.2	+	1	831	c.167T>C	c.(166-168)aTa>aCa	p.I56T	HEPH_ENST00000374727.3_Splice_Site_p.I59T|HEPH_ENST00000519389.1_Splice_Site_p.I110T|HEPH_ENST00000336279.5_Intron|HEPH_ENST00000441993.2_Splice_Site_p.I59T|HEPH_ENST00000419594.1_Splice_Site_p.I59T			Q9BQS7	HEPH_HUMAN	hephaestin	56	Plastocyanin-like 1.			DI -> QR (in Ref. 7; BAA31673). {ECO:0000305}.	cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						GACAGTGACATGTAGGTTTAA	0.522																																					p.I110T		Atlas-SNP	.											.	HEPH	224	.	0			c.T329C						PASS	.						83.0	52.0	63.0					X																	65390579		2203	4300	6503	SO:0001630	splice_region_variant	9843	exon2			GTGACATGTAGGT	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.167+1T>C	X.37:g.65390579T>C		200.0	0.0	0		158.0	54.0	0.341772	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	T	2.827	-0.243436	0.05906	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000458621;ENST00000441993;ENST00000419594;ENST00000343002;ENST00000425114	D;D;D;D;D;D;D	0.98807	-5.15;-5.15;-5.15;-5.15;-5.15;-5.15;-5.15	5.01	-4.52	0.03472	Cupredoxin (2);	1.081160	0.07043	N	0.830517	D	0.91123	0.7205	N	0.04508	-0.205	0.28301	N	0.923116	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	D	0.88495	0.3078	10	0.09590	T	0.72	.	0.9233	0.01319	0.3612:0.1545:0.1092:0.3751	.	110;59;56	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	T	110;59;56;59;59;56;56	ENSP00000430620:I110T;ENSP00000363859:I59T;ENSP00000396907:I56T;ENSP00000411687:I59T;ENSP00000413211:I59T;ENSP00000343939:I56T;ENSP00000398078:I56T	ENSP00000343939:I56T	I	+	2	0	HEPH	65307304	0.002000	0.14202	0.871000	0.34182	0.557000	0.35523	-2.384000	0.01063	-0.859000	0.04105	-0.438000	0.05819	ATA	.	.	none		0.522	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	Missense_Mutation
LRP5	4041	hgsc.bcm.edu	37	11	68193582	68193582	+	Silent	SNP	G	G	A	rs117289001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68193582G>A	ENST00000294304.7	+	16	3670	c.3564G>A	c.(3562-3564)cgG>cgA	p.R1188R		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1188	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|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 apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGGACAAGCGGACTCGCATCC	0.632													G|||	19	0.00379393	0.0	0.0086	5008	,	,		17781	0.0		0.0129	False		,,,				2504	0.0				p.R1188R		Atlas-SNP	.											.	LRP5	136	.	0			c.G3564A						PASS	.	G		11,4389	19.1+/-41.9	0,11,2189	99.0	86.0	90.0		3564	-1.0	0.8	11	dbSNP_132	90	110,8478	57.9+/-119.4	3,104,4187	no	coding-synonymous	LRP5	NM_002335.2		3,115,6376	AA,AG,GG		1.2809,0.25,0.9316		1188/1616	68193582	121,12867	2200	4294	6494	SO:0001819	synonymous_variant	4041	exon16			CAAGCGGACTCGC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3564G>A	11.37:g.68193582G>A		65.0	0.0	0		52.0	38.0	0.730769	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
CR1	1378	hgsc.bcm.edu	37	1	207669708	207669708	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207669708G>A	ENST00000367049.4	+	1	96	c.96G>A	c.(94-96)gtG>gtA	p.V32V	CR1_ENST00000367051.1_Silent_p.V32V|CR1_ENST00000367053.1_Silent_p.V32V|CR1_ENST00000400960.2_Silent_p.V32V|CR1_ENST00000367052.1_Silent_p.V32V|CR1_ENST00000367050.4_3'UTR	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	32					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CGGTTGTGGTGCTGCTTGCGC	0.741																																					p.V32V		Atlas-SNP	.											.	CR1	354	.	0			c.G96A						PASS	.						10.0	13.0	12.0					1																	207669708		1820	4065	5885	SO:0001819	synonymous_variant	1378	exon1			TGTGGTGCTGCTT	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.96G>A	1.37:g.207669708G>A		39.0	0.0	0		44.0	15.0	0.340909	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559458	0.27827	.	.	ENSG00000203710	ENST00000529814	.	.	.	3.59	2.67	0.31697	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50338	-0.8840	4	.	.	.	.	7.0064	0.24838	0.1239:0.0:0.8761:0.0	.	.	.	.	Y	8	.	.	C	+	2	0	CR1	205736331	0.998000	0.40836	0.834000	0.33040	0.918000	0.54935	3.349000	0.52217	1.078000	0.41014	0.591000	0.81541	TGC	.	.	none		0.741	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
ENDOG	2021	hgsc.bcm.edu	37	9	131584732	131584732	+	Missense_Mutation	SNP	C	C	T	rs61737987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584732C>T	ENST00000372642.4	+	3	948	c.737C>T	c.(736-738)aCc>aTc	p.T246I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	246					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										GAGCTCCGCACCTACGTGATG	0.592													C|||	5	0.000998403	0.0	0.0014	5008	,	,		21151	0.0		0.001	False		,,,				2504	0.0031				p.T246I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C737T						PASS	.	C	ILE/THR,	3,4401		0,3,2199	72.0	63.0	66.0		737,	5.6	1.0	9	dbSNP_129	66	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	89,	0,22,6480	TT,TC,CC		0.2209,0.0681,0.1692	benign,	246/298,	131584732	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			TCCGCACCTACGT	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.737C>T	9.37:g.131584732C>T	ENSP00000361725:p.Thr246Ile	151.0	0.0	0		139.0	71.0	0.510791	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.73	3.462148	0.63513	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.29397	1.57	5.63	5.63	0.86233	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063535	0.64402	D	0.000004	T	0.25344	0.0616	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.36030	0.216	T	0.22382	-1.0218	10	0.87932	D	0	-0.0021	18.6823	0.91551	0.0:1.0:0.0:0.0	rs61737987	246	Q14249	NUCG_HUMAN	I	246	ENSP00000361725:T246I	ENSP00000361725:T246I	T	+	2	0	ENDOG	130624553	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.227000	0.78070	2.651000	0.90000	0.455000	0.32223	ACC	C|0.998;T|0.002	0.002	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101592919	101592919	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:101592919C>T	ENST00000310954.6	-	8	1655	c.1369G>A	c.(1369-1371)Gca>Aca	p.A457T		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GTGAACAGTGCAAACTTCATT	0.378																																					p.A457T		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G1369A						PASS	.						109.0	108.0	108.0					5																	101592919		2203	4300	6503	SO:0001583	missense	353189	exon8			ACAGTGCAAACTT	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1369G>A	5.37:g.101592919C>T	ENSP00000309741:p.Ala457Thr	410.0	0.0	0		355.0	93.0	0.261972	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402413	0.42613	.	.	ENSG00000173930	ENST00000310954	T	0.80393	-1.37	5.78	3.75	0.43078	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.276470	0.30959	N	0.008529	T	0.68375	0.2994	L	0.39566	1.225	0.31887	N	0.617758	B	0.11235	0.004	B	0.18871	0.023	T	0.62520	-0.6837	10	0.19147	T	0.46	.	6.7535	0.23499	0.4703:0.4272:0.0:0.1024	.	457	Q6ZQN7	SO4C1_HUMAN	T	457	ENSP00000309741:A457T	ENSP00000309741:A457T	A	-	1	0	SLCO4C1	101620818	0.994000	0.37717	0.995000	0.50966	0.725000	0.41563	0.657000	0.24963	1.381000	0.46364	0.585000	0.79938	GCA	.	.	none		0.378	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
SLC6A6	6533	hgsc.bcm.edu	37	3	14489107	14489107	+	Missense_Mutation	SNP	G	G	A	rs62233560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14489107G>A	ENST00000454876.2	+	5	711	c.382G>A	c.(382-384)Gtt>Att	p.V128I	SLC6A6_ENST00000416216.2_Missense_Mutation_p.V128I|SLC6A6_ENST00000360861.3_Missense_Mutation_p.V128I|SLC6A6_ENST00000484191.1_3'UTR			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	128					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						CTATGCCTCCGTTGTAATTGT	0.547													A|||	27	0.00539137	0.0	0.0101	5008	,	,		21505	0.001		0.0129	False		,,,				2504	0.0061				p.V128I		Atlas-SNP	.											.	SLC6A6	58	.	0			c.G382A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	12,4394	825.1+/-416.5	0,12,2191	410.0	392.0	398.0		382,382,382	5.1	1.0	3	dbSNP_129	398	72,8528	816.0+/-406.9	2,68,4230	yes	missense,missense,missense	SLC6A6	NM_001134367.1,NM_001134368.1,NM_003043.3	29,29,29	2,80,6421	AA,AG,GG		0.8372,0.2724,0.6459	benign,benign,benign	128/621,128/201,128/621	14489107	84,12922	2203	4300	6503	SO:0001583	missense	6533	exon5			GCCTCCGTTGTAA		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.382G>A	3.37:g.14489107G>A	ENSP00000398063:p.Val128Ile	134.0	0.0	0		118.0	57.0	0.483051	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	CCDS33705.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	10	0.013192612137203167	A	5.409	0.260708	0.10239	0.002724	0.008372	ENSG00000131389	ENST00000454876;ENST00000360861;ENST00000416216	T;T;T	0.75938	-0.98;-0.98;-0.98	5.05	5.05	0.67936	.	0.106550	0.64402	N	0.000007	T	0.44414	0.1292	N	0.05608	-0.01	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.26018	-1.0115	10	0.17832	T	0.49	.	10.8576	0.46808	0.9255:0.0:0.0745:0.0	rs62233560	128	P31641	SC6A6_HUMAN	I	128	ENSP00000398063:V128I;ENSP00000354107:V128I;ENSP00000401167:V128I	ENSP00000354107:V128I	V	+	1	0	SLC6A6	14464111	1.000000	0.71417	0.999000	0.59377	0.076000	0.17211	2.449000	0.44935	0.778000	0.33520	-0.434000	0.05882	GTT	G|0.992;A|0.008	0.008	strong		0.547	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
PTPRQ	374462	hgsc.bcm.edu	37	12	80890246	80890246	+	Silent	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:80890246T>G	ENST00000266688.5	+	19	2196	c.2196T>G	c.(2194-2196)tcT>tcG	p.S732S				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	778	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CTGTAAGGTCTTACACCAGAT	0.328																																					p.S564S		Atlas-SNP	.											.	PTPRQ	119	.	0			c.T1692G						PASS	.						102.0	91.0	95.0					12																	80890246		692	1591	2283	SO:0001819	synonymous_variant	374462	exon11			AAGGTCTTACACC	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.2196T>G	12.37:g.80890246T>G		316.0	0.0	0		277.0	60.0	0.216606	NM_001145026		Silent	SNP	ENST00000266688.5	37		.	.	.	.	.	.	.	.	.	.	T	1.028	-0.682677	0.03353	.	.	ENSG00000139304	ENST00000532722	.	.	.	5.74	-11.5	0.00074	.	.	.	.	.	T	0.30978	0.0782	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40496	-0.9560	4	.	.	.	.	1.5	0.02474	0.2724:0.0888:0.2754:0.3634	.	.	.	.	R	433	.	.	L	+	2	0	PTPRQ	79414377	0.000000	0.05858	0.094000	0.20943	0.124000	0.20399	-1.949000	0.01532	-1.866000	0.01145	-0.649000	0.03915	CTT	.	.	none		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
FDX1L	112812	hgsc.bcm.edu	37	19	10426597	10426597	+	Missense_Mutation	SNP	T	T	C	rs62640397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10426597T>C	ENST00000393708.3	-	1	94	c.76A>G	c.(76-78)Aga>Gga	p.R26G	FDX1L_ENST00000494368.1_Intron|FDX1L_ENST00000541276.1_Missense_Mutation_p.R29G|CTD-2369P2.12_ENST00000586529.1_Intron|CTD-2369P2.10_ENST00000452032.2_Missense_Mutation_p.R26G|FDX1L_ENST00000492239.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	26					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			CCCCCAGGTCTGTTCCACCAG	0.677													T|||	106	0.0211661	0.0015	0.0058	5008	,	,		11423	0.0397		0.0328	False		,,,				2504	0.0276				p.R26G		Atlas-SNP	.											.	FDX1L	21	.	0			c.A76G						PASS	.	T	GLY/ARG	36,4366		0,36,2165	19.0	22.0	21.0		76	-2.5	0.0	19	dbSNP_129	21	269,8329		5,259,4035	yes	missense	FDX1L	NM_001031734.2	125	5,295,6200	CC,CT,TT		3.1286,0.8178,2.3462	benign	26/184	10426597	305,12695	2201	4299	6500	SO:0001583	missense	112812	exon1			CAGGTCTGTTCCA	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.76A>G	19.37:g.10426597T>C	ENSP00000377311:p.Arg26Gly	86.0	0.0	0		70.0	31.0	0.442857	NM_001031734	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	37	CCDS32905.1	56	0.02564102564102564	1	0.0020325203252032522	2	0.0055248618784530384	26	0.045454545454545456	27	0.03562005277044855	T	10.47	1.359917	0.24598	0.008178	0.031286	ENSG00000167807	ENST00000541276;ENST00000393708	.	.	.	4.14	-2.54	0.06307	.	0.296563	0.29956	N	0.010774	T	0.01976	0.0062	N	0.08118	0	0.19775	N	0.999957	B	0.06786	0.001	B	0.04013	0.001	T	0.06935	-1.0799	9	0.87932	D	0	-10.9532	3.6387	0.08158	0.11:0.0955:0.4395:0.355	.	26	Q6P4F2	ADXL_HUMAN	G	29;26	.	ENSP00000341665:R26G	R	-	1	2	FDX1L	10287597	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.952000	0.03881	-0.744000	0.04778	-2.293000	0.00265	AGA	T|0.980;C|0.020	0.020	strong		0.677	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
DTHD1	401124	hgsc.bcm.edu	37	4	36296443	36296443	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:36296443G>A	ENST00000456874.2	+	4	1108	c.1050G>A	c.(1048-1050)gtG>gtA	p.V350V	DTHD1_ENST00000357504.3_Silent_p.V185V|DTHD1_ENST00000507598.1_Silent_p.V390V	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	350					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						CAGCTCTGGTGGCACATTTAA	0.368																																					p.V350V		Atlas-SNP	.											.	DTHD1	63	.	0			c.G1050A						PASS	.						153.0	122.0	131.0					4																	36296443		692	1591	2283	SO:0001819	synonymous_variant	401124	exon4			TCTGGTGGCACAT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1050G>A	4.37:g.36296443G>A		162.0	0.0	0		134.0	60.0	0.447761	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			.	.	none		0.368	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
CCDC9	26093	hgsc.bcm.edu	37	19	47774680	47774680	+	Silent	SNP	C	C	G	rs117519030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47774680C>G	ENST00000221922.6	+	12	1563	c.1341C>G	c.(1339-1341)gcC>gcG	p.A447A		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	447							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		aggaACCAGCCCAAGACCACC	0.612													C|||	36	0.0071885	0.0023	0.0043	5008	,	,		14944	0.0		0.0249	False		,,,				2504	0.0051				p.A447A		Atlas-SNP	.											.	CCDC9	37	.	0			c.C1341G						PASS	.	C		23,4383		0,23,2180	109.0	105.0	106.0		1341	-1.1	0.0	19	dbSNP_132	106	311,8287		7,297,3995	no	coding-synonymous	CCDC9	NM_015603.2		7,320,6175	GG,GC,CC		3.6171,0.522,2.5684		447/532	47774680	334,12670	2203	4299	6502	SO:0001819	synonymous_variant	26093	exon12			ACCAGCCCAAGAC	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1341C>G	19.37:g.47774680C>G		44.0	0.0	0		55.0	30.0	0.545455	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.978;G|0.022	0.022	strong		0.612	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54645455	54645455	+	Missense_Mutation	SNP	C	C	G	rs142958762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54645455C>G	ENST00000230640.5	+	12	1549	c.1295C>G	c.(1294-1296)tCc>tGc	p.S432C	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.S331C	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	432	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				GATTGCTTATCCGATGAAGAT	0.313													C|||	11	0.00219649	0.0	0.0014	5008	,	,		19133	0.0		0.0099	False		,,,				2504	0.0				p.S432C	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.C1295G						PASS	.	C	CYS/SER	8,4398	14.3+/-33.2	0,8,2195	72.0	77.0	76.0		1295	5.5	1.0	5	dbSNP_134	76	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SKIV2L2	NM_015360.4	112	0,48,6455	GG,GC,CC		0.4651,0.1816,0.3691	probably-damaging	432/1043	54645455	48,12958	2203	4300	6503	SO:0001583	missense	23517	exon12			GCTTATCCGATGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1295C>G	5.37:g.54645455C>G	ENSP00000230640:p.Ser432Cys	165.0	0.0	0		171.0	98.0	0.573099	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	26.5	4.743788	0.89663	0.001816	0.004651	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.45276	0.9;0.9	5.53	5.53	0.82687	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65964	0.2742	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.947	T	0.76000	-0.3119	10	0.87932	D	0	-21.515	19.8173	0.96576	0.0:1.0:0.0:0.0	.	331;432	F5H7E2;P42285	.;SK2L2_HUMAN	C	432;331	ENSP00000230640:S432C;ENSP00000442583:S331C	ENSP00000230640:S432C	S	+	2	0	SKIV2L2	54681212	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.850000	0.69473	2.763000	0.94921	0.585000	0.79938	TCC	C|0.995;G|0.005	0.005	strong		0.313	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
GHRL	51738	hgsc.bcm.edu	37	3	10331519	10331519	+	Missense_Mutation	SNP	C	C	T	rs34911341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:10331519C>T	ENST00000335542.8	-	4	1022	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	GHRL_ENST00000450603.1_Missense_Mutation_p.R51Q|GHRL_ENST00000430179.1_Missense_Mutation_p.R50Q|GHRL_ENST00000422159.1_Missense_Mutation_p.R51Q|GHRL_ENST00000457360.1_Missense_Mutation_p.R51Q|GHRL_ENST00000439975.2_Intron|GHRL_ENST00000449554.2_Missense_Mutation_p.R50Q|GHRL_ENST00000476283.1_5'Flank|GHRLOS_ENST00000439539.3_RNA|GHRLOS_ENST00000605014.1_RNA|GHRLOS_ENST00000603771.1_RNA|GHRL_ENST00000287656.7_Missense_Mutation_p.R50Q|GHRL_ENST00000449238.2_Missense_Mutation_p.R38Q|GHRL_ENST00000437422.2_Missense_Mutation_p.R39Q|GHRL_ENST00000446937.2_Intron|GHRLOS_ENST00000605105.1_RNA|GHRL_ENST00000429122.1_Missense_Mutation_p.R51Q			Q9UBU3	GHRL_HUMAN	ghrelin/obestatin prepropeptide	51					actin polymerization or depolymerization (GO:0008154)|activation of MAPK activity (GO:0000187)|adult feeding behavior (GO:0008343)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|cortisol secretion (GO:0043400)|decidualization (GO:0046697)|dendrite development (GO:0016358)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|glucose metabolic process (GO:0006006)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of locomotion (GO:0040013)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of synapse assembly (GO:0051965)|regulation of cell proliferation (GO:0042127)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to estrogen (GO:0043627)|response to hormone (GO:0009725)	axon (GO:0030424)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|ghrelin receptor binding (GO:0031768)|growth hormone-releasing hormone activity (GO:0016608)|protein tyrosine kinase activator activity (GO:0030296)			breast(2)|large_intestine(1)|lung(1)|ovary(1)	5						TGCTAGAGCTCGGGGCTGCAG	0.567													C|||	13	0.00259585	0.0	0.0014	5008	,	,		17746	0.005		0.007	False		,,,				2504	0.0				p.R51Q		Atlas-SNP	.											.	GHRL	8	.	0			c.G152A	GRCh37	CM012814	GHRL	M	rs34911341	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	7,4399	14.3+/-33.2	0,7,2196	140.0	150.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	149,116,113,,152	4.9	1.0	3	dbSNP_126	147	53,8547	34.8+/-89.0	0,53,4247	yes	missense,missense,missense,intron,missense	GHRL	NM_001134941.1,NM_001134944.1,NM_001134945.1,NM_001134946.1,NM_016362.3	43,43,43,,43	0,60,6443	TT,TC,CC		0.6163,0.1589,0.4613	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	50/117,39/106,38/105,,51/118	10331519	60,12946	2203	4300	6503	SO:0001583	missense	51738	exon3			AGAGCTCGGGGCT	AF296558	CCDS33700.1, CCDS46747.1, CCDS46748.1, CCDS46749.1, CCDS46750.1	3p26-p25	2013-02-26	2008-07-02		ENSG00000157017	ENSG00000157017		"""Endogenous ligands"""	18129	protein-coding gene	gene with protein product	"""prepro-appetite regulatory hormone"""	605353	"""ghrelin, growth hormone secretagogue receptor ligand"""			10930375, 10604470, 16284174	Standard	NR_024133		Approved	MTLRP, ghrelin, obestatin	uc010hdj.2	Q9UBU3	OTTHUMG00000155360	ENST00000335542.8:c.152G>A	3.37:g.10331519C>T	ENSP00000335074:p.Arg51Gln	92.0	0.0	0		110.0	57.0	0.518182	NM_016362	A8CF34|A8CF38|A8CF42|A8DN29|A8DN30|Q86YP8|Q8TAT9|Q9H3R3	Missense_Mutation	SNP	ENST00000335542.8	37	CCDS33700.1	6	0.0027472527472527475	0	0.0	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	C	26.4	4.737997	0.89573	0.001589	0.006163	ENSG00000157017	ENST00000335542;ENST00000430179;ENST00000450603;ENST00000449554;ENST00000422159;ENST00000449238;ENST00000437422;ENST00000287656;ENST00000457360;ENST00000429122	T;T;T;T;T;T;T;T;T;T	0.62364	0.63;0.63;0.63;0.63;0.03;0.43;0.42;0.63;0.63;0.63	4.88	4.88	0.63580	Motilin/ghrelin (1);	0.000000	0.49305	D	0.000160	T	0.68796	0.3040	M	0.62088	1.915	0.43003	D	0.994528	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.996;0.998;0.996;0.999	T	0.73329	-0.4017	10	0.48119	T	0.1	-12.7683	13.3995	0.60874	0.0:1.0:0.0:0.0	rs34911341	38;39;51;50;51	Q9UBU3-4;Q9UBU3-3;Q9UBU3;Q9UBU3-2;Q86YP8	.;.;GHRL_HUMAN;.;.	Q	51;50;51;50;51;38;39;50;51;51	ENSP00000335074:R51Q;ENSP00000399922:R50Q;ENSP00000389192:R51Q;ENSP00000415521:R50Q;ENSP00000405464:R51Q;ENSP00000388145:R38Q;ENSP00000416768:R39Q;ENSP00000287656:R50Q;ENSP00000391406:R51Q;ENSP00000414819:R51Q	ENSP00000287656:R50Q	R	-	2	0	GHRL	10306519	0.997000	0.39634	0.981000	0.43875	0.957000	0.61999	3.731000	0.55013	2.531000	0.85337	0.655000	0.94253	CGA	C|0.996;T|0.004	0.004	strong		0.567	GHRL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339625.1	NM_016362	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998524	72998524	+	Missense_Mutation	SNP	C	C	T	rs200266026		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:72998524C>T	ENST00000580243.1	+	2	1510	c.1162C>T	c.(1162-1164)Ccg>Tcg	p.P388S	TSHZ1_ENST00000322038.5_Missense_Mutation_p.P343S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	388					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGCAGCGAACCCGTACGTCAC	0.627																																					p.P343S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C1027T						PASS	.						104.0	109.0	107.0					18																	72998524		2203	4300	6503	SO:0001583	missense	10194	exon2			GCGAACCCGTACG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1162C>T	18.37:g.72998524C>T	ENSP00000464391:p.Pro388Ser	131.0	0.0	0		98.0	35.0	0.357143	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	C	7.820	0.717534	0.15372	.	.	ENSG00000179981	ENST00000322038	T	0.12569	2.67	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.19846	0.0477	M	0.66939	2.045	0.58432	D	0.999994	P	0.48503	0.911	B	0.39840	0.311	T	0.03354	-1.1045	10	0.54805	T	0.06	-26.8549	18.8997	0.92437	0.0:1.0:0.0:0.0	.	388	Q6ZSZ6	TSH1_HUMAN	S	343	ENSP00000323584:P343S	ENSP00000323584:P343S	P	+	1	0	TSHZ1	71127512	1.000000	0.71417	0.995000	0.50966	0.313000	0.28021	7.343000	0.79319	2.452000	0.82932	0.561000	0.74099	CCG	.	.	weak		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
GPR133	283383	hgsc.bcm.edu	37	12	131475607	131475607	+	Missense_Mutation	SNP	C	C	A	rs137909892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:131475607C>A	ENST00000261654.5	+	7	1353	c.794C>A	c.(793-795)tCc>tAc	p.S265Y	GPR133_ENST00000535015.1_Missense_Mutation_p.S297Y|RP11-76C10.5_ENST00000542980.1_lincRNA	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	265					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		TTCATGACATCCACAGCAAGC	0.473													C|||	16	0.00319489	0.0	0.0	5008	,	,		19824	0.0		0.006	False		,,,				2504	0.0102				p.S265Y		Atlas-SNP	.											.	GPR133	136	.	0			c.C794A						PASS	.	C	TYR/SER	4,4402	8.1+/-20.4	0,4,2199	140.0	105.0	117.0		794	3.4	0.0	12	dbSNP_134	117	53,8547	34.3+/-88.2	1,51,4248	yes	missense	GPR133	NM_198827.3	144	1,55,6447	AA,AC,CC		0.6163,0.0908,0.4383	possibly-damaging	265/875	131475607	57,12949	2203	4300	6503	SO:0001583	missense	283383	exon7			TGACATCCACAGC	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.794C>A	12.37:g.131475607C>A	ENSP00000261654:p.Ser265Tyr	134.0	0.0	0		144.0	75.0	0.520833	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435607	0.25813	9.08E-4	0.006163	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015;ENST00000537600	T;T	0.46063	0.88;0.88	4.4	3.41	0.39046	.	0.630854	0.15230	N	0.273456	T	0.20292	0.0488	N	0.19112	0.55	0.22571	N	0.998973	B;P	0.35600	0.343;0.511	B;B	0.31751	0.116;0.135	T	0.18808	-1.0325	10	0.72032	D	0.01	.	11.8911	0.52630	0.0:0.8233:0.1767:0.0	.	297;265	B7ZLF7;Q6QNK2	.;GP133_HUMAN	Y	265;205;297;24	ENSP00000261654:S265Y;ENSP00000444425:S297Y	ENSP00000261654:S265Y	S	+	2	0	GPR133	130041560	0.001000	0.12720	0.006000	0.13384	0.002000	0.02628	0.878000	0.28126	2.395000	0.81488	0.557000	0.71058	TCC	C|0.997;A|0.003	0.003	strong		0.473	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
KIF2B	84643	hgsc.bcm.edu	37	17	51901244	51901244	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:51901244G>A	ENST00000268919.4	+	1	1006	c.850G>A	c.(850-852)Gcc>Acc	p.A284T		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	284	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CCAGTTCACCGCCCAGCCACT	0.572																																					p.A284T		Atlas-SNP	.											.	KIF2B	254	.	0			c.G850A						PASS	.						91.0	79.0	83.0					17																	51901244		2203	4300	6503	SO:0001583	missense	84643	exon1			TTCACCGCCCAGC	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.850G>A	17.37:g.51901244G>A	ENSP00000268919:p.Ala284Thr	96.0	0.0	0		86.0	27.0	0.313953	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686847	0.88639	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.18502	2.21	5.52	5.52	0.82312	Kinesin, motor domain (4);	0.000000	0.51477	D	0.000092	T	0.18425	0.0442	L	0.43923	1.385	0.58432	D	0.999998	P	0.41784	0.762	B	0.38880	0.284	T	0.01127	-1.1443	10	0.35671	T	0.21	.	18.3543	0.90352	0.0:0.0:1.0:0.0	.	284	Q8N4N8	KIF2B_HUMAN	T	284;172	ENSP00000268919:A284T	ENSP00000268919:A284T	A	+	1	0	KIF2B	49256243	1.000000	0.71417	0.964000	0.40570	0.833000	0.47200	5.606000	0.67641	2.739000	0.93911	0.655000	0.94253	GCC	.	.	none		0.572	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
FSTL5	56884	hgsc.bcm.edu	37	4	162680603	162680603	+	Silent	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:162680603A>T	ENST00000306100.5	-	6	1123	c.687T>A	c.(685-687)gcT>gcA	p.A229A	FSTL5_ENST00000536695.1_Silent_p.A228A|FSTL5_ENST00000379164.4_Silent_p.A228A|FSTL5_ENST00000427802.2_Silent_p.A228A	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	229	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		GGTGCTTGTCAGCATTAAAAT	0.333																																					p.A229A		Atlas-SNP	.											.	FSTL5	207	.	0			c.T687A						PASS	.						93.0	101.0	98.0					4																	162680603		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon6			CTTGTCAGCATTA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.687T>A	4.37:g.162680603A>T		239.0	0.0	0		210.0	52.0	0.247619	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			.	.	none		0.333	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
NSD1	64324	hgsc.bcm.edu	37	5	176638506	176638506	+	Missense_Mutation	SNP	G	G	C	rs28932179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176638506G>C	ENST00000439151.2	+	5	3151	c.3106G>C	c.(3106-3108)Gcc>Ccc	p.A1036P	NSD1_ENST00000347982.4_Missense_Mutation_p.A767P|NSD1_ENST00000361032.4_Missense_Mutation_p.A933P|NSD1_ENST00000354179.4_Missense_Mutation_p.A767P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1036			A -> P (in dbSNP:rs28932179). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TGCTTTTTCAGCCCAAATGGT	0.458			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.A1036P		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	NSD1_ENST00000439151,NS,carcinoma,-2,2	NSD1	416	2	0			c.G3106C						PASS	.	G	PRO/ALA,PRO/ALA	133,4273	94.8+/-133.5	3,127,2073	122.0	121.0	121.0		3106,2299	-7.9	0.0	5	dbSNP_125	121	209,8391	89.9+/-152.1	2,205,4093	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	27,27	5,332,6166	CC,CG,GG		2.4302,3.0186,2.6296	possibly-damaging,possibly-damaging	1036/2697,767/2428	176638506	342,12664	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTTCAGCCCAAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3106G>C	5.37:g.176638506G>C	ENSP00000395929:p.Ala1036Pro	136.0	0.0	0		144.0	67.0	0.465278	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	49	0.022435897435897436	24	0.04878048780487805	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	3.407	-0.121106	0.06838	0.030186	0.024302	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93547	-3.13;-3.13;-3.13;-3.24	4.58	-7.92	0.01160	.	0.885835	0.09644	N	0.774583	T	0.52869	0.1761	N	0.24115	0.695	0.09310	N	0.999999	P;P;B	0.40875	0.731;0.729;0.38	B;P;B	0.45232	0.277;0.474;0.147	T	0.72597	-0.4245	9	.	.	.	.	0.8308	0.01130	0.3731:0.1058:0.1991:0.3219	rs28932179	767;933;1036	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	P	767;1036;767;933	ENSP00000346111:A767P;ENSP00000395929:A1036P;ENSP00000343209:A767P;ENSP00000354310:A933P	.	A	+	1	0	NSD1	176571112	0.005000	0.15991	0.008000	0.14137	0.473000	0.32948	-0.404000	0.07205	-2.092000	0.00857	0.467000	0.42956	GCC	G|0.975;C|0.025	0.025	strong		0.458	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
CCR8	1237	hgsc.bcm.edu	37	3	39374151	39374151	+	Missense_Mutation	SNP	C	C	T	rs144913149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374151C>T	ENST00000326306.4	+	2	467	c.329C>T	c.(328-330)tCt>tTt	p.S110F	CCR8_ENST00000545843.1_Missense_Mutation_p.S27F|CCR8_ENST00000414803.1_Silent_p.V52V	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	110					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		AAAGTGGTGTCTGGCTTTTAT	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		24185	0.0		0.001	False		,,,				2504	0.0				p.S110F		Atlas-SNP	.											.	CCR8	34	.	0			c.C329T						PASS	.	C	PHE/SER	1,4405	2.1+/-5.4	0,1,2202	248.0	223.0	231.0		329	4.7	1.0	3	dbSNP_134	231	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CCR8	NM_005201.3	155	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	probably-damaging	110/356	39374151	16,12990	2203	4300	6503	SO:0001583	missense	1237	exon2			TGGTGTCTGGCTT	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.329C>T	3.37:g.39374151C>T	ENSP00000326432:p.Ser110Phe	416.0	0.0	0		354.0	180.0	0.508475	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.81	2.941871	0.53079	2.27E-4	0.001744	ENSG00000179934	ENST00000326306;ENST00000545843	T;T	0.37584	1.19;1.19	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.316313	0.30142	N	0.010316	T	0.59252	0.2180	M	0.79343	2.45	0.36556	D	0.872118	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.69676	-0.5081	10	0.87932	D	0	.	12.254	0.54613	0.1705:0.8294:0.0:0.0	.	110;27	P51685;Q3KNR3	CCR8_HUMAN;.	F	110;27	ENSP00000326432:S110F;ENSP00000440474:S27F	ENSP00000326432:S110F	S	+	2	0	CCR8	39349155	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	0.375000	0.20518	2.429000	0.82318	0.563000	0.77884	TCT	C|0.999;T|0.001	0.001	strong		0.493	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
S1PR5	53637	hgsc.bcm.edu	37	19	10624838	10624838	+	Missense_Mutation	SNP	C	C	T	rs150461309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10624838C>T	ENST00000439028.3	-	2	975	c.850G>A	c.(850-852)Gta>Ata	p.V284I	S1PR5_ENST00000333430.4_Missense_Mutation_p.V284I	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	284					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	TGCAGGAGTACAGGACAGGTG	0.657													C|||	24	0.00479233	0.0	0.0014	5008	,	,		15614	0.0169		0.004	False		,,,				2504	0.002				p.V284I		Atlas-SNP	.											.	S1PR5	33	.	0			c.G850A						PASS	.	C	ILE/VAL,ILE/VAL	2,4392	2.1+/-5.4	0,2,2195	34.0	32.0	32.0		850,850	1.8	0.2	19	dbSNP_134	32	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	S1PR5	NM_001166215.1,NM_030760.4	29,29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	benign,benign	284/399,284/399	10624838	11,12983	2197	4300	6497	SO:0001583	missense	53637	exon2			GGAGTACAGGACA	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	14299	protein-coding gene	gene with protein product		605146	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"""	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.850G>A	19.37:g.10624838C>T	ENSP00000416915:p.Val284Ile	80.0	0.0	0		63.0	30.0	0.47619	NM_030760	Q6NW11	Missense_Mutation	SNP	ENST00000439028.3	37	CCDS12240.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	0|0	0.0|0.0	14|14	0.024475524475524476|0.024475524475524476	3|3	0.00395778364116095|0.00395778364116095	C|C	0.204|0.204	-1.041896|-1.041896	0.01997|0.01997	4.55E-4|4.55E-4	0.001047|0.001047	ENSG00000180739|ENSG00000180739	ENST00000359134|ENST00000439028;ENST00000333430	.|T;T	.|0.36878	.|1.23;1.23	5.21|5.21	1.84|1.84	0.25277|0.25277	.|GPCR, rhodopsin-like superfamily (1);	.|0.440276	.|0.20594	.|U	.|0.089285	T|T	0.05318|0.05318	0.0141|0.0141	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	0.999994|0.999994	.|B	.|0.20459	.|0.045	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	6|10	0.87932|0.02654	D|T	0|1	.|.	1.7218|1.7218	0.02913|0.02913	0.147:0.4824:0.143:0.2276|0.147:0.4824:0.143:0.2276	.|.	.|284	.|Q9H228	.|S1PR5_HUMAN	Y|I	252|284	.|ENSP00000416915:V284I;ENSP00000328472:V284I	ENSP00000352045:C252Y|ENSP00000328472:V284I	C|V	-|-	2|1	0|0	S1PR5|S1PR5	10485838|10485838	0.000000|0.000000	0.05858|0.05858	0.163000|0.163000	0.22734|0.22734	0.520000|0.520000	0.34377|0.34377	-0.726000|-0.726000	0.04936|0.04936	0.194000|0.194000	0.20326|0.20326	0.491000|0.491000	0.48974|0.48974	TGT|GTA	C|0.997;T|0.003	0.003	strong		0.657	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760	
PSG8	440533	hgsc.bcm.edu	37	19	43262267	43262267	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43262267T>C	ENST00000306511.4	-	3	693	c.596A>G	c.(595-597)aAc>aGc	p.N199S	PSG8_ENST00000600709.1_5'UTR|PSG8_ENST00000406636.3_Missense_Mutation_p.N77S|PSG8_ENST00000404209.4_Missense_Mutation_p.N199S|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	199	Ig-like C2-type 1.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				GAGGGTCCTGTTGGTTTCAGA	0.517																																					p.N199S		Atlas-SNP	.											.	PSG8	101	.	0			c.A596G						PASS	.						269.0	276.0	274.0					19																	43262267		2203	4299	6502	SO:0001583	missense	440533	exon3			GTCCTGTTGGTTT	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.596A>G	19.37:g.43262267T>C	ENSP00000305005:p.Asn199Ser	95.0	0.0	0		90.0	39.0	0.433333	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	t	11.57	1.678127	0.29783	.	.	ENSG00000124467	ENST00000404209;ENST00000292109;ENST00000406636;ENST00000426252;ENST00000306511	T;T;T	0.15017	2.46;2.46;2.46	1.53	1.53	0.23141	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36936	0.0985	M	0.83223	2.63	0.09310	N	1	P;P;P;P	0.48089	0.624;0.683;0.884;0.905	P;P;P;P	0.62089	0.516;0.73;0.836;0.898	T	0.10291	-1.0636	9	0.87932	D	0	.	5.1071	0.14790	0.0:0.0:0.0:1.0	.	77;199;199;199	Q9UQ74-2;Q9UQ74;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.	S	199;74;77;11;199	ENSP00000385869:N199S;ENSP00000385081:N77S;ENSP00000305005:N199S	ENSP00000292109:N74S	N	-	2	0	PSG8	47954107	0.019000	0.18553	0.023000	0.16930	0.028000	0.11728	1.962000	0.40442	0.697000	0.31718	0.248000	0.18094	AAC	.	.	none		0.517	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
KIF17	57576	hgsc.bcm.edu	37	1	21044151	21044151	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21044151G>A	ENST00000247986.2	-	1	359	c.49C>T	c.(49-51)Cag>Tag	p.Q17*	KIF17_ENST00000400463.3_Nonsense_Mutation_p.Q17*|KIF17_ENST00000375044.1_5'Flank|SH2D5_ENST00000460804.1_5'Flank			Q9P2E2	KIF17_HUMAN	kinesin family member 17	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CGCTCCCGCTGGTTCATGGGA	0.741																																					p.Q17X		Atlas-SNP	.											.	KIF17	130	.	0			c.C49T						PASS	.						11.0	12.0	12.0					1																	21044151		2178	4261	6439	SO:0001587	stop_gained	57576	exon1			CCCGCTGGTTCAT	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.49C>T	1.37:g.21044151G>A	ENSP00000247986:p.Gln17*	13.0	0.0	0		13.0	6.0	0.461538	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Nonsense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	.	.	.	.	.	.	.	.	.	.	G	39	7.498382	0.98322	.	.	ENSG00000117245	ENST00000400463;ENST00000247986	.	.	.	4.11	3.16	0.36331	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	2.572	0.04797	0.1049:0.1814:0.5104:0.2033	.	.	.	.	X	17	.	ENSP00000247986:Q17X	Q	-	1	0	KIF17	20916738	0.969000	0.33509	1.000000	0.80357	0.824000	0.46624	1.130000	0.31393	0.865000	0.35603	0.485000	0.47835	CAG	.	.	none		0.741	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
NEB	4703	hgsc.bcm.edu	37	2	152389991	152389991	+	Intron	SNP	A	A	G	rs114218081	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152389991A>G	ENST00000172853.10	-	115	16462				NEB_ENST00000427231.2_Intron|NEB_ENST00000409198.1_Intron|NEB_ENST00000397345.3_Silent_p.L7128L|NEB_ENST00000603639.1_Silent_p.L7128L|NEB_ENST00000604864.1_Intron			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGAGCAGTCAACATATCTGGA	0.413													A|||	88	0.0175719	0.0393	0.0072	5008	,	,		22891	0.0		0.0268	False		,,,				2504	0.0041				p.L7163L		Atlas-SNP	.											.	NEB	1697	.	0			c.T21487C						PASS	.	A	,,	55,1329		3,49,640	218.0	170.0	185.0		,21382,	6.2	1.0	2	dbSNP_132	185	66,3116		0,66,1525	no	intron,coding-synonymous,intron	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	3,115,2165	GG,GA,AA		2.0742,3.974,2.65	,,	,7128/8526,	152389991	121,4445	692	1591	2283	SO:0001627	intron_variant	4703	exon144			CAGTCAACATATC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16314+737T>C	2.37:g.152389991A>G		127.0	0.0	0		102.0	46.0	0.45098	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.979;G|0.021	0.021	strong		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
MTTP	4547	hgsc.bcm.edu	37	4	100503136	100503136	+	Missense_Mutation	SNP	C	C	G	rs141736123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100503136C>G	ENST00000265517.5	+	2	339	c.136C>G	c.(136-138)Cgg>Ggg	p.R46G	MTTP_ENST00000422897.2_Missense_Mutation_p.R46G|MTTP_ENST00000511045.1_Missense_Mutation_p.R73G|MTTP_ENST00000457717.1_Missense_Mutation_p.R46G			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	46	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TCTTCTTGATCGGGGCAAAGG	0.468													C|||	63	0.0125799	0.0015	0.0115	5008	,	,		19440	0.0		0.0219	False		,,,				2504	0.0317				p.R46G		Atlas-SNP	.											.	MTTP	127	.	0			c.C136G						PASS	.	C	GLY/ARG	13,4393	20.2+/-43.8	0,13,2190	180.0	151.0	161.0		136	4.0	1.0	4	dbSNP_134	161	151,8449	73.2+/-135.9	1,149,4150	yes	missense	MTTP	NM_000253.2	125	1,162,6340	GG,GC,CC		1.7558,0.2951,1.261	benign	46/895	100503136	164,12842	2203	4300	6503	SO:0001583	missense	4547	exon3			CTTGATCGGGGCA		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.136C>G	4.37:g.100503136C>G	ENSP00000265517:p.Arg46Gly	163.0	0.0	0		151.0	70.0	0.463576	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	C	11.83	1.754473	0.31046	0.002951	0.017558	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.76	3.98	0.46160	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.458166	0.26052	N	0.026639	T	0.16642	0.0400	L	0.38838	1.175	0.33153	D	0.546014	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.15484	0.005;0.001;0.013	T	0.25606	-1.0127	10	0.21014	T	0.42	-12.0949	9.6418	0.39844	0.1303:0.5146:0.3551:0.0	.	73;46;46	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	G	56;73;46;46;46;46	ENSP00000426755:R56G;ENSP00000427679:R73G;ENSP00000400821:R46G;ENSP00000265517:R46G;ENSP00000407350:R46G	ENSP00000265517:R46G	R	+	1	2	MTTP	100722159	1.000000	0.71417	0.996000	0.52242	0.629000	0.37895	1.216000	0.32443	0.733000	0.32492	0.655000	0.94253	CGG	C|0.989;G|0.010;T|0.000	0.010	strong		0.468	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
TPX2	22974	hgsc.bcm.edu	37	20	30381700	30381700	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30381700G>A	ENST00000300403.6	+	14	2087	c.1559G>A	c.(1558-1560)gGg>gAg	p.G520E	TPX2_ENST00000340513.4_Missense_Mutation_p.G556E	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	520					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			CCACATTATGGGGTGCCTTTT	0.443																																					p.G520E		Atlas-SNP	.											.	TPX2	61	.	0			c.G1559A						PASS	.						171.0	176.0	174.0					20																	30381700		2203	4300	6503	SO:0001583	missense	22974	exon14			ATTATGGGGTGCC	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1559G>A	20.37:g.30381700G>A	ENSP00000300403:p.Gly520Glu	184.0	0.0	0		158.0	38.0	0.240506	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831487	0.91036	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.35236	1.32	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.63674	0.2531	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.57015	-0.7883	10	0.25751	T	0.34	-20.3066	19.545	0.95291	0.0:0.0:1.0:0.0	.	556;520	Q96RR5;Q9ULW0	.;TPX2_HUMAN	E	520;556	ENSP00000341145:G556E	ENSP00000300403:G520E	G	+	2	0	TPX2	29845361	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.527000	0.67123	2.861000	0.98227	0.655000	0.94253	GGG	.	.	none		0.443	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S|PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11.0	14.0	13.0		1948	-0.2	0.0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	13.0	0.0	0		26.0	12.0	0.461538	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
HSPA4	3308	hgsc.bcm.edu	37	5	132412424	132412424	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:132412424T>C	ENST00000304858.2	+	7	1031	c.742T>C	c.(742-744)Ttt>Ctt	p.F248L	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	248					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGTGAAGAATTTGGGAAGAA	0.373																																					p.F248L	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T742C						PASS	.						106.0	108.0	107.0					5																	132412424		2203	4300	6503	SO:0001583	missense	3308	exon7			GAAGAATTTGGGA	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.742T>C	5.37:g.132412424T>C	ENSP00000302961:p.Phe248Leu	166.0	0.0	0		109.0	19.0	0.174312	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	T	34	5.399231	0.96030	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.01295	5.04	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.12263	0.0298	M	0.91561	3.22	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.00403	-1.1761	10	0.87932	D	0	-10.5177	16.1924	0.82000	0.0:0.0:0.0:1.0	.	248	P34932	HSP74_HUMAN	L	248	ENSP00000302961:F248L	ENSP00000302961:F248L	F	+	1	0	HSPA4	132440323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.565000	0.82337	2.287000	0.76781	0.482000	0.46254	TTT	.	.	none		0.373	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
TRIM11	81559	hgsc.bcm.edu	37	1	228589861	228589861	+	Splice_Site	SNP	G	G	A	rs143926476		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228589861G>A	ENST00000284551.6	-	2	688	c.410C>T	c.(409-411)gCg>gTg	p.A137V	TRIM11_ENST00000366699.3_Splice_Site_p.A137V|TRIM11_ENST00000460651.1_5'Flank|TRIM11_ENST00000493030.2_Missense_Mutation_p.A12V	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	137					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				CTCCAGCTTCGCCTGCGGGAG	0.597																																					p.A137V		Atlas-SNP	.											.	TRIM11	38	.	0			c.C410T						PASS	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	57.0	48.0	51.0		410	0.3	0.4	1	dbSNP_134	51	0,8600		0,0,4300	no	missense-near-splice	TRIM11	NM_145214.2	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	137/469	228589861	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	81559	exon2			AGCTTCGCCTGCG	AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16281	protein-coding gene	gene with protein product		607868	"""tripartite motif-containing 11"""			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.409-1C>T	1.37:g.228589861G>A		143.0	0.0	0		132.0	31.0	0.234848	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.281017	0.23392	4.54E-4	0.0	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.57436	0.4;0.4	4.56	0.332	0.15938	.	0.734180	0.11649	N	0.542981	T	0.16342	0.0393	N	0.00605	-1.335	0.09310	N	0.999998	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.14578	0.001;0.011;0.0	T	0.18085	-1.0348	10	0.34782	T	0.22	.	1.8017	0.03073	0.3285:0.3588:0.2048:0.1079	.	137;137;137	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	V	137	ENSP00000284551:A137V;ENSP00000355660:A137V	ENSP00000284551:A137V	A	-	2	0	TRIM11	226656484	0.001000	0.12720	0.445000	0.26908	0.054000	0.15201	-0.571000	0.05889	0.469000	0.27268	-0.252000	0.11476	GCG	G|1.000;A|0.000	0.000	weak		0.597	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214	Missense_Mutation
MUSK	4593	hgsc.bcm.edu	37	9	113449489	113449489	+	Missense_Mutation	SNP	C	C	T	rs35142681	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113449489C>T	ENST00000374448.4	+	3	433	c.299C>T	c.(298-300)aCg>aTg	p.T100M	MUSK_ENST00000416899.2_Missense_Mutation_p.T100M|MUSK_ENST00000374439.1_5'Flank|MUSK_ENST00000374440.3_5'UTR|MUSK_ENST00000189978.5_Missense_Mutation_p.T100M	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	100	Ig-like 1.		T -> M (in dbSNP:rs35142681). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TACTGCTGCACGGCCAACAAT	0.517													C|||	49	0.00978435	0.0015	0.0216	5008	,	,		17374	0.0		0.0308	False		,,,				2504	0.001				p.T100M		Atlas-SNP	.											.	MUSK	112	.	0			c.C299T						PASS	.	C	MET/THR,MET/THR,MET/THR	29,4035		1,27,2004	181.0	187.0	185.0		299,299,299	-7.1	0.0	9	dbSNP_126	185	254,8152		3,248,3952	yes	missense,missense,missense	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	81,81,81	4,275,5956	TT,TC,CC		3.0217,0.7136,2.2694	benign,benign,benign	100/784,100/774,100/870	113449489	283,12187	2032	4203	6235	SO:0001583	missense	4593	exon3			GCTGCACGGCCAA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.299C>T	9.37:g.113449489C>T	ENSP00000363571:p.Thr100Met	212.0	0.0	0		157.0	157.0	1	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	29	0.013278388278388278	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	22	0.029023746701846966	C	11.55	1.672850	0.29693	0.007136	0.030217	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.68765	-0.35	6.05	-7.08	0.01558	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.734616	0.13377	N	0.392447	T	0.22322	0.0538	N	0.25245	0.725	0.33065	D	0.534608	B;B	0.28233	0.164;0.204	B;B	0.24701	0.055;0.053	T	0.07462	-1.0771	10	0.48119	T	0.1	.	13.5019	0.61462	0.0999:0.6723:0.0:0.2278	rs35142681	100;100	O15146;F5H6T2	MUSK_HUMAN;.	M	100	ENSP00000363571:T100M	ENSP00000189978:T100M	T	+	2	0	MUSK	112489310	0.014000	0.17966	0.006000	0.13384	0.988000	0.76386	0.205000	0.17356	-1.188000	0.02705	-0.355000	0.07637	ACG	C|0.983;T|0.017	0.017	strong		0.517	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
FAS	355	hgsc.bcm.edu	37	10	90771767	90771767	+	Missense_Mutation	SNP	G	G	A	rs56006128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90771767G>A	ENST00000355279.2	+	7	580	c.580G>A	c.(580-582)Gaa>Aaa	p.E194K	FAS_ENST00000352159.4_Missense_Mutation_p.E194K|FAS_ENST00000357339.2_Missense_Mutation_p.E173K|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000355740.2_Missense_Mutation_p.E194K			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	GAAGAGAAAGGAAGTACAGAA	0.358													G|||	3	0.000599042	0.0	0.0014	5008	,	,		20137	0.0		0.002	False		,,,				2504	0.0				p.E194K		Atlas-SNP	.											.	FAS	47	.	0			c.G580A	GRCh37	CM065175	FAS	M	rs56006128	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	104.0	107.0	106.0		580,517,580		0.0	10	dbSNP_129	106	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense	FAS	NM_000043.4,NM_152871.2,NM_152872.2	56,56,56	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	benign,benign,benign	194/336,173/315,194/221	90771767	32,12974	2203	4300	6503	SO:0001583	missense	355	exon7			AGAAAGGAAGTAC	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.580G>A	10.37:g.90771767G>A	ENSP00000347426:p.Glu194Lys	83.0	0.0	0		54.0	27.0	0.5	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.005	-2.233006	0.00277	6.81E-4	0.003372	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;T;D;T	0.92595	-3.07;-0.6;-2.09;-0.49	.	.	.	.	1209.270000	0.00166	U	0.000004	T	0.74489	0.3723	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.14805	0.001;0.0;0.011	B;B;B	0.01281	0.0;0.0;0.0	T	0.69895	-0.5021	8	0.28530	T	0.3	.	.	.	.	rs56006128	173;194;194	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	K	221;194;194;173;194;194	ENSP00000347979:E194K;ENSP00000345601:E194K;ENSP00000349896:E173K;ENSP00000347426:E194K	ENSP00000345601:E194K	E	+	1	0	FAS	90761747	.	.	0.010000	0.14722	0.014000	0.08584	.	.	0.119000	0.18210	0.121000	0.15741	GAA	G|0.999;A|0.001	0.001	strong		0.358	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	rs572028879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810609C>T	ENST00000288943.4	-	2	486	c.401G>A	c.(400-402)gGc>gAc	p.G134D	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	134	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GCCCTGGAAGCCGTCGAAGCC	0.697													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11195	0.0		0.0	False		,,,				2504	0.0				p.G134D		Atlas-SNP	.											.	DUSP2	20	.	0			c.G401A						PASS	.						15.0	20.0	18.0					2																	96810609		2094	4175	6269	SO:0001583	missense	1844	exon2			TGGAAGCCGTCGA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.401G>A	2.37:g.96810609C>T	ENSP00000288943:p.Gly134Asp	66.0	0.0	0		80.0	26.0	0.325	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	C	3.560	-0.089892	0.07053	.	.	ENSG00000158050	ENST00000288943	T	0.26373	1.74	4.31	2.38	0.29361	Rhodanese-like (5);	0.285507	0.32736	N	0.005712	T	0.26774	0.0655	L	0.58101	1.795	0.25586	N	0.986743	B	0.31459	0.324	B	0.37091	0.241	T	0.14504	-1.0470	10	0.28530	T	0.3	.	10.6808	0.45813	0.0:0.5226:0.4774:0.0	.	134	Q05923	DUS2_HUMAN	D	134	ENSP00000288943:G134D	ENSP00000288943:G134D	G	-	2	0	DUSP2	96174336	0.037000	0.19845	0.471000	0.27229	0.207000	0.24258	0.181000	0.16880	0.349000	0.23975	0.456000	0.33151	GGC	.	.	none		0.697	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117979606	117979606	+	Missense_Mutation	SNP	G	G	C	rs45441097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117979606G>C	ENST00000437212.3	+	7	792	c.578G>C	c.(577-579)tGt>tCt	p.C193S	TMPRSS4_ENST00000522824.1_Missense_Mutation_p.C188S|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.C153S|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.C46S|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.C191S			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	193	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TCCCTGCACTGTCTTGGTGAG	0.567													G|||	13	0.00259585	0.0	0.0086	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.001				p.C193S		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.G578C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS,SER/CYS	4,4396	8.1+/-20.4	0,4,2196	108.0	92.0	97.0		563,572,458,578	4.9	1.0	11	dbSNP_127	97	44,8548	28.5+/-78.6	0,44,4252	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	112,112,112,112	0,48,6448	CC,CG,GG		0.5121,0.0909,0.3695	probably-damaging,probably-damaging,probably-damaging,probably-damaging	188/433,191/436,153/398,193/438	117979606	48,12944	2200	4296	6496	SO:0001583	missense	56649	exon7			TGCACTGTCTTGG	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.578G>C	11.37:g.117979606G>C	ENSP00000416037:p.Cys193Ser	53.0	0.0	0		63.0	42.0	0.666667	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	20.7	4.036391	0.75617	9.09E-4	0.005121	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	D;T;D;D;D;D	0.98926	-5.24;0.26;-5.24;-5.24;-5.24;-5.24	4.93	4.93	0.64822	Speract/scavenger receptor-related (2);	0.000000	0.64402	D	0.000007	D	0.98839	0.9608	M	0.88640	2.97	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.996;0.997;0.999;0.998	D	0.95989	0.8984	10	0.87932	D	0	.	15.1719	0.72881	0.0:0.0:1.0:0.0	rs45441097	168;153;46;193;191	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	S	191;46;153;193;188;140	ENSP00000435184:C191S;ENSP00000428814:C46S;ENSP00000429209:C153S;ENSP00000416037:C193S;ENSP00000430547:C188S;ENSP00000428407:C140S	ENSP00000416037:C193S	C	+	2	0	TMPRSS4	117484816	0.998000	0.40836	0.964000	0.40570	0.803000	0.45373	5.377000	0.66184	2.564000	0.86499	0.561000	0.74099	TGT	G|0.997;C|0.003	0.003	strong		0.567	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
BCOR	54880	hgsc.bcm.edu	37	X	39932949	39932949	+	Silent	SNP	G	G	A	rs17145653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:39932949G>A	ENST00000378444.4	-	4	1878	c.1650C>T	c.(1648-1650)acC>acT	p.T550T	BCOR_ENST00000342274.4_Silent_p.T550T|BCOR_ENST00000397354.3_Silent_p.T550T|BCOR_ENST00000378455.4_Silent_p.T550T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	550					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TGACAGCATCGGTGCCGCCCA	0.572			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						G|||	11	0.00291391	0.0015	0.0014	3775	,	,		14756	0.0		0.007	False		,,,				2504	0.001				p.T550T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1650T						PASS	.	G	,,,	5,3828		0,5,0,1626,571	110.0	70.0	84.0		1650,1650,1650,1650	-11.2	0.0	X	dbSNP_123	84	76,6652		0,58,18,2370,1854	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	0,63,18,3996,2425	AA,AG,A,GG,G		1.1296,0.1304,0.767	,,,	550/1722,550/1704,550/1756,550/1722	39932949	81,10480	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			AGCATCGGTGCCG	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1650C>T	X.37:g.39932949G>A		119.0	1.0	0.00840336		74.0	73.0	0.986486	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			0|0.004;A|0.006	0.006	strong		0.572	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
LTBP1	4052	hgsc.bcm.edu	37	2	33623567	33623567	+	Silent	SNP	G	G	A	rs138835287		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:33623567G>A	ENST00000404816.2	+	34	5474	c.5121G>A	c.(5119-5121)ccG>ccA	p.P1707P	LTBP1_ENST00000390003.4_Silent_p.P1382P|LTBP1_ENST00000402934.1_Silent_p.P1326P|LTBP1_ENST00000354476.3_Silent_p.P1708P|LTBP1_ENST00000407925.1_Silent_p.P1381P|LTBP1_ENST00000418533.2_Silent_p.P1339P|LTBP1_ENST00000272273.5_Silent_p.P605P|LTBP1_ENST00000404525.1_Silent_p.P1328P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1707					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.P1708P(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ACTGCACTCCGTTGAATACCG	0.458													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21600	0.0		0.0	False		,,,				2504	0.0				p.P1707P		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,0,3	LTBP1	317	3	1	Substitution - coding silent(1)	lung(1)	c.G5121A						PASS	.	G	,,,,	0,4406		0,0,2203	123.0	99.0	107.0		4143,4017,3984,3858,5121	-9.1	0.0	2	dbSNP_134	107	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,	1381/1396,1339/1354,1328/1343,1286/1301,1707/1722	33623567	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon34			CACTCCGTTGAAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.5121G>A	2.37:g.33623567G>A		138.0	0.0	0		107.0	55.0	0.514019	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.999;A|0.001	0.001	strong		0.458	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
PCNT	5116	hgsc.bcm.edu	37	21	47860110	47860110	+	Missense_Mutation	SNP	G	G	A	rs563489032		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47860110G>A	ENST00000359568.5	+	42	9495	c.9388G>A	c.(9388-9390)Gtc>Atc	p.V3130I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3130	Interaction with NEK2.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CACCAGCAATGTCAAGGTAGG	0.542																																					p.V3130I		Atlas-SNP	.											.	PCNT	283	.	0			c.G9388A						PASS	.						59.0	66.0	63.0					21																	47860110		2203	4299	6502	SO:0001583	missense	5116	exon42			AGCAATGTCAAGG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.9388G>A	21.37:g.47860110G>A	ENSP00000352572:p.Val3130Ile	29.0	0.0	0		35.0	12.0	0.342857	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.094|5.094	0.202944|0.202944	0.09704|0.09704	.|.	.|.	ENSG00000160299|ENSG00000160299	ENST00000418394|ENST00000359568	.|T	.|0.01505	.|4.82	4.3|4.3	-4.62|-4.62	0.03370|0.03370	.|.	.|.	.|.	.|.	.|.	T|T	0.01092|0.01092	0.0036|0.0036	N|N	0.17474|0.17474	0.49|0.49	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17038	.|0.02;0.012	.|B;B	.|0.14578	.|0.011;0.005	T|T	0.48269|0.48269	-0.9050|-0.9050	5|9	.|0.16420	.|T	.|0.52	.|.	6.8565|6.8565	0.24044|0.24044	0.5669:0.0:0.3097:0.1234|0.5669:0.0:0.3097:0.1234	.|.	.|2933;3130	.|O95613-2;O95613	.|.;PCNT_HUMAN	I|I	110|3130	.|ENSP00000352572:V3130I	.|ENSP00000352572:V3130I	M|V	+|+	3|1	0|0	PCNT|PCNT	46684538|46684538	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-1.051000|-1.051000	0.03507|0.03507	-1.138000|-1.138000	0.02884|0.02884	-0.136000|-0.136000	0.14681|0.14681	ATG|GTC	.	.	none		0.542	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
AMPD1	270	hgsc.bcm.edu	37	1	115221116	115221116	+	Missense_Mutation	SNP	C	C	A	rs61752478	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115221116C>A	ENST00000520113.2	-	8	1044	c.1029G>T	c.(1027-1029)atG>atT	p.M343I	AMPD1_ENST00000353928.6_Missense_Mutation_p.M310I|AMPD1_ENST00000369538.3_Missense_Mutation_p.M339I			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	343					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GTTTCTGGTTCATGCAAGCGG	0.393													C|||	13	0.00259585	0.0008	0.0072	5008	,	,		21444	0.0		0.007	False		,,,				2504	0.0				p.M343I		Atlas-SNP	.											.	AMPD1	223	.	0			c.G1029T	GRCh37	CM041236	AMPD1	M	rs61752478	PASS	.	C	ILE/MET,ILE/MET	4,4402	8.1+/-20.4	0,4,2199	98.0	96.0	97.0		1029,1017	5.1	1.0	1	dbSNP_129	97	46,8554	30.7+/-82.3	0,46,4254	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	10,10	0,50,6453	AA,AC,CC		0.5349,0.0908,0.3844	probably-damaging,probably-damaging	343/781,339/777	115221116	50,12956	2203	4300	6503	SO:0001583	missense	270	exon8			CTGGTTCATGCAA	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1029G>T	1.37:g.115221116C>A	ENSP00000430075:p.Met343Ile	127.0	0.0	0		77.0	40.0	0.519481	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	28.9	4.960280	0.92791	9.08E-4	0.005349	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95482	-3.72;-3.72;-3.72	5.1	5.1	0.69264	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	M	0.83384	2.64	0.80722	D	1	P;D	0.57899	0.759;0.981	P;D	0.65773	0.576;0.938	D	0.98134	1.0432	10	0.87932	D	0	-20.3493	18.8767	0.92341	0.0:1.0:0.0:0.0	rs61752478	339;310	Q5TF02;P23109	.;AMPD1_HUMAN	I	343;339;310	ENSP00000430075:M343I;ENSP00000358551:M339I;ENSP00000316520:M310I	ENSP00000316520:M310I	M	-	3	0	AMPD1	115022639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.539000	0.85634	0.561000	0.74099	ATG	C|0.997;A|0.003	0.003	strong		0.393	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
ZSCAN9	7746	hgsc.bcm.edu	37	6	28195521	28195521	+	Silent	SNP	A	A	G	rs12197427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR|ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000527436.1_Silent_p.L158L	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					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)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70.0	64.0	66.0		474,474,474	-3.5	0.0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"""-"", ""Zinc fingers, C2H2-type"""	12984	protein-coding gene	gene with protein product		602246	"""zinc finger protein 193"""	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		200.0	0.0	0		160.0	77.0	0.48125	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299	
MAP1A	4130	hgsc.bcm.edu	37	15	43818115	43818115	+	Missense_Mutation	SNP	G	G	A	rs145659671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43818115G>A	ENST00000300231.5	+	4	4894	c.4444G>A	c.(4444-4446)Gac>Aac	p.D1482N	MAP1A_ENST00000399453.1_Missense_Mutation_p.D1482N|MAP1A_ENST00000382031.1_Missense_Mutation_p.D1720N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1482					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.D1482N(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GGAACAAAAGGACAGGGTCCT	0.448													G|||	11	0.00219649	0.0008	0.0086	5008	,	,		20845	0.0		0.003	False		,,,				2504	0.001				p.D1482N		Atlas-SNP	.											MAP1A,NS,carcinoma,0,1	MAP1A	189	1	1	Substitution - Missense(1)	pancreas(1)	c.G4444A						scavenged	.	G	ASN/ASP	14,3740		0,14,1863	92.0	92.0	92.0		4444	3.9	0.5	15	dbSNP_134	92	124,8086		0,124,3981	yes	missense	MAP1A	NM_002373.5	23	0,138,5844	AA,AG,GG		1.5104,0.3729,1.1535	probably-damaging	1482/2804	43818115	138,11826	1877	4105	5982	SO:0001583	missense	4130	exon4			CAAAAGGACAGGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4444G>A	15.37:g.43818115G>A	ENSP00000300231:p.Asp1482Asn	54.0	1.0	0.0185185		83.0	53.0	0.638554	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	12.86	2.064968	0.36470	0.003729	0.015104	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.23552	2.25;1.9;1.9	3.94	3.94	0.45596	.	.	.	.	.	T	0.32793	0.0841	M	0.71581	2.175	0.09310	N	1	D	0.67145	0.996	D	0.79784	0.993	T	0.12041	-1.0563	9	0.56958	D	0.05	-7.9541	13.1289	0.59369	0.0:0.1622:0.8377:0.0	.	1482	P78559	MAP1A_HUMAN	N	1720;1482;1482	ENSP00000371462:D1720N;ENSP00000382380:D1482N;ENSP00000300231:D1482N	ENSP00000300231:D1482N	D	+	1	0	MAP1A	41605407	0.002000	0.14202	0.509000	0.27700	0.039000	0.13416	0.567000	0.23608	2.166000	0.68216	0.563000	0.77884	GAC	G|0.992;A|0.008	0.008	strong		0.448	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
PTGS1	5742	hgsc.bcm.edu	37	9	125154660	125154660	+	Missense_Mutation	SNP	C	C	T	rs200295924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125154660C>T	ENST00000362012.2	+	11	1642	c.1637C>T	c.(1636-1638)cCg>cTg	p.P546L	PTGS1_ENST00000373698.5_Missense_Mutation_p.P437L|PTGS1_ENST00000223423.4_Missense_Mutation_p.P509L|PTGS1_ENST00000540753.1_Missense_Mutation_p.P484L	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	546					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TACTGGAAGCCGAGCACATTT	0.527																																					p.P546L		Atlas-SNP	.											.	PTGS1	84	.	0			c.C1637T						PASS	.						112.0	111.0	112.0					9																	125154660		2203	4300	6503	SO:0001583	missense	5742	exon11			GGAAGCCGAGCAC	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.1637C>T	9.37:g.125154660C>T	ENSP00000354612:p.Pro546Leu	272.0	0.0	0		230.0	57.0	0.247826	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178609	0.94846	.	.	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000373698	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.41	5.41	0.78517	.	0.096182	0.64402	D	0.000001	D	0.87370	0.6160	M	0.91920	3.255	0.80722	D	1	P;D;D	0.69078	0.939;0.995;0.997	P;D;D	0.68621	0.71;0.959;0.931	D	0.90078	0.4168	10	0.87932	D	0	-4.3937	18.2032	0.89846	0.0:1.0:0.0:0.0	.	484;546;509	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	L	484;546;509;437	ENSP00000437709:P484L;ENSP00000354612:P546L;ENSP00000223423:P509L;ENSP00000362802:P437L	ENSP00000223423:P509L	P	+	2	0	PTGS1	124194481	1.000000	0.71417	0.878000	0.34440	0.935000	0.57460	7.814000	0.86154	2.539000	0.85634	0.655000	0.94253	CCG	.	.	weak		0.527	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		
CC2D1B	200014	hgsc.bcm.edu	37	1	52822722	52822722	+	Missense_Mutation	SNP	G	G	A	rs201266966		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:52822722G>A	ENST00000371586.2	-	16	1985	c.1847C>T	c.(1846-1848)gCg>gTg	p.A616V	CC2D1B_ENST00000284376.3_Missense_Mutation_p.A610V|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000438831.1_5'UTR	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	616						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CACCTCCTCCGCCTTCTGGGA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		19738	0.0		0.0	False		,,,				2504	0.001				p.A616V		Atlas-SNP	.											CC2D1B,NS,carcinoma,0,1	CC2D1B	73	1	0			c.C1847T						PASS	.						59.0	57.0	58.0					1																	52822722		2202	4300	6502	SO:0001583	missense	200014	exon16			TCCTCCGCCTTCT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1847C>T	1.37:g.52822722G>A	ENSP00000360642:p.Ala616Val	164.0	0.0	0		173.0	84.0	0.485549	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.17|12.17	1.858338|1.858338	0.32791|0.32791	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371573|ENST00000438021;ENST00000450942	T;T|.	0.28895|.	1.59;1.59|.	5.65|5.65	4.73|4.73	0.59995|0.59995	.|.	0.170245|.	0.51477|.	N|.	0.000082|.	T|T	0.71685|0.71685	0.3369|0.3369	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B;B;B|.	0.21688|.	0.059;0.041;0.024|.	B;B;B|.	0.16722|.	0.012;0.016;0.008|.	T|T	0.69687|0.69687	-0.5078|-0.5078	10|5	0.59425|.	D|.	0.04|.	-3.3081|-3.3081	16.7669|16.7669	0.85526|0.85526	0.0692:0.0:0.9308:0.0|0.0692:0.0:0.9308:0.0	.|.	396;610;616|.	Q5T0G1;Q5T0F9-2;Q5T0F9|.	.;.;C2D1B_HUMAN|.	V|W	616;610;524|397;530	ENSP00000360642:A616V;ENSP00000284376:A610V|.	ENSP00000284376:A610V|.	A|R	-|-	2|1	0|2	CC2D1B|CC2D1B	52595310|52595310	1.000000|1.000000	0.71417|0.71417	0.797000|0.797000	0.32132|0.32132	0.144000|0.144000	0.21451|0.21451	5.830000|5.830000	0.69324|0.69324	0.953000|0.953000	0.37825|0.37825	-0.797000|-0.797000	0.03246|0.03246	GCG|CGG	G|0.997;A|0.003	0.003	weak		0.607	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
PIAS4	51588	hgsc.bcm.edu	37	19	4037723	4037723	+	Silent	SNP	G	G	A	rs140558761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4037723G>A	ENST00000262971.2	+	11	1498	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	461					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGGAAGCCGGGCGCCGATG	0.697													.|||	4	0.000798722	0.0	0.0	5008	,	,		12829	0.0		0.004	False		,,,				2504	0.0				p.P461P		Atlas-SNP	.											.	PIAS4	40	.	0			c.G1383A						PASS	.			1,4391		0,1,2195	22.0	23.0	23.0		1383	-8.8	0.0	19	dbSNP_134	23	26,8560		0,26,4267	no	coding-synonymous	PIAS4	NM_015897.2		0,27,6462	AA,AG,GG		0.3028,0.0228,0.208		461/511	4037723	27,12951	2196	4293	6489	SO:0001819	synonymous_variant	51588	exon11			GAAGCCGGGCGCC	AF077952	CCDS12118.1	19p13.3	2011-10-11						"""Zinc fingers, MIZ-type"""	17002	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 6"""	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.1383G>A	19.37:g.4037723G>A		53.0	0.0	0		80.0	43.0	0.5375	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897	
NUP210L	91181	hgsc.bcm.edu	37	1	153982536	153982536	+	Missense_Mutation	SNP	C	C	T	rs199611847		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153982536C>T	ENST00000368559.3	-	35	4913	c.4842G>A	c.(4840-4842)atG>atA	p.M1614I	NUP210L_ENST00000271854.3_Missense_Mutation_p.M1614I|NUP210L_ENST00000368553.1_Missense_Mutation_p.M547I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1614					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CATGGCACAGCATGAGGGTCG	0.423																																					p.M1614I		Atlas-SNP	.											.	NUP210L	181	.	0			c.G4842A						PASS	.	T	ILE/MET,ILE/MET	0,3736		0,0,1868	148.0	141.0	143.0		4842,4842	2.4	0.2	1		143	3,8209		0,3,4103	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	10,10	0,3,5971	TT,TC,CC		0.0365,0.0,0.0251	benign,benign	1614/1737,1614/1889	153982536	3,11945	1868	4106	5974	SO:0001583	missense	91181	exon35			GCACAGCATGAGG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.4842G>A	1.37:g.153982536C>T	ENSP00000357547:p.Met1614Ile	58.0	0.0	0		67.0	29.0	0.432836	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	c	0.029	-1.345824	0.01266	0.0	3.65E-4	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.18810	3.68;2.19;3.5	5.24	2.39	0.29439	.	1.290600	0.05075	N	0.482321	T	0.04092	0.0114	L	0.39898	1.24	0.20403	N	0.999903	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31586	-0.9938	10	0.02654	T	1	-12.129	5.8719	0.18809	0.1534:0.6865:0.0:0.1601	.	1614;1614	E7EP56;Q5VU65	.;P210L_HUMAN	I	1614;547;1614	ENSP00000357547:M1614I;ENSP00000357541:M547I;ENSP00000271854:M1614I	ENSP00000271854:M1614I	M	-	3	0	NUP210L	152249160	0.666000	0.27475	0.235000	0.24058	0.484000	0.33280	0.687000	0.25407	0.370000	0.24538	-0.224000	0.12420	ATG	.	.	weak		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
KIFC1	3833	hgsc.bcm.edu	37	6	33374015	33374015	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33374015G>A	ENST00000428849.2	+	8	2029	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	527	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						TCGGGCTGTGGCCCGCACAGC	0.597																																					p.A527T		Atlas-SNP	.											.	KIFC1	47	.	0			c.G1579A						PASS	.						60.0	71.0	67.0					6																	33374015		2202	4300	6502	SO:0001583	missense	3833	exon8			GCTGTGGCCCGCA	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"""Kinesins"""	6389	protein-coding gene	gene with protein product		603763	"""kinesin-like 2"""	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1579G>A	6.37:g.33374015G>A	ENSP00000393963:p.Ala527Thr	119.0	0.0	0		120.0	52.0	0.433333	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	g	25.6	4.651805	0.88056	.	.	ENSG00000237649	ENST00000428849	T	0.49139	0.79	5.29	4.43	0.53597	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.67192	0.2867	M	0.92833	3.35	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.72982	0.979;0.965	T	0.76225	-0.3037	10	0.87932	D	0	-5.1694	11.577	0.50866	0.0857:0.0:0.9143:0.0	.	519;527	B4E063;Q9BW19	.;KIFC1_HUMAN	T	527	ENSP00000393963:A527T	ENSP00000393963:A527T	A	+	1	0	KIFC1	33481993	1.000000	0.71417	0.999000	0.59377	0.871000	0.50021	6.592000	0.74095	1.461000	0.47929	0.558000	0.71614	GCC	.	.	none		0.597	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
P2RY8	286530	hgsc.bcm.edu	37	X	1584817	1584817	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:1584817C>T	ENST00000381297.4	-	2	845	c.635G>A	c.(634-636)tGt>tAt	p.C212Y	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCCGTGTAACAAGCCACGGT	0.657			T	CRLF2	"""B-ALL, Downs associated ALL"""																																p.C212Y		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.G635A						PASS	.						102.0	55.0	71.0					X																	1584817		2203	4295	6498	SO:0001583	missense	286530	exon2			GTGTAACAAGCCA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.635G>A	X.37:g.1584817C>T	ENSP00000370697:p.Cys212Tyr	84.0	0.0	0		68.0	27.0	0.397059	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	13.10	2.136811	0.37728	.	.	ENSG00000182162	ENST00000381297	T	0.42131	0.98	2.41	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.66557	0.2801	M	0.87682	2.9	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61436	-0.7063	10	0.87932	D	0	.	12.9335	0.58301	0.0:1.0:0.0:0.0	.	212	Q86VZ1	P2RY8_HUMAN	Y	212	ENSP00000370697:C212Y	ENSP00000370697:C212Y	C	-	2	0	P2RY8	1544817	1.000000	0.71417	0.993000	0.49108	0.058000	0.15608	6.011000	0.70760	0.838000	0.34948	0.279000	0.19357	TGT	.	.	none		0.657	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497900	32497900	+	Splice_Site	SNP	A	A	G	rs78612727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32497900A>G	ENST00000374975.3	-	1	163		c.e1+1			NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						ATGTGCACTTACGTCGGGTGT	0.522																																					.		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.100+2T>C						PASS	.						99.0	102.0	101.0					6																	32497900		2203	4300	6503	SO:0001630	splice_region_variant	3127	exon2			GCACTTACGTCGG		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.100+1T>C	6.37:g.32497900A>G		123.0	0.0	0		86.0	14.0	0.162791	NM_002125		Splice_Site	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	8.839	0.941693	0.18281	.	.	ENSG00000198502	ENST00000374975	.	.	.	4.54	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.35921	D	0.831832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4495	0.27229	0.8084:0.0:0.0:0.1916	.	.	.	.	.	-1	.	.	.	-	.	.	HLA-DRB5	32605878	0.985000	0.35326	0.199000	0.23439	0.019000	0.09904	2.123000	0.41996	1.909000	0.55274	0.397000	0.26171	.	A|0.994;G|0.006	0.006	strong		0.522	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	Intron
ZNF469	84627	hgsc.bcm.edu	37	16	88494603	88494603	+	Missense_Mutation	SNP	G	G	T	rs536586591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88494603G>T	ENST00000437464.1	+	1	725	c.725G>T	c.(724-726)aGc>aTc	p.S242I	ZNF469_ENST00000565624.1_Missense_Mutation_p.S242I	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	242	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GCTGAGAATAGCTTCCCAGGT	0.677													G|||	4	0.000798722	0.0	0.0	5008	,	,		11181	0.0		0.002	False		,,,				2504	0.002				p.S242I		Atlas-SNP	.											.	ZNF469	121	.	0			c.G725T						PASS	.						8.0	12.0	11.0					16																	88494603		688	1589	2277	SO:0001583	missense	84627	exon1			AGAATAGCTTCCC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.725G>T	16.37:g.88494603G>T	ENSP00000402343:p.Ser242Ile	115.0	0.0	0		101.0	66.0	0.653465	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041088	0.35989	.	.	ENSG00000225614	ENST00000437464	T	0.10288	2.89	4.34	1.27	0.21489	.	.	.	.	.	T	0.12646	0.0307	N	0.19112	0.55	0.22435	N	0.999101	D	0.61697	0.99	P	0.56398	0.797	T	0.20874	-1.0262	9	0.87932	D	0	.	7.2383	0.26082	0.3662:0.0:0.6338:0.0	.	242	Q96JG9	ZN469_HUMAN	I	242	ENSP00000402343:S242I	ENSP00000402343:S242I	S	+	2	0	ZNF469	87022104	0.993000	0.37304	0.755000	0.31263	0.617000	0.37484	0.285000	0.18883	0.003000	0.14656	0.462000	0.41574	AGC	.	.	none		0.677	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
DSG3	1830	hgsc.bcm.edu	37	18	29056063	29056063	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29056063C>T	ENST00000257189.4	+	16	2923	c.2840C>T	c.(2839-2841)tCc>tTc	p.S947F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	947					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GTGCAACCTTCCACTGCAGGC	0.517																																					p.S947F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2840T						PASS	.						156.0	141.0	146.0					18																	29056063		2203	4300	6503	SO:0001583	missense	1830	exon16			AACCTTCCACTGC	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2840C>T	18.37:g.29056063C>T	ENSP00000257189:p.Ser947Phe	89.0	0.0	0		67.0	16.0	0.238806	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.750220	0.69533	.	.	ENSG00000134757	ENST00000257189	T	0.80480	-1.38	5.54	5.54	0.83059	.	0.756022	0.11629	N	0.545016	D	0.85066	0.5612	L	0.58510	1.815	0.09310	N	0.999999	D	0.53619	0.961	P	0.57548	0.823	T	0.76553	-0.2917	10	0.87932	D	0	.	10.1776	0.42948	0.0:0.9051:0.0:0.0949	.	947	P32926	DSG3_HUMAN	F	947	ENSP00000257189:S947F	ENSP00000257189:S947F	S	+	2	0	DSG3	27310061	0.016000	0.18221	0.812000	0.32479	0.925000	0.55904	2.776000	0.47709	2.779000	0.95612	0.655000	0.94253	TCC	.	.	none		0.517	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
SCN10A	6336	hgsc.bcm.edu	37	3	38739416	38739416	+	Silent	SNP	C	C	T	rs145313578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38739416C>T	ENST00000449082.2	-	27	5294	c.5295G>A	c.(5293-5295)tcG>tcA	p.S1765S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1765					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CTGCAAAGTCCGAGAGAGCAG	0.498													C|||	4	0.000798722	0.0	0.0014	5008	,	,		19894	0.0		0.001	False		,,,				2504	0.002				p.S1765S		Atlas-SNP	.											SCN10A,NS,carcinoma,-1,2	SCN10A	359	2	0			c.G5295A						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	76.0	80.0	79.0		5295	-10.8	0.2	3	dbSNP_134	79	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	SCN10A	NM_006514.2		0,13,6490	TT,TC,CC		0.1395,0.0227,0.1		1765/1957	38739416	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon27			AAAGTCCGAGAGA	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5295G>A	3.37:g.38739416C>T		166.0	2.0	0.0120482		165.0	80.0	0.484848	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
KIAA1147	57189	hgsc.bcm.edu	37	7	141362558	141362558	+	Silent	SNP	G	G	T	rs375569681		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:141362558G>T	ENST00000536163.1	-	9	1265	c.1266C>A	c.(1264-1266)ggC>ggA	p.G422G	RP5-894A10.6_ENST00000602609.1_RNA|KIAA1147_ENST00000482493.1_Silent_p.G318G	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	422										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CTAGGCCCATGCCCCGGGCAT	0.527																																					p.G422G		Atlas-SNP	.											.	KIAA1147	32	.	0			c.C1266A						PASS	.	G		0,3818		0,0,1909	37.0	39.0	38.0		1266	5.4	1.0	7		38	2,8234		0,2,4116	no	coding-synonymous	KIAA1147	NM_001080392.1		0,2,6025	TT,TG,GG		0.0243,0.0,0.0166		422/456	141362558	2,12052	1909	4118	6027	SO:0001819	synonymous_variant	57189	exon9			GCCCATGCCCCGG	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1266C>A	7.37:g.141362558G>T		66.0	0.0	0		62.0	37.0	0.596774	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	37	CCDS47726.1																																																																																			.	.	weak		0.527	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1		
MINK1	50488	hgsc.bcm.edu	37	17	4797910	4797910	+	Missense_Mutation	SNP	G	G	A	rs79940062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4797910G>A	ENST00000355280.6	+	24	3095	c.2899G>A	c.(2899-2901)Gac>Aac	p.D967N	MINK1_ENST00000347992.7_Missense_Mutation_p.D938N|MINK1_ENST00000453408.3_Missense_Mutation_p.D947N	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGGCAGTGGGGACAGCATCCC	0.612													G|||	28	0.00559105	0.0008	0.0029	5008	,	,		20491	0.001		0.0179	False		,,,				2504	0.0061				p.D967N		Atlas-SNP	.											.	MINK1	110	.	0			c.G2899A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	16,4312		0,16,2148	47.0	51.0	50.0		2839,2788,2899,2812	5.3	1.0	17	dbSNP_133	50	160,8386		1,158,4114	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	23,23,23,23	1,174,6262	AA,AG,GG		1.8722,0.3697,1.3671	benign,benign,benign,benign	947/1313,930/1296,967/1333,938/1304	4797910	176,12698	2164	4273	6437	SO:0001583	missense	50488	exon24			AGTGGGGACAGCA	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2899G>A	17.37:g.4797910G>A	ENSP00000347427:p.Asp967Asn	103.0	0.0	0		95.0	40.0	0.421053	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	1	0.0017482517482517483	10	0.013192612137203167	G	21.1	4.091253	0.76756	0.003697	0.018722	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.74315	-0.83;-0.83;-0.83	5.26	5.26	0.73747	.	0.053262	0.64402	D	0.000001	T	0.73497	0.3594	M	0.65498	2.005	0.58432	D	0.999999	P;D;D;D	0.67145	0.952;0.996;0.993;0.996	P;D;D;D	0.73708	0.643;0.981;0.956;0.981	T	0.75451	-0.3313	10	0.22109	T	0.4	.	16.4095	0.83703	0.0:0.0:1.0:0.0	.	930;947;967;938	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	N	967;947;938	ENSP00000347427:D967N;ENSP00000406487:D947N;ENSP00000269296:D938N	ENSP00000269296:D938N	D	+	1	0	MINK1	4738686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.679000	0.74513	2.735000	0.93741	0.655000	0.94253	GAC	G|0.993;A|0.007	0.007	strong		0.612	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
NSD1	64324	hgsc.bcm.edu	37	5	176637471	176637471	+	Missense_Mutation	SNP	G	G	A	rs28932177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176637471G>A	ENST00000439151.2	+	5	2116	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	NSD1_ENST00000347982.4_Missense_Mutation_p.A422T|NSD1_ENST00000361032.4_Missense_Mutation_p.A588T|NSD1_ENST00000354179.4_Missense_Mutation_p.A422T	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	691			A -> T (in dbSNP:rs28932177). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TAGGTTTGCTGCCACAAACAC	0.393			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	65	0.0129792	0.0045	0.0086	5008	,	,		20290	0.0		0.0249	False		,,,				2504	0.0286				p.A691T		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G2071A						PASS	.	G	THR/ALA,THR/ALA	28,4378	35.2+/-66.4	1,26,2176	53.0	56.0	55.0		2071,1264	3.3	1.0	5	dbSNP_125	55	207,8393	89.7+/-151.9	2,203,4095	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	58,58	3,229,6271	AA,AG,GG		2.407,0.6355,1.8069	benign,benign	691/2697,422/2428	176637471	235,12771	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTGCTGCCACAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2071G>A	5.37:g.176637471G>A	ENSP00000395929:p.Ala691Thr	174.0	0.0	0		185.0	69.0	0.372973	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	10.58	1.390030	0.25118	0.006355	0.02407	ENSG00000165671	ENST00000354179;ENST00000355783;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.92752	-2.98;-2.98;-2.98;-3.1	5.1	3.31	0.37934	.	0.621198	0.16033	N	0.232761	T	0.59362	0.2188	N	0.08118	0	0.21822	N	0.999526	B;B;B	0.12630	0.006;0.006;0.001	B;B;B	0.12156	0.004;0.007;0.002	T	0.58719	-0.7587	9	.	.	.	.	4.2978	0.10910	0.182:0.0:0.592:0.226	rs28932177;rs28932177	422;588;691	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	T	422;422;691;422;588	ENSP00000346111:A422T;ENSP00000395929:A691T;ENSP00000343209:A422T;ENSP00000354310:A588T	.	A	+	1	0	NSD1	176570077	0.188000	0.23250	1.000000	0.80357	0.984000	0.73092	0.269000	0.18589	1.504000	0.48704	0.655000	0.94253	GCC	G|0.983;A|0.017	0.017	strong		0.393	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056277	26056277	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26056277T>G	ENST00000343677.2	-	1	422	c.380A>C	c.(379-381)aAa>aCa	p.K127T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	127					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						CTTCTTAGGTTTGGTTCCGCC	0.557																																					p.K127T		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A380C						PASS	.						57.0	68.0	65.0					6																	26056277		2202	4299	6501	SO:0001583	missense	3006	exon1			TTAGGTTTGGTTC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.380A>C	6.37:g.26056277T>G	ENSP00000339566:p.Lys127Thr	153.0	0.0	0		127.0	36.0	0.283465	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890388	0.33348	.	.	ENSG00000187837	ENST00000343677	T	0.19532	2.14	5.54	5.54	0.83059	.	0.120538	0.53938	D	0.000047	T	0.06325	0.0163	N	0.08118	0	0.58432	D	0.999999	B	0.25719	0.132	B	0.25759	0.063	T	0.14392	-1.0474	10	0.62326	D	0.03	-6.0558	15.1351	0.72558	0.0:0.0:0.0:1.0	.	127	P16403	H12_HUMAN	T	127	ENSP00000339566:K127T	ENSP00000339566:K127T	K	-	2	0	HIST1H1C	26164256	1.000000	0.71417	0.961000	0.40146	0.109000	0.19521	3.997000	0.57016	2.229000	0.72834	0.533000	0.62120	AAA	.	.	none		0.557	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
NUP210L	91181	hgsc.bcm.edu	37	1	154031134	154031134	+	Missense_Mutation	SNP	C	C	A	rs201928881		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154031134C>A	ENST00000368559.3	-	21	2957	c.2886G>T	c.(2884-2886)gaG>gaT	p.E962D	NUP210L_ENST00000368553.1_5'Flank|NUP210L_ENST00000271854.3_Missense_Mutation_p.E962D	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	962					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			GATCATAGACCTCCAAGGTAA	0.433																																					p.E962D		Atlas-SNP	.											.	NUP210L	181	.	0			c.G2886T						PASS	.	C	ASP/GLU,ASP/GLU	3,3683		0,3,1840	92.0	82.0	85.0		2886,2886	-0.5	1.0	1		85	19,8163		0,19,4072	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	45,45	0,22,5912	AA,AC,CC		0.2322,0.0814,0.1854	benign,benign	962/1737,962/1889	154031134	22,11846	1843	4091	5934	SO:0001583	missense	91181	exon21			ATAGACCTCCAAG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2886G>T	1.37:g.154031134C>A	ENSP00000357547:p.Glu962Asp	95.0	0.0	0		66.0	32.0	0.484848	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	9.212	1.031090	0.19590	8.14E-4	0.002322	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.07021	3.49;3.23	4.44	-0.504	0.11997	.	0.135069	0.33959	N	0.004391	T	0.02012	0.0063	L	0.44542	1.39	0.34482	D	0.703977	P;P	0.39665	0.651;0.682	B;B	0.32980	0.115;0.156	T	0.51787	-0.8661	10	0.33141	T	0.24	-24.0406	7.5347	0.27704	0.0:0.4383:0.0:0.5617	.	962;962	E7EP56;Q5VU65	.;P210L_HUMAN	D	962	ENSP00000357547:E962D;ENSP00000271854:E962D	ENSP00000271854:E962D	E	-	3	2	NUP210L	152297758	0.993000	0.37304	0.999000	0.59377	0.737000	0.42083	0.083000	0.14871	-0.010000	0.14271	0.591000	0.81541	GAG	.	.	weak		0.433	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
DAB2	1601	hgsc.bcm.edu	37	5	39381618	39381618	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:39381618G>A	ENST00000320816.6	-	11	1909	c.1442C>T	c.(1441-1443)cCc>cTc	p.P481L	DAB2_ENST00000339788.6_Missense_Mutation_p.P263L|DAB2_ENST00000545653.1_Missense_Mutation_p.P460L|DAB2_ENST00000509337.1_Missense_Mutation_p.P460L	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	481					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			CAGAGGGTTGGGCTGCAGGGC	0.532																																					p.P481L		Atlas-SNP	.											.	DAB2	124	.	0			c.C1442T						PASS	.						118.0	123.0	121.0					5																	39381618		2203	4300	6503	SO:0001583	missense	1601	exon11			GGGTTGGGCTGCA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1442C>T	5.37:g.39381618G>A	ENSP00000313391:p.Pro481Leu	88.0	0.0	0		123.0	43.0	0.349593	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212852	0.39102	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.37752	1.32;1.18;1.31;1.31	5.87	3.96	0.45880	.	0.775909	0.12796	N	0.438417	T	0.28200	0.0696	L	0.29908	0.895	0.44908	D	0.99792	B;B	0.15719	0.014;0.014	B;B	0.17979	0.013;0.02	T	0.04400	-1.0954	10	0.23891	T	0.37	-1.2282	13.2306	0.59941	0.0:0.1217:0.7521:0.1262	.	481;460	P98082;P98082-3	DAB2_HUMAN;.	L	481;263;460;460	ENSP00000313391:P481L;ENSP00000345508:P263L;ENSP00000439919:P460L;ENSP00000426245:P460L	ENSP00000313391:P481L	P	-	2	0	DAB2	39417375	1.000000	0.71417	0.991000	0.47740	0.841000	0.47740	2.304000	0.43655	1.587000	0.49959	0.655000	0.94253	CCC	.	.	none		0.532	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
KRT9	3857	hgsc.bcm.edu	37	17	39727894	39727894	+	Silent	SNP	A	A	G	rs115965791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39727894A>G	ENST00000246662.4	-	1	416	c.351T>C	c.(349-351)ggT>ggC	p.G117G	KRT9_ENST00000588431.1_Intron	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	117	Head.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				ctccagaaccaccaccaaagc	0.567													A|||	28	0.00559105	0.0015	0.0043	5008	,	,		12499	0.0		0.0129	False		,,,				2504	0.0102				p.G117G		Atlas-SNP	.											.	KRT9	78	.	0			c.T351C						PASS	.	A		8,4394		0,8,2193	142.0	171.0	161.0		351	-9.1	0.0	17	dbSNP_132	161	53,8537		0,53,4242	yes	coding-synonymous	KRT9	NM_000226.3		0,61,6435	GG,GA,AA		0.617,0.1817,0.4695		117/624	39727894	61,12931	2201	4295	6496	SO:0001819	synonymous_variant	3857	exon1			AGAACCACCACCA		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.351T>C	17.37:g.39727894A>G		81.0	0.0	0		75.0	37.0	0.493333	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
USH2A	7399	hgsc.bcm.edu	37	1	215956140	215956140	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215956140T>G	ENST00000307340.3	-	53	10911	c.10525A>C	c.(10525-10527)Aaa>Caa	p.K3509Q	USH2A_ENST00000366943.2_Missense_Mutation_p.K3509Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3509	Fibronectin type-III 20. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTGTCTATTTTGGTCCACGTA	0.403										HNSCC(13;0.011)																											p.K3509Q		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10525C						PASS	.						99.0	94.0	95.0					1																	215956140		2203	4300	6503	SO:0001583	missense	7399	exon53			CTATTTTGGTCCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.10525A>C	1.37:g.215956140T>G	ENSP00000305941:p.Lys3509Gln	125.0	0.0	0		97.0	30.0	0.309278	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.602549	0.46423	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53206	0.63;0.63	5.43	5.43	0.79202	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.313381	0.22314	U	0.061685	T	0.42359	0.1199	L	0.45137	1.4	0.23739	N	0.996979	P	0.50272	0.933	B	0.42386	0.386	T	0.35624	-0.9781	10	0.22706	T	0.39	.	15.4862	0.75569	0.0:0.0:0.0:1.0	.	3509	O75445	USH2A_HUMAN	Q	3509	ENSP00000305941:K3509Q;ENSP00000355910:K3509Q	ENSP00000305941:K3509Q	K	-	1	0	USH2A	214022763	1.000000	0.71417	0.021000	0.16686	0.401000	0.30781	3.818000	0.55678	2.063000	0.61619	0.533000	0.62120	AAA	.	.	none		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LRP1	4035	hgsc.bcm.edu	37	12	57597023	57597023	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57597023C>T	ENST00000243077.3	+	69	11237	c.10771C>T	c.(10771-10773)Cgc>Tgc	p.R3591C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3591	LDL-receptor class A 27. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CATCGCGGGGCGCTGGAAATG	0.672																																					p.R3591C		Atlas-SNP	.											LRP1,bladder,carcinoma,-1,1	LRP1	428	1	0			c.C10771T						PASS	.						36.0	34.0	35.0					12																	57597023		2199	4298	6497	SO:0001583	missense	4035	exon69			GCGGGGCGCTGGA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10771C>T	12.37:g.57597023C>T	ENSP00000243077:p.Arg3591Cys	112.0	0.0	0		89.0	25.0	0.280899	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939225	0.52972	.	.	ENSG00000123384	ENST00000243077;ENST00000555124	D;D	0.95656	-3.77;-3.77	5.06	4.15	0.48705	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.151987	0.40385	N	0.001116	D	0.98197	0.9404	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98813	1.0744	10	0.59425	D	0.04	.	13.6941	0.62567	0.1557:0.8443:0.0:0.0	.	3591	Q07954	LRP1_HUMAN	C	3591;172	ENSP00000243077:R3591C;ENSP00000451012:R172C	ENSP00000243077:R3591C	R	+	1	0	LRP1	55883290	0.172000	0.23043	1.000000	0.80357	0.384000	0.30261	0.760000	0.26475	1.325000	0.45301	0.650000	0.86243	CGC	.	.	none		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CHRM3	1131	hgsc.bcm.edu	37	1	240070855	240070855	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:240070855C>G	ENST00000255380.4	+	5	883	c.104C>G	c.(103-105)aCt>aGt	p.T35S		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	35					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GGAACCGTCACTCATTTCGGC	0.552																																					p.T35S		Atlas-SNP	.											.	CHRM3	118	.	0			c.C104G						PASS	.						77.0	77.0	77.0					1																	240070855		2203	4300	6503	SO:0001583	missense	1131	exon5			CCGTCACTCATTT	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.104C>G	1.37:g.240070855C>G	ENSP00000255380:p.Thr35Ser	138.0	0.0	0		123.0	32.0	0.260163	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	3.466	-0.108946	0.06924	.	.	ENSG00000133019	ENST00000255380;ENST00000448020	T;T	0.58210	0.35;1.64	5.6	5.6	0.85130	.	0.663883	0.14104	N	0.341213	T	0.29882	0.0747	N	0.02011	-0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.06338	-1.0832	10	0.19590	T	0.45	-4.5748	18.1624	0.89712	0.0:1.0:0.0:0.0	.	35	P20309	ACM3_HUMAN	S	35	ENSP00000255380:T35S;ENSP00000404764:T35S	ENSP00000255380:T35S	T	+	2	0	CHRM3	238137478	0.026000	0.19158	0.441000	0.26858	0.202000	0.24057	2.791000	0.47829	2.788000	0.95919	0.650000	0.86243	ACT	.	.	none		0.552	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
PMS1	5378	hgsc.bcm.edu	37	2	190728798	190728798	+	Missense_Mutation	SNP	A	A	G	rs201205478		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:190728798A>G	ENST00000441310.2	+	10	2419	c.2186A>G	c.(2185-2187)aAt>aGt	p.N729S	PMS1_ENST00000409823.3_Missense_Mutation_p.N690S|PMS1_ENST00000432292.3_Missense_Mutation_p.N553S|PMS1_ENST00000447232.2_Intron|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Missense_Mutation_p.N553S	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	729					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TTGATCCACAATCTCAGGTTT	0.333			"""Mis, N"""			"""colorectal, endometrial, ovarian"""		Direct reversal of damage;Mismatch excision repair (MMR)																													p.N729S		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.A2186G						PASS	.	A	SER/ASN,SER/ASN,	0,4406		0,0,2203	113.0	122.0	119.0		2186,2069,	3.1	1.0	2		119	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,intron	PMS1	NM_000534.4,NM_001128143.1,NM_001128144.1	46,46,	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign,benign,	729/933,690/894,	190728798	2,13004	2203	4300	6503	SO:0001583	missense	5378	exon10			TCCACAATCTCAG		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"""postmeiotic segregation increased (S. cerevisiae) 1"""	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.2186A>G	2.37:g.190728798A>G	ENSP00000406490:p.Asn729Ser	155.0	0.0	0		186.0	85.0	0.456989	NM_000534	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	37	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	9.300	1.052870	0.19907	0.0	2.33E-4	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000432292;ENST00000424307;ENST00000452382	T;T;T;T;D;T	0.85955	2.0;2.0;2.0;2.0;-2.05;2.02	5.45	3.11	0.35812	.	0.489617	0.25535	N	0.030017	T	0.64338	0.2589	N	0.04043	-0.29	0.19300	N	0.999974	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.52449	-0.8574	10	0.36615	T	0.2	-11.736	4.1444	0.10209	0.6036:0.0:0.2516:0.1448	.	729;690;729	Q4VAL4;Q5FBZ3;P54277	.;.;PMS1_HUMAN	S	553;729;553;690;553;668;117	ENSP00000406490:N729S;ENSP00000404492:N553S;ENSP00000387125:N690S;ENSP00000398378:N553S;ENSP00000389938:N668S;ENSP00000396232:N117S	ENSP00000376149:N553S	N	+	2	0	PMS1	190437043	0.996000	0.38824	1.000000	0.80357	0.975000	0.68041	0.494000	0.22467	0.528000	0.28580	0.524000	0.50904	AAT	.	.	weak		0.333	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2		
SGK2	10110	hgsc.bcm.edu	37	20	42199296	42199296	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42199296C>T	ENST00000341458.4	+	6	799	c.580C>T	c.(580-582)Ccc>Tcc	p.P194S	SGK2_ENST00000373077.1_Missense_Mutation_p.P133S|SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000373092.3_Missense_Mutation_p.P134S|SGK2_ENST00000426287.1_Missense_Mutation_p.P160S|SGK2_ENST00000373100.1_Missense_Mutation_p.P134S|SGK2_ENST00000423407.3_Missense_Mutation_p.P134S	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GTTCCTGGAGCCCCGGGCCAG	0.627																																					p.P194S		Atlas-SNP	.											.	SGK2	50	.	0			c.C580T						PASS	.						59.0	61.0	61.0					20																	42199296		2203	4300	6503	SO:0001583	missense	10110	exon6			CTGGAGCCCCGGG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.580C>T	20.37:g.42199296C>T	ENSP00000340608:p.Pro194Ser	77.0	0.0	0		87.0	4.0	0.045977	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852794	0.51270	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047564	0.85682	N	0.000000	T	0.48114	0.1482	N	0.17764	0.52	0.80722	D	1	B;B;P	0.37015	0.181;0.241;0.578	B;B;B	0.35971	0.049;0.143;0.215	T	0.44559	-0.9320	10	0.24483	T	0.36	.	17.7648	0.88475	0.0:1.0:0.0:0.0	.	160;194;134	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	S	134;134;133;133;134;194;160	ENSP00000362192:P134S;ENSP00000362184:P134S;ENSP00000362168:P133S;ENSP00000396222:P133S;ENSP00000392795:P134S;ENSP00000340608:P194S;ENSP00000412214:P160S	ENSP00000340608:P194S	P	+	1	0	SGK2	41632710	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.643000	0.83403	2.658000	0.90341	0.655000	0.94253	CCC	.	.	none		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1		
TTC21B	79809	hgsc.bcm.edu	37	2	166771842	166771842	+	Silent	SNP	A	A	G	rs138449110		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:166771842A>G	ENST00000243344.7	-	15	2144	c.2007T>C	c.(2005-2007)gaT>gaC	p.D669D		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	669				D -> G (in Ref. 4; BAB71404). {ECO:0000305}.	forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						CCCGTTCAATATCTCCTTGGG	0.413																																					p.D669D		Atlas-SNP	.											.	TTC21B	130	.	0			c.T2007C						PASS	.	A		0,4406		0,0,2203	153.0	154.0	154.0		2007	0.6	0.6	2	dbSNP_134	154	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TTC21B	NM_024753.3		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		669/1317	166771842	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	79809	exon15			TTCAATATCTCCT	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.2007T>C	2.37:g.166771842A>G		74.0	0.0	0		86.0	37.0	0.430233	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			A|1.000;G|0.000	0.000	weak		0.413	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24889664	24889664	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24889664C>T	ENST00000396432.2	-	14	3529	c.3043G>A	c.(3043-3045)Gac>Aac	p.D1015N	ARHGAP21_ENST00000493154.1_5'UTR|ARHGAP21_ENST00000320481.6_Missense_Mutation_p.D802N	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1014	Interaction with ARF1 and ARF6.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CATTCACAGTCGGACGTGGTG	0.478																																					p.D1015N		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.G3043A						PASS	.						118.0	112.0	114.0					10																	24889664		2203	4298	6501	SO:0001583	missense	57584	exon14			CACAGTCGGACGT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.3043G>A	10.37:g.24889664C>T	ENSP00000379709:p.Asp1015Asn	214.0	0.0	0		194.0	38.0	0.195876	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427131	0.83667	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	6.02	6.02	0.97574	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.86961	0.6059	L	0.39467	1.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.86018	0.1505	10	0.52906	T	0.07	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	1005;1014	F8W9U9;Q5T5U3	.;RHG21_HUMAN	N	1015;802;1005;1015;850	ENSP00000379709:D1015N;ENSP00000365604:D802N;ENSP00000365592:D1005N;ENSP00000405018:D1015N	ENSP00000365604:D802N	D	-	1	0	ARHGAP21	24929670	1.000000	0.71417	0.892000	0.35008	0.258000	0.26162	7.767000	0.85331	2.865000	0.98341	0.655000	0.94253	GAC	.	.	none		0.478	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
IQCE	23288	hgsc.bcm.edu	37	7	2649686	2649686	+	Missense_Mutation	SNP	C	C	T	rs368687600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2649686C>T	ENST00000402050.2	+	22	2162	c.1978C>T	c.(1978-1980)Ccc>Tcc	p.P660S	IQCE_ENST00000438376.2_Missense_Mutation_p.P644S|IQCE_ENST00000325979.7_Missense_Mutation_p.P595S|IQCE_ENST00000404984.1_Missense_Mutation_p.P609S	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	660						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		AGACCCCTCTCCCTCAGGGCC	0.597																																					p.P660S		Atlas-SNP	.											.	IQCE	66	.	0			c.C1978T						PASS	.	C	SER/PRO,SER/PRO	0,4082		0,0,2041	65.0	67.0	66.0		1930,1978	0.9	0.0	7		66	2,8352		0,2,4175	no	missense,missense	IQCE	NM_001100390.1,NM_152558.3	74,74	0,2,6216	TT,TC,CC		0.0239,0.0,0.0161	probably-damaging,probably-damaging	644/680,660/696	2649686	2,12434	2041	4177	6218	SO:0001583	missense	23288	exon22			CCCTCTCCCTCAG	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1978C>T	7.37:g.2649686C>T	ENSP00000385597:p.Pro660Ser	96.0	0.0	0		95.0	73.0	0.768421	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	C	3.946	-0.013165	0.07727	0.0	2.39E-4	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.11712	2.77;2.75;2.76;2.76	4.9	0.875	0.19130	.	2.223160	0.02320	N	0.072870	T	0.07413	0.0187	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.12837	0.004;0.008	T	0.32745	-0.9895	10	0.09590	T	0.72	.	5.0459	0.14483	0.0:0.4788:0.3314:0.1899	.	660;644	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	S	660;609;644;595	ENSP00000385597:P660S;ENSP00000385945:P609S;ENSP00000396178:P644S;ENSP00000313772:P595S	ENSP00000313772:P595S	P	+	1	0	IQCE	2616212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.116000	0.10724	-0.128000	0.11641	0.561000	0.74099	CCC	.	.	weak		0.597	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
SMARCA5	8467	hgsc.bcm.edu	37	4	144471249	144471249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:144471249A>G	ENST00000283131.3	+	23	3547	c.3085A>G	c.(3085-3087)Aag>Gag	p.K1029E		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	1029					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ACGAGGACCAAAGCCTTCAGT	0.358																																					p.K1029E		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A3085G						PASS	.						67.0	63.0	64.0					4																	144471249		2203	4300	6503	SO:0001583	missense	8467	exon23			GGACCAAAGCCTT	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.3085A>G	4.37:g.144471249A>G	ENSP00000283131:p.Lys1029Glu	61.0	0.0	0		66.0	14.0	0.212121	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017568	0.54576	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91011	-2.77	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.81973	0.4936	N	0.08118	0	0.46586	D	0.999116	B	0.26400	0.148	B	0.30029	0.11	T	0.78375	-0.2228	10	0.21014	T	0.42	-12.3435	16.1203	0.81346	1.0:0.0:0.0:0.0	.	1029	O60264	SMCA5_HUMAN	E	1029;972;972	ENSP00000283131:K1029E	ENSP00000283131:K1029E	K	+	1	0	SMARCA5	144690699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.877000	0.69675	2.274000	0.75844	0.533000	0.62120	AAG	.	.	none		0.358	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826663	34826663	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34826663G>A	ENST00000192788.5	+	14	2701	c.2530G>A	c.(2530-2532)Gtg>Atg	p.V844M	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.V844M	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	844							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CCTGAAGGAGGTGCTGCAGAG	0.537																																					p.V844M		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G2530A						PASS	.						123.0	120.0	121.0					6																	34826663		2021	4193	6214	SO:0001583	missense	54887	exon14			AAGGAGGTGCTGC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.2530G>A	6.37:g.34826663G>A	ENSP00000192788:p.Val844Met	133.0	0.0	0		130.0	32.0	0.246154	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972845	0.34848	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.17370	2.28;2.28	5.17	5.17	0.71159	.	0.207707	0.41396	D	0.000890	T	0.06600	0.0169	L	0.34521	1.04	0.31062	N	0.713971	B	0.31581	0.329	B	0.27170	0.077	T	0.10870	-1.0611	10	0.52906	T	0.07	-16.6036	13.7912	0.63143	0.0:0.0:0.8469:0.1531	.	844	Q6BDS2	URFB1_HUMAN	M	844	ENSP00000192788:V844M;ENSP00000400628:V844M	ENSP00000192788:V844M	V	+	1	0	UHRF1BP1	34934641	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.028000	0.41088	2.692000	0.91855	0.591000	0.81541	GTG	.	.	none		0.537	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
XPO5	57510	hgsc.bcm.edu	37	6	43514382	43514382	+	Silent	SNP	A	A	G	rs567618901		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43514382A>G	ENST00000265351.7	-	20	2478	c.2268T>C	c.(2266-2268)agT>agC	p.S756S	SCARNA15_ENST00000516409.1_RNA	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	756					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TTGGATTTCCACTGGATGTAT	0.458													A|||	1	0.000199681	0.0	0.0	5008	,	,		15773	0.001		0.0	False		,,,				2504	0.0				p.S756S		Atlas-SNP	.											XPO5,NS,carcinoma,-1,1	XPO5	79	1	0			c.T2268C						PASS	.						54.0	53.0	53.0					6																	43514382		1873	4102	5975	SO:0001819	synonymous_variant	57510	exon20			ATTTCCACTGGAT	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2268T>C	6.37:g.43514382A>G		142.0	0.0	0		98.0	43.0	0.438776	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			.	.	none		0.458	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
EML2	24139	hgsc.bcm.edu	37	19	46127999	46127999	+	Silent	SNP	C	C	T	rs36013288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46127999C>T	ENST00000245925.3	-	9	869	c.819G>A	c.(817-819)ggG>ggA	p.G273G	EML2_ENST00000589876.1_Silent_p.G273G|EML2_ENST00000587152.1_Silent_p.G474G|EML2_ENST00000536630.1_Silent_p.G420G|EML2_ENST00000586902.1_5'UTR	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	273	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CATAGAGGTTCCCCCCAGAGT	0.532													C|||	37	0.00738818	0.0	0.0115	5008	,	,		20477	0.0		0.0089	False		,,,				2504	0.0204				p.G474G		Atlas-SNP	.											EML2,NS,carcinoma,-1,1	EML2	64	1	0			c.G1422A						scavenged	.		,,	15,4391	21.2+/-45.6	0,15,2188	86.0	64.0	71.0		1422,1260,819	-0.9	1.0	19	dbSNP_126	71	70,8530	39.8+/-96.3	2,66,4232	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	2,81,6420	TT,TC,CC		0.814,0.3404,0.6535	,,	474/851,420/797,273/650	46127999	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	24139	exon12			GAGGTTCCCCCCA	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.819G>A	19.37:g.46127999C>T		85.0	1.0	0.0117647		72.0	34.0	0.472222	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																			C|0.993;T|0.007	0.007	strong		0.532	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
LRGUK	136332	hgsc.bcm.edu	37	7	133812351	133812351	+	Silent	SNP	T	T	C	rs61732215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:133812351T>C	ENST00000285928.2	+	1	300	c.231T>C	c.(229-231)gaT>gaC	p.D77D	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	77						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						CGGACGGAGATGAGGACCAGG	0.607													C|||	284	0.0567093	0.1717	0.0274	5008	,	,		16505	0.001		0.005	False		,,,				2504	0.0327				p.D77D		Atlas-SNP	.											.	LRGUK	113	.	0			c.T231C						PASS	.	C		710,3696	760.6+/-413.0	61,588,1554	82.0	79.0	80.0		231	-7.9	0.0	7	dbSNP_129	80	43,8557	817.4+/-406.9	0,43,4257	no	coding-synonymous	LRGUK	NM_144648.1		61,631,5811	CC,CT,TT		0.5,16.1144,5.7896		77/826	133812351	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon1			CGGAGATGAGGAC	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.231T>C	7.37:g.133812351T>C		139.0	0.0	0		147.0	73.0	0.496599	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.945;C|0.055	0.055	strong		0.607	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
RPAP1	26015	hgsc.bcm.edu	37	15	41819466	41819466	+	Missense_Mutation	SNP	G	G	A	rs35981448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41819466G>A	ENST00000304330.4	-	13	1761	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Missense_Mutation_p.R549C	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	549						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AGCACGTAGCGCAGCCGAGGC	0.617													G|||	14	0.00279553	0.0008	0.0014	5008	,	,		18252	0.0		0.006	False		,,,				2504	0.0061				p.R549C		Atlas-SNP	.											.	RPAP1	111	.	0			c.C1645T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	38.0	42.0	41.0		1645	5.3	1.0	15	dbSNP_126	41	49,8551	30.1+/-81.4	0,49,4251	yes	missense	RPAP1	NM_015540.2	180	0,56,6447	AA,AG,GG		0.5698,0.1589,0.4306	probably-damaging	549/1394	41819466	56,12950	2203	4300	6503	SO:0001583	missense	26015	exon13			CGTAGCGCAGCCG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1645C>T	15.37:g.41819466G>A	ENSP00000306123:p.Arg549Cys	91.0	0.0	0		74.0	37.0	0.5	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	G	20.3	3.958716	0.74016	0.001589	0.005698	ENSG00000103932	ENST00000304330	T	0.17691	2.26	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.32793	0.0841	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.10590	-1.0623	10	0.87932	D	0	-18.6742	13.8344	0.63400	0.0:0.0:0.8466:0.1534	rs35981448	549	Q9BWH6	RPAP1_HUMAN	C	549	ENSP00000306123:R549C	ENSP00000306123:R549C	R	-	1	0	RPAP1	39606758	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	5.777000	0.68931	2.659000	0.90383	0.655000	0.94253	CGC	G|0.996;A|0.004	0.004	strong		0.617	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
LRP1	4035	hgsc.bcm.edu	37	12	57550588	57550588	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57550588G>A	ENST00000243077.3	+	10	1912	c.1446G>A	c.(1444-1446)caG>caA	p.Q482Q		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	482	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AAAACGACCAGTATGGGAAGC	0.632																																					p.Q482Q		Atlas-SNP	.											.	LRP1	428	.	0			c.G1446A						PASS	.						44.0	40.0	42.0					12																	57550588		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon10			CGACCAGTATGGG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1446G>A	12.37:g.57550588G>A		57.0	0.0	0		47.0	5.0	0.106383	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CDKL4	344387	hgsc.bcm.edu	37	2	39440541	39440541	+	Splice_Site	SNP	G	G	A	rs375514414		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:39440541G>A	ENST00000395035.3	-	3	362	c.363C>T	c.(361-363)aaC>aaT	p.N121N	CDKL4_ENST00000378803.1_Splice_Site_p.N121N			Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	121	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|large_intestine(2)|liver(1)|lung(7)|ovary(1)	12		all_hematologic(82;0.248)				TGTTACTTACGTTATGTATAT	0.328													G|||	1	0.000199681	0.0	0.0	5008	,	,		18274	0.001		0.0	False		,,,				2504	0.0				p.N121N		Atlas-SNP	.											CDKL4,NS,carcinoma,0,1	CDKL4	30	1	0			c.C363T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	71.0	78.0	75.0		363	-4.6	0.9	2		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	CDKL4	NM_001009565.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		121/316	39440541	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	344387	exon3			ACTTACGTTATGT		CCDS33184.1	2p22.3	2011-11-04			ENSG00000205111	ENSG00000205111		"""Cyclin-dependent kinases"""	19287	protein-coding gene	gene with protein product							Standard	NM_001009565		Approved		uc002rrm.3	Q5MAI5	OTTHUMG00000133574	ENST00000395035.3:c.363+1C>T	2.37:g.39440541G>A		173.0	0.0	0		328.0	67.0	0.204268	NM_001009565	Q2NME9	Silent	SNP	ENST00000395035.3	37																																																																																				.	.	weak		0.328	CDKL4-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000331655.1	XM_293029	Silent
GPAT2	150763	hgsc.bcm.edu	37	2	96688916	96688916	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96688916G>A	ENST00000434632.1	-	20	2546	c.2087C>T	c.(2086-2088)cCg>cTg	p.P696L	FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000359548.4_Missense_Mutation_p.P696L|GPAT2_ENST00000453542.1_Missense_Mutation_p.P625L|GPAT2_ENST00000377137.3_Intron			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	696					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTTGAGCAGCGGGCTGAGCAG	0.652																																					p.P696L		Atlas-SNP	.											GPAT2,NS,carcinoma,+1,1	GPAT2	46	1	0			c.C2087T						scavenged	.						12.0	15.0	14.0					2																	96688916		1813	4047	5860	SO:0001583	missense	150763	exon19			AGCAGCGGGCTGA	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"""cancer/testis antigen 123"""					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.2087C>T	2.37:g.96688916G>A	ENSP00000389395:p.Pro696Leu	339.0	1.0	0.00294985		264.0	29.0	0.109848	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.365252	0.82463	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	D;D;T	0.83419	-1.72;-1.72;-0.81	5.44	5.44	0.79542	.	0.141914	0.49916	D	0.000123	D	0.89894	0.6847	M	0.64404	1.975	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.996;0.932;0.999;0.995	D	0.90665	0.4593	10	0.87932	D	0	-13.903	16.7485	0.85479	0.0:0.0:1.0:0.0	.	625;702;696;625	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	L	696;696;625	ENSP00000352547:P696L;ENSP00000389395:P696L;ENSP00000393770:P625L	ENSP00000352547:P696L	P	-	2	0	GPAT2	96052643	1.000000	0.71417	0.905000	0.35620	0.705000	0.40729	7.030000	0.76484	2.569000	0.86673	0.637000	0.83480	CCG	.	.	none		0.652	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328	
KRT17	3872	hgsc.bcm.edu	37	17	39777895	39777895	+	Nonsense_Mutation	SNP	T	T	A	rs146900210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39777895T>A	ENST00000311208.8	-	4	851	c.784A>T	c.(784-786)Aag>Tag	p.K262*	JUP_ENST00000540235.1_Nonsense_Mutation_p.K421*	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	262	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				TCTGCCATCTTCTCATACTGG	0.617																																					p.K262X	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.A784T						PASS	.	T	stop/LYS	0,4406		0,0,2203	122.0	105.0	111.0		784	1.5	1.0	17	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	no	stop-gained	KRT17	NM_000422.2		0,5,6498	AA,AT,TT		0.0581,0.0,0.0384		262/433	39777895	5,13001	2203	4300	6503	SO:0001587	stop_gained	3872	exon4			CCATCTTCTCATA	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.784A>T	17.37:g.39777895T>A	ENSP00000308452:p.Lys262*	307.0	1.0	0.00325733		347.0	172.0	0.495677	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Nonsense_Mutation	SNP	ENST00000311208.8	37	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726067	0.89298	0.0	5.81E-4	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	.	.	.	3.82	1.49	0.22878	.	0.000000	0.49305	D	0.000147	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9636	0.14080	0.0:0.1718:0.1573:0.6709	.	.	.	.	X	262;421	.	.	K	-	1	0	JUP;KRT17	37031421	0.014000	0.17966	0.998000	0.56505	0.970000	0.65996	0.145000	0.16157	0.160000	0.19432	0.533000	0.62120	AAG	T|1.000;A|0.000	0.000	strong		0.617	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422	
CETN3	1070	hgsc.bcm.edu	37	5	89703535	89703535	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:89703535A>C	ENST00000283122.3	-	2	258	c.134T>G	c.(133-135)aTa>aGa	p.I45R	CETN3_ENST00000522565.1_Missense_Mutation_p.I45R|CETN3_ENST00000522083.1_Missense_Mutation_p.I45R|CETN3_ENST00000522842.1_Missense_Mutation_p.I45R|CETN3_ENST00000522864.1_Missense_Mutation_p.I45R	NM_004365.2	NP_004356.2	O15182	CETN3_HUMAN	centrin, EF-hand protein, 3	45	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				centrosome cycle (GO:0007098)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|photoreceptor connecting cilium (GO:0032391)	calcium ion binding (GO:0005509)			lung(3)	3		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		ATGATAATCTATTGCTTCATC	0.269																																					p.I45R		Atlas-SNP	.											.	CETN3	16	.	0			c.T134G						PASS	.						100.0	96.0	97.0					5																	89703535		2200	4291	6491	SO:0001583	missense	1070	exon2			TAATCTATTGCTT	Y12473	CCDS4066.1, CCDS75274.1	5q14.3	2013-01-10	2010-06-24		ENSG00000153140	ENSG00000153140		"""EF-hand domain containing"""	1868	protein-coding gene	gene with protein product	"""CDC31 yeast homolog"", ""EF-hand superfamily member"""	602907	"""centrin, EF-hand protein, 3 (CDC31 yeast homolog)"""			9256449	Standard	XM_006714521		Approved	CEN3	uc003kjo.3	O15182	OTTHUMG00000131326	ENST00000283122.3:c.134T>G	5.37:g.89703535A>C	ENSP00000283122:p.Ile45Arg	342.0	0.0	0		332.0	122.0	0.36747	NM_004365	Q53YD2|Q9BS23	Missense_Mutation	SNP	ENST00000283122.3	37	CCDS4066.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845429	0.71603	.	.	ENSG00000153140	ENST00000283122;ENST00000522083;ENST00000522864;ENST00000522565;ENST00000522842	T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16	5.65	4.5	0.54988	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92156	0.7513	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.93002	0.6424	10	0.87932	D	0	.	10.5918	0.45314	0.925:0.0:0.075:0.0	.	45	O15182	CETN3_HUMAN	R	45	ENSP00000283122:I45R;ENSP00000428259:I45R;ENSP00000430361:I45R;ENSP00000430409:I45R;ENSP00000429875:I45R	ENSP00000283122:I45R	I	-	2	0	CETN3	89739291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.065000	0.93941	0.975000	0.38392	0.459000	0.35465	ATA	.	.	none		0.269	CETN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254097.1	NM_004365	
CLASRP	11129	hgsc.bcm.edu	37	19	45563695	45563695	+	Silent	SNP	G	G	A	rs147776329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45563695G>A	ENST00000221455.3	+	9	857	c.759G>A	c.(757-759)aaG>aaA	p.K253K	CLASRP_ENST00000391953.4_Silent_p.K191K|CLASRP_ENST00000544944.2_Silent_p.K253K	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	253					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						AGCATGCCAAGGCTCTTGAGG	0.602													G|||	20	0.00399361	0.0038	0.0058	5008	,	,		18973	0.0		0.0109	False		,,,				2504	0.0				p.K253K		Atlas-SNP	.											.	CLASRP	44	.	0			c.G759A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	126.0	102.0	110.0		759	3.6	1.0	19	dbSNP_134	110	114,8486	61.0+/-122.8	1,112,4187	no	coding-synonymous	CLASRP	NM_007056.2		1,131,6371	AA,AG,GG		1.3256,0.4312,1.0226		253/675	45563695	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon9			TGCCAAGGCTCTT	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.759G>A	19.37:g.45563695G>A		89.0	0.0	0		86.0	33.0	0.383721	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			G|0.991;A|0.009	0.009	strong		0.602	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
VPRBP	9730	hgsc.bcm.edu	37	3	51458204	51458204	+	Silent	SNP	G	G	A	rs150385433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:51458204G>A	ENST00000335891.5	-	7	882	c.873C>T	c.(871-873)tcC>tcT	p.S291S				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	740	Protein kinase-like.				B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TGGACAGTAAGGACAGGAGCA	0.557													G|||	16	0.00319489	0.0015	0.0058	5008	,	,		20267	0.0		0.0099	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	VPRBP	107	.	0			c.C2061T						PASS	.	G	,	3,4027		0,3,2012	224.0	213.0	217.0		2058,2061	-3.6	1.0	3	dbSNP_134	217	66,8310		0,66,4122	no	coding-synonymous,coding-synonymous	VPRBP	NM_001171904.1,NM_014703.2	,	0,69,6134	AA,AG,GG		0.788,0.0744,0.5562	,	686/1454,687/1455	51458204	69,12337	2015	4188	6203	SO:0001819	synonymous_variant	9730	exon14			CAGTAAGGACAGG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.873C>T	3.37:g.51458204G>A		153.0	0.0	0		121.0	69.0	0.570248	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	37																																																																																				G|0.995;A|0.005	0.005	strong		0.557	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
SOGA1	140710	hgsc.bcm.edu	37	20	35443768	35443768	+	Missense_Mutation	SNP	G	G	A	rs201600310		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:35443768G>A	ENST00000357779.3	-	5	1689	c.1363C>T	c.(1363-1365)Cgg>Tgg	p.R455W	SOGA1_ENST00000456801.2_Missense_Mutation_p.R296W|SOGA1_ENST00000237536.4_Missense_Mutation_p.R693W|SOGA1_ENST00000279034.6_Missense_Mutation_p.R455W			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	455					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TCATGCAGCCGGAAGTCAGCA	0.642																																					p.R693W		Atlas-SNP	.											.	SOGA1	136	.	0			c.C2077T						PASS	.						38.0	40.0	39.0					20																	35443768		2203	4300	6503	SO:0001583	missense	140710	exon5			GCAGCCGGAAGTC	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1363C>T	20.37:g.35443768G>A	ENSP00000350424:p.Arg455Trp	96.0	0.0	0		82.0	36.0	0.439024	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	G	12.03	1.815128	0.32053	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.18960	2.18;2.19;2.18;2.19	4.6	2.45	0.29901	.	0.356930	0.24426	N	0.038636	T	0.28400	0.0702	L	0.29908	0.895	0.22185	N	0.999303	D	0.76494	0.999	D	0.69307	0.963	T	0.02037	-1.1225	10	0.66056	D	0.02	-35.7471	8.495	0.33123	0.0:0.1348:0.5622:0.3029	.	455	O94964-4	.	W	693;455;296;455	ENSP00000237536:R693W;ENSP00000279034:R455W;ENSP00000413886:R296W;ENSP00000350424:R455W	ENSP00000237536:R693W	R	-	1	2	KIAA0889	34877182	0.915000	0.31059	0.960000	0.40013	0.382000	0.30200	1.264000	0.33015	1.137000	0.42214	0.313000	0.20887	CGG	G|0.998;A|0.002	0.002	weak		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
ARAP3	64411	hgsc.bcm.edu	37	5	141033870	141033870	+	Missense_Mutation	SNP	T	T	G	rs61749636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141033870T>G	ENST00000239440.4	-	33	4347	c.4282A>C	c.(4282-4284)Aca>Cca	p.T1428P	ARAP3_ENST00000508305.1_Missense_Mutation_p.T1259P|ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000522783.1_5'Flank|ARAP3_ENST00000513878.1_Missense_Mutation_p.T1077P|FCHSD1_ENST00000435817.2_5'Flank|FCHSD1_ENST00000519800.1_5'Flank	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1428			T -> P (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.T1428P(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CACTCCCGTGTGGTGGAGAAG	0.567													T|||	131	0.0261581	0.003	0.0519	5008	,	,		17472	0.0		0.0795	False		,,,				2504	0.0112				p.T1428P		Atlas-SNP	.											ARAP3,colon,carcinoma,+2,4	ARAP3	139	4	1	Substitution - Missense(1)	breast(1)	c.A4282C						PASS	.	T	PRO/THR	74,4332	65.3+/-102.7	1,72,2130	118.0	115.0	116.0		4282	0.0	0.0	5	dbSNP_129	116	650,7950	166.4+/-218.3	25,600,3675	yes	missense	ARAP3	NM_022481.5	38	26,672,5805	GG,GT,TT		7.5581,1.6795,5.5667	benign	1428/1545	141033870	724,12282	2203	4300	6503	SO:0001583	missense	64411	exon33			CCCGTGTGGTGGA	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4282A>C	5.37:g.141033870T>G	ENSP00000239440:p.Thr1428Pro	165.0	0.0	0		167.0	81.0	0.48503	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	88	0.040293040293040296	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	65	0.08575197889182058	T	1.173	-0.640433	0.03557	0.016795	0.075581	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.45668	0.89;0.89;0.89	4.01	0.00808	0.14073	.	0.594286	0.14268	N	0.330342	T	0.00724	0.0024	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10314	-1.0635	10	0.28530	T	0.3	.	6.0483	0.19772	0.1528:0.0:0.317:0.5302	rs61749636	1077;1259;1428	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	P	1259;1428;1077	ENSP00000421826:T1259P;ENSP00000239440:T1428P;ENSP00000421468:T1077P	ENSP00000239440:T1428P	T	-	1	0	ARAP3	141014054	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.295000	0.19065	0.002000	0.14630	0.533000	0.62120	ACA	T|0.952;G|0.048	0.048	strong		0.567	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
GK5	256356	hgsc.bcm.edu	37	3	141884493	141884493	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141884493G>A	ENST00000392993.2	-	16	1712	c.1561C>T	c.(1561-1563)Cgc>Tgc	p.R521C		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	521					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						TTCATGGAGCGTTTCACTGCT	0.393																																					p.R521C		Atlas-SNP	.											GK5,NS,carcinoma,+1,1	GK5	45	1	0			c.C1561T						PASS	.						218.0	199.0	205.0					3																	141884493		2203	4300	6503	SO:0001583	missense	256356	exon16			TGGAGCGTTTCAC	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"""Glycerol kinases"""	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.1561C>T	3.37:g.141884493G>A	ENSP00000418001:p.Arg521Cys	396.0	0.0	0		303.0	148.0	0.488449	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	37	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493597	0.84962	.	.	ENSG00000175066	ENST00000392993	D	0.91407	-2.84	5.98	5.11	0.69529	.	0.049681	0.85682	D	0.000000	D	0.93216	0.7839	M	0.84948	2.725	0.80722	D	1	D	0.59767	0.986	P	0.50537	0.643	D	0.93320	0.6692	10	0.49607	T	0.09	-12.3259	14.3523	0.66711	0.0723:0.0:0.9277:0.0	.	521	Q6ZS86	GLPK5_HUMAN	C	521	ENSP00000418001:R521C	ENSP00000418001:R521C	R	-	1	0	GK5	143367183	1.000000	0.71417	0.989000	0.46669	0.972000	0.66771	6.503000	0.73699	1.537000	0.49254	0.591000	0.81541	CGC	.	.	none		0.393	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
BCAT2	587	hgsc.bcm.edu	37	19	49309776	49309776	+	Missense_Mutation	SNP	G	G	C	rs117048185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49309776G>C	ENST00000316273.6	-	3	310	c.298C>G	c.(298-300)Cag>Gag	p.Q100E	BCAT2_ENST00000402551.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000599246.1_Intron|BCAT2_ENST00000597011.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000598162.1_Missense_Mutation_p.Q100E|BCAT2_ENST00000545387.2_Intron|BCAT2_ENST00000601496.1_5'Flank	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	100					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	CATGCCACCTGCAGGGAGTAG	0.607													G|||	30	0.00599042	0.0008	0.0072	5008	,	,		16606	0.0		0.0229	False		,,,				2504	0.001				p.Q100E		Atlas-SNP	.											.	BCAT2	35	.	0			c.C298G						PASS	.	G	,GLU/GLN	10,4396	15.5+/-35.6	0,10,2193	63.0	74.0	71.0		,298	5.3	1.0	19	dbSNP_132	71	120,8480	61.7+/-123.6	1,118,4181	yes	intron,missense	BCAT2	NM_001164773.1,NM_001190.3	,29	1,128,6374	CC,CG,GG		1.3953,0.227,0.9995	,benign	,100/393	49309776	130,12876	2203	4300	6503	SO:0001583	missense	587	exon3			CCACCTGCAGGGA	U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"""branched chain aminotransferase 2, mitochondrial"""	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.298C>G	19.37:g.49309776G>C	ENSP00000322991:p.Gln100Glu	86.0	0.0	0		85.0	45.0	0.529412	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	1.762	-0.486562	0.04352	0.00227	0.013953	ENSG00000105552	ENST00000316273;ENST00000402551	T;T	0.30448	1.53;1.53	5.26	5.26	0.73747	.	0.056271	0.64402	D	0.000001	T	0.05410	0.0143	N	0.02721	-0.515	0.43959	D	0.996633	B;B	0.23377	0.084;0.084	B;B	0.18263	0.021;0.021	T	0.13098	-1.0522	10	0.02654	T	1	-20.0097	12.4651	0.55753	0.0:0.1688:0.8312:0.0	.	100;100	Q53EW7;O15382	.;BCAT2_HUMAN	E	100;60	ENSP00000322991:Q100E;ENSP00000385161:Q60E	ENSP00000322991:Q100E	Q	-	1	0	BCAT2	54001588	0.995000	0.38212	1.000000	0.80357	0.499000	0.33736	2.479000	0.45197	2.627000	0.88993	0.555000	0.69702	CAG	G|0.990;C|0.010	0.010	strong		0.607	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
NCOA6	23054	hgsc.bcm.edu	37	20	33328372	33328372	+	Silent	SNP	C	C	T	rs141863711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33328372C>T	ENST00000374796.2	-	12	8258	c.5688G>A	c.(5686-5688)ccG>ccA	p.P1896P	NCOA6_ENST00000359003.2_Silent_p.P1896P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1896	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						AGGCAGTGCCCGGGCCCACAG	0.602																																					p.P1896P		Atlas-SNP	.											.	NCOA6	219	.	0			c.G5688A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	53.0	53.0	53.0		,5688	-11.3	0.0	20	dbSNP_134	53	0,8600		0,0,4300	no	intron,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	,1896/2064	33328372	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon11			AGTGCCCGGGCCC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5688G>A	20.37:g.33328372C>T		56.0	0.0	0		45.0	16.0	0.355556	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
ZNF217	7764	hgsc.bcm.edu	37	20	52192417	52192417	+	Silent	SNP	C	C	T	rs45439395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52192417C>T	ENST00000371471.2	-	4	3311	c.2886G>A	c.(2884-2886)ccG>ccA	p.P962P	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Silent_p.P962P			O75362	ZN217_HUMAN	zinc finger protein 217	962					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCGCCTGCGACGGATACACAC	0.562													C|||	11	0.00219649	0.0	0.0014	5008	,	,		20692	0.0		0.0099	False		,,,				2504	0.0				p.P962P		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2886A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	141.0	113.0	122.0		2886	-7.8	0.0	20	dbSNP_127	122	63,8537	39.8+/-96.3	0,63,4237	no	coding-synonymous	ZNF217	NM_006526.2		0,65,6438	TT,TC,CC		0.7326,0.0454,0.4998		962/1049	52192417	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			CTGCGACGGATAC	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2886G>A	20.37:g.52192417C>T		106.0	0.0	0		99.0	55.0	0.555556	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.997;T|0.003	0.003	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
MC1R	4157	hgsc.bcm.edu	37	16	89985950	89985950	+	Missense_Mutation	SNP	C	C	T	rs34158934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:89985950C>T	ENST00000555147.1	+	1	1664	c.284C>T	c.(283-285)aCg>aTg	p.T95M	RP11-566K11.4_ENST00000554623.1_RNA|TUBB3_ENST00000554444.1_5'Flank|TUBB3_ENST00000556922.1_Missense_Mutation_p.T95M|MC1R_ENST00000555427.1_Missense_Mutation_p.T95M|RP11-566K11.7_ENST00000570217.1_RNA	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	95			T -> M (in dbSNP:rs34158934).		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		GTGCTGGAGACGGCCGTCATC	0.627									Melanoma, Familial Clustering of				C|||	4	0.000798722	0.0023	0.0014	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T95M		Atlas-SNP	.											.	MC1R	20	.	0			c.C284T	GRCh37	CM062826	MC1R	M	rs34158934	PASS	.	C	MET/THR	3,4379		0,3,2188	46.0	56.0	52.0		284	3.9	0.8	16	dbSNP_126	52	5,8569		0,5,4282	yes	missense	MC1R	NM_002386.3	81	0,8,6470	TT,TC,CC		0.0583,0.0685,0.0617		95/318	89985950	8,12948	2191	4287	6478	SO:0001583	missense	4157	exon1	Familial Cancer Database		TGGAGACGGCCGT		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.284C>T	16.37:g.89985950C>T	ENSP00000451605:p.Thr95Met	114.0	0.0	0		115.0	67.0	0.582609	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711952	0.48517	6.85E-4	5.83E-4	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.01505	4.82;4.82;4.82	4.86	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38959	U	0.001519	T	0.02727	0.0082	L	0.41824	1.3	0.45914	D	0.998756	P	0.47034	0.889	P	0.46796	0.527	T	0.64368	-0.6424	9	.	.	.	.	10.5142	0.44879	0.0:0.836:0.0:0.164	rs34158934	95	Q01726	MSHR_HUMAN	M	95	ENSP00000451760:T95M;ENSP00000451560:T95M;ENSP00000451605:T95M	.	T	+	2	0	MC1R;RP11-566K11.2	88513451	0.902000	0.30710	0.785000	0.31869	0.215000	0.24574	1.867000	0.39499	1.057000	0.40506	0.455000	0.32223	ACG	C|0.995;T|0.005	0.005	strong		0.627	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
ADAM33	80332	hgsc.bcm.edu	37	20	3652365	3652365	+	Missense_Mutation	SNP	T	T	C	rs55687415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3652365T>C	ENST00000356518.2	-	16	2009	c.1768A>G	c.(1768-1770)Atg>Gtg	p.M590V	ADAM33_ENST00000350009.2_Missense_Mutation_p.M590V|ADAM33_ENST00000379861.4_Missense_Mutation_p.M590V|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	590	Cys-rich.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						ACTGGCACCATGTGCGGTGCG	0.637													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		20795	0.0		0.0	False		,,,				2504	0.0				p.M590V		Atlas-SNP	.											.	ADAM33	76	.	0			c.A1768G						PASS	.	T	VAL/MET,VAL/MET	82,4324		0,82,2121	42.0	33.0	36.0		1768,1768	0.5	0.0	20	dbSNP_129	36	4,8588		0,4,4292	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	21,21	0,86,6413	CC,CT,TT		0.0466,1.8611,0.6616	benign,benign	590/814,590/788	3652365	86,12912	2203	4296	6499	SO:0001583	missense	80332	exon16			GCACCATGTGCGG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.1768A>G	20.37:g.3652365T>C	ENSP00000348912:p.Met590Val	66.0	0.0	0		53.0	22.0	0.415094	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	T	4.955	0.177362	0.09443	0.018611	4.66E-4	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000428784;ENST00000439201	T;T;T	0.21031	2.03;2.03;2.03	5.46	0.539	0.17156	ADAM, cysteine-rich (2);	.	.	.	.	T	0.01835	0.0058	N	0.00926	-1.1	0.09310	N	0.999999	B;B;B;B	0.19073	0.033;0.001;0.001;0.001	B;B;B;B	0.14578	0.011;0.002;0.004;0.004	T	0.41520	-0.9504	9	0.16420	T	0.52	.	9.2387	0.37481	0.0:0.3775:0.0:0.6225	rs55687415;rs61753555	106;590;590;590	E9PEB2;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;ADA33_HUMAN;.	V	590;590;590;106;470	ENSP00000348912:M590V;ENSP00000369190:M590V;ENSP00000322550:M590V	ENSP00000322550:M590V	M	-	1	0	ADAM33	3600365	0.620000	0.27068	0.003000	0.11579	0.082000	0.17680	0.249000	0.18216	-0.185000	0.10550	0.459000	0.35465	ATG	T|0.992;C|0.008	0.008	strong		0.637	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
MAP7D1	55700	hgsc.bcm.edu	37	1	36636774	36636774	+	Silent	SNP	G	G	A	rs139650826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000373150.4_Silent_p.Q83Q|MAP7D1_ENST00000316156.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39.0	43.0	41.0		249	2.2	1.0	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.249G>A	1.37:g.36636774G>A		72.0	0.0	0		82.0	39.0	0.47561	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
OR5H2	79310	hgsc.bcm.edu	37	3	98002429	98002429	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98002429A>T	ENST00000355273.2	+	1	698	c.698A>T	c.(697-699)aAg>aTg	p.K233M	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						ATCCTAAAAAAGAAGTCTGTT	0.368																																					p.K233M		Atlas-SNP	.											OR5H2,NS,carcinoma,0,1	OR5H2	63	1	0			c.A698T						PASS	.						84.0	86.0	85.0					3																	98002429		2203	4300	6503	SO:0001583	missense	79310	exon1			TAAAAAAGAAGTC		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"""GPCR / Class A : Olfactory receptors"""	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.698A>T	3.37:g.98002429A>T	ENSP00000347418:p.Lys233Met	169.0	0.0	0		137.0	39.0	0.284672	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	A	0.025	-1.380780	0.01204	.	.	ENSG00000197938	ENST00000355273	T	0.00032	8.88	3.03	-5.67	0.02444	GPCR, rhodopsin-like superfamily (1);	0.347490	0.20667	N	0.087917	T	0.00039	0.0001	N	0.00642	-1.3	0.09310	N	1	B	0.29232	0.238	B	0.32211	0.142	T	0.47923	-0.9079	10	0.02654	T	1	.	0.6655	0.00849	0.2024:0.1404:0.235:0.4222	.	233	Q8NGV7	OR5H2_HUMAN	M	233	ENSP00000347418:K233M	ENSP00000347418:K233M	K	+	2	0	OR5H2	99485119	0.000000	0.05858	0.003000	0.11579	0.036000	0.12997	-0.051000	0.11885	-0.806000	0.04398	0.338000	0.21704	AAG	.	.	none		0.368	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
CHST4	10164	hgsc.bcm.edu	37	16	71570847	71570847	+	Missense_Mutation	SNP	G	G	A	rs148657245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71570847G>A	ENST00000338482.5	+	3	610	c.267G>A	c.(265-267)atG>atA	p.M89I	CHST4_ENST00000572450.1_Missense_Mutation_p.M89I|RP11-510M2.5_ENST00000568523.1_RNA|CHST4_ENST00000539698.3_Missense_Mutation_p.M89I|ZNF19_ENST00000568446.1_Intron			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	89					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CCGCCTGGATGCTGCACATGG	0.582													G|||	17	0.00339457	0.0	0.0	5008	,	,		17368	0.0		0.0129	False		,,,				2504	0.0041				p.M89I		Atlas-SNP	.											.	CHST4	47	.	0			c.G267A						PASS	.	G	ILE/MET,ILE/MET	7,4389	12.9+/-30.5	0,7,2191	90.0	93.0	92.0		267,267	-2.5	0.0	16	dbSNP_134	92	95,8505	54.0+/-114.7	1,93,4206	yes	missense,missense	CHST4	NM_001166395.1,NM_005769.2	10,10	1,100,6397	AA,AG,GG		1.1047,0.1592,0.7849	benign,benign	89/387,89/387	71570847	102,12894	2198	4300	6498	SO:0001583	missense	10164	exon2			CTGGATGCTGCAC	AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"""Sulfotransferases, membrane-bound"""	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.267G>A	16.37:g.71570847G>A	ENSP00000341206:p.Met89Ile	181.0	0.0	0		205.0	131.0	0.639024	NM_001166395	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	3.265	-0.150351	0.06585	0.001592	0.011047	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.81499	-1.5;-1.5	6.0	-2.45	0.06481	Sulfotransferase domain (1);	1.694150	0.02602	N	0.101171	T	0.55353	0.1915	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43845	-0.9366	10	0.34782	T	0.22	-3.2597	3.7124	0.08425	0.1301:0.4236:0.2298:0.2165	.	89	Q8NCG5	CHST4_HUMAN	I	89	ENSP00000341206:M89I;ENSP00000441204:M89I	ENSP00000341206:M89I	M	+	3	0	CHST4	70128348	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.112000	0.15479	-0.681000	0.05204	-0.878000	0.02970	ATG	G|0.993;A|0.007	0.007	strong		0.582	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769	
MFHAS1	9258	hgsc.bcm.edu	37	8	8749318	8749318	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8749318A>G	ENST00000276282.6	-	1	1837	c.1251T>C	c.(1249-1251)caT>caC	p.H417H		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	417	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CTGCAGCCTTATGCCCCATCA	0.617																																					p.H417H	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T1251C						PASS	.						48.0	43.0	44.0					8																	8749318		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGCCTTATGCCCC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1251T>C	8.37:g.8749318A>G		42.0	0.0	0		36.0	17.0	0.472222	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.617	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
WDR25	79446	hgsc.bcm.edu	37	14	100996337	100996337	+	Missense_Mutation	SNP	G	G	A	rs144754220		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:100996337G>A	ENST00000335290.6	+	7	1820	c.1594G>A	c.(1594-1596)Gcc>Acc	p.A532T	WDR25_ENST00000554998.1_Missense_Mutation_p.A532T|WDR25_ENST00000557502.1_3'UTR|WDR25_ENST00000402312.3_Missense_Mutation_p.A532T|WDR25_ENST00000542471.2_Missense_Mutation_p.A275T	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	532										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CTCCGTCCTCGCCACCTGCTC	0.617																																					p.A532T		Atlas-SNP	.											.	WDR25	37	.	0			c.G1594A						PASS	.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	75.0	68.0	71.0		1594,1594	4.8	1.0	14	dbSNP_134	71	0,8600		0,0,4300	no	missense,missense	WDR25	NM_001161476.1,NM_024515.4	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	532/545,532/545	100996337	1,13005	2203	4300	6503	SO:0001583	missense	79446	exon7			GTCCTCGCCACCT	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.1594G>A	14.37:g.100996337G>A	ENSP00000334148:p.Ala532Thr	98.0	0.0	0		91.0	20.0	0.21978	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693621	0.88735	2.27E-4	0.0	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	T;T;T;T	0.70282	4.69;4.69;4.69;-0.47	4.83	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.133172	0.49305	D	0.000150	D	0.85982	0.5824	M	0.92077	3.27	0.58432	D	0.999996	D;D	0.89917	1.0;0.997	P;P	0.59546	0.859;0.834	D	0.89565	0.3809	10	0.62326	D	0.03	-12.8885	17.0452	0.86500	0.0:0.0:1.0:0.0	.	275;532	Q64LD2-2;Q64LD2	.;WDR25_HUMAN	T	532;532;532;275	ENSP00000450661:A532T;ENSP00000385540:A532T;ENSP00000334148:A532T;ENSP00000441903:A275T	ENSP00000334148:A532T	A	+	1	0	WDR25	100066090	1.000000	0.71417	0.964000	0.40570	0.626000	0.37791	9.336000	0.96533	2.388000	0.81334	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.617	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
GPAM	57678	hgsc.bcm.edu	37	10	113926224	113926224	+	Missense_Mutation	SNP	A	A	G	rs35019520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:113926224A>G	ENST00000348367.4	-	12	1354	c.1157T>C	c.(1156-1158)aTt>aCt	p.I386T	GPAM_ENST00000423155.1_Missense_Mutation_p.I386T|GPAM_ENST00000369425.1_Missense_Mutation_p.I386T			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	386			I -> T (in dbSNP:rs35019520).		acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		TAACATTCTAATAACACCTCT	0.388													A|||	37	0.00738818	0.0008	0.0086	5008	,	,		20081	0.0		0.0219	False		,,,				2504	0.0082				p.I386T	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.T1157C						PASS	.	A	THR/ILE	11,4395	17.9+/-39.9	0,11,2192	240.0	207.0	218.0		1157	4.7	1.0	10	dbSNP_126	218	109,8491	59.1+/-120.7	1,107,4192	yes	missense	GPAM	NM_020918.4	89	1,118,6384	GG,GA,AA		1.2674,0.2497,0.9227	benign	386/829	113926224	120,12886	2203	4300	6503	SO:0001583	missense	57678	exon12			ATTCTAATAACAC	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1157T>C	10.37:g.113926224A>G	ENSP00000265276:p.Ile386Thr	108.0	0.0	0		108.0	38.0	0.351852	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	A	14.69	2.610145	0.46527	0.002497	0.012674	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.42900	0.96;0.96;0.96	5.87	4.69	0.59074	.	0.159420	0.56097	D	0.000036	T	0.12305	0.0299	N	0.08118	0	0.29156	N	0.878052	B;B	0.19817	0.039;0.039	B;B	0.18871	0.023;0.023	T	0.04737	-1.0930	10	0.22706	T	0.39	-19.2312	14.4037	0.67068	0.8693:0.1307:0.0:0.0	rs35019520	386;386	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	T	386	ENSP00000265276:I386T;ENSP00000409242:I386T;ENSP00000358433:I386T	ENSP00000265276:I386T	I	-	2	0	GPAM	113916214	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	5.730000	0.68546	2.247000	0.74100	0.523000	0.50628	ATT	A|0.990;G|0.010	0.010	strong		0.388	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
NDUFA9	4704	hgsc.bcm.edu	37	12	4768290	4768290	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4768290G>A	ENST00000266544.5	+	5	519	c.499G>A	c.(499-501)Gtt>Att	p.V167I	RP11-500M8.7_ENST00000536588.1_3'UTR	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa	167					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|sodium ion transport (GO:0006814)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						ATTCATTCATGTTTCACATCT	0.358																																					p.V167I	Colon(75;996 1244 23946 25294 29232)	Atlas-SNP	.											.	NDUFA9	45	.	0			c.G499A						PASS	.						69.0	73.0	72.0					12																	4768290		2203	4300	6503	SO:0001583	missense	4704	exon5			ATTCATGTTTCAC	AF050641	CCDS8532.1	12p13.3	2011-09-14	2002-08-29		ENSG00000139180	ENSG00000139180		"""Mitochondrial respiratory chain complex / Complex I"", ""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	7693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 22E, member 1"", ""complex I 39kDa subunit"""	603834	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (39kD)"""	NDUFS2L		8486360, 19027726	Standard	NM_005002		Approved	SDR22E1, CI-39k	uc001qnc.3	Q16795		ENST00000266544.5:c.499G>A	12.37:g.4768290G>A	ENSP00000266544:p.Val167Ile	101.0	0.0	0		67.0	30.0	0.447761	NM_005002	Q14076|Q2NKX0	Missense_Mutation	SNP	ENST00000266544.5	37	CCDS8532.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731929	0.30684	.	.	ENSG00000139180	ENST00000266544	D	0.93189	-3.18	5.26	3.43	0.39272	NAD(P)-binding domain (1);NmrA-like (1);	0.304583	0.38005	N	0.001857	D	0.85898	0.5804	N	0.17922	0.545	0.80722	D	1	B;B	0.15473	0.013;0.013	B;B	0.25987	0.065;0.065	T	0.76515	-0.2931	10	0.27082	T	0.32	-11.9884	7.2226	0.25997	0.3375:0.0:0.6625:0.0	.	167;167	A8K4V2;Q16795	.;NDUA9_HUMAN	I	167	ENSP00000266544:V167I	ENSP00000266544:V167I	V	+	1	0	NDUFA9	4638551	0.989000	0.36119	0.984000	0.44739	0.576000	0.36127	0.932000	0.28884	0.707000	0.31934	0.585000	0.79938	GTT	.	.	none		0.358	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398900.2	NM_005002	
RAD54B	25788	hgsc.bcm.edu	37	8	95423464	95423464	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:95423464A>G	ENST00000336148.5	-	4	508	c.384T>C	c.(382-384)gtT>gtC	p.V128V		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	128					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TACACCAAACAACACTGAAAT	0.328								Direct reversal of damage;Homologous recombination																													p.V128V		Atlas-SNP	.											.	RAD54B	88	.	0			c.T384C						PASS	.						100.0	101.0	101.0					8																	95423464		2202	4297	6499	SO:0001819	synonymous_variant	25788	exon4			CCAAACAACACTG	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.384T>C	8.37:g.95423464A>G		259.0	0.0	0		240.0	111.0	0.4625	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			.	.	none		0.328	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
VIPR2	7434	hgsc.bcm.edu	37	7	158828692	158828692	+	Missense_Mutation	SNP	C	C	T	rs145308657		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158828692C>T	ENST00000262178.2	-	8	945	c.760G>A	c.(760-762)Gtc>Atc	p.V254I	VIPR2_ENST00000377633.3_Missense_Mutation_p.V238I|VIPR2_ENST00000402066.1_Missense_Mutation_p.V395I	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	254					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CCGATGCAGACGGTGGGGAGG	0.612																																					p.V254I	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.G760A						PASS	.	T	ILE/VAL	0,4406		0,0,2203	66.0	50.0	55.0		760	-2.9	0.0	7	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	yes	missense	VIPR2	NM_003382.4	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	254/439	158828692	2,13004	2203	4300	6503	SO:0001583	missense	7434	exon8			TGCAGACGGTGGG	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.760G>A	7.37:g.158828692C>T	ENSP00000262178:p.Val254Ile	68.0	0.0	0		56.0	29.0	0.517857	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Missense_Mutation	SNP	ENST00000262178.2	37	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	c	4.973	0.180779	0.09443	0.0	2.33E-4	ENSG00000106018	ENST00000262178;ENST00000377633;ENST00000402066	T;T;T	0.51574	0.7;0.7;0.7	4.72	-2.87	0.05700	GPCR, family 2-like (1);	0.479321	0.17044	N	0.189218	T	0.23133	0.0559	N	0.16602	0.42	0.09310	N	0.999991	B	0.24882	0.113	B	0.22880	0.042	T	0.16305	-1.0407	9	.	.	.	.	6.6287	0.22845	0.0:0.3749:0.1336:0.4915	.	254	P41587	VIPR2_HUMAN	I	254;238;395	ENSP00000262178:V254I;ENSP00000366860:V238I;ENSP00000384497:V395I	.	V	-	1	0	VIPR2	158521453	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.497000	0.02289	-0.616000	0.05671	-1.616000	0.00795	GTC	C|1.000;T|0.000	0.000	weak		0.612	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
PLCD4	84812	hgsc.bcm.edu	37	2	219492952	219492952	+	Splice_Site	SNP	C	C	T	rs61733653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219492952C>T	ENST00000450993.2	+	7	1312	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	PLCD4_ENST00000417849.1_Splice_Site_p.R325W|PLCD4_ENST00000432688.1_Splice_Site_p.R325W	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	325	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGGATATATACGGTGCAGTGG	0.517													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		20599	0.0		0.0089	False		,,,				2504	0.0031				p.R325W		Atlas-SNP	.											.	PLCD4	51	.	0			c.C973T						PASS	.	C	TRP/ARG	17,4047		0,17,2015	121.0	116.0	117.0		973	2.9	1.0	2	dbSNP_129	117	95,8281		1,93,4094	yes	missense-near-splice	PLCD4	NM_032726.3	101	1,110,6109	TT,TC,CC		1.1342,0.4183,0.9003	probably-damaging	325/763	219492952	112,12328	2032	4188	6220	SO:0001630	splice_region_variant	84812	exon7			TATATACGGTGCA	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.974+1C>T	2.37:g.219492952C>T		107.0	0.0	0		80.0	45.0	0.5625	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	17.58	3.425437	0.62733	0.004183	0.011342	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.64618	-0.11;-0.11;-0.11	4.7	2.91	0.33838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.112622	0.56097	N	0.000021	T	0.70613	0.3244	M	0.86651	2.83	0.38031	D	0.935157	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.74717	-0.3571	10	0.87932	D	0	.	4.4431	0.11584	0.2899:0.5284:0.0:0.1817	rs61733653	325;325	B7Z5V4;Q9BRC7	.;PLCD4_HUMAN	W	325	ENSP00000388631:R325W;ENSP00000396942:R325W;ENSP00000396185:R325W	ENSP00000251959:R325W	R	+	1	2	PLCD4	219201196	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	1.641000	0.37197	0.600000	0.29862	-0.262000	0.10625	CGG	C|0.994;T|0.006	0.006	strong		0.517	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		Missense_Mutation
USP48	84196	hgsc.bcm.edu	37	1	22033020	22033020	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22033020C>T	ENST00000308271.9	-	17	2799	c.2151G>A	c.(2149-2151)aaG>aaA	p.K717K	USP48_ENST00000374732.3_Silent_p.K255K|USP48_ENST00000400301.1_Silent_p.K717K|USP48_ENST00000529637.1_Silent_p.K729K	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	717	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		GGAGAGAAGTCTTTTGCTCGT	0.388																																					p.K717K		Atlas-SNP	.											USP48,colon,carcinoma,0,1	USP48	91	1	0			c.G2151A						PASS	.						131.0	133.0	132.0					1																	22033020		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon17			AGAAGTCTTTTGC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2151G>A	1.37:g.22033020C>T		198.0	0.0	0		199.0	63.0	0.316583	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			.	.	none		0.388	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
FAT3	120114	hgsc.bcm.edu	37	11	92088524	92088524	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:92088524C>T	ENST00000298047.6	+	1	3263	c.3246C>T	c.(3244-3246)atC>atT	p.I1082I	FAT3_ENST00000541502.1_Silent_p.I1082I|FAT3_ENST00000525166.1_Silent_p.I932I|FAT3_ENST00000409404.2_Silent_p.I1082I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1082	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGTACTCCATCAGGGATGGCA	0.463										TCGA Ovarian(4;0.039)																											p.I1082I		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3246T						PASS	.						108.0	105.0	106.0					11																	92088524		2055	4207	6262	SO:0001819	synonymous_variant	120114	exon1			CTCCATCAGGGAT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3246C>T	11.37:g.92088524C>T		114.0	0.0	0		102.0	32.0	0.313726	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
DTX1	1840	hgsc.bcm.edu	37	12	113496151	113496151	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496151C>G	ENST00000257600.3	+	1	657	c.154C>G	c.(154-156)Ctg>Gtg	p.L52V		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	52	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TGAGAACGTGCTGAAGGAGGA	0.647																																					p.L52V		Atlas-SNP	.											.	DTX1	83	.	0			c.C154G						PASS	.						121.0	106.0	111.0					12																	113496151		2203	4300	6503	SO:0001583	missense	1840	exon1			AACGTGCTGAAGG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.154C>G	12.37:g.113496151C>G	ENSP00000257600:p.Leu52Val	83.0	0.0	0		79.0	13.0	0.164557	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569791	0.65765	.	.	ENSG00000135144	ENST00000257600	T	0.46819	0.86	3.9	3.9	0.45041	WWE domain (2);WWE domain, subgroup (1);	0.093779	0.43919	U	0.000507	T	0.31606	0.0802	N	0.16478	0.41	0.39022	D	0.95976	B	0.29481	0.245	B	0.28305	0.088	T	0.19128	-1.0315	10	0.25106	T	0.35	-0.2273	14.8783	0.70513	0.0:1.0:0.0:0.0	.	52	Q86Y01	DTX1_HUMAN	V	52	ENSP00000257600:L52V	ENSP00000257600:L52V	L	+	1	2	DTX1	111980534	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.362000	0.52314	2.021000	0.59480	0.555000	0.69702	CTG	.	.	none		0.647	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
LRPPRC	10128	hgsc.bcm.edu	37	2	44201315	44201315	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201315A>T	ENST00000260665.7	-	9	1186	c.1129T>A	c.(1129-1131)Tta>Ata	p.L377I	LRPPRC_ENST00000409659.1_Missense_Mutation_p.L377I|LRPPRC_ENST00000409946.1_Missense_Mutation_p.L377I	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	377					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAGTGTTGTAAAAAGAAACTG	0.358																																					p.L377I		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1129A						PASS	.						98.0	96.0	97.0					2																	44201315		2203	4300	6503	SO:0001583	missense	10128	exon9			GTTGTAAAAAGAA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1129T>A	2.37:g.44201315A>T	ENSP00000260665:p.Leu377Ile	342.0	0.0	0		550.0	65.0	0.118182	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.901542	0.52227	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70399	0.32;0.26;0.29;-0.48	6.08	1.21	0.21127	.	0.000000	0.64402	D	0.000004	T	0.69753	0.3146	L	0.46157	1.445	0.47621	D	0.999471	P;B;D	0.67145	0.955;0.097;0.996	P;B;P	0.59703	0.753;0.054;0.862	T	0.64659	-0.6355	10	0.40728	T	0.16	-13.0937	4.796	0.13272	0.5914:0.0:0.2803:0.1283	.	277;351;377	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	I	277;377;377;377;351	ENSP00000260665:L377I;ENSP00000386234:L377I;ENSP00000386562:L377I;ENSP00000403637:L351I	ENSP00000260665:L377I	L	-	1	2	LRPPRC	44054819	1.000000	0.71417	0.456000	0.27044	0.944000	0.59088	3.419000	0.52728	0.194000	0.20326	0.482000	0.46254	TTA	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
DCLRE1C	64421	hgsc.bcm.edu	37	10	14987181	14987181	+	Missense_Mutation	SNP	C	C	A	rs138077101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:14987181C>A	ENST00000378278.2	-	3	206	c.169G>T	c.(169-171)Gtt>Ttt	p.V57F	DCLRE1C_ENST00000357717.2_Intron|DCLRE1C_ENST00000378249.1_5'UTR|DCLRE1C_ENST00000378255.1_5'UTR|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.V57F|DCLRE1C_ENST00000453695.2_5'UTR|DCLRE1C_ENST00000378258.1_5'UTR|DCLRE1C_ENST00000378254.1_5'UTR|DCLRE1C_ENST00000378246.2_5'UTR|DCLRE1C_ENST00000396817.2_5'UTR			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	57					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						TATAGATAAACCTTCAAGCTG	0.308								Non-homologous end-joining																													p.V57F		Atlas-SNP	.											.	DCLRE1C	136	.	0			c.G169T						PASS	.	C	PHE/VAL,,,	0,4406		0,0,2203	45.0	46.0	46.0		169,,,	5.2	1.0	10	dbSNP_134	46	8,8592	5.7+/-21.5	0,8,4292	yes	missense,utr-5,utr-5,utr-5	DCLRE1C	NM_001033855.1,NM_001033857.1,NM_001033858.1,NM_022487.2	50,,,	0,8,6495	AA,AC,CC		0.093,0.0,0.0615	probably-damaging,,,	57/693,,,	14987181	8,12998	2203	4300	6503	SO:0001583	missense	64421	exon3			GATAAACCTTCAA	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.169G>T	10.37:g.14987181C>A	ENSP00000367527:p.Val57Phe	138.0	0.0	0		117.0	53.0	0.452991	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843519	0.91197	0.0	9.3E-4	ENSG00000152457	ENST00000378289;ENST00000378278	T;T	0.76316	-1.01;-1.01	5.19	5.19	0.71726	Beta-lactamase-like (1);	0.115748	0.64402	D	0.000016	D	0.83774	0.5327	L	0.47078	1.49	0.80722	D	1	P;P	0.48350	0.897;0.909	P;P	0.60789	0.712;0.879	T	0.82967	-0.0194	10	0.44086	T	0.13	.	18.7242	0.91708	0.0:1.0:0.0:0.0	.	57;57	Q96SD1-4;Q96SD1	.;DCR1C_HUMAN	F	57	ENSP00000367538:V57F;ENSP00000367527:V57F	ENSP00000367527:V57F	V	-	1	0	DCLRE1C	15027187	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	2.687000	0.46976	2.604000	0.88044	0.573000	0.79308	GTT	C|1.000;A|0.000	0.000	strong		0.308	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	
INSR	3643	hgsc.bcm.edu	37	19	7150532	7150532	+	Missense_Mutation	SNP	G	G	A	rs143523271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7150532G>A	ENST00000302850.5	-	11	2385	c.2243C>T	c.(2242-2244)tCa>tTa	p.S748L	INSR_ENST00000341500.5_Intron	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	748					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACCAGTGCCTGAAGAGGTTTT	0.592																																					p.S748L		Atlas-SNP	.											.	INSR	265	.	0			c.C2243T						PASS	.	G	LEU/SER,	1,4405	2.1+/-5.4	0,1,2202	77.0	68.0	71.0		2243,	4.2	0.5	19	dbSNP_134	71	12,8588	9.1+/-34.3	0,12,4288	yes	missense,intron	INSR	NM_000208.2,NM_001079817.1	145,	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign,	748/1383,	7150532	13,12993	2203	4300	6503	SO:0001583	missense	3643	exon11			GTGCCTGAAGAGG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2243C>T	19.37:g.7150532G>A	ENSP00000303830:p.Ser748Leu	51.0	0.0	0		51.0	21.0	0.411765	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	G	5.384	0.256032	0.10185	2.27E-4	0.001395	ENSG00000171105	ENST00000302850	T	0.75704	-0.96	5.23	4.2	0.49525	Fibronectin, type III (2);	0.753844	0.10277	U	0.693994	T	0.63954	0.2555	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.54316	-0.8312	10	0.33940	T	0.23	.	9.578	0.39470	0.0959:0.0:0.9041:0.0	.	748	P06213	INSR_HUMAN	L	748	ENSP00000303830:S748L	ENSP00000303830:S748L	S	-	2	0	INSR	7101532	0.977000	0.34250	0.504000	0.27639	0.048000	0.14542	2.692000	0.47018	1.202000	0.43218	0.643000	0.83706	TCA	G|0.999;A|0.001	0.001	strong		0.592	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
PARL	55486	hgsc.bcm.edu	37	3	183551309	183551309	+	Silent	SNP	C	C	T	rs140027735		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183551309C>T	ENST00000317096.4	-	9	1059	c.999G>A	c.(997-999)gcG>gcA	p.A333A	PARL_ENST00000435888.1_Silent_p.A249A|PARL_ENST00000311101.5_Silent_p.A283A	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	333					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CAAGATGTGCCGCATGATCAA	0.488																																					p.A333A		Atlas-SNP	.											PARL,NS,carcinoma,-2,1	PARL	32	1	0			c.G999A						PASS	.						117.0	101.0	106.0					3																	183551309		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon9			ATGTGCCGCATGA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.999G>A	3.37:g.183551309C>T		272.0	0.0	0		249.0	79.0	0.317269	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.958|9.958	1.222020|1.222020	0.22457|0.22457	.|.	.|.	ENSG00000175193|ENSG00000175193	ENST00000417784|ENST00000418450	.|.	.|.	.|.	5.63|5.63	0.535|0.535	0.17133|0.17133	.|.	.|.	.|.	.|.	.|.	T|T	0.42131|0.42131	0.1189|0.1189	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24297|0.24297	-1.0164|-1.0164	4|4	.|.	.|.	.|.	-14.8538|-14.8538	1.496|1.496	0.02467|0.02467	0.1357:0.2209:0.1255:0.5179|0.1357:0.2209:0.1255:0.5179	.|.	.|.	.|.	.|.	S|Q	125|66	.|.	.|.	G|R	-|-	1|2	0|0	PARL|PARL	185034003|185034003	0.871000|0.871000	0.30034|0.30034	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	-0.009000|-0.009000	0.12765|0.12765	0.149000|0.149000	0.19098|0.19098	-0.238000|-0.238000	0.12139|0.12139	GGC|CGG	C|1.000;A|0.000	.	alt		0.488	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
SLC16A7	9194	hgsc.bcm.edu	37	12	60168491	60168491	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:60168491T>G	ENST00000261187.4	+	4	579	c.415T>G	c.(415-417)Ttc>Gtc	p.F139V	SLC16A7_ENST00000552024.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000547379.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000543448.1_Missense_Mutation_p.F40V|SLC16A7_ENST00000552432.1_Missense_Mutation_p.F139V	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	139					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	TGGCAAATACTTCTATAGGAA	0.398																																					p.F139V		Atlas-SNP	.											.	SLC16A7	82	.	0			c.T415G						PASS	.						77.0	73.0	74.0					12																	60168491		2203	4300	6503	SO:0001583	missense	9194	exon5			AAATACTTCTATA	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.415T>G	12.37:g.60168491T>G	ENSP00000261187:p.Phe139Val	257.0	0.0	0		209.0	44.0	0.210526	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592137	0.86953	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448;ENST00000548444	T;T;T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2;0.2;0.2	5.87	5.87	0.94306	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	H	0.95745	3.715	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	D	0.88302	0.2950	9	.	.	.	.	16.2631	0.82557	0.0:0.0:0.0:1.0	.	139	O60669	MOT2_HUMAN	V	139;139;139;139;139;40;24	ENSP00000449547:F139V;ENSP00000448071:F139V;ENSP00000448742:F139V;ENSP00000446722:F139V;ENSP00000261187:F139V;ENSP00000443731:F40V;ENSP00000447814:F24V	.	F	+	1	0	SLC16A7	58454758	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	8.040000	0.89188	2.239000	0.73571	0.528000	0.53228	TTC	.	.	none		0.398	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
TTC30A	92104	hgsc.bcm.edu	37	2	178482771	178482771	+	Missense_Mutation	SNP	C	C	T	rs59353759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178482771C>T	ENST00000355689.5	-	1	923	c.659G>A	c.(658-660)cGc>cAc	p.R220H	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	220					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AGGATGCTGGCGGATGCCACG	0.542													C|||	171	0.0341454	0.0408	0.013	5008	,	,		21101	0.0109		0.0199	False		,,,				2504	0.0787				p.R220H		Atlas-SNP	.											.	TTC30A	60	.	0			c.G659A						PASS	.	C	HIS/ARG	184,4222	119.6+/-157.3	4,176,2023	71.0	70.0	70.0		659	5.8	1.0	2	dbSNP_129	70	154,8446	73.8+/-136.5	2,150,4148	no	missense	TTC30A	NM_152275.3	29	6,326,6171	TT,TC,CC		1.7907,4.1761,2.5988	benign	220/666	178482771	338,12668	2203	4300	6503	SO:0001583	missense	92104	exon1			TGCTGGCGGATGC	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.659G>A	2.37:g.178482771C>T	ENSP00000347915:p.Arg220His	161.0	0.0	0		166.0	81.0	0.487952	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	40	0.018315018315018316	14	0.028455284552845527	7	0.019337016574585635	5	0.008741258741258742	14	0.018469656992084433	C	11.45	1.642016	0.29157	0.041761	0.017907	ENSG00000197557	ENST00000355689	T	0.21543	2.0	5.78	5.78	0.91487	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.138754	0.64402	D	0.000006	T	0.05731	0.0150	M	0.71920	2.185	0.51482	D	0.99992	B	0.28512	0.214	B	0.21917	0.037	T	0.01626	-1.1309	10	0.59425	D	0.04	.	9.433	0.38622	0.0:0.8764:0.0:0.1236	rs59353759;rs61997200	220	Q86WT1	TT30A_HUMAN	H	220	ENSP00000347915:R220H	ENSP00000347915:R220H	R	-	2	0	TTC30A	178191017	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	2.932000	0.48940	2.755000	0.94549	0.549000	0.68633	CGC	C|0.974;T|0.026	0.026	strong		0.542	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
MTSS1	9788	hgsc.bcm.edu	37	8	125568485	125568485	+	Silent	SNP	C	C	T	rs145509745		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125568485C>T	ENST00000518547.1	-	12	1865	c.1392G>A	c.(1390-1392)tcG>tcA	p.S464S	MTSS1_ENST00000524090.1_Silent_p.S354S|MTSS1_ENST00000325064.5_Silent_p.S468S|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Silent_p.S182S|MTSS1_ENST00000378017.3_Silent_p.S439S|MTSS1_ENST00000431961.2_Silent_p.S182S|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000395508.2_Silent_p.S238S	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	464					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGGTGGCAGCCGATACAGTCA	0.642																																					p.S464S	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.G1392A						PASS	.	C		0,4406		0,0,2203	78.0	66.0	70.0		1392	-6.7	0.8	8	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTSS1	NM_014751.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		464/756	125568485	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon12			GGCAGCCGATACA	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1392G>A	8.37:g.125568485C>T		149.0	0.0	0		131.0	68.0	0.519084	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	C	8.528	0.870352	0.17322	0.0	1.16E-4	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	4.65	-6.73	0.01749	.	.	.	.	.	T	0.37839	0.1018	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39663	-0.9603	4	.	.	.	-9.0128	3.2915	0.06950	0.2562:0.1322:0.0856:0.526	.	.	.	.	S	252;247	.	.	G	-	1	0	MTSS1	125637666	0.000000	0.05858	0.803000	0.32268	0.967000	0.64934	-3.210000	0.00556	-1.401000	0.02058	-0.538000	0.04264	GGC	C|1.000;T|0.000	0.000	weak		0.642	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
TLN2	83660	hgsc.bcm.edu	37	15	63111778	63111778	+	Missense_Mutation	SNP	G	G	A	rs138463845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63111778G>A	ENST00000561311.1	+	52	7065	c.6835G>A	c.(6835-6837)Ggc>Agc	p.G2279S	TLN2_ENST00000306829.6_Missense_Mutation_p.G2279S			Q9Y4G6	TLN2_HUMAN	talin 2	2279					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GCGAGTCGCCGGCGCTGTGAC	0.562													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		18034	0.0		0.005	False		,,,				2504	0.0				p.G2279S		Atlas-SNP	.											TLN2,NS,carcinoma,-2,2	TLN2	253	2	0			c.G6835A						scavenged	.	G	SER/GLY	8,4398	14.3+/-33.2	0,8,2195	57.0	60.0	59.0		6835	4.5	0.0	15	dbSNP_134	59	64,8536	39.3+/-95.6	0,64,4236	yes	missense	TLN2	NM_015059.2	56	0,72,6431	AA,AG,GG		0.7442,0.1816,0.5536	benign	2279/2543	63111778	72,12934	2203	4300	6503	SO:0001583	missense	83660	exon50			GTCGCCGGCGCTG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6835G>A	15.37:g.63111778G>A	ENSP00000453508:p.Gly2279Ser	45.0	2.0	0.0444444		49.0	29.0	0.591837	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	4.821	0.152577	0.09185	0.001816	0.007442	ENSG00000171914	ENST00000306829	T	0.64803	-0.12	5.38	4.46	0.54185	.	0.218055	0.45361	D	0.000378	T	0.23806	0.0576	N	0.02916	-0.46	0.09310	N	0.999999	B	0.14438	0.01	B	0.06405	0.002	T	0.15009	-1.0452	10	0.05620	T	0.96	-15.6397	10.7611	0.46266	0.2001:0.0:0.7999:0.0	.	2279	Q9Y4G6	TLN2_HUMAN	S	2279	ENSP00000303476:G2279S	ENSP00000303476:G2279S	G	+	1	0	TLN2	60898831	0.994000	0.37717	0.029000	0.17559	0.423000	0.31445	4.826000	0.62715	1.270000	0.44297	0.561000	0.74099	GGC	G|0.995;A|0.005	0.005	strong		0.562	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
PRF1	5551	hgsc.bcm.edu	37	10	72360457	72360457	+	Missense_Mutation	SNP	G	G	A	rs151232299		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72360457G>A	ENST00000441259.1	-	2	362	c.202C>T	c.(202-204)Cgg>Tgg	p.R68W	PRF1_ENST00000373209.2_Missense_Mutation_p.R68W	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	68	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CCGTCGGGCCGCAGGAACCTT	0.682			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.R68W		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,right_upper_lobe,carcinoma,+2,1	PRF1	64	1	0			c.C202T						PASS	.	G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	41.0	41.0	41.0		202,202	1.6	0.9	10	dbSNP_134	41	0,8600		0,0,4300	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	68/556,68/556	72360457	1,13005	2203	4300	6503	SO:0001583	missense	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CGGGCCGCAGGAA	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.202C>T	10.37:g.72360457G>A	ENSP00000398568:p.Arg68Trp	252.0	0.0	0		239.0	91.0	0.380753	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210912	0.58343	2.27E-4	0.0	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91740	-2.9;-2.9	5.7	1.58	0.23477	Membrane attack complex component/perforin (MACPF) domain (1);	0.257519	0.37530	N	0.002057	D	0.93523	0.7933	M	0.83692	2.655	0.18873	N	0.999984	D	0.89917	1.0	P	0.61722	0.893	D	0.86042	0.1520	10	0.87932	D	0	-20.3888	1.6559	0.02782	0.161:0.1295:0.3914:0.3181	.	68	P14222	PERF_HUMAN	W	68	ENSP00000362305:R68W;ENSP00000398568:R68W	ENSP00000316746:R68W	R	-	1	2	PRF1	72030463	0.000000	0.05858	0.910000	0.35882	0.562000	0.35680	0.342000	0.19926	0.014000	0.14944	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.682	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
BAI2	576	hgsc.bcm.edu	37	1	32221612	32221612	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:32221612C>T	ENST00000373658.3	-	4	1167	c.826G>A	c.(826-828)Gag>Aag	p.E276K	BAI2_ENST00000398538.1_Missense_Mutation_p.E264K|BAI2_ENST00000398542.1_Missense_Mutation_p.E264K|BAI2_ENST00000373655.2_Missense_Mutation_p.E276K|BAI2_ENST00000257070.4_Missense_Mutation_p.E276K|BAI2_ENST00000527361.1_Missense_Mutation_p.E276K|MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000398547.1_Missense_Mutation_p.E264K|BAI2_ENST00000398556.3_Missense_Mutation_p.E279K	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	276					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TATCTCATCTCGGTTGTGAAC	0.642																																					p.E276K		Atlas-SNP	.											.	BAI2	128	.	0			c.G826A						PASS	.						61.0	65.0	64.0					1																	32221612		2203	4300	6503	SO:0001583	missense	576	exon4			TCATCTCGGTTGT	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.826G>A	1.37:g.32221612C>T	ENSP00000362762:p.Glu276Lys	171.0	0.0	0		121.0	54.0	0.446281	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662416	0.29515	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T	0.44083	1.61;1.81;0.99;0.99;1.97;0.93;0.93;1.01;1.59;1.45	5.33	5.33	0.75918	.	0.000000	0.42053	D	0.000761	T	0.30479	0.0766	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.24426	0.103;0.06;0.012;0.012;0.001;0.007	B;B;B;B;B;B	0.15052	0.01;0.012;0.001;0.006;0.0;0.0	T	0.04870	-1.0921	10	0.29301	T	0.29	.	16.3081	0.82856	0.0:1.0:0.0:0.0	.	264;276;264;264;276;276	A2A3C3;O60241-4;O60241-3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	K	279;264;276;276;264;276;276;264;269;310	ENSP00000381564:E279K;ENSP00000381555:E264K;ENSP00000362762:E276K;ENSP00000362759:E276K;ENSP00000381550:E264K;ENSP00000257070:E276K;ENSP00000435397:E276K;ENSP00000381548:E264K;ENSP00000410921:E269K;ENSP00000437219:E310K	ENSP00000257070:E276K	E	-	1	0	BAI2	31994199	0.978000	0.34361	1.000000	0.80357	0.996000	0.88848	2.427000	0.44740	2.667000	0.90743	0.561000	0.74099	GAG	.	.	none		0.642	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
KIAA0930	23313	hgsc.bcm.edu	37	22	45608215	45608215	+	Intron	SNP	G	G	A	rs150665432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45608215G>A	ENST00000336156.5	-	2	130				KIAA0930_ENST00000496226.1_5'UTR|KIAA0930_ENST00000492273.1_Nonsense_Mutation_p.Q4*|KIAA0930_ENST00000443310.3_Intron|KIAA0930_ENST00000251993.7_Nonsense_Mutation_p.Q4*|KIAA0930_ENST00000391627.2_Intron	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930											endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						GCAGCAGCCTGAGAGCCCATG	0.637													G|||	10	0.00199681	0.0015	0.0029	5008	,	,		16127	0.0		0.004	False		,,,				2504	0.002				p.Q4X		Atlas-SNP	.											.	KIAA0930	43	.	0			c.C10T						PASS	.	G	,stop/GLN	3,4401	6.2+/-15.9	0,3,2199	32.0	32.0	32.0		,10	-1.5	0.0	22	dbSNP_134	32	35,8563	23.4+/-69.3	1,33,4265	yes	intron,stop-gained	KIAA0930	NM_001009880.1,NM_015264.1	,	1,36,6464	AA,AG,GG		0.4071,0.0681,0.2923	,	,4/410	45608215	38,12964	2202	4299	6501	SO:0001627	intron_variant	23313	exon1			CAGCCTGAGAGCC	AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 9"""	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.65-227C>T	22.37:g.45608215G>A		123.0	0.0	0		85.0	47.0	0.552941	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Nonsense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	1	0.0017482517482517483	5	0.006596306068601583	G	15.73	2.919233	0.52546	6.81E-4	0.004071	ENSG00000100364	ENST00000251993	.	.	.	2.41	-1.47	0.08772	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	4.8647	0.13602	0.1506:0.3861:0.4633:0.0	.	.	.	.	X	4	.	ENSP00000251993:Q4X	Q	-	1	0	KIAA0930	43986879	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.788000	0.04614	-0.192000	0.10432	-0.258000	0.10820	CAG	G|0.996;A|0.004	0.004	strong		0.637	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880	
FAT2	2196	hgsc.bcm.edu	37	5	150930205	150930205	+	Silent	SNP	C	C	T	rs35489594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150930205C>T	ENST00000261800.5	-	7	4536	c.4524G>A	c.(4522-4524)acG>acA	p.T1508T		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1508	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTTTCCCACCGTTACCAGGA	0.522													C|||	6	0.00119808	0.0	0.0014	5008	,	,		21811	0.0		0.004	False		,,,				2504	0.001				p.T1508T		Atlas-SNP	.											.	FAT2	465	.	0			c.G4524A						PASS	.	C		11,4395	15.5+/-35.6	0,11,2192	96.0	87.0	90.0		4524	-10.5	0.8	5	dbSNP_126	90	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	FAT2	NM_001447.2		0,84,6419	TT,TC,CC		0.8488,0.2497,0.6459		1508/4350	150930205	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon7			TCCCACCGTTACC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.4524G>A	5.37:g.150930205C>T		142.0	0.0	0		134.0	60.0	0.447761	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.995;T|0.005	0.005	strong		0.522	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
LIMK1	3984	hgsc.bcm.edu	37	7	73520264	73520264	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73520264T>C	ENST00000336180.2	+	6	719	c.668T>C	c.(667-669)aTc>aCc	p.I223T	LIMK1_ENST00000418310.1_Missense_Mutation_p.I253T|LIMK1_ENST00000538333.3_Missense_Mutation_p.I189T	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	223	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	GGAGACCGGATCTTGGAAATC	0.607																																					p.I223T		Atlas-SNP	.											.	LIMK1	55	.	0			c.T668C						PASS	.						104.0	89.0	94.0					7																	73520264		2203	4300	6503	SO:0001583	missense	3984	exon6			ACCGGATCTTGGA	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.668T>C	7.37:g.73520264T>C	ENSP00000336740:p.Ile223Thr	81.0	0.0	0		78.0	16.0	0.205128	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363859	0.82353	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.97	4.97	0.65823	PDZ/DHR/GLGF (4);	0.051007	0.85682	D	0.000000	T	0.71685	0.3369	M	0.81341	2.54	0.80722	D	1	P;D;D	0.63046	0.852;0.992;0.992	B;D;D	0.68483	0.433;0.958;0.958	T	0.76356	-0.2989	10	0.87932	D	0	-30.7731	12.6805	0.56918	0.0:0.0:0.0:1.0	.	118;189;223	Q59FA3;B7Z6I8;P53667	.;.;LIMK1_HUMAN	T	253;223;223;189;189	ENSP00000409717:I253T;ENSP00000336740:I223T;ENSP00000396480:I189T;ENSP00000444452:I189T	ENSP00000336740:I223T	I	+	2	0	LIMK1	73158200	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.676000	0.84012	1.898000	0.54952	0.524000	0.50904	ATC	.	.	none		0.607	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:136834138T>C	ENST00000394945.1	-	2	279	c.110A>G	c.(109-111)aAt>aGt	p.N37S	SPOCK1_ENST00000282223.7_Missense_Mutation_p.N37S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	37					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTCTAGGAAATTGCCGTGGTT	0.682													T|||	19	0.00379393	0.0	0.0058	5008	,	,		9286	0.0		0.0129	False		,,,				2504	0.002				p.N37S		Atlas-SNP	.											.	SPOCK1	58	.	0			c.A110G						PASS	.	T	SER/ASN	9,4397		0,9,2194	22.0	21.0	22.0		110	3.7	1.0	5	dbSNP_132	22	106,8492		3,100,4196	yes	missense	SPOCK1	NM_004598.3	46	3,109,6390	CC,CT,TT		1.2328,0.2043,0.8843	benign	37/440	136834138	115,12889	2203	4299	6502	SO:0001583	missense	6695	exon2			AGGAAATTGCCGT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.110A>G	5.37:g.136834138T>C	ENSP00000378401:p.Asn37Ser	43.0	0.0	0		40.0	23.0	0.575	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	24.2	4.510460	0.85389	0.002043	0.012328	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.58940	0.3;0.3;0.34	3.66	3.66	0.41972	.	0.344437	0.23803	N	0.044419	T	0.33498	0.0865	L	0.51914	1.62	0.27215	N	0.959807	B	0.15930	0.015	B	0.14578	0.011	T	0.44112	-0.9349	10	0.56958	D	0.05	.	10.3639	0.44012	0.0:0.0:0.0:1.0	.	37	Q08629	TICN1_HUMAN	S	37	ENSP00000378401:N37S;ENSP00000282223:N37S;ENSP00000424517:N37S	ENSP00000282223:N37S	N	-	2	0	SPOCK1	136862037	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.481000	0.53179	1.439000	0.47511	0.379000	0.24179	AAT	T|0.991;C|0.009	0.009	strong		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062222	144062222	+	Silent	SNP	G	G	A	rs201478085		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:144062222G>A	ENST00000056217.5	+	2	2634	c.2460G>A	c.(2458-2460)ccG>ccA	p.P820P	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	820					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P820P(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					CTGATTTGCCGCAGCCCCACC	0.607																																					p.P820P		Atlas-SNP	.											ARHGEF5,NS,carcinoma,+2,2	ARHGEF5	73	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G2460A						scavenged	.						2.0	3.0	3.0					7																	144062222		1307	2929	4236	SO:0001819	synonymous_variant	7984	exon2			TTTGCCGCAGCCC	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.2460G>A	7.37:g.144062222G>A		165.0	0.0	0		151.0	27.0	0.178808	NM_005435	A6NNJ2|Q6ZML7	Silent	SNP	ENST00000056217.5	37	CCDS34771.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.555218	0.00918	.	.	ENSG00000050327	ENST00000474817	.	.	.	3.89	-7.77	0.01227	.	.	.	.	.	T	0.16171	0.0389	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	T	0.16129	-1.0413	4	.	.	.	0.9342	2.0231	0.03513	0.2015:0.1496:0.4066:0.2422	.	.	.	.	H	74	.	.	R	+	2	0	ARHGEF5	143693155	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.255000	0.00538	-2.388000	0.00588	-1.365000	0.01206	CGC	G|0.995;A|0.005	0.005	weak		0.607	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
PTPRN2	5799	hgsc.bcm.edu	37	7	157929370	157929370	+	Missense_Mutation	SNP	C	C	T	rs55645575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157929370C>T	ENST00000389418.4	-	8	1159	c.1150G>A	c.(1150-1152)Gac>Aac	p.D384N	PTPRN2_ENST00000404321.2_Missense_Mutation_p.D407N|PTPRN2_ENST00000389416.4_Missense_Mutation_p.D367N|PTPRN2_ENST00000389413.3_Missense_Mutation_p.D384N|PTPRN2_ENST00000409483.1_Missense_Mutation_p.D346N	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	384					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTATCATCGTCGTCCTGCACT	0.443													C|||	27	0.00539137	0.0	0.0072	5008	,	,		17715	0.0		0.0159	False		,,,				2504	0.0061				p.D384N		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G1150A						PASS	.		ASN/ASP,ASN/ASP,ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	194.0	151.0	166.0		1150,1099,1150	-0.7	0.0	7	dbSNP_129	166	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	23,23,23	1,141,6361	TT,TC,CC		1.5116,0.2951,1.0995	benign,benign,benign	384/1016,367/999,384/987	157929370	143,12863	2203	4300	6503	SO:0001583	missense	5799	exon8			CATCGTCGTCCTG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1150G>A	7.37:g.157929370C>T	ENSP00000374069:p.Asp384Asn	99.0	0.0	0		88.0	32.0	0.363636	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	4.357	0.065672	0.08388	0.002951	0.015116	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.13;4.11;4.13;4.13;4.12	4.47	-0.709	0.11237	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.002;0.003;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.001	T	0.49194	-0.8965	9	0.17832	T	0.49	.	4.3322	0.11069	0.1523:0.4773:0.0:0.3704	rs55645575	407;346;384;367;384	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	N	346;384;367;384;407	ENSP00000387114:D346N;ENSP00000374064:D384N;ENSP00000374067:D367N;ENSP00000374069:D384N;ENSP00000385464:D407N	ENSP00000374064:D384N	D	-	1	0	PTPRN2	157622131	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.080000	0.14802	-0.123000	0.11745	-1.747000	0.00681	GAC	C|0.989;T|0.011	0.011	strong		0.443	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PRR11	55771	hgsc.bcm.edu	37	17	57247133	57247133	+	Missense_Mutation	SNP	G	G	A	rs145780567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:57247133G>A	ENST00000262293.4	+	2	332	c.20G>A	c.(19-21)cGa>cAa	p.R7Q		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	7						cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TTCAAACAACGAAGACGAAAG	0.338													G|||	15	0.00299521	0.0	0.0058	5008	,	,		14982	0.001		0.0099	False		,,,				2504	0.0				p.R7Q		Atlas-SNP	.											PRR11,NS,carcinoma,+1,1	PRR11	36	1	0			c.G20A						PASS	.	G	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	62.0	60.0	61.0		20	1.2	0.4	17	dbSNP_134	61	78,8522	43.6+/-101.6	0,78,4222	yes	missense	PRR11	NM_018304.3	43	0,89,6414	AA,AG,GG		0.907,0.2497,0.6843	benign	7/361	57247133	89,12917	2203	4300	6503	SO:0001583	missense	55771	exon2			AACAACGAAGACG		CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.20G>A	17.37:g.57247133G>A	ENSP00000262293:p.Arg7Gln	101.0	0.0	0		86.0	47.0	0.546512	NM_018304	Q9NUZ7|Q9NXE9	Missense_Mutation	SNP	ENST00000262293.4	37	CCDS11614.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	G	4.777	0.144546	0.09134	0.002497	0.00907	ENSG00000068489	ENST00000262293	.	.	.	4.38	1.17	0.20885	.	0.450854	0.18874	N	0.128767	T	0.19765	0.0475	L	0.32530	0.975	0.18873	N	0.999986	B	0.23490	0.086	B	0.14578	0.011	T	0.12319	-1.0552	9	0.49607	T	0.09	-2.239	6.1076	0.20081	0.3479:0.0:0.6521:0.0	.	7	Q96HE9	PRR11_HUMAN	Q	7	.	ENSP00000262293:R7Q	R	+	2	0	PRR11	54601915	1.000000	0.71417	0.357000	0.25798	0.008000	0.06430	0.486000	0.22340	0.182000	0.20032	0.561000	0.74099	CGA	G|0.994;A|0.006	0.006	strong		0.338	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304	
OR9G1	390174	hgsc.bcm.edu	37	11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	rs78340277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186.0	171.0	176.0		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	257.0	0.0	0		227.0	85.0	0.374449	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
FAM208B	54906	hgsc.bcm.edu	37	10	5803349	5803349	+	Silent	SNP	A	A	C	rs543461908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5803349A>C	ENST00000328090.5	+	19	7714	c.7089A>C	c.(7087-7089)cgA>cgC	p.R2363R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2363																	GTGACTCTCGATCATCAACAA	0.388																																					p.R2363R		Atlas-SNP	.											C10orf18,NS,carcinoma,+2,2	.	.	2	0			c.A7089C						PASS	.						128.0	120.0	122.0					10																	5803349		1889	4118	6007	SO:0001819	synonymous_variant	54906	exon19			CTCTCGATCATCA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7089A>C	10.37:g.5803349A>C		119.0	0.0	0		120.0	28.0	0.233333	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	37	CCDS41485.1																																																																																			.	.	none		0.388	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
ING4	51147	hgsc.bcm.edu	37	12	6760367	6760367	+	Silent	SNP	C	C	T	rs76327967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6760367C>T	ENST00000396807.4	-	8	782	c.744G>A	c.(742-744)aaG>aaA	p.K248K	ING4_ENST00000486287.1_5'UTR|ING4_ENST00000412586.2_Silent_p.K245K|ING4_ENST00000341550.4_Silent_p.K247K|ING4_ENST00000446105.2_Silent_p.K244K|ING4_ENST00000444704.2_Silent_p.K224K|ING4_ENST00000423703.2_3'UTR	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4	248					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						TTATCTATTTCTTCTTCCGTT	0.527													C|||	361	0.0720847	0.1815	0.0677	5008	,	,		20926	0.0179		0.0298	False		,,,				2504	0.0266				p.K248K		Atlas-SNP	.											.	ING4	31	.	0			c.G744A						PASS	.	C	,,,,,	762,3644	310.0+/-291.3	54,654,1495	98.0	89.0	92.0		744,735,732,672,,741	4.0	1.0	12	dbSNP_131	92	327,8273	113.5+/-173.5	4,319,3977	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	ING4	NM_001127582.1,NM_001127583.1,NM_001127584.1,NM_001127585.1,NM_001127586.1,NM_016162.3	,,,,,	58,973,5472	TT,TC,CC		3.8023,17.2946,8.3731	,,,,,	248/250,245/247,244/246,224/226,,247/249	6760367	1089,11917	2203	4300	6503	SO:0001819	synonymous_variant	51147	exon8			CTATTTCTTCTTC	AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"""Zinc fingers, PHD-type"""	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.744G>A	12.37:g.6760367C>T		131.0	0.0	0		110.0	45.0	0.409091	NM_001127582	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Silent	SNP	ENST00000396807.4	37	CCDS44813.1																																																																																			C|0.923;T|0.077	0.077	strong		0.527	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287	
PIGW	284098	hgsc.bcm.edu	37	17	34893655	34893655	+	Missense_Mutation	SNP	C	C	G	rs61755368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34893655C>G	ENST00000592983.1	+	2	1285	c.705C>G	c.(703-705)caC>caG	p.H235Q	MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000586007.1_5'Flank|PIGW_ENST00000328396.2_Missense_Mutation_p.H235Q|MYO19_ENST00000431794.3_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	235					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATGGAGTTCACTGGAACTTTT	0.368													C|||	5	0.000998403	0.0	0.0	5008	,	,		20498	0.0		0.005	False		,,,				2504	0.0				p.H235Q		Atlas-SNP	.											.	PIGW	50	.	0			c.C705G						PASS	.	C	GLN/HIS	6,4390	9.9+/-24.2	0,6,2192	75.0	79.0	77.0		705	2.7	1.0	17	dbSNP_129	77	60,8538	35.3+/-89.8	0,60,4239	yes	missense	PIGW	NM_178517.3	24	0,66,6431	GG,GC,CC		0.6978,0.1365,0.5079	probably-damaging	235/505	34893655	66,12928	2198	4299	6497	SO:0001583	missense	284098	exon2			AGTTCACTGGAAC	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"""Phosphatidylinositol glycan anchor biosynthesis"""	23213	protein-coding gene	gene with protein product		610275	"""phosphatidylinositol glycan, class W"""			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.705C>G	17.37:g.34893655C>G	ENSP00000468778:p.His235Gln	125.0	0.0	0		114.0	57.0	0.5	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	37	CCDS11313.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	16.95	3.262679	0.59431	0.001365	0.006978	ENSG00000184886	ENST00000328396	.	.	.	5.79	2.71	0.32032	.	0.000000	0.85682	D	0.000000	T	0.76543	0.4002	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82206	-0.0572	8	.	.	.	-6.0044	10.914	0.47124	0.0:0.793:0.0:0.207	rs61755368	235	Q7Z7B1	PIGW_HUMAN	Q	235	.	.	H	+	3	2	PIGW	31967768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.970000	0.29383	0.802000	0.34089	0.561000	0.74099	CAC	C|0.995;G|0.005	0.005	strong		0.368	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517	
S100PBP	64766	hgsc.bcm.edu	37	1	33292008	33292008	+	Missense_Mutation	SNP	G	G	A	rs61739743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33292008G>A	ENST00000373475.5	+	3	562	c.308G>A	c.(307-309)aGc>aAc	p.S103N	S100PBP_ENST00000398243.3_Missense_Mutation_p.S103N|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000373476.1_Missense_Mutation_p.S103N	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TCATCGTACAGCCTGGGACCA	0.473													G|||	35	0.00698882	0.0182	0.0072	5008	,	,		19748	0.0		0.006	False		,,,				2504	0.0				p.S103N		Atlas-SNP	.											.	S100PBP	31	.	0			c.G308A						PASS	.	G	ASN/SER,ASN/SER	72,4334	62.3+/-99.4	1,70,2132	56.0	52.0	53.0		308,308	0.1	0.1	1	dbSNP_129	53	65,8535	39.8+/-96.3	0,65,4235	yes	missense,missense	S100PBP	NM_001017406.1,NM_022753.2	46,46	1,135,6367	AA,AG,GG		0.7558,1.6341,1.0534	benign,benign	103/342,103/409	33292008	137,12869	2203	4300	6503	SO:0001583	missense	64766	exon3			CGTACAGCCTGGG	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"""S100P binding protein 1"""	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.308G>A	1.37:g.33292008G>A	ENSP00000362574:p.Ser103Asn	110.0	0.0	0		82.0	36.0	0.439024	NM_001256121		Missense_Mutation	SNP	ENST00000373475.5	37	CCDS30666.1	16	0.007326007326007326	11	0.022357723577235773	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.857	0.159396	0.09236	0.016341	0.007558	ENSG00000116497	ENST00000530710;ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689;ENST00000526230;ENST00000531256;ENST00000482212	.	.	.	5.32	0.136	0.14780	.	0.673278	0.15732	N	0.247367	T	0.12860	0.0312	N	0.20986	0.625	0.09310	N	0.999997	B;B	0.19583	0.037;0.008	B;B	0.22386	0.039;0.009	T	0.12066	-1.0562	9	0.45353	T	0.12	-0.1643	5.5651	0.17167	0.2246:0.2654:0.51:0.0	rs61739743	103;103	A8MTZ6;Q96BU1	.;S1PBP_HUMAN	N	103	.	ENSP00000349117:S103N	S	+	2	0	S100PBP	33064595	0.603000	0.26924	0.082000	0.20525	0.073000	0.16967	0.412000	0.21131	-0.034000	0.13713	0.655000	0.94253	AGC	G|0.990;A|0.010	0.010	strong		0.473	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753	
IGFN1	91156	hgsc.bcm.edu	37	1	201163305	201163305	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs189690117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163305C>A	ENST00000295591.8	+	0	161				IGFN1_ENST00000335211.4_Missense_Mutation_p.P11T|IGFN1_ENST00000451870.2_Missense_Mutation_p.P11T			Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1							nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GTCCCACATCCCTGGAGTGAG	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18650	0.0		0.004	False		,,,				2504	0.0				p.P11T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C31A						PASS	.						30.0	36.0	34.0					1																	201163305		692	1591	2283			91156	exon3			CACATCCCTGGAG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000295591.8:c.-8490C>A	1.37:g.201163305C>A		123.0	0.0	0		116.0	116.0	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000295591.8	37		2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	15.73	2.921085	0.52653	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.63096	0.23;-0.02	4.55	4.55	0.56014	.	.	.	.	.	T	0.69287	0.3094	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.72620	-0.4238	7	0.62326	D	0.03	.	14.2363	0.65929	0.0:1.0:0.0:0.0	.	.	.	.	T	11	ENSP00000334714:P11T;ENSP00000398386:P11T	ENSP00000334714:P11T	P	+	1	0	IGFN1	199429928	0.289000	0.24334	0.730000	0.30809	0.517000	0.34286	2.800000	0.47900	2.058000	0.61347	0.637000	0.83480	CCT	C|0.999;A|0.001	0.001	strong		0.607	IGFN1-201	KNOWN	basic	protein_coding	protein_coding		NM_178275	
NFIX	4784	hgsc.bcm.edu	37	19	13183882	13183882	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13183882C>G	ENST00000592199.1	+	3	581	c.581C>G	c.(580-582)tCa>tGa	p.S194*	NFIX_ENST00000585575.1_Nonsense_Mutation_p.S186*|NFIX_ENST00000587760.1_Nonsense_Mutation_p.S186*|NFIX_ENST00000358552.3_Nonsense_Mutation_p.S193*|NFIX_ENST00000397661.2_Nonsense_Mutation_p.S194*|NFIX_ENST00000360105.4_Nonsense_Mutation_p.S197*|NFIX_ENST00000587260.1_Nonsense_Mutation_p.S193*|AC007787.2_ENST00000588095.1_RNA|NFIX_ENST00000588228.1_Nonsense_Mutation_p.S147*|NFIX_ENST00000588680.1_3'UTR			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	194					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			TCAGATAGTTCAAACCAGCAA	0.557																																					p.S202X		Atlas-SNP	.											.	NFIX	61	.	0			c.C605G						PASS	.						142.0	144.0	143.0					19																	13183882		2032	4166	6198	SO:0001587	stop_gained	4784	exon3			ATAGTTCAAACCA	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.581C>G	19.37:g.13183882C>G	ENSP00000467512:p.Ser194*	120.0	0.0	0		105.0	27.0	0.257143	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Nonsense_Mutation	SNP	ENST00000592199.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.568508	0.96540	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000438869;ENST00000358552	.	.	.	4.59	4.59	0.56863	.	0.156010	0.44483	D	0.000442	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	14.6799	0.69009	0.0:1.0:0.0:0.0	.	.	.	.	X	194;194;197;147;193	.	ENSP00000264825:S197X	S	+	2	0	NFIX	13044882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.505000	0.73708	2.280000	0.76307	0.462000	0.41574	TCA	.	.	none		0.557	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501	
C8orf74	203076	hgsc.bcm.edu	37	8	10532188	10532188	+	Silent	SNP	T	T	C	rs61729951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10532188T>C	ENST00000304519.5	+	2	110	c.81T>C	c.(79-81)ctT>ctC	p.L27L	RP1L1_ENST00000329335.3_Intron|C8orf74_ENST00000524025.1_3'UTR	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	27										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGCGGAGGCTTCTGAACTGGG	0.577													T|||	23	0.00459265	0.0008	0.0072	5008	,	,		16259	0.0		0.0149	False		,,,				2504	0.002				p.L27L		Atlas-SNP	.											.	C8orf74	28	.	0			c.T81C						PASS	.	T		17,3793		0,17,1888	39.0	43.0	42.0		81	-1.6	0.4	8	dbSNP_129	42	163,8101		3,157,3972	no	coding-synonymous	C8orf74	NM_001040032.1		3,174,5860	CC,CT,TT		1.9724,0.4462,1.4908		27/295	10532188	180,11894	1905	4132	6037	SO:0001819	synonymous_variant	203076	exon2			GAGGCTTCTGAAC	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.81T>C	8.37:g.10532188T>C		144.0	0.0	0		137.0	105.0	0.766423	NM_001040032	A2RUD6	Silent	SNP	ENST00000304519.5	37	CCDS47800.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	1.640	-0.516781	0.04200	0.004462	0.019724	ENSG00000171060	ENST00000521818	.	.	.	5.06	-1.65	0.08291	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26950	-1.0088	4	.	.	.	.	7.5808	0.27963	0.0:0.3943:0.3278:0.2779	rs61729951	.	.	.	P	26	.	.	S	+	1	0	C8orf74	10569598	0.002000	0.14202	0.397000	0.26308	0.201000	0.24016	-0.558000	0.05978	-0.316000	0.08690	-0.495000	0.04643	TCT	T|0.992;C|0.008	0.008	strong		0.577	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
FAR1	84188	hgsc.bcm.edu	37	11	13743325	13743325	+	Silent	SNP	A	A	G	rs34341612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:13743325A>G	ENST00000354817.3	+	10	1320	c.1176A>G	c.(1174-1176)gaA>gaG	p.E392E	FAR1_ENST00000532502.1_Silent_p.E16E	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	392					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						TGTTTCTTGAATATTTCACAA	0.303													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		16434	0.0		0.0119	False		,,,				2504	0.0143				p.E392E		Atlas-SNP	.											.	FAR1	40	.	0			c.A1176G						PASS	.	A		9,4387	15.5+/-35.6	0,9,2189	85.0	84.0	84.0		1176	0.2	1.0	11	dbSNP_126	84	123,8459	63.5+/-125.6	0,123,4168	no	coding-synonymous	FAR1	NM_032228.5		0,132,6357	GG,GA,AA		1.4332,0.2047,1.0171		392/516	13743325	132,12846	2198	4291	6489	SO:0001819	synonymous_variant	84188	exon10			TCTTGAATATTTC	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	26222	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 1"""		"""male sterility domain containing 2"""	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.1176A>G	11.37:g.13743325A>G		70.0	0.0	0		49.0	32.0	0.653061	NM_032228	D3DQW8|Q5CZA3	Silent	SNP	ENST00000354817.3	37	CCDS7813.1																																																																																			A|0.990;G|0.010	0.010	strong		0.303	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228	
STOX1	219736	hgsc.bcm.edu	37	10	70641785	70641785	+	Missense_Mutation	SNP	T	T	C	rs377656965		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70641785T>C	ENST00000298596.6	+	2	465	c.382T>C	c.(382-384)Tgt>Cgt	p.C128R	STOX1_ENST00000399165.4_Missense_Mutation_p.C128R|STOX1_ENST00000421961.2_Missense_Mutation_p.C18R|STOX1_ENST00000399162.2_Missense_Mutation_p.C128R|STOX1_ENST00000399169.4_Missense_Mutation_p.C128R	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	128						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGTTCTTTGCTGTGCTATATC	0.368																																					p.C128R		Atlas-SNP	.											.	STOX1	75	.	0			c.T382C						PASS	.	T	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	0,3730		0,0,1865	166.0	152.0	156.0		382,382,382,52,382	5.6	1.0	10		156	1,8199		0,1,4099	no	missense,missense,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	180,180,180,180,180	0,1,5964	CC,CT,TT		0.0122,0.0,0.0084	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	128/228,128/170,128/990,18/880,128/990	70641785	1,11929	1865	4100	5965	SO:0001583	missense	219736	exon2			CTTTGCTGTGCTA	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.382T>C	10.37:g.70641785T>C	ENSP00000298596:p.Cys128Arg	175.0	0.0	0		160.0	73.0	0.45625	NM_001130160	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328142	0.41197	0.0	1.22E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000399165;ENST00000399162;ENST00000421961	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.57	5.57	0.84162	Storkhead-box protein, winged-helix domain (1);	0.149142	0.45867	U	0.000336	T	0.68970	0.3059	L	0.36672	1.1	0.80722	D	1	P;P;P	0.48503	0.627;0.911;0.627	B;P;B	0.45753	0.216;0.492;0.14	T	0.72381	-0.4311	10	0.59425	D	0.04	.	11.934	0.52864	0.0:0.0702:0.0:0.9298	.	128;128;128	Q6ZVD7-3;Q6ZVD7;Q6ZVD7-2	.;STOX1_HUMAN;.	R	128;128;128;128;18	ENSP00000382121:C128R;ENSP00000298596:C128R;ENSP00000382118:C128R;ENSP00000382115:C128R;ENSP00000394509:C18R	ENSP00000298596:C128R	C	+	1	0	STOX1	70311791	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.709000	0.47160	2.242000	0.73789	0.482000	0.46254	TGT	.	.	none		0.368	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
DIAPH3	81624	hgsc.bcm.edu	37	13	60413550	60413550	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:60413550G>T	ENST00000400324.4	-	23	2990	c.2770C>A	c.(2770-2772)Cag>Aag	p.Q924K	DIAPH3_ENST00000400319.1_Missense_Mutation_p.Q854K|DIAPH3_ENST00000267215.4_Missense_Mutation_p.Q924K|DIAPH3_ENST00000377908.2_Missense_Mutation_p.Q913K|DIAPH3_ENST00000400330.1_Missense_Mutation_p.Q924K|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.Q878K	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	924	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CTTCCCATCTGCCTCAAATTC	0.403																																					p.Q924K		Atlas-SNP	.											.	DIAPH3	139	.	0			c.C2770A						PASS	.						82.0	77.0	79.0					13																	60413550		1842	4094	5936	SO:0001583	missense	81624	exon23			CCATCTGCCTCAA	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2770C>A	13.37:g.60413550G>T	ENSP00000383178:p.Gln924Lys	68.0	0.0	0		52.0	10.0	0.192308	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470488	0.84533	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	T;T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37;2.37	5.19	5.19	0.71726	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.058535	0.64402	D	0.000001	T	0.29223	0.0727	L	0.58969	1.84	0.51482	D	0.999927	B;D	0.55605	0.014;0.972	B;P	0.49361	0.01;0.608	T	0.01397	-1.1365	10	0.48119	T	0.1	.	19.0719	0.93143	0.0:0.0:1.0:0.0	.	661;924	Q9NSV4-1;Q9NSV4	.;DIAP3_HUMAN	K	924;924;913;878;854;913;854;878;924;661;924	ENSP00000383178:Q924K;ENSP00000383184:Q924K;ENSP00000367141:Q913K;ENSP00000383173:Q854K;ENSP00000383174:Q878K;ENSP00000267215:Q924K	ENSP00000267214:Q661K	Q	-	1	0	DIAPH3	59311551	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.414000	0.97362	2.585000	0.87301	0.591000	0.81541	CAG	.	.	none		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559058	140559058	+	Silent	SNP	G	G	A	rs17844495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559058G>A	ENST00000239444.2	+	1	1688	c.1443G>A	c.(1441-1443)tcG>tcA	p.S481S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	481	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAGAGACTCGGGCACCAACG	0.662																																					p.S481S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G1443A						PASS	.						85.0	131.0	115.0					5																	140559058		2203	4296	6499	SO:0001819	synonymous_variant	56128	exon1			AGACTCGGGCACC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1443G>A	5.37:g.140559058G>A		228.0	0.0	0		261.0	41.0	0.157088	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			G|0.680;A|0.320	0.320	strong		0.662	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TGM7	116179	hgsc.bcm.edu	37	15	43569097	43569097	+	Missense_Mutation	SNP	C	C	T	rs146833656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43569097C>T	ENST00000452443.2	-	12	1940	c.1936G>A	c.(1936-1938)Gaa>Aaa	p.E646K		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	646					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CCGCTTCCTTCCAGCACCATC	0.592													C|||	12	0.00239617	0.0008	0.0086	5008	,	,		21418	0.0		0.004	False		,,,				2504	0.001				p.E646K		Atlas-SNP	.											.	TGM7	86	.	0			c.G1936A						PASS	.	C	LYS/GLU	15,4389	22.3+/-47.3	0,15,2187	111.0	90.0	97.0		1936	5.1	1.0	15	dbSNP_134	97	104,8494	56.8+/-118.0	0,104,4195	yes	missense	TGM7	NM_052955.2	56	0,119,6382	TT,TC,CC		1.2096,0.3406,0.9152	probably-damaging	646/711	43569097	119,12883	2202	4299	6501	SO:0001583	missense	116179	exon12			TTCCTTCCAGCAC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1936G>A	15.37:g.43569097C>T	ENSP00000389466:p.Glu646Lys	69.0	0.0	0		84.0	63.0	0.75	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	23.4	4.409135	0.83340	0.003406	0.012096	ENSG00000159495	ENST00000452443	T	0.37584	1.19	5.13	5.13	0.70059	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.233909	0.35378	N	0.003260	T	0.55273	0.1910	M	0.86864	2.845	0.44668	D	0.997653	D	0.67145	0.996	D	0.63192	0.912	T	0.68443	-0.5407	10	0.72032	D	0.01	-23.3696	16.0633	0.80853	0.0:1.0:0.0:0.0	.	646	Q96PF1	TGM7_HUMAN	K	646	ENSP00000389466:E646K	ENSP00000389466:E646K	E	-	1	0	TGM7	41356389	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.641000	0.67881	2.375000	0.81037	0.585000	0.79938	GAA	C|0.992;T|0.008	0.008	strong		0.592	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
SOCS1	8651	hgsc.bcm.edu	37	16	11348810	11348810	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11348810C>T	ENST00000332029.2	-	2	676	c.526G>A	c.(526-528)Gag>Aag	p.E176K	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	176	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.Y64fs*1(1)|p.R127_*212del(1)|p.V171_R179del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CGGCACAGCTCCTGCAGCGGC	0.726			"""F, O"""		"""Hodgkin Lymphoma, PMBL"""																																p.E176K	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,+2,1	SOCS1	84	1	7	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(7)	c.G526A						PASS	.						6.0	7.0	7.0					16																	11348810		2122	4174	6296	SO:0001583	missense	8651	exon2			ACAGCTCCTGCAG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.526G>A	16.37:g.11348810C>T	ENSP00000329418:p.Glu176Lys	12.0	0.0	0		17.0	11.0	0.647059	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.726616	0.89298	.	.	ENSG00000185338	ENST00000332029	T	0.45276	0.9	4.13	4.13	0.48395	SOCS protein, C-terminal (4);	0.126789	0.51477	U	0.000085	T	0.56746	0.2006	M	0.77616	2.38	0.53688	D	0.999977	P	0.38677	0.642	P	0.48334	0.574	T	0.64863	-0.6307	10	0.72032	D	0.01	-30.4191	15.5539	0.76177	0.0:1.0:0.0:0.0	.	176	O15524	SOCS1_HUMAN	K	176	ENSP00000329418:E176K	ENSP00000329418:E176K	E	-	1	0	SOCS1	11256311	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.578000	0.46051	2.141000	0.66446	0.462000	0.41574	GAG	.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1		
PLPPR1	54886	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221.0	202.0	208.0		34,34	5.9	1.0	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	246.0	0.0	0		227.0	111.0	0.488987	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
FUK	197258	hgsc.bcm.edu	37	16	70512349	70512349	+	Missense_Mutation	SNP	G	G	A	rs17886060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70512349G>A	ENST00000288078.6	+	21	3048	c.2816G>A	c.(2815-2817)cGg>cAg	p.R939Q	FUK_ENST00000378912.2_Missense_Mutation_p.R945Q|FUK_ENST00000571514.1_Missense_Mutation_p.R430Q	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	939			R -> Q (in dbSNP:rs17886060). {ECO:0000269|Ref.3}.|R -> W (in dbSNP:rs17883248). {ECO:0000269|Ref.3}.			cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				CGCCTGGCTCGGAACCTGCTG	0.647													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		18862	0.0		0.0109	False		,,,				2504	0.0072				p.R939Q		Atlas-SNP	.											.	FUK	72	.	0			c.G2816A						PASS	.	G	GLN/ARG	7,4041		0,7,2017	60.0	65.0	63.0		2816	5.7	1.0	16	dbSNP_124	63	120,8240		1,118,4061	yes	missense	FUK	NM_145059.2	43	1,125,6078	AA,AG,GG		1.4354,0.1729,1.0235	probably-damaging	939/1085	70512349	127,12281	2024	4180	6204	SO:0001583	missense	197258	exon21			TGGCTCGGAACCT		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.2816G>A	16.37:g.70512349G>A	ENSP00000288078:p.Arg939Gln	87.0	0.0	0		73.0	49.0	0.671233	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	16.72	3.200151	0.58126	0.001729	0.014354	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	D;D	0.93712	-3.27;-3.27	5.65	5.65	0.86999	.	0.050215	0.85682	D	0.000000	D	0.96021	0.8704	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.926;0.926	D	0.95082	0.8214	10	0.59425	D	0.04	-30.887	19.7405	0.96228	0.0:0.0:1.0:0.0	rs17886060;rs17886060	945;845;939	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	Q	939;945;253	ENSP00000288078:R939Q;ENSP00000368192:R945Q	ENSP00000288078:R939Q	R	+	2	0	FUK	69069850	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	6.263000	0.72521	2.655000	0.90218	0.655000	0.94253	CGG	G|0.990;A|0.010	0.010	strong		0.647	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178700038	178700038	+	Missense_Mutation	SNP	C	C	G	rs146064587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178700038C>G	ENST00000251582.7	-	3	663	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.E188Q	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	188	Poly-Glu.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		ATGAAGAACTCCTCCTCCTCC	0.602																																					p.E188Q		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G562C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	81.0	78.0	79.0		562,562	5.0	1.0	5	dbSNP_134	79	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	188/1212,188/567	178700038	2,13004	2203	4300	6503	SO:0001583	missense	9509	exon3			AGAACTCCTCCTC	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.562G>C	5.37:g.178700038C>G	ENSP00000251582:p.Glu188Gln	50.0	0.0	0		59.0	25.0	0.423729	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430513	0.83776	0.0	2.33E-4	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.07327	3.2;3.2	4.96	4.96	0.65561	Peptidase M12B, propeptide (1);	0.000000	0.37178	N	0.002212	T	0.25568	0.0622	M	0.62154	1.92	0.44660	D	0.997649	D;D	0.89917	0.998;1.0	D;D	0.91635	0.994;0.999	T	0.00389	-1.1770	10	0.59425	D	0.04	.	13.7201	0.62720	0.0:1.0:0.0:0.0	.	188;188	O95450-2;O95450	.;ATS2_HUMAN	Q	188	ENSP00000251582:E188Q;ENSP00000274609:E188Q	ENSP00000251582:E188Q	E	-	1	0	ADAMTS2	178632644	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.753000	0.68736	2.284000	0.76573	0.561000	0.74099	GAG	C|1.000;G|0.000	0.000	weak		0.602	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
MUC4	4585	hgsc.bcm.edu	37	3	195505247	195505247	+	Silent	SNP	G	G	T	rs76650792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505247G>T	ENST00000346145.4	-	2	201	c.162C>A	c.(160-162)atC>atA	p.I54I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Silent_p.I4290I|MUC4_ENST00000475231.1_Silent_p.I4290I	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1047					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGTGGAAATGATGGTCTGGG	0.592													.|||	112	0.0223642	0.0121	0.0562	5008	,	,		8996	0.005		0.0497	False		,,,				2504	0.002				p.I4290I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12870A						PASS	.	G	,,	66,4336	60.5+/-97.4	2,62,2137	225.0	175.0	192.0		162,12870,	-4.7	0.0	3	dbSNP_131	192	379,8209	123.9+/-182.7	9,361,3924	no	coding-synonymous,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	11,423,6061	TT,TG,GG		4.4131,1.4993,3.4257	,,	54/1177,4290/5413,	195505247	445,12545	2201	4294	6495	SO:0001819	synonymous_variant	4585	exon3			GGAAATGATGGTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.162C>A	3.37:g.195505247G>T		296.0	0.0	0		285.0	136.0	0.477193	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			G|0.967;T|0.033	0.033	strong		0.592	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
MYH14	79784	hgsc.bcm.edu	37	19	50771511	50771511	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50771511C>T	ENST00000596571.1	+	21	2797	c.2797C>T	c.(2797-2799)Cgc>Tgc	p.R933C	MYH14_ENST00000425460.1_Missense_Mutation_p.R941C|MYH14_ENST00000376970.2_Missense_Mutation_p.R966C|MYH14_ENST00000601313.1_Missense_Mutation_p.R974C|MYH14_ENST00000598205.1_Missense_Mutation_p.R941C|MYH14_ENST00000440075.2_Missense_Mutation_p.R974C|MYH14_ENST00000262269.8_Missense_Mutation_p.R974C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	933			R -> L (in PNMHH). {ECO:0000269|PubMed:21480433}.		actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCTGGCAGCCCGCAAGCAGGA	0.657																																					p.R974C		Atlas-SNP	.											.	MYH14	261	.	0			c.C2920T						PASS	.						20.0	29.0	26.0					19																	50771511		2140	4241	6381	SO:0001583	missense	79784	exon24			GCAGCCCGCAAGC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2797C>T	19.37:g.50771511C>T	ENSP00000472819:p.Arg933Cys	109.0	0.0	0		78.0	47.0	0.602564	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608866	0.66558	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	3.9	3.9	0.45041	.	.	.	.	.	D	0.90307	0.6968	M	0.75884	2.315	0.80722	D	1	P;P;P	0.44690	0.713;0.59;0.841	B;B;B	0.34180	0.126;0.059;0.177	D	0.90702	0.4621	9	0.72032	D	0.01	.	9.075	0.36515	0.2192:0.7808:0.0:0.0	.	974;933;941	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	933;974;966;941;933;974	ENSP00000406273:R974C;ENSP00000366169:R966C;ENSP00000407879:R941C;ENSP00000262269:R974C	ENSP00000262269:R974C	R	+	1	0	MYH14	55463323	0.779000	0.28652	1.000000	0.80357	0.892000	0.51952	2.109000	0.41863	2.180000	0.69256	0.561000	0.74099	CGC	.	.	none		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
ATHL1	80162	hgsc.bcm.edu	37	11	290050	290050	+	Silent	SNP	G	G	A	rs139686173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:290050G>A	ENST00000409548.2	+	2	349	c.234G>A	c.(232-234)gaG>gaA	p.E78E	RP11-326C3.2_ENST00000533924.1_RNA|RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409479.1_Silent_p.E78E|ATHL1_ENST00000409655.1_5'UTR|RP11-326C3.2_ENST00000534742.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	78					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGCTGACCGAGACCTTCGCCC	0.677													G|||	45	0.00898562	0.0015	0.0187	5008	,	,		14729	0.0		0.0149	False		,,,				2504	0.0153				p.E78E		Atlas-SNP	.											.	ATHL1	88	.	0			c.G234A						PASS	.	G		4,1378		0,4,687	25.0	34.0	31.0		234	3.8	0.4	11	dbSNP_134	31	62,3120		0,62,1529	no	coding-synonymous	ATHL1	NM_025092.4		0,66,2216	AA,AG,GG		1.9485,0.2894,1.4461		78/738	290050	66,4498	691	1591	2282	SO:0001819	synonymous_variant	80162	exon2			GACCGAGACCTTC	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.234G>A	11.37:g.290050G>A		36.0	0.0	0		52.0	14.0	0.269231	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.986;A|0.014	0.014	strong		0.677	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
OR2T12	127064	hgsc.bcm.edu	37	1	248458187	248458187	+	Missense_Mutation	SNP	G	G	A	rs200352170		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248458187G>A	ENST00000317996.1	-	1	693	c.694C>T	c.(694-696)Cgc>Tgc	p.R232C		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			GCCTTCTTGCGGGCTTCTGTA	0.522																																					p.R232C		Atlas-SNP	.											.	OR2T12	113	.	0			c.C694T						PASS	.						100.0	94.0	96.0					1																	248458187		2203	4300	6503	SO:0001583	missense	127064	exon1			TCTTGCGGGCTTC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.694C>T	1.37:g.248458187G>A	ENSP00000324583:p.Arg232Cys	402.0	0.0	0		363.0	97.0	0.267218	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	10.81	1.454126	0.26161	.	.	ENSG00000177201	ENST00000317996	T	0.00337	8.05	1.55	0.316	0.15857	GPCR, rhodopsin-like superfamily (1);	0.870947	0.09313	U	0.819284	T	0.00384	0.0012	M	0.85945	2.785	0.09310	N	0.999998	B	0.24368	0.102	B	0.24269	0.052	T	0.31833	-0.9929	10	0.59425	D	0.04	.	7.1649	0.25685	0.0:0.0:0.5344:0.4655	.	232	Q8NG77	O2T12_HUMAN	C	232	ENSP00000324583:R232C	ENSP00000324583:R232C	R	-	1	0	OR2T12	246524810	0.000000	0.05858	0.169000	0.22859	0.670000	0.39368	-0.554000	0.06006	0.645000	0.30675	0.175000	0.17021	CGC	G|0.999;A|0.001	0.001	weak		0.522	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
POLQ	10721	hgsc.bcm.edu	37	3	121212484	121212484	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121212484C>T	ENST00000264233.5	-	15	2491	c.2363G>A	c.(2362-2364)gGc>gAc	p.G788D		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	788					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CCTCTGGATGCCAAACGTAAG	0.468								DNA polymerases (catalytic subunits)																													p.G788D	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											POLQ,caecum,carcinoma,0,1	POLQ	273	1	0			c.G2363A						scavenged	.						76.0	74.0	75.0					3																	121212484		2203	4300	6503	SO:0001583	missense	10721	exon15			TGGATGCCAAACG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2363G>A	3.37:g.121212484C>T	ENSP00000264233:p.Gly788Asp	118.0	0.0	0		71.0	3.0	0.0422535	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132722	0.94517	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.72505	-0.66	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.88779	0.6529	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91345	0.5100	10	0.87932	D	0	.	19.3309	0.94288	0.0:1.0:0.0:0.0	.	788	O75417	DPOLQ_HUMAN	D	411;788;924	ENSP00000264233:G788D	ENSP00000264233:G788D	G	-	2	0	POLQ	122695174	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.337000	0.79256	2.648000	0.89879	0.650000	0.86243	GGC	.	.	none		0.468	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
SALL1	6299	hgsc.bcm.edu	37	16	51174432	51174432	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:51174432T>C	ENST00000251020.4	-	2	1734	c.1701A>G	c.(1699-1701)atA>atG	p.I567M	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.I470M|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	567					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TGATGAAGGGTATGAGGCTTG	0.612																																					p.I567M	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A1701G						PASS	.						45.0	50.0	48.0					16																	51174432		2198	4300	6498	SO:0001583	missense	6299	exon2			GAAGGGTATGAGG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1701A>G	16.37:g.51174432T>C	ENSP00000251020:p.Ile567Met	88.0	0.0	0		64.0	29.0	0.453125	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	8.110	0.778639	0.16120	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.05996	3.36;3.38	5.32	-10.6	0.00265	.	0.257755	0.45126	D	0.000388	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.22386	0.039	T	0.29518	-1.0009	10	0.72032	D	0.01	.	6.6511	0.22963	0.0662:0.2679:0.4445:0.2214	.	567	Q9NSC2	SALL1_HUMAN	M	567;470;531	ENSP00000251020:I567M;ENSP00000407914:I470M	ENSP00000251020:I567M	I	-	3	3	SALL1	49731933	0.000000	0.05858	0.164000	0.22755	0.998000	0.95712	-3.833000	0.00355	-2.099000	0.00849	0.455000	0.32223	ATA	.	.	none		0.612	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
NCAPD2	9918	hgsc.bcm.edu	37	12	6638197	6638197	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6638197C>T	ENST00000315579.5	+	27	4363	c.3564C>T	c.(3562-3564)acC>acT	p.T1188T	NCAPD2_ENST00000545962.1_Silent_p.T1143T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1188					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						CTTTCCACACCATCATGAAGT	0.527																																					p.T1188T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3564T						PASS	.						55.0	61.0	59.0					12																	6638197		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon27			CCACACCATCATG	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.3564C>T	12.37:g.6638197C>T		84.0	0.0	0		67.0	23.0	0.343284	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			.	.	none		0.527	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
EIF4G2	1982	hgsc.bcm.edu	37	11	10827592	10827592	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:10827592T>A	ENST00000526148.1	-	4	620	c.110A>T	c.(109-111)gAg>gTg	p.E37V	EIF4G2_ENST00000525681.1_Missense_Mutation_p.E37V|EIF4G2_ENST00000525995.1_5'UTR|EIF4G2_ENST00000396525.2_Missense_Mutation_p.E37V|EIF4G2_ENST00000339995.5_Missense_Mutation_p.E37V	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CCCCAGGAACTCGCTGATTAA	0.403																																					p.E37V		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A110T						PASS	.						97.0	93.0	95.0					11																	10827592		2201	4294	6495	SO:0001583	missense	1982	exon4			AGGAACTCGCTGA	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.110A>T	11.37:g.10827592T>A	ENSP00000433664:p.Glu37Val	203.0	0.0	0		205.0	48.0	0.234146	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949046	0.92660	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416;ENST00000532082;ENST00000524932;ENST00000532570;ENST00000526591;ENST00000530211;ENST00000527526;ENST00000530702	T;T;T;T;T;T;T;T	0.49139	2.11;2.11;2.11;2.11;1.79;1.82;1.82;0.79	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52435	0.1734	N	0.24115	0.695	0.51233	D	0.999912	D;D	0.65815	0.995;0.995	P;P	0.60682	0.878;0.878	T	0.64533	-0.6385	9	0.87932	D	0	-8.5634	15.356	0.74428	0.0:0.0:0.0:1.0	.	37;110	P78344;B4DZF2	IF4G2_HUMAN;.	V	37;37;37;37;110;37;37;37;37;37;37;37;15	ENSP00000433664:E37V;ENSP00000433371:E37V;ENSP00000340281:E37V;ENSP00000379778:E37V;ENSP00000431583:E37V;ENSP00000433121:E37V;ENSP00000435523:E37V;ENSP00000431511:E37V	ENSP00000340281:E37V	E	-	2	0	EIF4G2	10784168	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	2.023000	0.59567	0.455000	0.32223	GAG	.	.	none		0.403	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
RASSF6	166824	hgsc.bcm.edu	37	4	74459206	74459206	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74459206A>C	ENST00000342081.3	-	4	475	c.345T>G	c.(343-345)ttT>ttG	p.F115L	RASSF6_ENST00000395777.2_Missense_Mutation_p.F83L|RASSF6_ENST00000335049.5_Missense_Mutation_p.F71L|RASSF6_ENST00000307439.5_Missense_Mutation_p.F83L	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	115					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TCATACTAGTAAAAGAAGAGA	0.363																																					p.F115L		Atlas-SNP	.											.	RASSF6	68	.	0			c.T345G						PASS	.						115.0	115.0	115.0					4																	74459206		2203	4300	6503	SO:0001583	missense	166824	exon4			ACTAGTAAAAGAA	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.345T>G	4.37:g.74459206A>C	ENSP00000340578:p.Phe115Leu	117.0	0.0	0		101.0	20.0	0.19802	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	37	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	A	6.548	0.469333	0.12461	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	4.87	-1.98	0.07480	.	0.620622	0.17776	N	0.162414	T	0.20700	0.0498	L	0.34521	1.04	0.09310	N	0.999999	B;B;B	0.16166	0.013;0.013;0.016	B;B;B	0.19148	0.024;0.014;0.015	T	0.33624	-0.9861	10	0.10636	T	0.68	-3.5922	9.1491	0.36951	0.4954:0.0:0.5046:0.0	.	71;83;115	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	L	83;115;83;71	ENSP00000303877:F83L;ENSP00000340578:F115L;ENSP00000379123:F83L;ENSP00000335582:F71L	ENSP00000303877:F83L	F	-	3	2	RASSF6	74678070	0.159000	0.22864	0.029000	0.17559	0.029000	0.11900	-0.191000	0.09601	-0.624000	0.05611	0.443000	0.29094	TTT	.	.	none		0.363	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
KRT73	319101	hgsc.bcm.edu	37	12	53002197	53002197	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53002197C>T	ENST00000305748.3	-	9	1440	c.1406G>A	c.(1405-1407)gGg>gAg	p.G469E	RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	469	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		AAAGCCAGCCCCTGTGCCTGC	0.612																																					p.G469E		Atlas-SNP	.											.	KRT73	101	.	0			c.G1406A						PASS	.						41.0	39.0	40.0					12																	53002197		2203	4300	6503	SO:0001583	missense	319101	exon9			CCAGCCCCTGTGC	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.1406G>A	12.37:g.53002197C>T	ENSP00000307014:p.Gly469Glu	75.0	0.0	0		69.0	9.0	0.130435	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570160	0.65765	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.82893	-1.58;-1.66	4.88	4.88	0.63580	.	0.185839	0.26421	N	0.024464	T	0.74473	0.3721	L	0.46819	1.47	0.09310	N	0.999999	P	0.39216	0.664	B	0.35607	0.206	T	0.64287	-0.6443	10	0.09338	T	0.73	.	13.7369	0.62824	0.0:1.0:0.0:0.0	.	469	Q86Y46	K2C73_HUMAN	E	469;214	ENSP00000307014:G469E;ENSP00000449081:G214E	ENSP00000307014:G469E	G	-	2	0	KRT73	51288464	0.031000	0.19500	0.210000	0.23637	0.137000	0.21094	1.906000	0.39887	2.709000	0.92574	0.655000	0.94253	GGG	.	.	none		0.612	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
FKBP15	23307	hgsc.bcm.edu	37	9	115936860	115936860	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115936860G>A	ENST00000238256.3	-	22	2344	c.2227C>T	c.(2227-2229)Ctc>Ttc	p.L743F		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	743					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CTTTCTGAGAGGTTCTTAGGA	0.443																																					p.L743F		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,+1,2	FKBP15	128	2	0			c.C2227T						PASS	.						65.0	63.0	64.0					9																	115936860		1882	4104	5986	SO:0001583	missense	23307	exon22			CTGAGAGGTTCTT	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2227C>T	9.37:g.115936860G>A	ENSP00000238256:p.Leu743Phe	219.0	0.0	0		133.0	39.0	0.293233	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	g	20.6	4.021430	0.75275	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.29397	1.57;1.58	6.07	6.07	0.98685	.	.	.	.	.	T	0.57227	0.2039	M	0.72894	2.215	0.39987	D	0.974995	D;P	0.89917	1.0;0.788	D;B	0.76575	0.988;0.257	T	0.58194	-0.7679	9	0.72032	D	0.01	-11.325	18.151	0.89674	0.0:0.0:1.0:0.0	.	324;743	B4DVS2;Q5T1M5	.;FKB15_HUMAN	F	768;743	ENSP00000416158:L768F;ENSP00000238256:L743F	ENSP00000238256:L743F	L	-	1	0	FKBP15	114976681	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.051000	0.57412	2.890000	0.99128	0.586000	0.80456	CTC	.	.	none		0.443	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
OBSCN	84033	hgsc.bcm.edu	37	1	228452016	228452016	+	Missense_Mutation	SNP	G	G	C	rs185523702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228452016G>C	ENST00000422127.1	+	16	4829	c.4785G>C	c.(4783-4785)gaG>gaC	p.E1595D	OBSCN_ENST00000570156.2_Missense_Mutation_p.E1779D|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.E1595D|OBSCN_ENST00000359599.6_Missense_Mutation_p.E251D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1595	Ig-like 16.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGTGCAGGAGGCAGGCCAGG	0.642													G|||	20	0.00399361	0.0008	0.0086	5008	,	,		18329	0.0		0.0119	False		,,,				2504	0.001				p.E1779D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G5337C						PASS	.	G	ASP/GLU,ASP/GLU	12,4228		0,12,2108	44.0	52.0	50.0		4785,4785	3.8	1.0	1		50	165,8287		3,159,4064	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	45,45	3,171,6172	CC,CG,GG		1.9522,0.283,1.3946	possibly-damaging,possibly-damaging	1595/7969,1595/6621	228452016	177,12515	2120	4226	6346	SO:0001583	missense	84033	exon18			GCAGGAGGCAGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.4785G>C	1.37:g.228452016G>C	ENSP00000409493:p.Glu1595Asp	319.0	0.0	0		309.0	147.0	0.475728	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	.	1.509	-0.549977	0.03996	0.00283	0.019522	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04317	3.65;3.65;3.65	4.69	3.77	0.43336	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.306226	0.28595	N	0.014790	T	0.01387	0.0045	N	0.16037	0.36	0.80722	D	1	B;B	0.30439	0.018;0.279	B;B	0.23716	0.029;0.048	T	0.52403	-0.8580	10	0.11794	T	0.64	.	13.1743	0.59617	0.1471:0.0:0.8529:0.0	.	1595;1595	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	1595;1595;251	ENSP00000284548:E1595D;ENSP00000409493:E1595D;ENSP00000352613:E251D	ENSP00000284548:E1595D	E	+	3	2	OBSCN	226518639	0.000000	0.05858	0.996000	0.52242	0.001000	0.01503	-0.150000	0.10189	0.601000	0.29879	-1.579000	0.00862	GAG	G|0.990;C|0.010	0.010	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
USP39	10713	hgsc.bcm.edu	37	2	85843348	85843348	+	Silent	SNP	C	C	T	rs11544042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85843348C>T	ENST00000323701.6	+	1	40	c.30C>T	c.(28-30)cgC>cgT	p.R10R	USP39_ENST00000409025.1_Silent_p.R10R|USP39_ENST00000409470.1_Silent_p.R10R|USP39_ENST00000459775.1_Intron|USP39_ENST00000409766.3_Silent_p.R10R|USP39_ENST00000450066.2_Intron	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	10	Arg-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						GGGAGTCTCGCGGTTCCACTC	0.706													C|||	267	0.0533147	0.1036	0.0548	5008	,	,		12680	0.001		0.0775	False		,,,				2504	0.0133				p.R10R		Atlas-SNP	.											.	USP39	33	.	0			c.C30T						PASS	.	C		365,3963		13,339,1812	7.0	8.0	8.0		30	-4.3	1.0	2	dbSNP_120	8	528,7964		12,504,3730	no	coding-synonymous	USP39	NM_006590.2		25,843,5542	TT,TC,CC		6.2176,8.4335,6.9657		10/566	85843348	893,11927	2164	4246	6410	SO:0001819	synonymous_variant	10713	exon1			GTCTCGCGGTTCC	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"""Ubiquitin-specific peptidases"""	20071	protein-coding gene	gene with protein product	"""snRNP assembly defective 1 homolog (S.cerevisiae)"", ""small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"""	611594	"""ubiquitin specific protease 39"""			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.30C>T	2.37:g.85843348C>T		50.0	0.0	0		60.0	33.0	0.55	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Silent	SNP	ENST00000323701.6	37	CCDS33234.1																																																																																			C|0.936;T|0.064	0.064	strong		0.706	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590	
TFDP2	7029	hgsc.bcm.edu	37	3	141678667	141678667	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141678667G>A	ENST00000489671.1	-	11	1330	c.900C>T	c.(898-900)ttC>ttT	p.F300F	TFDP2_ENST00000495310.1_Silent_p.F203F|TFDP2_ENST00000486111.1_Silent_p.F240F|TFDP2_ENST00000467072.1_Silent_p.F240F|TFDP2_ENST00000310282.6_Silent_p.F240F|TFDP2_ENST00000477292.1_Silent_p.F164F|TFDP2_ENST00000397991.4_Silent_p.F272F|TFDP2_ENST00000479040.1_Silent_p.F239F|TFDP2_ENST00000499676.2_Silent_p.F240F|TFDP2_ENST00000317104.7_Silent_p.F224F			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	300	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|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)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						TGTCAAAATTGAAAAGATACT	0.403																																					p.F300F		Atlas-SNP	.											.	TFDP2	44	.	0			c.C900T						PASS	.						96.0	91.0	92.0					3																	141678667		1932	4165	6097	SO:0001819	synonymous_variant	7029	exon11			AAAATTGAAAAGA	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.900C>T	3.37:g.141678667G>A		93.0	0.0	0		87.0	4.0	0.045977	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1	.	.	.	.	.	.	.	.	.	.	G	9.486	1.099510	0.20552	.	.	ENSG00000114126	ENST00000474279	.	.	.	5.69	-4.06	0.03986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.5996	14.6009	0.68441	0.5011:0.0:0.4989:0.0	.	.	.	.	X	14	.	.	Q	-	1	0	TFDP2	143161357	1.000000	0.71417	0.491000	0.27477	0.959000	0.62525	1.103000	0.31062	-0.748000	0.04753	-0.379000	0.06801	CAA	.	.	none		0.403	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
MAGEA4	4103	hgsc.bcm.edu	37	X	151092968	151092968	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151092968G>T	ENST00000360243.2	+	3	1099	c.832G>T	c.(832-834)Gct>Tct	p.A278S	MAGEA4_ENST00000393921.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A278S|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A278S|MAGEA4_ENST00000393920.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370335.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A278S	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	278	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					GGGTCCAAGGGCTCTGGCTGA	0.547																																					p.A278S		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G832T						PASS	.						130.0	128.0	129.0					X																	151092968		2203	4300	6503	SO:0001583	missense	4103	exon3			CCAAGGGCTCTGG		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.832G>T	X.37:g.151092968G>T	ENSP00000353379:p.Ala278Ser	158.0	0.0	0		95.0	32.0	0.336842	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.519751	0.44866	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4;3.4	2.55	1.68	0.24146	.	0.050169	0.85682	D	0.000000	T	0.19725	0.0474	M	0.83692	2.655	0.09310	N	1	D	0.56968	0.978	D	0.68943	0.961	T	0.02893	-1.1097	9	.	.	.	.	4.7785	0.13190	0.1844:0.0:0.8156:0.0	.	278	P43358	MAGA4_HUMAN	S	278	ENSP00000276344:A278S;ENSP00000377498:A278S;ENSP00000359362:A278S;ENSP00000377497:A278S;ENSP00000359365:A278S;ENSP00000359360:A278S;ENSP00000353379:A278S	.	A	+	1	0	MAGEA4	150843624	0.192000	0.23301	0.009000	0.14445	0.021000	0.10359	0.444000	0.21661	0.500000	0.27991	0.292000	0.19580	GCT	.	.	none		0.547	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
TLE3	7090	hgsc.bcm.edu	37	15	70351154	70351154	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:70351154C>T	ENST00000558939.1	-	11	2143	c.766G>A	c.(766-768)Gac>Aac	p.D256N	TLE3_ENST00000559191.1_Intron|TLE3_ENST00000559048.1_Splice_Site_p.D261N|TLE3_ENST00000440567.3_Splice_Site_p.D249N|TLE3_ENST00000317509.8_Splice_Site_p.D256N|TLE3_ENST00000557907.1_Splice_Site_p.D256N|TLE3_ENST00000539550.1_Splice_Site_p.D200N|TLE3_ENST00000558201.1_Splice_Site_p.D262N|TLE3_ENST00000558379.1_Splice_Site_p.D256N|TLE3_ENST00000560589.1_Splice_Site_p.D200N|TLE3_ENST00000451782.2_Splice_Site_p.D256N|TLE3_ENST00000559929.1_Splice_Site_p.D266N|TLE3_ENST00000442299.2_Splice_Site_p.D256N|TLE3_ENST00000557997.1_Splice_Site_p.D256N|TLE3_ENST00000560939.1_Splice_Site_p.D261N	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	256	CCN domain.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GTTGCGGGGTCCTGAAAACAC	0.612																																					p.D256N		Atlas-SNP	.											.	TLE3	104	.	0			c.G766A						PASS	.						17.0	19.0	18.0					15																	70351154		1935	4130	6065	SO:0001630	splice_region_variant	7090	exon11			CGGGGTCCTGAAA	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.766-1G>A	15.37:g.70351154C>T		56.0	0.0	0		40.0	15.0	0.375	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.902492	0.72754	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.53857	0.82;0.87;0.92;0.87;0.6	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.68449	0.3002	L	0.56340	1.77	0.80722	D	1	D;B;B;B;P;B;P;B	0.61080	0.989;0.021;0.264;0.011;0.552;0.053;0.823;0.019	D;B;B;B;B;B;P;B	0.66497	0.944;0.019;0.16;0.02;0.34;0.043;0.733;0.03	T	0.68161	-0.5482	10	0.54805	T	0.06	-0.4451	19.143	0.93452	0.0:1.0:0.0:0.0	.	249;256;256;256;256;256;261;200	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	N	256;256;256;249;200	ENSP00000390007:D256N;ENSP00000394717:D256N;ENSP00000319233:D256N;ENSP00000415057:D249N;ENSP00000442594:D200N	ENSP00000319233:D256N	D	-	1	0	TLE3	68138208	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.559000	0.82265	2.764000	0.94973	0.555000	0.69702	GAC	.	.	none		0.612	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	Missense_Mutation
SPAST	6683	hgsc.bcm.edu	37	2	32289034	32289034	+	Missense_Mutation	SNP	C	C	A	rs121908517		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32289034C>A	ENST00000315285.3	+	1	259	c.134C>A	c.(133-135)cCg>cAg	p.P45Q	SPAST_ENST00000345662.1_Missense_Mutation_p.P45Q	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					cccgAGTCGCCGCATAAGCGG	0.716																																					p.P45Q		Atlas-SNP	.											SPAST,NS,carcinoma,-1,2	SPAST	61	2	0			c.C134A	GRCh37	CM045939	SPAST	M	rs121908517	PASS	.	C	,GLN/PRO,GLN/PRO	0,4402		0,0,2201	24.0	25.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,134,134	3.2	1.0	2	dbSNP_133	25	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense,missense	SPAST,HP11026	XM_003403507.1,NM_199436.1,NM_014946.3	,76,76	0,3,6498	AA,AC,CC		0.0349,0.0,0.0231	,benign,benign	,45/585,45/617	32289034	3,12999	2201	4300	6501	SO:0001583	missense	6683	exon1			AGTCGCCGCATAA	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.134C>A	2.37:g.32289034C>A	ENSP00000320885:p.Pro45Gln	35.0	0.0	0		61.0	25.0	0.409836	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.390692	0.25118	0.0	3.49E-4	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.93426	-3.22;-3.15	4.15	3.25	0.37280	.	0.196102	0.35235	N	0.003354	D	0.84279	0.5437	N	0.14661	0.345	0.35379	A	0.789784	B;B	0.22276	0.067;0.067	B;B	0.14578	0.011;0.011	T	0.81831	-0.0752	9	0.59425	D	0.04	-20.6852	6.4706	0.22005	0.1824:0.722:0.0:0.0957	.	45;45	E5KRP6;Q9UBP0	.;SPAST_HUMAN	Q	45	ENSP00000340817:P45Q;ENSP00000320885:P45Q	ENSP00000320885:P45Q	P	+	2	0	SPAST	32142538	1.000000	0.71417	0.998000	0.56505	0.046000	0.14306	1.604000	0.36804	0.846000	0.35142	0.637000	0.83480	CCG	C|1.000;A|0.000	0.000	weak		0.716	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436	
SLC32A1	140679	hgsc.bcm.edu	37	20	37353743	37353743	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:37353743A>G	ENST00000217420.1	+	1	639	c.376A>G	c.(376-378)Acc>Gcc	p.T126A		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	126					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CTGGAACGTGACCAACGCCAT	0.677																																					p.T126A		Atlas-SNP	.											.	SLC32A1	81	.	0			c.A376G						PASS	.						38.0	40.0	39.0					20																	37353743		2147	4214	6361	SO:0001583	missense	140679	exon1			AACGTGACCAACG	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"""Solute carriers"""	11018	protein-coding gene	gene with protein product			"""vesicular inhibitory amino acid transporter"""	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.376A>G	20.37:g.37353743A>G	ENSP00000217420:p.Thr126Ala	108.0	0.0	0		83.0	25.0	0.301205	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436764	0.83885	.	.	ENSG00000101438	ENST00000217420	T	0.02216	4.39	5.19	4.08	0.47627	.	0.152435	0.64402	N	0.000018	T	0.07458	0.0188	M	0.64170	1.965	0.80722	D	1	P	0.51933	0.949	P	0.58331	0.837	T	0.04885	-1.0920	10	0.59425	D	0.04	-41.9776	9.2152	0.37342	0.9126:0.0:0.0874:0.0	.	126	Q9H598	VIAAT_HUMAN	A	126	ENSP00000217420:T126A	ENSP00000217420:T126A	T	+	1	0	SLC32A1	36787157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.020000	0.93667	0.811000	0.34303	0.459000	0.35465	ACC	.	.	none		0.677	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552	
RBPJL	11317	hgsc.bcm.edu	37	20	43942698	43942698	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43942698G>A	ENST00000343694.3	+	8	853	c.781G>A	c.(781-783)Gac>Aac	p.D261N	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372743.1_Missense_Mutation_p.D261N|RBPJL_ENST00000372741.3_Missense_Mutation_p.D261N	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	261					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGCCCAAGGAGACTTCCCACC	0.587																																					p.D261N		Atlas-SNP	.											.	RBPJL	67	.	0			c.G781A						PASS	.						129.0	127.0	127.0					20																	43942698		2203	4300	6503	SO:0001583	missense	11317	exon8			CAAGGAGACTTCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.781G>A	20.37:g.43942698G>A	ENSP00000341243:p.Asp261Asn	71.0	0.0	0		53.0	22.0	0.415094	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744830	0.49151	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	T;T;T	0.29397	1.57;1.57;1.57	5.25	5.25	0.73442	Beta-trefoil (2);	0.129253	0.51477	D	0.000092	T	0.28962	0.0719	N	0.25485	0.75	0.46260	D	0.998959	P;B	0.47484	0.896;0.303	P;B	0.46172	0.506;0.128	T	0.01334	-1.1382	10	0.36615	T	0.2	-39.329	16.168	0.81785	0.0:0.0:1.0:0.0	.	261;261	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	N	261	ENSP00000361828:D261N;ENSP00000361826:D261N;ENSP00000341243:D261N	ENSP00000341243:D261N	D	+	1	0	RBPJL	43376112	1.000000	0.71417	1.000000	0.80357	0.313000	0.28021	6.631000	0.74277	2.724000	0.93272	0.563000	0.77884	GAC	.	.	none		0.587	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
OR4A47	403253	hgsc.bcm.edu	37	11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	rs76991989	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148.0	144.0	145.0		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	143.0	0.0	0		116.0	90.0	0.775862	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
ZNF598	90850	hgsc.bcm.edu	37	16	2048564	2048564	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2048564T>C	ENST00000563630.1	-	12	2461	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	ZNF598_ENST00000431526.1_Missense_Mutation_p.Y795C|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Missense_Mutation_p.Y740C			Q86UK7	ZN598_HUMAN	zinc finger protein 598	795	Pro-rich.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						ACTCTTGTAATACTGGGCTGC	0.652																																					p.Y795C		Atlas-SNP	.											.	ZNF598	55	.	0			c.A2384G						PASS	.						7.0	8.0	8.0					16																	2048564		1863	4080	5943	SO:0001583	missense	90850	exon14			TTGTAATACTGGG	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2219A>G	16.37:g.2048564T>C	ENSP00000455882:p.Tyr740Cys	123.0	0.0	0		98.0	49.0	0.5	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		.	.	.	.	.	.	.	.	.	.	.	13.41	2.228427	0.39399	.	.	ENSG00000167962	ENST00000431526	T	0.44881	0.91	5.29	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.73360	-0.4007	10	0.87932	D	0	-18.8123	9.7829	0.40660	0.0:0.0812:0.0:0.9188	.	795;787	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	C	795	ENSP00000411409:Y795C	ENSP00000411409:Y795C	Y	-	2	0	ZNF598	1988565	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.301000	0.78850	2.000000	0.58554	0.379000	0.24179	TAT	.	.	none		0.652	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
ATM	472	hgsc.bcm.edu	37	11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	rs1801516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1853N(10)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTACTCCAAGATACAAATGA	0.388			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75.0	72.0	73.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1.0	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	126.0	0.0	0		91.0	15.0	0.164835	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
SLC9A5	6553	hgsc.bcm.edu	37	16	67300058	67300058	+	Silent	SNP	G	G	A	rs61744117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67300058G>A	ENST00000299798.11	+	15	2213	c.2148G>A	c.(2146-2148)aaG>aaA	p.K716K	CTC-277H1.7_ENST00000573063.1_RNA	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	716					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		AGACAGAGAAGGAGGACGATG	0.562													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20520	0.0		0.003	False		,,,				2504	0.0				p.K716K		Atlas-SNP	.											.	SLC9A5	82	.	0			c.G2148A						PASS	.	G		1,4181		0,1,2090	117.0	124.0	121.0		2148	2.2	1.0	16	dbSNP_129	121	23,8393		0,23,4185	no	coding-synonymous	SLC9A5	NM_004594.2		0,24,6275	AA,AG,GG		0.2733,0.0239,0.1905		716/897	67300058	24,12574	2091	4208	6299	SO:0001819	synonymous_variant	6553	exon15			AGAGAAGGAGGAC		CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"""Solute carriers"""	11078	protein-coding gene	gene with protein product		600477	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 5"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 5"""			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.2148G>A	16.37:g.67300058G>A		153.0	0.0	0		200.0	113.0	0.565	NM_004594	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
DMD	1756	hgsc.bcm.edu	37	X	32486756	32486756	+	Silent	SNP	C	C	T	rs1800268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:32486756C>T	ENST00000357033.4	-	23	3227	c.3021G>A	c.(3019-3021)tcG>tcA	p.S1007S	DMD_ENST00000378677.2_Silent_p.S1003S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1007					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GCGCTTTCTTCGACATCTCTT	0.408													C|||	33	0.00874172	0.0	0.013	3775	,	,		11926	0.0		0.0159	False		,,,				2504	0.0082				p.S1007S		Atlas-SNP	.											.	DMD	2127	.	0			c.G3021A						PASS	.	C	,,,,	15,3818		0,12,3,1619,568	75.0	68.0	70.0		2997,3021,2652,3009,2652	-2.5	0.9	X	dbSNP_89	70	112,6616		0,87,25,2341,1847	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	0,99,28,3960,2415	TT,TC,T,CC,C		1.6647,0.3913,1.2025	,,,,	999/3678,1007/3686,884/3563,1003/3682,884/3563	32486756	127,10434	2202	4300	6502	SO:0001819	synonymous_variant	1756	exon23			TTTCTTCGACATC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3021G>A	X.37:g.32486756C>T		420.0	0.0	0		238.0	238.0	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.989;T|0.011	0.011	strong		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
DNM2	1785	hgsc.bcm.edu	37	19	10870486	10870486	+	Splice_Site	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10870486A>G	ENST00000355667.6	+	2	314	c.234A>G	c.(232-234)acA>acG	p.T78T	DNM2_ENST00000314646.5_Splice_Site_p.T78T|DNM2_ENST00000389253.4_Splice_Site_p.T78T|DNM2_ENST00000585892.1_Splice_Site_p.T78T|DNM2_ENST00000359692.6_Splice_Site_p.T78T|DNM2_ENST00000408974.4_Splice_Site_p.T78T	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	78	Dynamin-type G.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			TCTCAAAAACAGGTAAAATGG	0.587			"""F, N, Splice, Mis, O"""		ETP ALL																																p.T78T		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.A234G						PASS	.						101.0	107.0	105.0					19																	10870486		2203	4300	6503	SO:0001630	splice_region_variant	1785	exon2			AAAAACAGGTAAA		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.235+1A>G	19.37:g.10870486A>G		122.0	0.0	0		102.0	43.0	0.421569	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																			.	.	none		0.587	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	Silent
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94.0	95.0	94.0		3049,2881	3.7	1.0	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	174.0	0.0	0		141.0	60.0	0.425532	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
PPP1R7	5510	hgsc.bcm.edu	37	2	242122130	242122130	+	Silent	SNP	A	A	G	rs113069444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242122130A>G	ENST00000234038.6	+	10	1449	c.975A>G	c.(973-975)acA>acG	p.T325T	PPP1R7_ENST00000407025.1_Silent_p.T325T|PPP1R7_ENST00000272983.8_Silent_p.T282T	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	325					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		GCCTGGAGACAGTGTACCTGG	0.602													A|||	3	0.000599042	0.0	0.0	5008	,	,		19210	0.0		0.003	False		,,,				2504	0.0				p.T325T	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											PPP1R7,NS,carcinoma,+2,1	PPP1R7	35	1	0			c.A975G						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	127.0	116.0	120.0		975	-10.4	0.1	2	dbSNP_132	120	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	PPP1R7	NM_002712.1		0,29,6474	GG,GA,AA		0.3023,0.0681,0.223		325/361	242122130	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5510	exon10			GGAGACAGTGTAC	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9295	protein-coding gene	gene with protein product		602877	"""protein phosphatase 1, regulatory (inhibitor) subunit 7"""			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.975A>G	2.37:g.242122130A>G		81.0	0.0	0		64.0	26.0	0.40625	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	A|A	6.902|6.902	0.536047|0.536047	0.13188|0.13188	6.81E-4|6.81E-4	0.003023|0.003023	ENSG00000115685|ENSG00000115685	ENST00000450367|ENST00000415769	.|.	.|.	.|.	5.19|5.19	-10.4|-10.4	0.00318|0.00318	.|.	.|.	.|.	.|.	.|.	T|T	0.41373|0.41373	0.1156|0.1156	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.54002|0.54002	-0.8358|-0.8358	4|4	.|.	.|.	.|.	-12.923|-12.923	5.0645|5.0645	0.14574|0.14574	0.3682:0.4119:0.0765:0.1434|0.3682:0.4119:0.0765:0.1434	.|.	.|.	.|.	.|.	R|G	300|47	.|.	.|.	Q|S	+|+	2|1	0|0	PPP1R7|PPP1R7	241770803|241770803	0.000000|0.000000	0.05858|0.05858	0.124000|0.124000	0.21820|0.21820	0.701000|0.701000	0.40568|0.40568	-5.138000|-5.138000	0.00147|0.00147	-3.714000|-3.714000	0.00117|0.00117	-1.258000|-1.258000	0.01471|0.01471	CAG|AGT	A|0.997;G|0.002;T|0.000	0.002	strong		0.602	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712	
UTP20	27340	hgsc.bcm.edu	37	12	101674926	101674926	+	Silent	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101674926T>G	ENST00000261637.4	+	2	252	c.78T>G	c.(76-78)gtT>gtG	p.V26V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	26					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TGGGGAATGTTAATATTGATA	0.303																																					p.V26V		Atlas-SNP	.											.	UTP20	222	.	0			c.T78G						PASS	.						82.0	83.0	82.0					12																	101674926		2203	4299	6502	SO:0001819	synonymous_variant	27340	exon2			GAATGTTAATATT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.78T>G	12.37:g.101674926T>G		119.0	0.0	0		111.0	31.0	0.279279	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			.	.	none		0.303	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
FGFR2	2263	hgsc.bcm.edu	37	10	123325034	123325034	+	Silent	SNP	C	C	T	rs1047101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123325034C>T	ENST00000358487.5	-	3	566	c.294G>A	c.(292-294)acG>acA	p.T98T	FGFR2_ENST00000346997.2_Silent_p.T98T|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000369056.1_Silent_p.T98T|FGFR2_ENST00000351936.6_Silent_p.T98T|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000359354.2_Silent_p.T98T|FGFR2_ENST00000369061.4_Silent_p.T98T|FGFR2_ENST00000369060.4_Silent_p.T98T|FGFR2_ENST00000457416.2_Silent_p.T98T|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000360144.3_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	98	Ig-like C2-type 1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	AGTCTCTAGGCGTGGCGCCCT	0.537		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				C|||	17	0.00339457	0.0015	0.0058	5008	,	,		17879	0.0		0.0099	False		,,,				2504	0.001				p.T98T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G294A						PASS	.	C	,,,,,,,,	7,4399	12.9+/-30.5	0,7,2196	175.0	150.0	158.0		294,294,294,,,294,,,294	-0.8	1.0	10	dbSNP_86	158	79,8521	46.3+/-105.2	1,77,4222	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,intron,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	1,84,6418	TT,TC,CC		0.9186,0.1589,0.6612	,,,,,,,,	98/822,98/770,98/710,,,98/706,,,98/823	123325034	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon3	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	TCTAGGCGTGGCG	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.294G>A	10.37:g.123325034C>T		154.0	0.0	0		161.0	87.0	0.540373	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|0.993;T|0.007	0.007	strong		0.537	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
ALG1	56052	hgsc.bcm.edu	37	16	5132659	5132659	+	Missense_Mutation	SNP	C	C	T	rs74910062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:5132659C>T	ENST00000262374.5	+	11	1203	c.1172C>T	c.(1171-1173)gCt>gTt	p.A391V	ALG1_ENST00000588623.1_Missense_Mutation_p.A280V|ALG1_ENST00000544428.1_Missense_Mutation_p.A280V	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	391					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				CCTGTGTGTGCTGTGAACTTC	0.597													C|||	37	0.00738818	0.0212	0.0029	5008	,	,		20282	0.004		0.001	False		,,,				2504	0.002				p.A391V		Atlas-SNP	.											.	ALG1	35	.	0			c.C1172T						PASS	.						95.0	71.0	79.0					16																	5132659		2087	3975	6062	SO:0001583	missense	56052	exon11			TGTGTGCTGTGAA	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.1172C>T	16.37:g.5132659C>T	ENSP00000262374:p.Ala391Val	17.0	0.0	0		17.0	7.0	0.411765	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214278	0.79352	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.79141	-1.24;-1.24	5.28	5.28	0.74379	Glycosyl transferase, family 1 (1);	0.000000	0.85682	D	0.000000	D	0.90345	0.6979	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92258	0.5814	10	0.87932	D	0	-20.3409	17.5165	0.87775	0.0:1.0:0.0:0.0	.	280;391	B4DP08;Q9BT22	.;ALG1_HUMAN	V	391;280	ENSP00000262374:A391V;ENSP00000440019:A280V	ENSP00000262374:A391V	A	+	2	0	ALG1	5072660	1.000000	0.71417	0.702000	0.30337	0.479000	0.33129	7.176000	0.77643	2.474000	0.83562	0.555000	0.69702	GCT	.	.	weak		0.597	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
MUC6	4588	hgsc.bcm.edu	37	11	1027995	1027995	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1027995G>C	ENST00000421673.2	-	15	1868	c.1818C>G	c.(1816-1818)caC>caG	p.H606Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	606	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCACTGTGGCGTGGCACCTCT	0.667																																					p.H606Q		Atlas-SNP	.											.	MUC6	408	.	0			c.C1818G						PASS	.						29.0	34.0	32.0					11																	1027995		2115	4236	6351	SO:0001583	missense	4588	exon15			TGTGGCGTGGCAC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.1818C>G	11.37:g.1027995G>C	ENSP00000406861:p.His606Gln	106.0	0.0	0		110.0	17.0	0.154545	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	7.821	0.717831	0.15372	.	.	ENSG00000184956	ENST00000421673	T	0.79845	-1.31	4.93	-2.13	0.07144	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.31847	U	0.006963	D	0.85575	0.5728	M	0.86420	2.815	0.18873	N	0.999982	D	0.61080	0.989	D	0.66351	0.943	T	0.76277	-0.3018	10	0.87932	D	0	.	3.0196	0.06071	0.3712:0.1112:0.4057:0.112	.	606	Q6W4X9	MUC6_HUMAN	Q	606	ENSP00000406861:H606Q	ENSP00000406861:H606Q	H	-	3	2	MUC6	1017995	0.000000	0.05858	0.008000	0.14137	0.098000	0.18820	-0.761000	0.04751	-0.607000	0.05738	-1.564000	0.00881	CAC	.	.	none		0.667	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000430669.2_Silent_p.T179T|PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000375274.2_Silent_p.T244T|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000468211.2_Silent_p.T179T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	245					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GGAGGTATGCTGTCCCAGACT	0.388													T|||	47	0.00938498	0.0023	0.0202	5008	,	,		17942	0.0		0.0249	False		,,,				2504	0.0051				p.T245T		Atlas-SNP	.											.	PTCH1	1850	.	0			c.A735G						PASS	.	T	,,,,,,	30,4376	34.3+/-65.2	0,30,2173	84.0	70.0	75.0		735,537,732,282,282,282,282	-2.5	1.0	9	dbSNP_89	75	329,8271	115.2+/-175.0	4,321,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	4,351,6148	CC,CT,TT		3.8256,0.6809,2.7603	,,,,,,	245/1448,179/1382,244/1447,94/1297,94/1297,94/1297,94/1297	98244242	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon5			GTATGCTGTCCCA	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.735A>G	9.37:g.98244242T>C		91.0	0.0	0		94.0	42.0	0.446809	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.976;C|0.024	0.024	strong		0.388	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
MYH1	4619	hgsc.bcm.edu	37	17	10401064	10401064	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10401064C>A	ENST00000226207.5	-	31	4446	c.4352G>T	c.(4351-4353)aGg>aTg	p.R1451M	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1451				R -> T (in Ref. 4; CAA27380). {ECO:0000305}.	muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						ATCAAAGTTCCTTTGCTTTTT	0.443																																					p.R1451M		Atlas-SNP	.											.	MYH1	403	.	0			c.G4352T						PASS	.						119.0	117.0	118.0					17																	10401064		2203	4300	6503	SO:0001583	missense	4619	exon31			AAGTTCCTTTGCT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.4352G>T	17.37:g.10401064C>A	ENSP00000226207:p.Arg1451Met	166.0	0.0	0		155.0	40.0	0.258065	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169376	0.57584	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	T	0.80393	-1.37	5.65	5.65	0.86999	Myosin tail (1);	0.138860	0.32593	U	0.005888	D	0.91686	0.7372	H	0.96748	3.875	0.41280	D	0.986904	D	0.71674	0.998	D	0.70016	0.967	D	0.92699	0.6173	10	0.87932	D	0	.	7.7121	0.28684	0.0:0.8062:0.0:0.1938	.	1451	P12882	MYH1_HUMAN	M	1451;540	ENSP00000226207:R1451M	ENSP00000226207:R1451M	R	-	2	0	MYH1	10341789	0.929000	0.31497	1.000000	0.80357	0.903000	0.53119	1.648000	0.37271	2.811000	0.96726	0.655000	0.94253	AGG	.	.	none		0.443	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
KLHL32	114792	hgsc.bcm.edu	37	6	97423931	97423931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97423931G>A	ENST00000369261.4	+	3	445	c.82G>A	c.(82-84)Gtc>Atc	p.V28I	KLHL32_ENST00000539200.1_Missense_Mutation_p.V28I|KLHL32_ENST00000544166.1_5'UTR|KLHL32_ENST00000536676.1_Missense_Mutation_p.V28I	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	28										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		CAATGACAGTGTCCTGGCAGC	0.493																																					p.V28I		Atlas-SNP	.											.	KLHL32	85	.	0			c.G82A						PASS	.						82.0	69.0	73.0					6																	97423931		2203	4300	6503	SO:0001583	missense	114792	exon3			GACAGTGTCCTGG	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.82G>A	6.37:g.97423931G>A	ENSP00000358265:p.Val28Ile	87.0	0.0	0		83.0	23.0	0.277108	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181059	0.78677	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200;ENST00000369254	T;T;T;T	0.70749	-0.51;1.97;1.97;-0.51	5.14	5.14	0.70334	BTB/POZ fold (2);	0.055908	0.64402	N	0.000001	T	0.61438	0.2347	N	0.24115	0.695	0.80722	D	1	P;P;B;P	0.50156	0.517;0.932;0.397;0.9	B;P;B;B	0.61592	0.227;0.891;0.281;0.323	T	0.57740	-0.7759	10	0.07325	T	0.83	.	18.7846	0.91949	0.0:0.0:1.0:0.0	.	28;28;28;28	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	I	28	ENSP00000358265:V28I;ENSP00000440382:V28I;ENSP00000441527:V28I;ENSP00000358258:V28I	ENSP00000358258:V28I	V	+	1	0	KLHL32	97530652	1.000000	0.71417	0.990000	0.47175	0.702000	0.40608	9.263000	0.95617	2.674000	0.91012	0.591000	0.81541	GTC	.	.	none		0.493	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
TMCO4	255104	hgsc.bcm.edu	37	1	20073019	20073019	+	Silent	SNP	C	C	T	rs34281331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20073019C>T	ENST00000294543.6	-	9	928	c.687G>A	c.(685-687)gcG>gcA	p.A229A	TMCO4_ENST00000375122.2_Silent_p.A229A|TMCO4_ENST00000375127.1_Silent_p.A229A	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	229						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGCCCAGAGCCGCTGCCCCGG	0.587													C|||	207	0.0413339	0.0242	0.0735	5008	,	,		17314	0.0605		0.0179	False		,,,				2504	0.046				p.A229A		Atlas-SNP	.											.	TMCO4	46	.	0			c.G687A						PASS	.	C		86,4320	68.1+/-105.8	0,86,2117	22.0	22.0	22.0		687	-10.3	0.0	1	dbSNP_126	22	150,8446	66.3+/-128.7	1,148,4149	no	coding-synonymous	TMCO4	NM_181719.4		1,234,6266	TT,TC,CC		1.745,1.9519,1.8151		229/635	20073019	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	255104	exon9			CAGAGCCGCTGCC		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.687G>A	1.37:g.20073019C>T		374.0	1.0	0.0026738		372.0	185.0	0.497312	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.587	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37732509	37732509	+	Silent	SNP	G	G	A	rs369997427		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:37732509G>A	ENST00000330843.4	-	3	1158	c.1146C>T	c.(1144-1146)tcC>tcT	p.S382S	RAB11FIP1_ENST00000287263.4_Silent_p.S382S|RAB11FIP1_ENST00000523182.1_5'Flank|RAB11FIP1_ENST00000522727.1_Silent_p.S234S|RAB11FIP1_ENST00000524118.1_Silent_p.S234S	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	382					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGGAAGATTCGGAGAGCTGCC	0.567																																					p.S382S		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C1146T						PASS	.						59.0	60.0	60.0					8																	37732509		2203	4300	6503	SO:0001819	synonymous_variant	80223	exon3			AGATTCGGAGAGC	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.1146C>T	8.37:g.37732509G>A		90.0	0.0	0		87.0	24.0	0.275862	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																			.	.	weak		0.567	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
CMYA5	202333	hgsc.bcm.edu	37	5	79029025	79029025	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79029025T>C	ENST00000446378.2	+	2	4468	c.4437T>C	c.(4435-4437)tcT>tcC	p.S1479S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1479					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAACATCATCTTCTCAGCATT	0.388																																					p.S1479S		Atlas-SNP	.											CMYA5_ENST00000446378,NS,carcinoma,+1,2	CMYA5	643	2	0			c.T4437C						PASS	.						90.0	88.0	88.0					5																	79029025		1853	4095	5948	SO:0001819	synonymous_variant	202333	exon2			ATCATCTTCTCAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.4437T>C	5.37:g.79029025T>C		103.0	0.0	0		74.0	16.0	0.216216	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.388	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
PFKP	5214	hgsc.bcm.edu	37	10	3178001	3178001	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3178001G>A	ENST00000381125.4	+	21	2272	c.2196G>A	c.(2194-2196)gtG>gtA	p.V732V	PFKP_ENST00000381075.2_Silent_p.V724V|PFKP_ENST00000381072.1_Silent_p.V150V|PITRM1_ENST00000464395.1_5'Flank	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	732	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TTCAACCTGTGGCAGAGCTGA	0.403																																					p.V732V		Atlas-SNP	.											.	PFKP	182	.	0			c.G2196A						PASS	.						78.0	78.0	78.0					10																	3178001		2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			ACCTGTGGCAGAG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.2196G>A	10.37:g.3178001G>A		112.0	0.0	0		118.0	37.0	0.313559	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	g	2.795	-0.250360	0.05867	.	.	ENSG00000067057	ENST00000433193	.	.	.	4.92	2.06	0.26882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.47	0.11708	0.2166:0.0:0.5125:0.271	.	.	.	.	X	85	.	.	W	+	2	0	PFKP	3168001	0.798000	0.28890	0.791000	0.31998	0.487000	0.33371	0.615000	0.24329	0.506000	0.28125	-0.361000	0.07541	TGG	.	.	none		0.403	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
ENTPD7	57089	hgsc.bcm.edu	37	10	101458487	101458487	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101458487A>G	ENST00000370489.4	+	10	1385	c.1207A>G	c.(1207-1209)Ata>Gta	p.I403V		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	403						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		ACTCAATGGCATATATCAATC	0.517																																					p.I403V		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A1207G						PASS	.						88.0	81.0	83.0					10																	101458487		2203	4300	6503	SO:0001583	missense	57089	exon10			AATGGCATATATC	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.1207A>G	10.37:g.101458487A>G	ENSP00000359520:p.Ile403Val	247.0	0.0	0		153.0	76.0	0.496732	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	A	2.485	-0.318732	0.05386	.	.	ENSG00000198018	ENST00000370489	T	0.08282	3.11	4.79	4.79	0.61399	.	0.069391	0.64402	D	0.000010	T	0.02807	0.0084	N	0.02697	-0.525	0.32828	D	0.503591	B	0.02656	0.0	B	0.04013	0.001	T	0.25779	-1.0122	10	0.02654	T	1	-0.8043	8.8175	0.35004	0.9146:0.0:0.0854:0.0	.	403	Q9NQZ7	ENTP7_HUMAN	V	403	ENSP00000359520:I403V	ENSP00000359520:I403V	I	+	1	0	ENTPD7	101448477	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	2.569000	0.45973	2.022000	0.59522	0.533000	0.62120	ATA	.	.	none		0.517	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
SCTR	6344	hgsc.bcm.edu	37	2	120199139	120199139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:120199139C>T	ENST00000019103.5	-	12	1444	c.1177G>A	c.(1177-1179)Ggg>Agg	p.G393R		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	393					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CTCACCTCCCCATTGAGGAAG	0.602																																					p.G393R		Atlas-SNP	.											.	SCTR	45	.	0			c.G1177A						PASS	.						81.0	67.0	72.0					2																	120199139		2203	4300	6503	SO:0001583	missense	6344	exon12			CCTCCCCATTGAG		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.1177G>A	2.37:g.120199139C>T	ENSP00000019103:p.Gly393Arg	53.0	0.0	0		48.0	23.0	0.479167	NM_002980	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466290	0.63625	.	.	ENSG00000080293	ENST00000019103	T	0.79454	-1.27	4.78	2.02	0.26589	GPCR, family 2, secretin-like, conserved site (1);	0.104147	0.42420	N	0.000703	D	0.86818	0.6024	M	0.84511	2.7	0.46654	D	0.999149	D	0.89917	1.0	D	0.83275	0.996	D	0.85446	0.1158	10	0.87932	D	0	.	8.9316	0.35675	0.0:0.7531:0.0:0.2469	.	393	P47872	SCTR_HUMAN	R	393	ENSP00000019103:G393R	ENSP00000019103:G393R	G	-	1	0	SCTR	119915609	0.823000	0.29233	0.748000	0.31131	0.800000	0.45204	1.860000	0.39428	0.237000	0.21200	-0.140000	0.14226	GGG	.	.	none		0.602	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
GLO1	2739	hgsc.bcm.edu	37	6	38650631	38650631	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38650631T>C	ENST00000373365.4	-	4	415	c.329A>G	c.(328-330)gAt>gGt	p.D110G	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	110					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	CTGGGTCTCATCATCTTCAGT	0.368																																					p.D110G		Atlas-SNP	.											.	GLO1	12	.	0			c.A329G						PASS	.						161.0	131.0	141.0					6																	38650631		2203	4300	6503	SO:0001583	missense	2739	exon4			GTCTCATCATCTT	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"""glyoxalase domain containing 1"""	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.329A>G	6.37:g.38650631T>C	ENSP00000362463:p.Asp110Gly	82.0	0.0	0		95.0	5.0	0.0526316	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Missense_Mutation	SNP	ENST00000373365.4	37	CCDS4837.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959074	0.92726	.	.	ENSG00000124767	ENST00000373365	T	0.69561	-0.41	5.95	5.95	0.96441	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.043159	0.85682	D	0.000000	T	0.79969	0.4538	M	0.85462	2.755	0.80722	D	1	D	0.61080	0.989	D	0.65773	0.938	D	0.83766	0.0217	10	0.87932	D	0	-26.0981	16.0971	0.81132	0.0:0.0:0.0:1.0	.	110	Q04760	LGUL_HUMAN	G	110	ENSP00000362463:D110G	ENSP00000362463:D110G	D	-	2	0	GLO1	38758609	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.140000	0.77322	2.279000	0.76181	0.533000	0.62120	GAT	.	.	none		0.368	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
USP54	159195	hgsc.bcm.edu	37	10	75258558	75258558	+	Silent	SNP	G	G	A	rs61749235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75258558G>A	ENST00000339859.4	-	23	4984	c.4884C>T	c.(4882-4884)acC>acT	p.T1628T	USP54_ENST00000408019.1_Silent_p.T1628T|RP11-137L10.6_ENST00000442133.4_RNA|RP11-137L10.6_ENST00000595935.1_RNA|USP54_ENST00000428547.1_Silent_p.T1478T|PPP3CB_ENST00000394829.2_5'Flank|PPP3CB_ENST00000394828.2_5'Flank|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000600607.1_RNA|RP11-137L10.6_ENST00000593790.1_RNA|PPP3CB_ENST00000342558.3_5'Flank|USP54_ENST00000497106.1_5'UTR|RP11-137L10.6_ENST00000600206.1_RNA|RP11-137L10.6_ENST00000600887.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000422491.2_Silent_p.T763T|USP54_ENST00000394811.2_Silent_p.T669T|PPP3CB_ENST00000394822.2_5'Flank|PPP3CB_ENST00000360663.5_5'Flank|RP11-137L10.6_ENST00000596320.1_RNA|RP11-137L10.6_ENST00000422977.1_RNA|PPP3CB_ENST00000545874.1_5'Flank			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1628					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					GAGGACCAGGGGTTCGGGACC	0.547													G|||	37	0.00738818	0.0	0.013	5008	,	,		15599	0.0		0.0159	False		,,,				2504	0.0123				p.T1628T	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.C4884T						PASS	.	G		22,4384	29.9+/-59.1	0,22,2181	89.0	87.0	88.0		4884	-1.0	0.6	10	dbSNP_129	88	154,8446	74.2+/-136.8	1,152,4147	no	coding-synonymous	USP54	NM_152586.3		1,174,6328	AA,AG,GG		1.7907,0.4993,1.3532		1628/1685	75258558	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	159195	exon22			ACCAGGGGTTCGG	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"""Ubiquitin-specific peptidases"""	23513	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 29"", ""ubiquitin specific protease 54"""	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.4884C>T	10.37:g.75258558G>A		130.0	0.0	0		99.0	98.0	0.989899	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Silent	SNP	ENST00000339859.4	37	CCDS7329.2																																																																																			G|0.989;A|0.011	0.011	strong		0.547	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586	
BRINP2	57795	hgsc.bcm.edu	37	1	177242695	177242695	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:177242695G>T	ENST00000361539.4	+	5	1053	c.741G>T	c.(739-741)ttG>ttT	p.L247F	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	247	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GTTCTGTCTTGGTACAGAGTC	0.448																																					p.L247F		Atlas-SNP	.											.	FAM5B	191	.	0			c.G741T						PASS	.						85.0	77.0	79.0					1																	177242695		2203	4300	6503	SO:0001583	missense	57795	exon5			TGTCTTGGTACAG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.741G>T	1.37:g.177242695G>T	ENSP00000354481:p.Leu247Phe	209.0	0.0	0		190.0	35.0	0.184211	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015662	0.75161	.	.	ENSG00000198797	ENST00000361539	T	0.27402	1.67	5.39	4.44	0.53790	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.64402	D	0.000002	T	0.54647	0.1871	M	0.74647	2.275	0.58432	D	0.999999	D;D	0.71674	0.995;0.998	D;D	0.83275	0.954;0.996	T	0.58940	-0.7547	10	0.87932	D	0	-11.3146	13.6873	0.62524	0.0:0.0:0.7267:0.2733	.	142;247	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	F	247	ENSP00000354481:L247F	ENSP00000354481:L247F	L	+	3	2	FAM5B	175509318	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.030000	0.41108	2.537000	0.85549	0.655000	0.94253	TTG	.	.	none		0.448	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
MTIF2	4528	hgsc.bcm.edu	37	2	55470662	55470662	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:55470662A>G	ENST00000263629.4	-	12	1769	c.1454T>C	c.(1453-1455)cTg>cCg	p.L485P	MTIF2_ENST00000403721.1_Missense_Mutation_p.L485P|MTIF2_ENST00000394600.3_Missense_Mutation_p.L485P	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	485					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CTTCTTCCACAGTAGATGGCC	0.383																																					p.L485P		Atlas-SNP	.											.	MTIF2	64	.	0			c.T1454C						PASS	.						188.0	184.0	185.0					2																	55470662		2203	4300	6503	SO:0001583	missense	4528	exon12			TTCCACAGTAGAT	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1454T>C	2.37:g.55470662A>G	ENSP00000263629:p.Leu485Pro	256.0	0.0	0		422.0	328.0	0.777251	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	A	4.188	0.033551	0.08101	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.58358	0.34;0.34;0.34;0.87	5.6	1.63	0.23807	.	0.432007	0.27700	N	0.018206	T	0.28267	0.0698	N	0.08118	0	0.38365	D	0.944718	B	0.16802	0.019	B	0.22601	0.04	T	0.05784	-1.0864	10	0.36615	T	0.2	0.6749	7.0519	0.25077	0.2056:0.0:0.2629:0.5315	.	485	P46199	IF2M_HUMAN	P	485;485;485;163	ENSP00000384481:L485P;ENSP00000263629:L485P;ENSP00000378099:L485P;ENSP00000403492:L163P	ENSP00000263629:L485P	L	-	2	0	MTIF2	55324166	1.000000	0.71417	0.995000	0.50966	0.052000	0.14988	0.787000	0.26858	0.381000	0.24851	-0.275000	0.10095	CTG	.	.	none		0.383	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
SGK1	6446	hgsc.bcm.edu	37	6	134494426	134494426	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494426G>T	ENST00000237305.7	-	5	491	c.403C>A	c.(403-405)Ctg>Atg	p.L135M	SGK1_ENST00000528577.1_Missense_Mutation_p.L163M|SGK1_ENST00000413996.3_Missense_Mutation_p.L149M|SGK1_ENST00000367857.5_Missense_Mutation_p.L125M|SGK1_ENST00000367858.5_Missense_Mutation_p.L230M|SGK1_ENST00000475719.2_Missense_Mutation_p.L135M|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	135	Glu/Lys-rich.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCTTTTTCAGGATTGCTTTC	0.378																																					p.L230M		Atlas-SNP	.											.	SGK1	387	.	0			c.C688A						PASS	.						114.0	113.0	113.0					6																	134494426		2203	4300	6503	SO:0001583	missense	6446	exon7			TTTTCAGGATTGC	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.403C>A	6.37:g.134494426G>T	ENSP00000237305:p.Leu135Met	175.0	0.0	0		103.0	31.0	0.300971	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149912	0.57151	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;1.88	6.17	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.54481	0.1861	L	0.42686	1.345	0.80722	D	1	B;B;B;B;B;B	0.32918	0.24;0.386;0.389;0.099;0.39;0.121	B;B;P;B;B;B	0.44673	0.179;0.291;0.457;0.111;0.408;0.177	T	0.61262	-0.7098	10	0.54805	T	0.06	.	15.9715	0.80025	0.0648:0.0:0.9352:0.0	.	163;149;135;125;230;135	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	M	230;149;135;125;163;135	ENSP00000356832:L230M;ENSP00000396242:L149M;ENSP00000237305:L135M;ENSP00000356831:L125M;ENSP00000434450:L163M;ENSP00000434302:L135M	ENSP00000237305:L135M	L	-	1	2	SGK1	134536119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.089000	0.57685	1.599000	0.50093	0.655000	0.94253	CTG	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
AGTPBP1	23287	hgsc.bcm.edu	37	9	88204462	88204462	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:88204462A>G	ENST00000357081.3	-	20	2847	c.2703T>C	c.(2701-2703)taT>taC	p.Y901Y	AGTPBP1_ENST00000376109.3_Silent_p.Y913Y|AGTPBP1_ENST00000376083.3_Silent_p.Y861Y|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	901					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGATATGTTCATAATAATTAG	0.378																																					p.Y861Y		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.T2583C						PASS	.						133.0	129.0	130.0					9																	88204462		2203	4300	6503	SO:0001819	synonymous_variant	23287	exon20			ATGTTCATAATAA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.2703T>C	9.37:g.88204462A>G		142.0	0.0	0		119.0	48.0	0.403361	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				.	.	none		0.378	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
GCKR	2646	hgsc.bcm.edu	37	2	27741665	27741665	+	Missense_Mutation	SNP	G	G	A	rs141361209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27741665G>A	ENST00000264717.2	+	17	1496	c.1433G>A	c.(1432-1434)cGt>cAt	p.R478H	GCKR_ENST00000424318.2_Missense_Mutation_p.R288H	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	478	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)	p.R478L(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					AAGTTCCAGCGTGAGCTAAGC	0.473													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19790	0.0		0.002	False		,,,				2504	0.0				p.R478H		Atlas-SNP	.											GCKR,NS,carcinoma,0,1	GCKR	73	1	1	Substitution - Missense(1)	lung(1)	c.G1433A						PASS	.	G	HIS/ARG	1,4405		0,1,2202	105.0	101.0	103.0		1433	1.2	1.0	2	dbSNP_134	103	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GCKR	NM_001486.3	29	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign	478/626	27741665	4,13002	2203	4300	6503	SO:0001583	missense	2646	exon17			TCCAGCGTGAGCT	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1433G>A	2.37:g.27741665G>A	ENSP00000264717:p.Arg478His	107.0	0.0	0		123.0	46.0	0.373984	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	7.777	0.708592	0.15239	2.27E-4	3.49E-4	ENSG00000084734	ENST00000264717;ENST00000424318	D;D	0.83419	-1.72;-1.72	3.76	1.18	0.20946	Sugar isomerase (SIS) (1);	0.265072	0.33075	N	0.005308	T	0.58793	0.2147	N	0.25144	0.715	0.28844	N	0.896431	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.47045	-0.9147	10	0.11182	T	0.66	0.0223	9.1221	0.36793	0.1699:0.0:0.8301:0.0	.	288;476;478	F5H1P6;A8K731;Q14397	.;.;GCKR_HUMAN	H	478;288	ENSP00000264717:R478H;ENSP00000409109:R288H	ENSP00000264717:R478H	R	+	2	0	GCKR	27595169	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.557000	0.36299	0.269000	0.21961	0.561000	0.74099	CGT	G|0.999;A|0.001	0.001	strong		0.473	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486	
ZNF93	81931	hgsc.bcm.edu	37	19	20026163	20026163	+	Silent	SNP	G	G	C	rs150804499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20026163G>C	ENST00000343769.5	+	2	106	c.78G>C	c.(76-78)cgG>cgC	p.R26R	ZNF93_ENST00000591366.1_Silent_p.R26R|ZNF93_ENST00000592160.1_Silent_p.R26R|AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						CTGCACAGCGGAATCTATATA	0.398													g|||	44	0.00878594	0.0008	0.0115	5008	,	,		15681	0.0		0.0119	False		,,,				2504	0.0235				p.R26R		Atlas-SNP	.											.	ZNF93	81	.	0			c.G78C						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	144.0	147.0	146.0		78	-1.7	0.3	19	dbSNP_134	146	98,8502	55.2+/-116.2	1,96,4203	no	coding-synonymous	ZNF93	NM_031218.3		1,107,6395	CC,CG,GG		1.1395,0.2497,0.8381		26/621	20026163	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon2			ACAGCGGAATCTA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.78G>C	19.37:g.20026163G>C		27.0	0.0	0		27.0	14.0	0.518519	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			G|0.991;C|0.009	0.009	strong		0.398	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
RASA3	22821	hgsc.bcm.edu	37	13	114795333	114795333	+	Missense_Mutation	SNP	C	C	T	rs200024629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114795333C>T	ENST00000334062.7	-	5	524	c.403G>A	c.(403-405)Gag>Aag	p.E135K	RASA3_ENST00000389544.4_Missense_Mutation_p.E103K|RASA3_ENST00000542651.1_Missense_Mutation_p.R103Q	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	135	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			GTGATGACCTCGCTCAGCCGC	0.647													c|||	1	0.000199681	0.0008	0.0	5008	,	,		18381	0.0		0.0	False		,,,				2504	0.0				p.E135K		Atlas-SNP	.											.	RASA3	83	.	0			c.G403A						PASS	.						110.0	66.0	81.0					13																	114795333		2201	4297	6498	SO:0001583	missense	22821	exon5			TGACCTCGCTCAG		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.403G>A	13.37:g.114795333C>T	ENSP00000335029:p.Glu135Lys	43.0	0.0	0		48.0	23.0	0.479167	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.5|21.5	4.163421|4.163421	0.78226|0.78226	.|.	.|.	ENSG00000185989|ENSG00000185989	ENST00000334062;ENST00000389544|ENST00000542651	D;D|T	0.86164|0.17054	-1.97;-2.08|2.3	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.31606|0.31606	0.0802|0.0802	L|L	0.60455|0.60455	1.87|1.87	0.38497|0.38497	D|D	0.948117|0.948117	P|.	0.40660|.	0.726|.	B|.	0.39503|.	0.301|.	T|T	0.07290|0.07290	-1.0780|-1.0780	9|6	.|.	.|.	.|.	.|.	16.3374|16.3374	0.83068|0.83068	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	135|.	Q14644|.	RASA3_HUMAN|.	K|Q	135;103|103	ENSP00000335029:E135K;ENSP00000374195:E103K|ENSP00000439008:R103Q	.|.	E|R	-|-	1|2	0|0	RASA3|RASA3	113813435|113813435	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.916000|0.916000	0.54674|0.54674	6.028000|6.028000	0.70889|0.70889	2.207000|2.207000	0.71202|0.71202	0.561000|0.561000	0.74099|0.74099	GAG|CGA	C|1.000;T|0.000	0.000	strong		0.647	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
MSRB3	253827	hgsc.bcm.edu	37	12	65857078	65857078	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:65857078C>T	ENST00000355192.3	+	6	681	c.555C>T	c.(553-555)gcC>gcT	p.A185A	MSRB3_ENST00000535664.1_Silent_p.A178A|MSRB3_ENST00000308259.5_Silent_p.A178A	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	185					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		CCAGCCCGGCCCAGGCAGACA	0.473																																					p.A185A		Atlas-SNP	.											.	MSRB3	80	.	0			c.C555T						PASS	.						49.0	47.0	48.0					12																	65857078		2203	4300	6503	SO:0001819	synonymous_variant	253827	exon6			CCCGGCCCAGGCA	BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"""deafness, autosomal recessive 74"""	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.555C>T	12.37:g.65857078C>T		113.0	0.0	0		75.0	27.0	0.36	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Silent	SNP	ENST00000355192.3	37	CCDS8973.1																																																																																			.	.	none		0.473	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080	
BMP2K	55589	hgsc.bcm.edu	37	4	79832870	79832870	+	Missense_Mutation	SNP	A	A	T	rs116710382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79832870A>T	ENST00000335016.5	+	16	3335	c.3169A>T	c.(3169-3171)Aat>Tat	p.N1057Y	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1057					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AGATAGGGGGAATGTCTTACA	0.522													A|||	19	0.00379393	0.0	0.0101	5008	,	,		20274	0.0		0.0119	False		,,,				2504	0.0				p.N1057Y		Atlas-SNP	.											.	BMP2K	169	.	0			c.A3169T						PASS	.	A	TYR/ASN	5,3897		0,5,1946	101.0	101.0	101.0		3169	1.3	0.0	4	dbSNP_132	101	61,8203		0,61,4071	yes	missense	BMP2K	NM_198892.1	143	0,66,6017	TT,TA,AA		0.7381,0.1281,0.5425	benign	1057/1162	79832870	66,12100	1951	4132	6083	SO:0001583	missense	55589	exon16			AGGGGGAATGTCT	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.3169A>T	4.37:g.79832870A>T	ENSP00000334836:p.Asn1057Tyr	151.0	0.0	0		135.0	70.0	0.518519	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	A|A	3.678|3.678	-0.066194|-0.066194	0.07273|0.07273	0.001281|0.001281	0.007381|0.007381	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000335016	.|T	.|0.43688	.|0.94	5.41|5.41	1.3|1.3	0.21679|0.21679	.|.	.|1.089200	.|0.07033	.|N	.|0.828802	T|T	0.24198|0.24198	0.0586|0.0586	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.26400	.|0.148	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	5|10	.|0.44086	.|T	.|0.13	-1.0317|-1.0317	13.6768|13.6768	0.62458|0.62458	0.4465:0.5535:0.0:0.0|0.4465:0.5535:0.0:0.0	.|.	.|1057	.|Q9NSY1	.|BMP2K_HUMAN	V|Y	749|1057	.|ENSP00000334836:N1057Y	.|ENSP00000334836:N1057Y	E|N	+|+	2|1	0|0	BMP2K|BMP2K	80051894|80051894	0.407000|0.407000	0.25352|0.25352	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	2.601000|2.601000	0.46249|0.46249	0.336000|0.336000	0.23639|0.23639	0.397000|0.397000	0.26171|0.26171	GAA|AAT	A|0.993;T|0.007	0.007	strong		0.522	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
DST	667	hgsc.bcm.edu	37	6	56494071	56494071	+	Silent	SNP	A	A	G	rs112640831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56494071A>G	ENST00000361203.3	-	28	3826	c.3819T>C	c.(3817-3819)aaT>aaC	p.N1273N	DST_ENST00000370769.4_Silent_p.N1273N|DST_ENST00000244364.6_Silent_p.N947N|DST_ENST00000446842.2_Silent_p.N947N|DST_ENST00000370754.5_Silent_p.N1451N|DST_ENST00000312431.6_Silent_p.N1273N|DST_ENST00000518935.1_Silent_p.N947N|DST_ENST00000370765.6_Silent_p.N947N|DST_ENST00000370788.2_Silent_p.N1273N|DST_ENST00000421834.2_Silent_p.N1273N			Q03001	DYST_HUMAN	dystonin	1273					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCACATGAACATTTTGCCACC	0.338													A|||	53	0.0105831	0.0015	0.0101	5008	,	,		18282	0.0		0.0268	False		,,,				2504	0.0174				p.N947N		Atlas-SNP	.											.	DST	1427	.	0			c.T2841C						PASS	.	A	,	33,4373	37.6+/-69.7	0,33,2170	276.0	228.0	244.0		2841,2841	-1.0	1.0	6	dbSNP_132	244	360,8240	120.2+/-179.5	9,342,3949	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	9,375,6119	GG,GA,AA		4.186,0.749,3.0217	,	947/2650,947/5172	56494071	393,12613	2203	4300	6503	SO:0001819	synonymous_variant	667	exon18			ATGAACATTTTGC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3819T>C	6.37:g.56494071A>G		168.0	0.0	0		128.0	66.0	0.515625	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				A|0.974;G|0.026;T|0.000	0.026	strong		0.338	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
NEB	4703	hgsc.bcm.edu	37	2	152382759	152382759	+	Silent	SNP	T	T	C	rs61730765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152382759T>C	ENST00000172853.10	-	121	17007	c.16860A>G	c.(16858-16860)aaA>aaG	p.K5620K	NEB_ENST00000427231.2_Silent_p.K7321K|NEB_ENST00000409198.1_Silent_p.K5620K|NEB_ENST00000397345.3_Silent_p.K7321K|NEB_ENST00000603639.1_Silent_p.K7321K|NEB_ENST00000604864.1_Silent_p.K7321K			P20929	NEBU_HUMAN	nebulin	5620					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CCTTGACATGTTTCTCTTTGT	0.488													T|||	107	0.0213658	0.0537	0.0072	5008	,	,		16984	0.0		0.0268	False		,,,				2504	0.0041				p.K7356K		Atlas-SNP	.											.	NEB	1697	.	0			c.A22068G						PASS	.	T	,,	176,3694		7,162,1766	64.0	65.0	65.0		21963,21963,16860	-3.7	1.0	2	dbSNP_129	65	159,8093		2,155,3969	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	9,317,5735	CC,CT,TT		1.9268,4.5478,2.7636	,,	7321/8526,7321/8526,5620/6670	152382759	335,11787	1935	4126	6061	SO:0001819	synonymous_variant	4703	exon150			GACATGTTTCTCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16860A>G	2.37:g.152382759T>C		130.0	0.0	0		103.0	47.0	0.456311	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				T|0.975;C|0.025	0.025	strong		0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
C14orf37	145407	hgsc.bcm.edu	37	14	58605156	58605156	+	Silent	SNP	G	G	A	rs61748937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605156G>A	ENST00000267485.7	-	2	1115	c.921C>T	c.(919-921)gcC>gcT	p.A307A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	307						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TTAAGGCAGAGGCAGCTGGAA	0.517													G|||	17	0.00339457	0.0015	0.0029	5008	,	,		21146	0.0		0.0109	False		,,,				2504	0.002				p.A307A		Atlas-SNP	.											.	C14orf37	87	.	0			c.C921T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	93.0	97.0	96.0		921	0.4	0.0	14	dbSNP_129	96	134,8466	68.0+/-130.5	1,132,4167	no	coding-synonymous	C14orf37	NM_001001872.2		1,140,6362	AA,AG,GG		1.5581,0.1816,1.0918		307/775	58605156	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			GGCAGAGGCAGCT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.921C>T	14.37:g.58605156G>A		218.0	0.0	0		175.0	98.0	0.56	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
OR5L1	219437	hgsc.bcm.edu	37	11	55579068	55579068	+	Silent	SNP	C	C	T	rs575553149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579068C>T	ENST00000333973.2	+	1	215	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TGTTAGCCAACCTGGGCATGA	0.498																																					p.N42N		Atlas-SNP	.											OR5L1,colon,carcinoma,0,3	OR5L1	145	3	0			c.C126T						scavenged	.						325.0	285.0	299.0					11																	55579068		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			AGCCAACCTGGGC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.126C>T	11.37:g.55579068C>T		113.0	0.0	0		143.0	8.0	0.0559441	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			.	.	none		0.498	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272482	11272482	+	Missense_Mutation	SNP	G	G	A	rs72650691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11272482G>A	ENST00000409790.1	+	24	3327	c.3097G>A	c.(3097-3099)Gcc>Acc	p.A1033T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A120T	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCCGGCTGCCGCCTGCACAGA	0.687													G|||	4	0.000798722	0.0008	0.0029	5008	,	,		15009	0.0		0.001	False		,,,				2504	0.0				p.A1033T		Atlas-SNP	.											CLEC16A,NS,carcinoma,-1,1	CLEC16A	101	1	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3097A						PASS	.	G	THR/ALA	2,4080		0,2,2039	10.0	13.0	12.0		3097	1.3	0.0	16	dbSNP_130	12	20,8320		0,20,4150	yes	missense	CLEC16A	NM_015226.2	58	0,22,6189	AA,AG,GG		0.2398,0.049,0.1771	benign	1033/1054	11272482	22,12400	2041	4170	6211	SO:0001583	missense	23274	exon23			GCTGCCGCCTGCA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.3097G>A	16.37:g.11272482G>A	ENSP00000387122:p.Ala1033Thr	12.0	0.0	0		13.0	13.0	1	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	8.999	0.979594	0.18812	4.9E-4	0.002398	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44482	0.92	4.4	1.28	0.21552	.	1.314290	0.04911	N	0.453315	T	0.23846	0.0577	N	0.08118	0	0.09310	N	1	B;B	0.20261	0.043;0.0	B;B	0.10450	0.005;0.0	T	0.19910	-1.0291	10	0.23302	T	0.38	-0.2189	8.3364	0.32217	0.2744:0.0:0.7256:0.0	.	120;1033	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1033;1033;120	ENSP00000387122:A1033T	ENSP00000371244:A120T	A	+	1	0	CLEC16A	11179983	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.320000	0.19540	0.440000	0.26502	-0.794000	0.03295	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62194238C>T	ENST00000467148.1	-	8	6006	c.5937G>A	c.(5935-5937)ccG>ccA	p.P1979P	HELZ2_ENST00000427522.2_Silent_p.P1410P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1979					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCTGCCCCTGCGGCGTCCGTG	0.657													C|||	71	0.0141773	0.0008	0.0303	5008	,	,		15702	0.001		0.0408	False		,,,				2504	0.0072				p.P1979P		Atlas-SNP	.											.	.	.	.	0			c.G5937A						PASS	.	C	,	23,4271		0,23,2124	10.0	11.0	11.0		5937,4230	-9.2	0.0	20	dbSNP_126	11	243,8151		3,237,3957	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	3,260,6081	TT,TC,CC		2.8949,0.5356,2.0965	,	1979/2650,1410/2081	62194238	266,12422	2147	4197	6344	SO:0001819	synonymous_variant	85441	exon9			CCCCTGCGGCGTC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.5937G>A	20.37:g.62194238C>T		83.0	0.0	0		99.0	38.0	0.383838	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.984;T|0.016	0.016	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
MAGI1	9223	hgsc.bcm.edu	37	3	65464386	65464386	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:65464386C>G	ENST00000497477.2	-	4	637	c.638G>C	c.(637-639)gGc>gCc	p.G213A	MAGI1_ENST00000402939.2_Missense_Mutation_p.G213A|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000330909.8_Missense_Mutation_p.G213A|MAGI1_ENST00000483466.1_Missense_Mutation_p.G213A			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	213	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CTGCTTAGAGCCAGACTGAAG	0.527																																					p.G213A		Atlas-SNP	.											.	MAGI1	481	.	0			c.G638C						PASS	.						165.0	143.0	151.0					3																	65464386		2203	4300	6503	SO:0001583	missense	9223	exon4			TTAGAGCCAGACT	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.638G>C	3.37:g.65464386C>G	ENSP00000424369:p.Gly213Ala	169.0	0.0	0		146.0	38.0	0.260274	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.85|10.85	1.467724|1.467724	0.26335|0.26335	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477	.|T;T;T;T;T	.|0.42900	.|0.96;0.96;2.35;0.96;0.96	5.89|5.89	5.89|5.89	0.94794|0.94794	.|Guanylate kinase/L-type calcium channel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52613|0.52613	0.1745|0.1745	L|L	0.35854|0.35854	1.095|1.095	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P;P	.|0.52692	.|0.944;0.907;0.955;0.893;0.951;0.656	.|P;B;P;B;D;P	.|0.63113	.|0.599;0.395;0.725;0.303;0.911;0.465	T|T	0.25257|0.25257	-1.0137|-1.0137	5|10	.|0.11485	.|T	.|0.65	-22.988|-22.988	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|213;213;213;213;213;213	.|Q96QZ7-6;Q96QZ7;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;MAGI1_HUMAN;.;.;.;.	P|A	94|213;213;109;88;213;213	.|ENSP00000385450:G213A;ENSP00000331157:G213A;ENSP00000418177:G88A;ENSP00000420323:G213A;ENSP00000424369:G213A	.|ENSP00000331157:G213A	A|G	-|-	1|2	0|0	MAGI1|MAGI1	65439426|65439426	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.770000|5.770000	0.68873|0.68873	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.	none		0.527	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
DGKH	160851	hgsc.bcm.edu	37	13	42803315	42803315	+	Silent	SNP	G	G	A	rs376522940		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42803315G>A	ENST00000337343.4	+	30	3675	c.3654G>A	c.(3652-3654)tcG>tcA	p.S1218S	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_3'UTR|DGKH_ENST00000536612.1_Silent_p.S1082S|DGKH_ENST00000261491.5_3'UTR|DGKH_ENST00000379274.2_Silent_p.S1098S	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1218					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CTCCACAGTCGGAGGTGTAAT	0.413																																					p.S1218S		Atlas-SNP	.											.	DGKH	106	.	0			c.G3654A						PASS	.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	76.0	77.0	77.0		,3294,3246,,3654	-4.6	0.0	13		77	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	,1098/1101,1082/1085,,1218/1221	42803315	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon30			ACAGTCGGAGGTG	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3654G>A	13.37:g.42803315G>A		71.0	0.0	0		67.0	10.0	0.149254	NM_178009	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			.	.	weak		0.413	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
MYLK2	85366	hgsc.bcm.edu	37	20	30414621	30414621	+	Silent	SNP	C	C	T	rs6089088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30414621C>T	ENST00000375994.2	+	7	1377	c.1104C>T	c.(1102-1104)ttC>ttT	p.F368F	MYLK2_ENST00000375985.4_Silent_p.F368F|MYLK2_ENST00000468730.1_3'UTR			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	368	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GAGAGCTCTTCGAGAGGATTG	0.592													C|||	41	0.0081869	0.0008	0.013	5008	,	,		19225	0.0		0.0209	False		,,,				2504	0.0102				p.F368F		Atlas-SNP	.											.	MYLK2	76	.	0			c.C1104T						PASS	.	C		25,4381	32.6+/-62.9	0,25,2178	124.0	99.0	108.0		1104	1.4	1.0	20	dbSNP_114	108	186,8414	84.0+/-146.5	0,186,4114	no	coding-synonymous	MYLK2	NM_033118.3		0,211,6292	TT,TC,CC		2.1628,0.5674,1.6223		368/597	30414621	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	85366	exon8			GCTCTTCGAGAGG	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"""skeletal muscle myosin light chain kinase"""	606566	"""myosin light chain kinase 2, skeletal muscle"""				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1104C>T	20.37:g.30414621C>T		175.0	0.0	0		159.0	75.0	0.471698	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	37	CCDS13191.1																																																																																			C|0.986;T|0.014	0.014	strong		0.592	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118	
PTGIS	5740	hgsc.bcm.edu	37	20	48156249	48156249	+	Silent	SNP	G	G	A	rs61322884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:48156249G>A	ENST00000244043.4	-	5	560	c.531C>T	c.(529-531)taC>taT	p.Y177Y	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	177					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	AAAGAGTCAGGTAGCCGGCTC	0.602													G|||	56	0.0111821	0.0015	0.0173	5008	,	,		16309	0.0		0.0358	False		,,,				2504	0.0061				p.Y177Y		Atlas-SNP	.											.	PTGIS	60	.	0			c.C531T						PASS	.	G		17,4387	21.2+/-45.6	0,17,2185	34.0	34.0	34.0		531	4.2	1.0	20	dbSNP_129	34	259,8341	98.6+/-160.1	2,255,4043	no	coding-synonymous	PTGIS	NM_000961.3		2,272,6228	AA,AG,GG		3.0116,0.386,2.1224		177/501	48156249	276,12728	2202	4300	6502	SO:0001819	synonymous_variant	5740	exon5			AGTCAGGTAGCCG		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.531C>T	20.37:g.48156249G>A		36.0	0.0	0		31.0	19.0	0.612903	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
PCSK1	5122	hgsc.bcm.edu	37	5	95751785	95751785	+	Missense_Mutation	SNP	T	T	C	rs6232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:95751785T>C	ENST00000311106.3	-	6	898	c.661A>G	c.(661-663)Aat>Gat	p.N221D	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.N174D	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	221	Peptidase S8.		N -> D (associated with susceptibility to obesity; induces a 10.4% reduction of activity (P = 0.03) when compared to the wild-type enzyme; dbSNP:rs6232). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:18604207}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TTGTGATTATTTGCTTGCATG	0.373													T|||	105	0.0209665	0.0023	0.0259	5008	,	,		20477	0.002		0.0328	False		,,,				2504	0.0501				p.N221D		Atlas-SNP	.											.	PCSK1	93	.	0			c.A661G	GRCh37	CM083013	PCSK1	M	rs6232	PASS	.	T	ASP/ASN,ASP/ASN	44,4362	45.3+/-79.5	0,44,2159	170.0	161.0	164.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	661,520	6.1	1.0	5	dbSNP_52	164	431,8169	132.5+/-190.1	9,413,3878	yes	missense,missense	PCSK1	NM_000439.4,NM_001177875.1	23,23	9,457,6037	CC,CT,TT		5.0116,0.9986,3.6522	benign,benign	221/754,174/707	95751785	475,12531	2203	4300	6503	SO:0001583	missense	5122	exon6			GATTATTTGCTTG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.661A>G	5.37:g.95751785T>C	ENSP00000308024:p.Asn221Asp	170.0	0.0	0		168.0	80.0	0.47619	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	39	0.017857142857142856	1	0.0020325203252032522	7	0.019337016574585635	2	0.0034965034965034965	29	0.03825857519788918	T	16.91	3.253847	0.59212	0.009986	0.050116	ENSG00000175426	ENST00000311106;ENST00000508626	D;D	0.87650	-2.28;-2.28	6.06	6.06	0.98353	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.041262	0.85682	D	0.000000	T	0.57460	0.2055	M	0.62088	1.915	0.48040	D	0.999572	B	0.19445	0.036	B	0.23852	0.049	T	0.72760	-0.4196	10	0.36615	T	0.2	-28.6369	16.2708	0.82618	0.0:0.0:0.0:1.0	rs6232;rs17470938;rs57975876;rs6232	221	P29120	NEC1_HUMAN	D	221;174	ENSP00000308024:N221D;ENSP00000421600:N174D	ENSP00000308024:N221D	N	-	1	0	PCSK1	95777541	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.656000	0.67988	2.324000	0.78689	0.533000	0.62120	AAT	T|0.968;C|0.032	0.032	strong		0.373	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
SAMD4B	55095	hgsc.bcm.edu	37	19	39873858	39873858	+	Silent	SNP	T	T	G	rs140996761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:39873858T>G	ENST00000314471.6	+	15	3018	c.1983T>G	c.(1981-1983)gtT>gtG	p.V661V	SAMD4B_ENST00000598913.1_Silent_p.V661V|SAMD4B_ENST00000596368.1_Intron	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	661					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			ACTGCCCGGTTCCTGGGCCTG	0.562													t|||	12	0.00239617	0.0	0.0014	5008	,	,		20343	0.0		0.0109	False		,,,				2504	0.0				p.V661V		Atlas-SNP	.											.	SAMD4B	48	.	0			c.T1983G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	150.0	116.0	128.0		1983	0.1	1.0	19	dbSNP_134	128	72,8528	42.6+/-100.3	1,70,4229	no	coding-synonymous	SAMD4B	NM_018028.2		1,74,6428	GG,GT,TT		0.8372,0.0908,0.5843		661/695	39873858	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	55095	exon15			CCCGGTTCCTGGG		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.1983T>G	19.37:g.39873858T>G		162.0	0.0	0		105.0	52.0	0.495238	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	6.377	0.437719	0.12104	9.08E-4	0.008372	ENSG00000179134	ENST00000429637	.	.	.	4.2	0.092	0.14470	.	.	.	.	.	T	0.47820	0.1466	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54846	-0.8232	5	0.87932	D	0	.	2.9929	0.05989	0.1656:0.441:0.2913:0.1021	.	.	.	.	A	661	.	ENSP00000387732:S661A	S	+	1	0	SAMD4B	44565698	0.999000	0.42202	1.000000	0.80357	0.583000	0.36354	0.404000	0.20999	0.368000	0.24481	-0.805000	0.03199	TCC	T|0.996;G|0.004	0.004	strong		0.562	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133966522	133966522	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:133966522G>A	ENST00000298622.4	+	16	2200	c.2062G>A	c.(2062-2064)Gaa>Aaa	p.E688K	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	688						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GACCTTGGCCGAAAAGGTAAC	0.597																																					p.E688K		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G2062A						PASS	.						116.0	81.0	93.0					10																	133966522		2200	4293	6493	SO:0001583	missense	282973	exon16			TTGGCCGAAAAGG	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.2062G>A	10.37:g.133966522G>A	ENSP00000298622:p.Glu688Lys	96.0	0.0	0		106.0	27.0	0.254717	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366941	0.82463	.	.	ENSG00000188385	ENST00000298622	T	0.30714	1.52	4.01	4.01	0.46588	.	.	.	.	.	T	0.49592	0.1566	M	0.68317	2.08	0.49798	D	0.999825	D;D	0.89917	1.0;0.997	D;P	0.64506	0.926;0.715	T	0.46414	-0.9193	9	0.21540	T	0.41	.	16.1506	0.81618	0.0:0.0:1.0:0.0	.	125;688	Q5VZ66-2;Q5VZ66	.;JKIP3_HUMAN	K	688	ENSP00000298622:E688K	ENSP00000298622:E688K	E	+	1	0	JAKMIP3	133816512	1.000000	0.71417	0.876000	0.34364	0.450000	0.32258	9.219000	0.95173	1.780000	0.52325	0.479000	0.44913	GAA	.	.	none		0.597	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
ANO4	121601	hgsc.bcm.edu	37	12	101520847	101520847	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101520847G>A	ENST00000392977.3	+	27	3077	c.2867G>A	c.(2866-2868)tGa>tAa	p.*956*	ANO4_ENST00000299222.9_Silent_p.*476*|ANO4_ENST00000392979.3_Silent_p.*921*|ANO4_ENST00000550015.1_Silent_p.*476*			Q32M45	ANO4_HUMAN	anoctamin 4	0					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GAGTGGCCGTGACCATGTAGG	0.483										HNSCC(74;0.22)																											p.X921X		Atlas-SNP	.											.	ANO4	183	.	0			c.G2762A						PASS	.						91.0	61.0	71.0					12																	101520847		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon26			GGCCGTGACCATG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2867G>A	12.37:g.101520847G>A		94.0	0.0	0		84.0	22.0	0.261905	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																				.	.	none		0.483	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
OR56A1	120796	hgsc.bcm.edu	37	11	6048408	6048408	+	Missense_Mutation	SNP	C	C	A	rs151331727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6048408C>A	ENST00000316650.5	-	1	563	c.527G>T	c.(526-528)tGt>tTt	p.C176F		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTTTCCCCACAGTAATGGAG	0.453													.|||	15	0.00299521	0.0	0.0014	5008	,	,		23480	0.0		0.0139	False		,,,				2504	0.0				p.C176F		Atlas-SNP	.											.	OR56A1	73	.	0			c.G527T						PASS	.	C	PHE/CYS	4,4398	8.1+/-20.4	0,4,2197	107.0	101.0	103.0		527	3.3	0.9	11	dbSNP_134	103	69,8523	41.2+/-98.3	0,69,4227	yes	missense	OR56A1	NM_001001917.2	205	0,73,6424	AA,AC,CC		0.8031,0.0909,0.5618	probably-damaging	176/319	6048408	73,12921	2201	4296	6497	SO:0001583	missense	120796	exon1			TCCCCACAGTAAT	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"""GPCR / Class A : Olfactory receptors"""	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.527G>T	11.37:g.6048408C>A	ENSP00000321246:p.Cys176Phe	133.0	0.0	0		163.0	36.0	0.220859	NM_001001917	B2RNI2|Q6IFL0	Missense_Mutation	SNP	ENST00000316650.5	37	CCDS31405.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.479	0.859298	0.17178	9.09E-4	0.008031	ENSG00000180934	ENST00000316650	T	0.00211	8.54	4.27	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000276	T	0.00300	0.0009	M	0.85945	2.785	0.28249	N	0.925365	B	0.31989	0.35	B	0.44163	0.443	T	0.00860	-1.1537	10	0.72032	D	0.01	.	13.1758	0.59626	0.0:0.8382:0.1618:0.0	.	176	Q8NGH5	O56A1_HUMAN	F	176	ENSP00000321246:C176F	ENSP00000321246:C176F	C	-	2	0	OR56A1	6004984	0.990000	0.36364	0.893000	0.35052	0.276000	0.26787	3.002000	0.49496	1.113000	0.41760	0.655000	0.94253	TGT	C|0.996;A|0.004	0.004	strong		0.453	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917	
FIGN	55137	hgsc.bcm.edu	37	2	164467750	164467750	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:164467750A>T	ENST00000333129.3	-	3	906	c.592T>A	c.(592-594)Tat>Aat	p.Y198N	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'Flank	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	198					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						TGGCTACTATAAGTAGAATGC	0.537																																					p.Y198N		Atlas-SNP	.											.	FIGN	106	.	0			c.T592A						PASS	.						70.0	76.0	74.0					2																	164467750		2038	4192	6230	SO:0001583	missense	55137	exon3			TACTATAAGTAGA	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.592T>A	2.37:g.164467750A>T	ENSP00000333836:p.Tyr198Asn	120.0	0.0	0		105.0	30.0	0.285714	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	17.94	3.511293	0.64522	.	.	ENSG00000182263	ENST00000333129	T	0.40225	1.04	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.60689	0.2288	M	0.66939	2.045	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.60510	-0.7249	10	0.48119	T	0.1	-9.4916	16.8061	0.85666	1.0:0.0:0.0:0.0	.	198	Q5HY92	FIGN_HUMAN	N	198	ENSP00000333836:Y198N	ENSP00000333836:Y198N	Y	-	1	0	FIGN	164175996	1.000000	0.71417	0.972000	0.41901	0.984000	0.73092	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TAT	.	.	none		0.537	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
KDM4C	23081	hgsc.bcm.edu	37	9	6981115	6981115	+	Missense_Mutation	SNP	G	G	A	rs35049841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:6981115G>A	ENST00000381309.3	+	9	1677	c.1112G>A	c.(1111-1113)cGa>cAa	p.R371Q	KDM4C_ENST00000381306.3_Missense_Mutation_p.R371Q|KDM4C_ENST00000442236.2_Missense_Mutation_p.R190Q|RP11-403H13.1_ENST00000445708.1_RNA|KDM4C_ENST00000535193.1_Missense_Mutation_p.R393Q|KDM4C_ENST00000543771.1_Missense_Mutation_p.R371Q|KDM4C_ENST00000536108.1_Missense_Mutation_p.R190Q|KDM4C_ENST00000428870.2_Missense_Mutation_p.R58Q	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	371					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AAAGCATCCCGAAGGTAATGA	0.453													G|||	2	0.000399361	0.0	0.0014	5008	,	,		19729	0.0		0.001	False		,,,				2504	0.0				p.R393Q		Atlas-SNP	.											.	KDM4C	186	.	0			c.G1178A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	70.0	62.0	65.0		1112,1112,1178,1112	-4.8	0.0	9	dbSNP_126	65	37,8563	24.6+/-71.5	0,37,4263	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	43,43,43,43	0,37,6466	AA,AG,GG		0.4302,0.0,0.2845	benign,benign,benign,benign	371/1048,371/814,393/836,371/1057	6981115	37,12969	2203	4300	6503	SO:0001583	missense	23081	exon9			CATCCCGAAGGTA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1112G>A	9.37:g.6981115G>A	ENSP00000370710:p.Arg371Gln	47.0	0.0	0		23.0	8.0	0.347826	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	10.47	1.358960	0.24598	0.0	0.004302	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.19532	2.25;2.26;2.43;2.33;2.64;2.14;3.43	5.47	-4.79	0.03200	.	0.954910	0.08712	N	0.904774	T	0.14657	0.0354	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B	0.47106	0.196;0.89;0.158;0.011;0.045	B;B;B;B;B	0.41466	0.026;0.358;0.039;0.007;0.017	T	0.11275	-1.0594	10	0.13470	T	0.59	-1.4792	15.7963	0.78412	0.7358:0.0:0.2642:0.0	rs35049841;rs61752861	190;371;393;371;371	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	Q	393;371;371;371;190;190;58	ENSP00000442382:R393Q;ENSP00000445427:R371Q;ENSP00000370710:R371Q;ENSP00000370707:R371Q;ENSP00000409353:R190Q;ENSP00000440656:R190Q;ENSP00000405739:R58Q	ENSP00000370707:R371Q	R	+	2	0	KDM4C	6971115	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-0.028000	0.12350	-1.432000	0.01979	-0.225000	0.12378	CGA	G|0.998;A|0.002	0.002	strong		0.453	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019974	107019974	+	Missense_Mutation	SNP	C	C	T	rs372866009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:107019974C>T	ENST00000369063.3	-	9	1553	c.1088G>A	c.(1087-1089)cGg>cAg	p.R363Q	RTN4IP1_ENST00000539449.1_3'UTR|RTN4IP1_ENST00000498091.1_5'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	363						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.R363L(1)		breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		AATAACTGGCCGGATCTGTAA	0.418																																					p.R363Q		Atlas-SNP	.											RTN4IP1,NS,carcinoma,0,1	RTN4IP1	31	1	1	Substitution - Missense(1)	lung(1)	c.G1088A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	92.0	95.0	94.0		1088	-2.2	0.9	6		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	RTN4IP1	NM_032730.4	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	363/397	107019974	2,13004	2203	4300	6503	SO:0001583	missense	84816	exon9			ACTGGCCGGATCT	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1088G>A	6.37:g.107019974C>T	ENSP00000358059:p.Arg363Gln	96.0	0.0	0		71.0	26.0	0.366197	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Missense_Mutation	SNP	ENST00000369063.3	37	CCDS5056.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.439632	0.25900	0.0	2.33E-4	ENSG00000130347	ENST00000369063	T	0.24908	1.83	6.02	-2.25	0.06888	.	0.687056	0.15173	N	0.276506	T	0.06645	0.0170	L	0.33245	0.995	0.30421	N	0.7781	B	0.19583	0.037	B	0.12837	0.008	T	0.35847	-0.9772	10	0.31617	T	0.26	-0.4612	12.1462	0.54024	0.0:0.3328:0.0:0.6672	.	363	Q8WWV3	RT4I1_HUMAN	Q	363	ENSP00000358059:R363Q	ENSP00000358059:R363Q	R	-	2	0	RTN4IP1	107126667	0.011000	0.17503	0.894000	0.35097	0.910000	0.53928	-0.027000	0.12371	-0.270000	0.09285	-0.355000	0.07637	CGG	.	.	weak		0.418	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
ZNF235	9310	hgsc.bcm.edu	37	19	44791537	44791537	+	Missense_Mutation	SNP	G	G	A	rs149947768		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44791537G>A	ENST00000291182.4	-	5	2153	c.2051C>T	c.(2050-2052)aCg>aTg	p.T684M	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	684					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)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				CTGCTGACACGTATAGGGTTT	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		21663	0.0		0.001	False		,,,				2504	0.0				p.T684M		Atlas-SNP	.											.	ZNF235	60	.	0			c.C2051T						PASS	.	G	MET/THR	0,4406		0,0,2203	127.0	116.0	120.0		2051	1.1	0.1	19	dbSNP_134	120	10,8590	7.1+/-27.0	0,10,4290	yes	missense	ZNF235	NM_004234.4	81	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	benign	684/739	44791537	10,12996	2203	4300	6503	SO:0001583	missense	9310	exon5			TGACACGTATAGG	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.2051C>T	19.37:g.44791537G>A	ENSP00000291182:p.Thr684Met	147.0	0.0	0		86.0	41.0	0.476744	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	G	6.572	0.473837	0.12521	0.0	0.001163	ENSG00000159917	ENST00000391957;ENST00000291182;ENST00000359844	T	0.19806	2.12	4.97	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.171331	0.28203	N	0.016214	T	0.14270	0.0345	L	0.37697	1.125	0.09310	N	1	B;B	0.28470	0.086;0.213	B;B	0.24701	0.012;0.055	T	0.18493	-1.0335	10	0.62326	D	0.03	-1.4434	7.5912	0.28023	0.0867:0.0:0.5441:0.3692	.	680;684	Q14590-2;Q14590	.;ZN235_HUMAN	M	684;684;576	ENSP00000291182:T684M	ENSP00000291182:T684M	T	-	2	0	ZNF235	49483377	0.000000	0.05858	0.100000	0.21137	0.510000	0.34073	-0.585000	0.05794	0.616000	0.30141	0.313000	0.20887	ACG	G|0.998;A|0.002	0.002	strong		0.493	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
HTT	3064	hgsc.bcm.edu	37	4	3107140	3107140	+	Silent	SNP	C	C	T	rs184820567		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3107140C>T	ENST00000355072.5	+	5	730	c.585C>T	c.(583-585)caC>caT	p.H195H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	195					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCTGGCTCACCTGGTTCGGC	0.527													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.H195H		Atlas-SNP	.											.	HTT	221	.	0			c.C585T						PASS	.	C		0,4288		0,0,2144	111.0	116.0	114.0		585	3.4	1.0	4		114	3,8537		0,3,4267	no	coding-synonymous	HTT	NM_002111.6		0,3,6411	TT,TC,CC		0.0351,0.0,0.0234		195/3143	3107140	3,12825	2144	4270	6414	SO:0001819	synonymous_variant	3064	exon5			GGCTCACCTGGTT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.585C>T	4.37:g.3107140C>T		182.0	0.0	0		145.0	70.0	0.482759	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
NACAD	23148	hgsc.bcm.edu	37	7	45123857	45123857	+	Missense_Mutation	SNP	A	A	G	rs7790844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:45123857A>G	ENST00000490531.2	-	2	1941	c.1922T>C	c.(1921-1923)gTt>gCt	p.V641A		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	641					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V641A(1)		breast(1)|endometrium(2)|skin(2)	5						CGGTGTCATAACGGAGTCCTG	0.597																																					p.V641A		Atlas-SNP	.											NACAD,NS,carcinoma,0,1	NACAD	44	1	1	Substitution - Missense(1)	endometrium(1)	c.T1922C						scavenged	.						4.0	5.0	5.0					7																	45123857		604	1531	2135	SO:0001583	missense	23148	exon2			GTCATAACGGAGT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1922T>C	7.37:g.45123857A>G	ENSP00000420477:p.Val641Ala	13.0	1.0	0.0769231		9.0	7.0	0.777778	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	a	1.045	-0.677539	0.03378	.	.	ENSG00000136274	ENST00000490531	T	0.12039	2.72	1.41	0.403	0.16350	.	3.406300	0.02110	N	0.054755	T	0.06050	0.0157	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30327	-0.9982	9	0.07482	T	0.82	.	5.5804	0.17247	0.3401:0.0:0.6599:0.0	rs7790844;rs7790844	641	O15069	NACAD_HUMAN	A	641	ENSP00000420477:V641A	ENSP00000420477:V641A	V	-	2	0	NACAD	45090382	.	.	0.002000	0.10522	0.107000	0.19398	.	.	-0.244000	0.09639	-0.665000	0.03846	GTT	A|0.007;G|0.993	0.993	strong		0.597	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ATP12A	479	hgsc.bcm.edu	37	13	25255705	25255705	+	Silent	SNP	C	C	A	rs41288276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51.0	54.0	53.0		15,15	-6.3	0.0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.15C>A	13.37:g.25255705C>A		83.0	0.0	0		71.0	36.0	0.507042	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
ITFG2	55846	hgsc.bcm.edu	37	12	2930731	2930731	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2930731C>T	ENST00000228799.2	+	8	955	c.816C>T	c.(814-816)ggC>ggT	p.G272G	ITFG2_ENST00000542548.1_Silent_p.G160G|ITFG2_ENST00000419778.2_Silent_p.G95G	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	272					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			AGAGTAGTGGCTCTGGCCTCT	0.607																																					p.G272G		Atlas-SNP	.											.	ITFG2	38	.	0			c.C816T						PASS	.						89.0	78.0	82.0					12																	2930731		2203	4300	6503	SO:0001819	synonymous_variant	55846	exon8			TAGTGGCTCTGGC	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.816C>T	12.37:g.2930731C>T		125.0	0.0	0		97.0	4.0	0.0412371	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Silent	SNP	ENST00000228799.2	37	CCDS8513.1																																																																																			.	.	none		0.607	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463	
ZNF460	10794	hgsc.bcm.edu	37	19	57802116	57802116	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57802116C>T	ENST00000360338.3	+	3	529	c.207C>T	c.(205-207)gcC>gcT	p.A69A	ZNF460_ENST00000537645.1_Silent_p.A28A	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CTCATCTGGCCTTGCCTGAGG	0.483																																					p.A69A		Atlas-SNP	.											.	ZNF460	59	.	0			c.C207T						PASS	.						71.0	64.0	66.0					19																	57802116		2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TCTGGCCTTGCCT	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.207C>T	19.37:g.57802116C>T		140.0	0.0	0		140.0	33.0	0.235714	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			.	.	none		0.483	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590139	140590139	+	Missense_Mutation	SNP	G	G	A	rs145232861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140590139G>A	ENST00000239450.2	+	1	1849	c.1660G>A	c.(1660-1662)Gcc>Acc	p.A554T	PCDHB12_ENST00000541609.1_Missense_Mutation_p.A217T	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	554	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGCTGGACGCCAACGACAA	0.711													G|||	11	0.00219649	0.0	0.0014	5008	,	,		16609	0.0		0.0099	False		,,,				2504	0.0				p.A554T		Atlas-SNP	.											.	PCDHB12	179	.	0			c.G1660A						PASS	.	G	THR/ALA	6,4392		0,6,2193	23.0	27.0	26.0		1660	2.5	1.0	5	dbSNP_134	26	29,8559		0,29,4265	no	missense	PCDHB12	NM_018932.3	58	0,35,6458	AA,AG,GG		0.3377,0.1364,0.2695	benign	554/796	140590139	35,12951	2199	4294	6493	SO:0001583	missense	56124	exon1			CTGGACGCCAACG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1660G>A	5.37:g.140590139G>A	ENSP00000239450:p.Ala554Thr	158.0	0.0	0		126.0	73.0	0.579365	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	8.941	0.965816	0.18583	0.001364	0.003377	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.03181	4.02;4.02	3.41	2.5	0.30297	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.02533	0.0077	N	0.13352	0.335	0.09310	N	0.999998	B	0.34015	0.435	B	0.23716	0.048	T	0.46442	-0.9191	9	0.40728	T	0.16	.	12.3896	0.55350	0.0:0.481:0.519:0.0	.	554	Q9Y5F1	PCDBC_HUMAN	T	217;554;174	ENSP00000440199:A217T;ENSP00000239450:A554T	ENSP00000239450:A554T	A	+	1	0	PCDHB12	140570323	0.000000	0.05858	0.953000	0.39169	0.995000	0.86356	0.135000	0.15952	0.525000	0.28522	0.485000	0.47835	GCC	G|0.875;A|0.125	0.125	strong		0.711	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
LAMA5	3911	hgsc.bcm.edu	37	20	60901762	60901762	+	Missense_Mutation	SNP	C	C	T	rs11699758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60901762C>T	ENST00000252999.3	-	40	5335	c.5269G>A	c.(5269-5271)Gtt>Att	p.V1757I		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1757	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CCACGGTGAACGTGGCCAGGC	0.657													C|||	73	0.0145767	0.0121	0.0231	5008	,	,		18170	0.0		0.0368	False		,,,				2504	0.0041				p.V1757I		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5269A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	71.0	54.0	60.0		5269	-1.0	0.0	20	dbSNP_120	60	254,8344	99.0+/-160.6	3,248,4048	yes	missense	LAMA5	NM_005560.3	29	5,343,6154	TT,TC,CC		2.9542,2.2469,2.7145	benign	1757/3696	60901762	353,12651	2203	4299	6502	SO:0001583	missense	3911	exon40			GGTGAACGTGGCC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5269G>A	20.37:g.60901762C>T	ENSP00000252999:p.Val1757Ile	170.0	0.0	0		144.0	79.0	0.548611	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	42	0.019230769230769232	8	0.016260162601626018	14	0.03867403314917127	0	0.0	20	0.026385224274406333	C	0.464	-0.887824	0.02511	0.022469	0.029542	ENSG00000130702	ENST00000252999	T	0.36157	1.27	5.12	-1.04	0.10068	Laminin B type IV (2);Laminin B, subgroup (1);	0.497398	0.22077	N	0.064941	T	0.03915	0.0110	N	0.17474	0.49	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.13953	-1.0490	10	0.25106	T	0.35	.	7.414	0.27034	0.0:0.4374:0.2158:0.3468	rs11699758	1757	O15230	LAMA5_HUMAN	I	1757	ENSP00000252999:V1757I	ENSP00000252999:V1757I	V	-	1	0	LAMA5	60335157	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.028000	0.12350	-0.054000	0.13266	-0.355000	0.07637	GTT	C|0.974;T|0.026	0.026	strong		0.657	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
EIF2AK1	27102	hgsc.bcm.edu	37	7	6080686	6080686	+	Missense_Mutation	SNP	A	A	T	rs34909691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6080686A>T	ENST00000199389.6	-	9	1102	c.956T>A	c.(955-957)cTt>cAt	p.L319H	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.L195H|EIF2AK1_ENST00000495565.1_5'UTR	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> H (in dbSNP:rs34909691). {ECO:0000269|PubMed:17344846}.		negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GGTCGACTCAAGTTCACCAGA	0.458													A|||	45	0.00898562	0.0008	0.0173	5008	,	,		16878	0.0		0.0179	False		,,,				2504	0.0143				p.L319H		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.T956A						PASS	.	A	HIS/LEU,HIS/LEU	15,4391		0,15,2188	164.0	161.0	162.0		953,956	-1.8	0.0	7	dbSNP_126	162	193,8407		2,189,4109	yes	missense,missense	EIF2AK1	NM_001134335.1,NM_014413.3	99,99	2,204,6297	TT,TA,AA		2.2442,0.3404,1.5993	benign,benign	318/630,319/631	6080686	208,12798	2203	4300	6503	SO:0001583	missense	27102	exon9			GACTCAAGTTCAC	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.956T>A	7.37:g.6080686A>T	ENSP00000199389:p.Leu319His	187.0	0.0	0		178.0	137.0	0.769663	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	21	0.009615384615384616	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	7.886	0.731364	0.15507	0.003404	0.022442	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.68624	-0.27;-0.34	5.36	-1.8	0.07907	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.737749	0.14214	N	0.333889	T	0.23649	0.0572	N	0.14661	0.345	0.09310	N	1	B;P;B	0.34826	0.003;0.471;0.401	B;B;B	0.33196	0.005;0.159;0.151	T	0.22208	-1.0223	10	0.15499	T	0.54	-0.6525	6.7447	0.23454	0.2399:0.4967:0.0:0.2635	rs34909691;rs61731539	195;318;319	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	H	319;195	ENSP00000199389:L319H;ENSP00000445784:L195H	ENSP00000199389:L319H	L	-	2	0	EIF2AK1	6047212	0.000000	0.05858	0.013000	0.15412	0.024000	0.10985	0.404000	0.20999	0.018000	0.15052	0.533000	0.62120	CTT	A|0.978;T|0.022	0.022	strong		0.458	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
CDHR3	222256	hgsc.bcm.edu	37	7	105636765	105636765	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105636765C>T	ENST00000317716.9	+	6	758	c.678C>T	c.(676-678)atC>atT	p.I226I	CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000541203.1_Intron|CDHR3_ENST00000478080.1_Silent_p.I138I|CDHR3_ENST00000542731.1_Silent_p.I226I|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AGGTGAACATCGTGAACCTCA	0.587																																					p.I226I		Atlas-SNP	.											.	CDHR3	153	.	0			c.C678T						PASS	.						41.0	44.0	43.0					7																	105636765		2011	4165	6176	SO:0001819	synonymous_variant	222256	exon6			GAACATCGTGAAC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.678C>T	7.37:g.105636765C>T		42.0	0.0	0		51.0	4.0	0.0784314	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																			.	.	none		0.587	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
CYP4F3	4051	hgsc.bcm.edu	37	19	15760035	15760035	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15760035C>G	ENST00000221307.8	+	6	638	c.591C>G	c.(589-591)ctC>ctG	p.L197L	CYP4F3_ENST00000591058.1_Silent_p.L197L|CYP4F3_ENST00000586182.2_Silent_p.L197L|CYP4F3_ENST00000585846.1_Silent_p.L197L	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	197					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						ACATCAGCCTCATGACCTTGG	0.577																																					p.L197L		Atlas-SNP	.											.	CYP4F3	69	.	0			c.C591G						PASS	.						124.0	107.0	113.0					19																	15760035		2203	4300	6503	SO:0001819	synonymous_variant	4051	exon6			CAGCCTCATGACC	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.591C>G	19.37:g.15760035C>G		105.0	0.0	0		125.0	36.0	0.288	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			.	.	none		0.577	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
CTBS	1486	hgsc.bcm.edu	37	1	85029085	85029085	+	Missense_Mutation	SNP	A	A	G	rs143993403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:85029085A>G	ENST00000370630.5	-	6	860	c.812T>C	c.(811-813)aTt>aCt	p.I271T	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	271					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		GACTTTTGCAATGGTACAAAC	0.363													A|||	7	0.00139776	0.0	0.0	5008	,	,		12899	0.0		0.007	False		,,,				2504	0.0				p.I271T		Atlas-SNP	.											.	CTBS	24	.	0			c.T812C						PASS	.	A	THR/ILE	2,4394		0,2,2196	42.0	46.0	44.0		812	0.2	1.0	1	dbSNP_134	44	31,8567		0,31,4268	yes	missense	CTBS	NM_004388.2	89	0,33,6464	GG,GA,AA		0.3605,0.0455,0.254	benign	271/386	85029085	33,12961	2198	4299	6497	SO:0001583	missense	1486	exon6			TTTGCAATGGTAC	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.812T>C	1.37:g.85029085A>G	ENSP00000359664:p.Ile271Thr	120.0	0.0	0		97.0	42.0	0.43299	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	15.09	2.730266	0.48939	4.55E-4	0.003605	ENSG00000117151	ENST00000370630	T	0.05081	3.5	5.39	0.206	0.15208	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.218455	0.46758	N	0.000269	T	0.02610	0.0079	L	0.43598	1.365	0.33049	D	0.532445	P	0.38420	0.63	B	0.42625	0.393	T	0.44651	-0.9314	10	0.22109	T	0.4	-10.2359	11.7481	0.51832	0.8713:0.0:0.1287:0.0	.	271	Q01459	DIAC_HUMAN	T	271	ENSP00000359664:I271T	ENSP00000359659:I180T	I	-	2	0	CTBS	84801673	0.997000	0.39634	0.992000	0.48379	0.887000	0.51463	3.142000	0.50601	-0.226000	0.09899	0.528000	0.53228	ATT	A|0.997;G|0.003	0.003	strong		0.363	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57562804G>A	ENST00000258214.2	-	2	532	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	96				R -> W (in Ref. 2; AAH08285/AAH09941). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCGACCACCGGCGCATGGTC	0.731													A|||	5008	1.0	1.0	1.0	5008	,	,		3757	1.0		1.0	False		,,,				2504	1.0				p.R96W		Atlas-SNP	.											.	CCDC102A	22	.	0			c.C286T						PASS	.						8.0	10.0	9.0					16																	57562804		1834	3717	5551	SO:0001583	missense	92922	exon2			ACCACCGGCGCAT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.286C>T	16.37:g.57562804G>A	ENSP00000258214:p.Arg96Trp	0.0	0.0	.		4.0	4.0	1	NM_033212	Q9BT74	Missense_Mutation	SNP	ENST00000258214.2	37	CCDS10784.1	2180	0.9981684981684982	492	1.0	360	0.994475138121547	570	0.9965034965034965	758	1.0	A	10.17	1.277909	0.23307	.	.	ENSG00000135736	ENST00000258214	T	0.37752	1.18	4.82	4.82	0.62117	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00049	-2.415	0.40217	P	0.022302999999999962	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	9	0.33141	T	0.24	-23.2491	9.5348	0.39216	0.9152:0.0:0.0848:0.0	rs12935069;rs12935069	96	Q96A19	C102A_HUMAN	W	96	ENSP00000258214:R96W	ENSP00000258214:R96W	R	-	1	2	CCDC102A	56120305	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.801000	0.75170	0.698000	0.31739	-0.556000	0.04195	CGG	G|0.001;A|0.999	0.999	strong		0.731	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
PDE4A	5141	hgsc.bcm.edu	37	19	10531491	10531491	+	Silent	SNP	C	C	T	rs117495488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10531491C>T	ENST00000352831.6	+	1	161	c.51C>T	c.(49-51)ccC>ccT	p.P17P	PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000592685.1_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	17					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	TGTCACTGCCCGGGCCCCGGG	0.726													C|||	34	0.00678914	0.0	0.0	5008	,	,		8964	0.0278		0.004	False		,,,				2504	0.002				p.P17P		Atlas-SNP	.											.	PDE4A	236	.	0			c.C51T						PASS	.	C		0,2670		0,0,1335	7.0	8.0	8.0		51	-7.6	0.9	19	dbSNP_132	8	6,6434		0,6,3214	no	coding-synonymous	PDE4A	NM_001111307.1		0,6,4549	TT,TC,CC		0.0932,0.0,0.0659		17/887	10531491	6,9104	1335	3220	4555	SO:0001819	synonymous_variant	5141	exon1			ACTGCCCGGGCCC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.51C>T	19.37:g.10531491C>T		2.0	0.0	0		32.0	18.0	0.5625	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	37	CCDS45961.1																																																																																			C|0.987;T|0.013	0.013	strong		0.726	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
CCKBR	887	hgsc.bcm.edu	37	11	6291466	6291466	+	Silent	SNP	A	A	G	rs77873910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6291466A>G	ENST00000334619.2	+	3	745	c.552A>G	c.(550-552)ctA>ctG	p.L184L	CCKBR_ENST00000525014.1_3'UTR|CCKBR_ENST00000525462.1_Silent_p.L184L|CCKBR_ENST00000532715.1_Silent_p.L100L	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	184					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TGTCCGGACTACTCATGGTGC	0.667													A|||	44	0.00878594	0.0045	0.0187	5008	,	,		2100	0.0		0.0159	False		,,,				2504	0.0092				p.L184L		Atlas-SNP	.											CCKBR_ENST00000525462,NS,carcinoma,+2,2	CCKBR	232	2	0			c.A552G						PASS	.	A		32,4370	36.8+/-68.6	0,32,2169	59.0	49.0	53.0		552	3.2	1.0	11	dbSNP_131	53	155,8437	73.5+/-136.2	1,153,4142	no	coding-synonymous	CCKBR	NM_176875.2		1,185,6311	GG,GA,AA		1.804,0.7269,1.4391		184/448	6291466	187,12807	2201	4296	6497	SO:0001819	synonymous_variant	887	exon3			CGGACTACTCATG	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"""GPCR / Class A : Cholecystokinin receptors"""	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.552A>G	11.37:g.6291466A>G		70.0	0.0	0		77.0	16.0	0.207792	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Silent	SNP	ENST00000334619.2	37	CCDS7761.1																																																																																			A|0.986;G|0.014	0.014	strong		0.667	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	
NEK11	79858	hgsc.bcm.edu	37	3	130799314	130799314	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130799314C>G	ENST00000510769.1	+	3	471	c.218C>G	c.(217-219)aCt>aGt	p.T73S	NEK11_ENST00000508196.1_Missense_Mutation_p.T73S|NEK11_ENST00000383366.4_Missense_Mutation_p.T73S|NEK11_ENST00000507910.1_Missense_Mutation_p.T73S|NEK11_ENST00000510688.1_Missense_Mutation_p.T73S|NEK11_ENST00000511262.1_Missense_Mutation_p.T73S|NEK11_ENST00000356918.4_Missense_Mutation_p.T73S|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000429253.2_Missense_Mutation_p.T73S					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						CCAAATGAAACTGTACAGGCC	0.368																																					p.T73S		Atlas-SNP	.											.	NEK11	76	.	0			c.C218G						PASS	.						76.0	74.0	75.0					3																	130799314		2203	4300	6503	SO:0001583	missense	79858	exon4			ATGAAACTGTACA	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.218C>G	3.37:g.130799314C>G	ENSP00000421549:p.Thr73Ser	77.0	0.0	0		70.0	18.0	0.257143	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	37		.	.	.	.	.	.	.	.	.	.	C	12.87	2.067808	0.36470	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.77	4.89	0.63831	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000050	T	0.49847	0.1581	N	0.21240	0.645	0.80722	D	1	P;P;P;P;B	0.49635	0.573;0.513;0.698;0.926;0.063	B;B;B;B;B	0.39935	0.138;0.287;0.161;0.314;0.037	T	0.55927	-0.8063	10	0.54805	T	0.06	.	17.0528	0.86524	0.0:0.8732:0.1268:0.0	.	73;73;73;73;73	Q8NG66-3;E9PHI8;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;NEK11_HUMAN;.	S	73	ENSP00000421549:T73S;ENSP00000397180:T73S;ENSP00000349389:T73S;ENSP00000423458:T73S;ENSP00000425114:T73S;ENSP00000372857:T73S;ENSP00000426662:T73S;ENSP00000421851:T73S	ENSP00000349389:T73S	T	+	2	0	NEK11	132282004	1.000000	0.71417	0.983000	0.44433	0.330000	0.28571	3.946000	0.56644	1.415000	0.47037	0.655000	0.94253	ACT	.	.	none		0.368	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187629137A>G	ENST00000441802.2	-	2	2054	c.1845T>C	c.(1843-1845)ttT>ttC	p.F615F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	615	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGTTTAAACTAAAGAAATCCA	0.433										HNSCC(5;0.00058)			A|||	78	0.0155751	0.0	0.0101	5008	,	,		20191	0.0258		0.0368	False		,,,				2504	0.0082				p.F615F	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1845C						PASS	.	A		23,3713		0,23,1845	68.0	63.0	64.0		1845	-1.3	0.6	4	dbSNP_111	64	305,7891		4,297,3797	no	coding-synonymous	FAT1	NM_005245.3		4,320,5642	GG,GA,AA		3.7213,0.6156,2.7489		615/4589	187629137	328,11604	1868	4098	5966	SO:0001819	synonymous_variant	2195	exon2			TAAACTAAAGAAA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1845T>C	4.37:g.187629137A>G		69.0	0.0	0		62.0	23.0	0.370968	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CSNK2A1	1457	hgsc.bcm.edu	37	20	472938	472938	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:472938G>A	ENST00000217244.3	-	9	956	c.581C>T	c.(580-582)tCc>tTc	p.S194F	CSNK2A1_ENST00000349736.5_Missense_Mutation_p.S194F|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.S58F|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.S194F	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GAAGTATCGGGAAGCAACTCG	0.408																																					p.S194F		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.C581T						PASS	.						87.0	80.0	83.0					20																	472938		2203	4298	6501	SO:0001583	missense	1457	exon8			TATCGGGAAGCAA	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.581C>T	20.37:g.472938G>A	ENSP00000217244:p.Ser194Phe	78.0	0.0	0		60.0	16.0	0.266667	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901024	0.92035	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.54279	3.06;3.06;3.06;0.58	4.84	4.84	0.62591	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095477	0.85682	D	0.000000	T	0.81083	0.4749	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86825	0.2007	10	0.87932	D	0	-7.1666	17.471	0.87646	0.0:0.0:1.0:0.0	.	194	P68400	CSK21_HUMAN	F	194;194;194;194;58	ENSP00000383086:S194F;ENSP00000339247:S194F;ENSP00000217244:S194F;ENSP00000383076:S58F	ENSP00000217244:S194F	S	-	2	0	CSNK2A1	420938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.562000	0.98145	2.679000	0.91253	0.655000	0.94253	TCC	.	.	none		0.408	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	
RPTOR	57521	hgsc.bcm.edu	37	17	78820351	78820351	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78820351G>A	ENST00000306801.3	+	11	1653	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	RPTOR_ENST00000544334.2_Missense_Mutation_p.E431K|RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000537330.1_Missense_Mutation_p.E246K	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	431					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						AAACCCACCCGAACAGCTGCC	0.627																																					p.E431K		Atlas-SNP	.											.	RPTOR	122	.	0			c.G1291A						PASS	.						145.0	112.0	123.0					17																	78820351		2203	4300	6503	SO:0001583	missense	57521	exon11			CCACCCGAACAGC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1291G>A	17.37:g.78820351G>A	ENSP00000307272:p.Glu431Lys	76.0	0.0	0		88.0	27.0	0.306818	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.912856	0.92178	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T;T	0.34472	1.36;1.36;1.36	4.92	4.92	0.64577	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68778	0.3038	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.998	D;D;P	0.85130	0.956;0.997;0.843	T	0.74390	-0.3681	10	0.35671	T	0.21	.	17.7008	0.88294	0.0:0.0:1.0:0.0	.	431;246;431	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	K	246;431;431	ENSP00000440947:E246K;ENSP00000307272:E431K;ENSP00000442479:E431K	ENSP00000307272:E431K	E	+	1	0	RPTOR	76434946	1.000000	0.71417	0.834000	0.33040	0.611000	0.37282	8.736000	0.91554	2.267000	0.75376	0.467000	0.42956	GAA	.	.	none		0.627	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
SPPL2A	84888	hgsc.bcm.edu	37	15	51017488	51017488	+	Silent	SNP	G	G	T	rs140457962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:51017488G>T	ENST00000261854.5	-	12	1453	c.1179C>A	c.(1177-1179)atC>atA	p.I393I	SPPL2A_ENST00000559293.1_5'UTR	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	393					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		CTGAGAAATAGATCAGTTTTG	0.338													G|||	8	0.00159744	0.0008	0.0	5008	,	,		17872	0.0		0.007	False		,,,				2504	0.0				p.I393I	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1179A						PASS	.	G		6,4386	11.4+/-27.6	0,6,2190	104.0	101.0	102.0		1179	-2.8	0.8	15	dbSNP_134	102	77,8511	44.9+/-103.4	0,77,4217	no	coding-synonymous	SPPL2A	NM_032802.3		0,83,6407	TT,TG,GG		0.8966,0.1366,0.6394		393/521	51017488	83,12897	2196	4294	6490	SO:0001819	synonymous_variant	84888	exon12			GAAATAGATCAGT		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1179C>A	15.37:g.51017488G>T		229.0	0.0	0		223.0	127.0	0.569507	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.995;T|0.005	0.005	strong		0.338	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
BRINP1	1620	hgsc.bcm.edu	37	9	121930344	121930344	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:121930344C>T	ENST00000265922.3	-	8	1765	c.1304G>A	c.(1303-1305)aGc>aAc	p.S435N	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	435					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CATGGCGCAGCTGTTGTTCCC	0.632																																					p.S435N		Atlas-SNP	.											.	DBC1	194	.	0			c.G1304A						PASS	.						31.0	31.0	31.0					9																	121930344		2203	4300	6503	SO:0001583	missense	1620	exon8			GCGCAGCTGTTGT	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1304G>A	9.37:g.121930344C>T	ENSP00000265922:p.Ser435Asn	106.0	0.0	0		115.0	16.0	0.13913	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239289	0.58995	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.54479	0.57	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	L	0.40543	1.245	0.80722	D	1	D	0.53885	0.963	P	0.49853	0.624	T	0.55166	-0.8183	10	0.46703	T	0.11	-29.9476	19.8211	0.96595	0.0:1.0:0.0:0.0	.	435	O60477	DBC1_HUMAN	N	435	ENSP00000265922:S435N	ENSP00000265922:S435N	S	-	2	0	DBC1	120970165	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.947000	0.56652	2.687000	0.91594	0.655000	0.94253	AGC	.	.	none		0.632	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
DCC	1630	hgsc.bcm.edu	37	18	50278563	50278563	+	Silent	SNP	T	T	C	rs112141078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:50278563T>C	ENST00000442544.2	+	2	847	c.231T>C	c.(229-231)gaT>gaC	p.D77D	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	77	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GGAAGAAAGATGGCATTCATC	0.507													T|||	33	0.00658946	0.0015	0.0115	5008	,	,		17210	0.0		0.0209	False		,,,				2504	0.002				p.D77D		Atlas-SNP	.											.	DCC	360	.	0			c.T231C						PASS	.	T		27,4379	35.2+/-66.4	0,27,2176	104.0	98.0	100.0		231	0.1	1.0	18	dbSNP_132	100	215,8385	91.1+/-153.3	2,211,4087	no	coding-synonymous	DCC	NM_005215.3		2,238,6263	CC,CT,TT		2.5,0.6128,1.8607		77/1448	50278563	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon2			GAAAGATGGCATT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.231T>C	18.37:g.50278563T>C		110.0	0.0	0		98.0	43.0	0.438776	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			T|0.986;C|0.014	0.014	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
HIST1H2BI	8346	hgsc.bcm.edu	37	6	26273368	26273368	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26273368C>G	ENST00000377733.2	+	1	225	c.165C>G	c.(163-165)atC>atG	p.I55M	HIST1H3G_ENST00000305910.3_5'Flank	NM_003525.2	NP_003516.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bi	55					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(1)|lung(8)|urinary_tract(1)	16						ACACCGGCATCTCGTCCAAGG	0.562																																					p.I55M		Atlas-SNP	.											.	HIST1H2BI	29	.	0			c.C165G						PASS	.						215.0	203.0	207.0					6																	26273368		2203	4300	6503	SO:0001583	missense	8346	exon1			CGGCATCTCGTCC	Z80782	CCDS4603.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000168242	ENSG00000278588		"""Histones / Replication-dependent"""	4756	protein-coding gene	gene with protein product		602807	"""H2B histone family, member K"", ""histone 1, H2bi"""	H2BFK		9119399, 12408966	Standard	NM_003525		Approved	H2B/k	uc003nhk.3	P62807	OTTHUMG00000014448	ENST00000377733.2:c.165C>G	6.37:g.26273368C>G	ENSP00000366962:p.Ile55Met	109.0	0.0	0		108.0	22.0	0.203704	NM_003525	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000377733.2	37	CCDS4603.1	.	.	.	.	.	.	.	.	.	.	.	16.73	3.205259	0.58234	.	.	ENSG00000168242	ENST00000377733	T	0.73152	-0.72	4.5	2.68	0.31781	.	.	.	.	.	T	0.73401	0.3582	M	0.89904	3.07	0.27866	N	0.940224	.	.	.	.	.	.	T	0.68550	-0.5379	7	0.87932	D	0	.	10.0332	0.42114	0.0:0.8284:0.0:0.1716	.	.	.	.	M	55	ENSP00000366962:I55M	ENSP00000366962:I55M	I	+	3	3	HIST1H2BI	26381347	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	1.163000	0.31798	0.335000	0.23614	0.563000	0.77884	ATC	.	.	none		0.562	HIST1H2BI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040111.1	NM_003525	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671411	31671411	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671411C>T	ENST00000375483.3	+	3	408	c.408C>T	c.(406-408)ctC>ctT	p.L136L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	136	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ACAGGGGCCTCGGGCGATACA	0.627																																					p.L136L		Atlas-SNP	.											.	.	.	.	0			c.C408T						PASS	.						59.0	57.0	58.0					20																	31671411		2203	4300	6503	SO:0001819	synonymous_variant	149954	exon3			GGGCCTCGGGCGA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.408C>T	20.37:g.31671411C>T		215.0	0.0	0		178.0	48.0	0.269663	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			.	.	none		0.627	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
IL5RA	3568	hgsc.bcm.edu	37	3	3139910	3139910	+	Silent	SNP	T	T	C	rs141948767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3139910T>C	ENST00000446632.2	-	6	1006	c.432A>G	c.(430-432)tcA>tcG	p.S144S	IL5RA_ENST00000383846.1_Silent_p.S144S|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000311981.8_Silent_p.S144S|IL5RA_ENST00000430514.2_Silent_p.S144S|IL5RA_ENST00000438560.1_Silent_p.S144S|IL5RA_ENST00000256452.3_Silent_p.S144S|IL5RA_ENST00000456302.1_Silent_p.S144S|IL5RA_ENST00000418488.2_Silent_p.S144S	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	144					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		ACCTTAAACGTGAATAATTGT	0.423													T|||	5	0.000998403	0.0	0.0029	5008	,	,		21487	0.0		0.003	False		,,,				2504	0.0				p.S144S	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.A432G						PASS	.	T	,,,,,	5,4401	9.9+/-24.2	0,5,2198	208.0	215.0	213.0		432,432,432,432,432,432	-8.4	0.0	3	dbSNP_134	213	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL5RA	NM_000564.4,NM_175724.2,NM_175725.2,NM_175726.3,NM_175727.2,NM_175728.2	,,,,,	0,28,6475	CC,CT,TT		0.2674,0.1135,0.2153	,,,,,	144/421,144/334,144/336,144/421,144/334,144/336	3139910	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	3568	exon6			TAAACGTGAATAA	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.432A>G	3.37:g.3139910T>C		268.0	0.0	0		244.0	109.0	0.446721	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Silent	SNP	ENST00000446632.2	37	CCDS2559.1																																																																																			T|0.998;C|0.002	0.002	strong		0.423	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
ZMYND10	51364	hgsc.bcm.edu	37	3	50379257	50379257	+	Missense_Mutation	SNP	G	G	A	rs142613783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:50379257G>A	ENST00000231749.3	-	10	2377	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000490675.1_5'UTR|RASSF1_ENST00000357043.2_5'Flank|RASSF1_ENST00000488024.1_5'Flank|ZMYND10_ENST00000360165.3_Missense_Mutation_p.R364W	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	369	Interaction with LRRC6.		R -> W (in dbSNP:rs142613783). {ECO:0000269|Ref.1}.		inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCCTGCAGCCGCAGGTCCTGC	0.627										TSP Lung(30;0.18)			G|||	9	0.00179712	0.0	0.0014	5008	,	,		20400	0.0		0.006	False		,,,				2504	0.002				p.R369W		Atlas-SNP	.											.	ZMYND10	37	.	0			c.C1105T						PASS	.	G	TRP/ARG	7,4399	12.9+/-30.5	0,7,2196	42.0	42.0	42.0		1105	2.2	1.0	3	dbSNP_134	42	67,8533	39.8+/-96.3	0,67,4233	yes	missense	ZMYND10	NM_015896.2	101	0,74,6429	AA,AG,GG		0.7791,0.1589,0.569	probably-damaging	369/441	50379257	74,12932	2203	4300	6503	SO:0001583	missense	51364	exon10			GCAGCCGCAGGTC	U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"""Zinc fingers, MYND-type"""	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.1105C>T	3.37:g.50379257G>A	ENSP00000231749:p.Arg369Trp	70.0	0.0	0		60.0	31.0	0.516667	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	12.24	1.879643	0.33162	0.001589	0.007791	ENSG00000004838	ENST00000231749;ENST00000360165	.	.	.	5.11	2.16	0.27623	.	0.226724	0.41194	D	0.000924	T	0.57007	0.2024	M	0.72894	2.215	0.23468	N	0.997615	D;D	0.89917	0.992;1.0	P;D	0.67725	0.765;0.953	T	0.60105	-0.7328	9	0.87932	D	0	-31.184	14.5087	0.67769	0.0:0.0:0.3974:0.6026	.	364;369	O75800-2;O75800	.;ZMY10_HUMAN	W	369;364	.	ENSP00000231749:R369W	R	-	1	2	ZMYND10	50354261	0.663000	0.27448	0.964000	0.40570	0.168000	0.22595	1.029000	0.30140	0.131000	0.18576	0.462000	0.41574	CGG	G|0.995;A|0.005	0.005	strong		0.627	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896	
NRXN1	9378	hgsc.bcm.edu	37	2	50464109	50464109	+	Splice_Site	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50464109C>A	ENST00000406316.2	-	18	4841		c.e18-1		NRXN1_ENST00000406859.3_Splice_Site|NRXN1_ENST00000401710.1_Splice_Site|NRXN1_ENST00000401669.2_Splice_Site|NRXN1_ENST00000402717.3_Splice_Site|NRXN1_ENST00000405472.3_Splice_Site|NRXN1_ENST00000404971.1_Splice_Site|NRXN1_ENST00000331040.5_Splice_Site|NRXN1_ENST00000342183.5_Splice_Site	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTCGTCCCAGCTGGAAAACAA	0.413																																					.		Atlas-SNP	.											.	NRXN1	1118	.	0			c.3485-1G>T						PASS	.						79.0	76.0	77.0					2																	50464109		2203	4300	6503	SO:0001630	splice_region_variant	9378	exon20			TCCCAGCTGGAAA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3365-1G>T	2.37:g.50464109C>A		80.0	0.0	0		160.0	35.0	0.21875	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Splice_Site	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488228	0.84854	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7969	0.96490	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NRXN1	50317613	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.731000	0.84895	2.679000	0.91253	0.650000	0.86243	.	.	.	none		0.413	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		Intron
SAMSN1	64092	hgsc.bcm.edu	37	21	15873026	15873026	+	Missense_Mutation	SNP	T	T	C	rs62227165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:15873026T>C	ENST00000400566.1	-	6	673	c.592A>G	c.(592-594)Aca>Gca	p.T198A	SAMSN1_ENST00000285670.2_Missense_Mutation_p.T266A|SAMSN1_ENST00000400564.1_Missense_Mutation_p.T30A|SAMSN1_ENST00000463807.1_5'Flank	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	198	SH3.				negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		CCCATTGGTGTTTTGCAAATA	0.378													T|||	30	0.00599042	0.0008	0.0202	5008	,	,		20252	0.0		0.0149	False		,,,				2504	0.0				p.T266A		Atlas-SNP	.											.	SAMSN1	112	.	0			c.A796G						PASS	.	T	ALA/THR	21,3673		0,21,1826	193.0	170.0	177.0		592	5.8	1.0	21	dbSNP_129	177	203,8003		2,199,3902	yes	missense	SAMSN1	NM_022136.3	58	2,220,5728	CC,CT,TT		2.4738,0.5685,1.8824	probably-damaging	198/374	15873026	224,11676	1847	4103	5950	SO:0001583	missense	64092	exon7			TTGGTGTTTTGCA	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.592A>G	21.37:g.15873026T>C	ENSP00000383411:p.Thr198Ala	188.0	0.0	0		223.0	141.0	0.632287	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	T	21.6	4.169451	0.78452	0.005685	0.024738	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T;T	0.29917	3.22;3.22;1.55	5.77	5.77	0.91146	Src homology-3 domain (2);Variant SH3 (1);	0.046352	0.85682	D	0.000000	T	0.26810	0.0656	N	0.21142	0.635	0.44067	D	0.996815	P;D;D	0.71674	0.954;0.998;0.983	P;D;P	0.80764	0.761;0.994;0.895	T	0.26538	-1.0100	10	0.59425	D	0.04	-17.7917	16.0902	0.81086	0.0:0.0:0.0:1.0	rs62227165	30;266;198	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	A	266;198;30	ENSP00000285670:T266A;ENSP00000383411:T198A;ENSP00000383409:T30A	ENSP00000285670:T266A	T	-	1	0	SAMSN1	14794897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.226000	0.58606	2.194000	0.70268	0.528000	0.53228	ACA	T|0.985;C|0.015	0.015	strong		0.378	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		
MLLT1	4298	hgsc.bcm.edu	37	19	6222552	6222552	+	Silent	SNP	C	C	T	rs139655596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6222552C>T	ENST00000252674.7	-	6	853	c.690G>A	c.(688-690)tcG>tcA	p.S230S		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	230					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CCAGCTTCCGCGAGGTGTCCT	0.647			T	MLL	AL								C|||	64	0.0127796	0.0023	0.0173	5008	,	,		11334	0.004		0.0258	False		,,,				2504	0.0194				p.S230S		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	.	MLLT1	47	.	0			c.G690A						PASS	.	C		23,4381	29.9+/-59.1	0,23,2179	36.0	35.0	36.0		690	-9.6	0.0	19	dbSNP_134	36	220,8378	90.6+/-152.8	1,218,4080	no	coding-synonymous	MLLT1	NM_005934.3		1,241,6259	TT,TC,CC		2.5587,0.5223,1.8689		230/560	6222552	243,12759	2202	4299	6501	SO:0001819	synonymous_variant	4298	exon6			CTTCCGCGAGGTG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.690G>A	19.37:g.6222552C>T		30.0	0.0	0		27.0	15.0	0.555556	NM_005934	Q14768	Silent	SNP	ENST00000252674.7	37	CCDS12160.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934	
LRRC27	80313	hgsc.bcm.edu	37	10	134151131	134151131	+	Silent	SNP	G	G	T	rs116451295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134151131G>T	ENST00000368614.3	+	3	378	c.273G>T	c.(271-273)ccG>ccT	p.P91P	LRRC27_ENST00000368613.4_Silent_p.P91P|LRRC27_ENST00000368612.1_Silent_p.P29P|LRRC27_ENST00000392638.2_Silent_p.P91P|LRRC27_ENST00000368610.3_Silent_p.P29P|LRRC27_ENST00000344079.5_Silent_p.P91P|LRRC27_ENST00000368615.3_Silent_p.P91P|LRRC27_ENST00000356571.4_Silent_p.P91P|LRRC27_ENST00000432555.2_5'UTR	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	91								p.P91P(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	18		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		AGTTGCTTCCGAACCTGACTT	0.408													G|||	85	0.0169728	0.0015	0.0115	5008	,	,		16328	0.001		0.0129	False		,,,				2504	0.0624				p.P91P		Atlas-SNP	.											LRRC27,rectum,carcinoma,0,2	LRRC27	64	2	2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	c.G273T						PASS	.	G	,,,	15,4391	23.3+/-48.9	0,15,2188	105.0	99.0	101.0		273,273,273,273	-9.5	0.0	10	dbSNP_132	101	198,8402	86.6+/-149.0	5,188,4107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRC27	NM_001143757.1,NM_001143758.1,NM_001143759.1,NM_030626.2	,,,	5,203,6295	TT,TG,GG		2.3023,0.3404,1.6377	,,,	91/531,91/384,91/384,91/531	134151131	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80313	exon3			GCTTCCGAACCTG	AB051461	CCDS31316.1, CCDS44496.1	10q26.3	2013-09-20			ENSG00000148814	ENSG00000148814			29346	protein-coding gene	gene with protein product						11214970	Standard	NM_030626		Approved	KIAA1674	uc010quw.1	Q9C0I9	OTTHUMG00000019284	ENST00000368614.3:c.273G>T	10.37:g.134151131G>T		146.0	0.0	0		118.0	56.0	0.474576	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Silent	SNP	ENST00000368614.3	37	CCDS31316.1	16	0.007326007326007326	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	0.061	-1.225056	0.01530	0.003404	0.023023	ENSG00000148814	ENST00000450442	.	.	.	4.73	-9.47	0.00594	.	.	.	.	.	T	0.28599	0.0708	.	.	.	0.53005	D	0.999965	.	.	.	.	.	.	T	0.60398	-0.7271	4	.	.	.	-20.1907	6.1334	0.20217	0.2244:0.4943:0.2025:0.0788	.	.	.	.	L	43	.	.	R	+	2	0	LRRC27	134001121	0.957000	0.32711	0.005000	0.12908	0.040000	0.13550	-0.274000	0.08537	-4.666000	0.00037	-1.623000	0.00790	CGA	G|0.984;T|0.016	0.016	strong		0.408	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462	
LRP1	4035	hgsc.bcm.edu	37	12	57587714	57587714	+	Missense_Mutation	SNP	C	C	T	rs367968116		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587714C>T	ENST00000243077.3	+	48	8303	c.7837C>T	c.(7837-7839)Cgg>Tgg	p.R2613W	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2613	LDL-receptor class A 13. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GTTCCGCTGCCGGGACGGGAC	0.607																																					p.R2613W		Atlas-SNP	.											LRP1,NS,lymphoid_neoplasm,-1,1	LRP1	428	1	0			c.C7837T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	97.0	89.0	92.0		7837	4.2	1.0	12		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP1	NM_002332.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2613/4545	57587714	1,13005	2203	4300	6503	SO:0001583	missense	4035	exon48			CGCTGCCGGGACG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7837C>T	12.37:g.57587714C>T	ENSP00000243077:p.Arg2613Trp	108.0	0.0	0		105.0	38.0	0.361905	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803636	0.50315	0.0	1.16E-4	ENSG00000123384	ENST00000243077	D	0.95690	-3.78	5.09	4.19	0.49359	.	0.164278	0.37261	N	0.002175	D	0.96617	0.8896	M	0.62088	1.915	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	D	0.96868	0.9637	10	0.66056	D	0.02	.	14.7368	0.69422	0.0:0.8543:0.1457:0.0	.	2613	Q07954	LRP1_HUMAN	W	2613	ENSP00000243077:R2613W	ENSP00000243077:R2613W	R	+	1	2	LRP1	55873981	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	1.355000	0.34068	1.368000	0.46115	0.650000	0.86243	CGG	.	.	weak		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PRR21	643905	hgsc.bcm.edu	37	2	240982389	240982389	+	Missense_Mutation	SNP	C	C	G	rs143417758		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982389C>G	ENST00000408934.1	-	1	10	c.11G>C	c.(10-12)tGt>tCt	p.C4S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	4										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						TGTGGATGAACAGGCATGCAT	0.567																																					p.C4S		Atlas-SNP	.											.	PRR21	53	.	0			c.G11C						PASS	.						73.0	62.0	65.0					2																	240982389		2172	4269	6441	SO:0001583	missense	643905	exon1			GATGAACAGGCAT	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.11G>C	2.37:g.240982389C>G	ENSP00000386166:p.Cys4Ser	29.0	0.0	0		12.0	7.0	0.583333	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	c	5.954	0.359922	0.11296	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.37752	1.18;1.18	0.149	0.149	0.14863	.	.	.	.	.	T	0.18173	0.0436	N	0.08118	0	0.19945	N	0.999941	P	0.37500	0.597	B	0.39119	0.291	T	0.15435	-1.0437	8	0.42905	T	0.14	.	.	.	.	.	4	Q8WXC7	PRR21_HUMAN	S	4	ENSP00000386166:C4S;ENSP00000418240:C4S	ENSP00000386166:C4S	C	-	2	0	PRR21	240631062	0.000000	0.05858	0.009000	0.14445	0.017000	0.09413	-0.776000	0.04674	0.192000	0.20272	0.195000	0.17529	TGT	.	.	weak		0.567	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
RAB40B	10966	hgsc.bcm.edu	37	17	80616397	80616397	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80616397C>T	ENST00000571995.1	-	5	666	c.535G>A	c.(535-537)Ggg>Agg	p.G179R	RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000538809.2_Missense_Mutation_p.M128I|RAB40B_ENST00000571880.1_5'Flank	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	179	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2)	10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CGGTCCATCCCATGCCGCAGC	0.662																																					p.G179R		Atlas-SNP	.											.	RAB40B	24	.	0			c.G535A						PASS	.						65.0	66.0	66.0					17																	80616397		2203	4300	6503	SO:0001583	missense	10966	exon5			CCATCCCATGCCG	U05227	CCDS11816.1	17q25.3	2014-08-12			ENSG00000141542	ENSG00000141542		"""RAB, member RAS oncogene"""	18284	protein-coding gene	gene with protein product						11697911	Standard	NM_006822		Approved	SEC4L, RAR	uc002kft.3	Q12829	OTTHUMG00000177806	ENST00000571995.1:c.535G>A	17.37:g.80616397C>T	ENSP00000461785:p.Gly179Arg	126.0	0.0	0		119.0	31.0	0.260504	NM_006822	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	37	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.716630	0.68844	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.24	4.24	0.50183	SOCS protein, C-terminal (1);	0.000000	0.64402	D	0.000003	T	0.62600	0.2441	L	0.47716	1.5	0.43412	D	0.995555	B	0.25609	0.13	B	0.36567	0.228	T	0.64702	-0.6345	9	0.51188	T	0.08	.	17.0842	0.86606	0.0:1.0:0.0:0.0	.	179	Q12829	RB40B_HUMAN	R	179;213	.	ENSP00000269347:G179R	G	-	1	0	RAB40B	78209686	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.573000	0.82421	2.283000	0.76528	0.591000	0.81541	GGG	.	.	none		0.662	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1		
ZNF587	84914	hgsc.bcm.edu	37	19	58371202	58371202	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58371202C>T	ENST00000339656.5	+	3	1604	c.1422C>T	c.(1420-1422)ggC>ggT	p.G474G	ZNF814_ENST00000596604.1_Intron|ZNF587_ENST00000419854.1_Silent_p.G431G|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G473G|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	474					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		AATTATTTGGCAATAAGCACA	0.433																																					p.G474G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.C1422T						PASS	.						154.0	150.0	151.0					19																	58371202		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATTTGGCAATAAG	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1422C>T	19.37:g.58371202C>T		180.0	0.0	0		224.0	13.0	0.0580357	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			.	.	none		0.433	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ELOVL1	64834	hgsc.bcm.edu	37	1	43830438	43830438	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43830438A>G	ENST00000372458.3	-	5	463	c.346T>C	c.(346-348)Ttc>Ctc	p.F116L	ELOVL1_ENST00000413844.2_Missense_Mutation_p.F89L|ELOVL1_ENST00000470769.1_5'UTR	NM_001256399.1|NM_001256402.1|NM_022821.3	NP_001243328.1|NP_001243331.1|NP_073732.1	Q9BW60	ELOV1_HUMAN	ELOVL fatty acid elongase 1	116					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|prostate(1)	4	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AACTTGGAGAAGAGGAAGAGC	0.498																																					p.F116L		Atlas-SNP	.											.	ELOVL1	18	.	0			c.T346C						PASS	.						112.0	123.0	119.0					1																	43830438		2203	4300	6503	SO:0001583	missense	64834	exon5			TGGAGAAGAGGAA	AK001653	CCDS485.1, CCDS57987.1	1p34	2011-05-25	2011-05-25		ENSG00000066322	ENSG00000066322			14418	protein-coding gene	gene with protein product		611813	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1"""				Standard	NM_022821		Approved	Ssc1	uc031pmf.1	Q9BW60	OTTHUMG00000007422	ENST00000372458.3:c.346T>C	1.37:g.43830438A>G	ENSP00000361536:p.Phe116Leu	93.0	0.0	0		79.0	42.0	0.531646	NM_001256399	B4DP24|Q53HT2|Q5JUY3|Q8WXU3|Q9NVD9|Q9Y396	Missense_Mutation	SNP	ENST00000372458.3	37	CCDS485.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.837426	0.50951	.	.	ENSG00000066322	ENST00000372458;ENST00000413844	T;T	0.16073	2.37;2.37	5.77	4.65	0.58169	.	0.042915	0.85682	N	0.000000	T	0.18002	0.0432	L	0.45470	1.425	0.80722	D	1	B;B	0.13145	0.001;0.007	B;B	0.28465	0.011;0.09	T	0.02844	-1.1103	10	0.38643	T	0.18	0.4038	10.9623	0.47393	0.9261:0.0:0.0739:0.0	.	89;116	B4DP24;Q9BW60	.;ELOV1_HUMAN	L	116;89	ENSP00000361536:F116L;ENSP00000416024:F89L	ENSP00000361536:F116L	F	-	1	0	ELOVL1	43603025	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.126000	0.57937	1.026000	0.39733	0.533000	0.62120	TTC	.	.	none		0.498	ELOVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019496.1	NM_022821	
CCDC168	643677	hgsc.bcm.edu	37	13	103388880	103388880	+	Missense_Mutation	SNP	T	T	C	rs17592459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103388880T>C	ENST00000322527.2	-	1	279	c.280A>G	c.(280-282)Atg>Gtg	p.M94V		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	94			M -> V (in dbSNP:rs17592459).														AGATGTGGCATAAAGCTTCTT	0.413													T|||	122	0.024361	0.003	0.0216	5008	,	,		24116	0.0		0.0408	False		,,,				2504	0.0634				p.M4723V		Atlas-SNP	.											.	.	.	.	0			c.A14167G						PASS	.	T	VAL/MET	6,1378		0,6,686	250.0	192.0	210.0		14167	-2.3	0.0	13	dbSNP_123	210	116,3066		3,110,1478	yes	missense	CCDC168	NM_001146197.1	21	3,116,2164	CC,CT,TT		3.6455,0.4335,2.6719	benign	4723/7082	103388880	122,4444	692	1591	2283	SO:0001583	missense	643677	exon4			GTGGCATAAAGCT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.280A>G	13.37:g.103388880T>C	ENSP00000320232:p.Met94Val	197.0	0.0	0		164.0	81.0	0.493902	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		42	0.019230769230769232	4	0.008130081300813009	8	0.022099447513812154	0	0.0	30	0.0395778364116095	T	0.007	-2.011250	0.00422	0.004335	0.036455	ENSG00000175820	ENST00000322527	T	0.02631	4.22	4.0	-2.27	0.06846	.	1.931660	0.02917	N	0.137481	T	0.00384	0.0012	N	0.10874	0.06	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.37384	-0.9708	10	0.02654	T	1	.	3.0766	0.06248	0.3203:0.2667:0.0:0.413	rs17592459;rs52821179;rs17592459	94	Q8NDH2	CC168_HUMAN	V	94	ENSP00000320232:M94V	ENSP00000320232:M94V	M	-	1	0	CCDC168	102186881	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.063000	0.11655	-0.568000	0.06038	-0.464000	0.05259	ATG	T|0.978;C|0.022	0.022	strong		0.413	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
EAF1	85403	hgsc.bcm.edu	37	3	15477872	15477872	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477872A>C	ENST00000396842.2	+	5	975	c.550A>C	c.(550-552)Att>Ctt	p.I184L	EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000595975.1_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000593876.1_RNA|EAF1_ENST00000432764.2_Missense_Mutation_p.I83L	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	184	Necessary for transactivation activity.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						AGTTGACATTATTGAACAAAT	0.483																																					p.I184L		Atlas-SNP	.											.	EAF1	16	.	0			c.A550C						PASS	.						46.0	47.0	47.0					3																	15477872		2203	4300	6503	SO:0001583	missense	85403	exon5			GACATTATTGAAC	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.550A>C	3.37:g.15477872A>C	ENSP00000380054:p.Ile184Leu	158.0	0.0	0		168.0	35.0	0.208333	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885242	0.91814	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.67	5.67	0.87782	.	0.091650	0.64402	D	0.000001	T	0.62368	0.2422	M	0.65975	2.015	0.58432	D	0.999999	B;B	0.15473	0.013;0.011	B;B	0.17722	0.019;0.003	T	0.60347	-0.7281	9	0.49607	T	0.09	-10.8435	14.8972	0.70651	1.0:0.0:0.0:0.0	.	83;184	B4E3F5;Q96JC9	.;EAF1_HUMAN	L	184;83	.	ENSP00000380054:I184L	I	+	1	0	EAF1	15452876	1.000000	0.71417	0.966000	0.40874	0.886000	0.51366	8.962000	0.93254	2.159000	0.67721	0.454000	0.30748	ATT	.	.	none		0.483	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
DMBT1	1755	hgsc.bcm.edu	37	10	124358421	124358421	+	Missense_Mutation	SNP	G	G	A	rs368405942		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124358421G>A	ENST00000338354.3	+	26	3194	c.3088G>A	c.(3088-3090)Gtc>Atc	p.V1030I	DMBT1_ENST00000368909.3_Missense_Mutation_p.V1030I|DMBT1_ENST00000330163.4_Missense_Mutation_p.V531I|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000344338.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000368956.2_Missense_Mutation_p.V531I			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1030	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TGCCAATGTCGTCTGCAGGCA	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V1030I	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G3088A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	0,4072		0,0,2036	260.0	259.0	259.0		1591,3088,3058	2.6	0.9	10		259	2,8420		0,2,4209	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	29,29,29	0,2,6245	AA,AG,GG		0.0237,0.0,0.016	possibly-damaging,possibly-damaging,possibly-damaging	531/1786,1030/2414,1020/2404	124358421	2,12492	2036	4211	6247	SO:0001583	missense	1755	exon26			AATGTCGTCTGCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.3088G>A	10.37:g.124358421G>A	ENSP00000342210:p.Val1030Ile	62.0	0.0	0		43.0	14.0	0.325581	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	G	16.84	3.233595	0.58886	0.0	2.37E-4	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09	3.57	2.63	0.31362	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.725684	0.11251	N	0.583638	T	0.60143	0.2246	M	0.69248	2.105	0.80722	D	1	D;D;P;P	0.76494	0.99;0.999;0.923;0.938	P;D;B;B	0.74674	0.606;0.984;0.154;0.24	T	0.52540	-0.8562	10	0.38643	T	0.18	.	11.4562	0.50183	0.0924:0.0:0.9076:0.0	.	1030;531;1020;1030	Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	I	1030;1030;1030;1030;1030;1030;531;1020;531;531;1030;1020;531	ENSP00000342210:V1030I;ENSP00000343175:V1020I;ENSP00000327747:V531I;ENSP00000357905:V1030I;ENSP00000357951:V1020I;ENSP00000357952:V531I	ENSP00000331522:V531I	V	+	1	0	DMBT1	124348411	1.000000	0.71417	0.922000	0.36590	0.566000	0.35808	7.239000	0.78182	0.585000	0.29608	0.558000	0.71614	GTC	.	.	none		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
E2F2	1870	hgsc.bcm.edu	37	1	23845566	23845566	+	Missense_Mutation	SNP	G	G	A	rs139052092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:23845566G>A	ENST00000361729.2	-	5	1220	c.794C>T	c.(793-795)aCa>aTa	p.T265I	E2F2_ENST00000487237.1_5'UTR	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	265	Dimerization. {ECO:0000255}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		GGCAATCACTGTCTGCTCCTT	0.532													G|||	5	0.000998403	0.0	0.0	5008	,	,		20103	0.0		0.005	False		,,,				2504	0.0				p.T265I		Atlas-SNP	.											.	E2F2	31	.	0			c.C794T						PASS	.	G	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	113.0	97.0	103.0		794	6.1	1.0	1	dbSNP_134	103	27,8573	19.2+/-60.6	0,27,4273	yes	missense	E2F2	NM_004091.3	89	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging	265/438	23845566	29,12977	2203	4300	6503	SO:0001583	missense	1870	exon5			ATCACTGTCTGCT	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.794C>T	1.37:g.23845566G>A	ENSP00000355249:p.Thr265Ile	126.0	0.0	0		128.0	64.0	0.5	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	35	5.445078	0.96187	4.54E-4	0.00314	ENSG00000007968	ENST00000361729	D	0.87412	-2.25	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.89234	0.6657	M	0.63428	1.95	0.80722	D	1	P	0.51240	0.943	P	0.48189	0.57	D	0.88744	0.3245	10	0.49607	T	0.09	-19.7296	19.2232	0.93806	0.0:0.0:1.0:0.0	.	265	Q14209	E2F2_HUMAN	I	265	ENSP00000355249:T265I	ENSP00000355249:T265I	T	-	2	0	E2F2	23718153	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	9.803000	0.99136	2.885000	0.99019	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.532	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091	
WDFY4	57705	hgsc.bcm.edu	37	10	49987998	49987998	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:49987998C>T	ENST00000325239.5	+	18	3437	c.3410C>T	c.(3409-3411)cCt>cTt	p.P1137L	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1137						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						GTCATGGAACCTGAGGATGAC	0.567																																					p.P1137L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C3410T						PASS	.						126.0	112.0	116.0					10																	49987998		692	1591	2283	SO:0001583	missense	57705	exon19			TGGAACCTGAGGA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.3410C>T	10.37:g.49987998C>T	ENSP00000320563:p.Pro1137Leu	79.0	0.0	0		79.0	26.0	0.329114	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943757	0.53079	.	.	ENSG00000128815	ENST00000426033;ENST00000325239	T	0.56444	0.46	5.71	4.81	0.61882	.	.	.	.	.	T	0.37320	0.0999	N	0.24115	0.695	0.80722	D	1	B	0.20052	0.041	B	0.20184	0.028	T	0.14062	-1.0486	8	.	.	.	.	12.1701	0.54152	0.0:0.9213:0.0:0.0787	.	1137	Q6ZS81	WDFY4_HUMAN	L	1137	ENSP00000320563:P1137L	.	P	+	2	0	WDFY4	49658004	1.000000	0.71417	0.816000	0.32577	0.917000	0.54804	4.981000	0.63819	1.422000	0.47177	0.561000	0.74099	CCT	.	.	none		0.567	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259598	69259598	+	Splice_Site	SNP	C	C	T	rs563928424		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69259598C>T	ENST00000439696.2	-	1	359		c.e1+1		ZFP36L1_ENST00000555997.1_5'Flank|ZFP36L1_ENST00000336440.3_Splice_Site	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CCCCCCTTTACCTTGCATAAA	0.517													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14835	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.57+1G>A						PASS	.						163.0	168.0	166.0					14																	69259598		2203	4300	6503	SO:0001630	splice_region_variant	677	exon2			CCTTTACCTTGCA	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.57+1G>A	14.37:g.69259598C>T		63.0	0.0	0		34.0	6.0	0.176471	NM_004926	Q13851	Splice_Site	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882604	0.72410	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000553375	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0951	0.81114	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZFP36L1	68329351	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.059000	0.64306	2.065000	0.61736	0.561000	0.74099	.	.	.	none		0.517	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		Intron
NAV3	89795	hgsc.bcm.edu	37	12	78574783	78574783	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:78574783C>A	ENST00000397909.2	+	30	5823	c.5650C>A	c.(5650-5652)Ctt>Att	p.L1884I	NAV3_ENST00000266692.7_Missense_Mutation_p.L1685I|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000536525.2_Missense_Mutation_p.L1862I|NAV3_ENST00000228327.6_Missense_Mutation_p.L1862I			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1884	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GTCATTAGGACTTTCTCTAAA	0.488										HNSCC(70;0.22)																											p.L1862I		Atlas-SNP	.											.	NAV3	506	.	0			c.C5584A						PASS	.						116.0	117.0	117.0					12																	78574783		2000	4164	6164	SO:0001583	missense	89795	exon29			TTAGGACTTTCTC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5650C>A	12.37:g.78574783C>A	ENSP00000381007:p.Leu1884Ile	120.0	0.0	0		103.0	18.0	0.174757	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.9|27.9	4.869227|4.869227	0.91587|0.91587	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.32023|.	1.53;1.51;1.52;1.47;2.32|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.36034|.	U|.	0.002827|.	T|T	0.76285|0.76285	0.3966|0.3966	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.998;0.996;0.999;0.998|.	D;D;D;D|.	0.83275|.	0.949;0.986;0.996;0.99|.	T|T	0.72404|0.72404	-0.4304|-0.4304	10|5	0.59425|.	D|.	0.04|.	-12.5593|-12.5593	20.547|20.547	0.99278|0.99278	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1862;1685;1884;1862|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	I|N	1862;1884;1862;1685;476;484|756	ENSP00000446132:L1862I;ENSP00000381007:L1884I;ENSP00000228327:L1862I;ENSP00000266692:L1685I;ENSP00000448303:L484I|.	ENSP00000228327:L1862I|.	L|T	+|+	1|2	0|0	NAV3|NAV3	77098914|77098914	1.000000|1.000000	0.71417|0.71417	0.417000|0.417000	0.26559|0.26559	0.868000|0.868000	0.49771|0.49771	7.487000|7.487000	0.81328|0.81328	2.850000|2.850000	0.98022|0.98022	0.650000|0.650000	0.86243|0.86243	CTT|ACT	.	.	none		0.488	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
MCL1	4170	hgsc.bcm.edu	37	1	150550920	150550920	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150550920A>C	ENST00000369026.2	-	2	795	c.736T>G	c.(736-738)Ttg>Gtg	p.L246V	MCL1_ENST00000464132.1_5'UTR|MCL1_ENST00000307940.3_Intron	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	246					apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ACTCGAGACAACGATTTCACA	0.478																																					p.L246V		Atlas-SNP	.											.	MCL1	27	.	0			c.T736G						PASS	.						106.0	108.0	107.0					1																	150550920		2203	4300	6503	SO:0001583	missense	4170	exon2			GAGACAACGATTT	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"""myeloid cell leukemia sequence 1 (BCL2-related)"""			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.736T>G	1.37:g.150550920A>C	ENSP00000358022:p.Leu246Val	154.0	0.0	0		107.0	28.0	0.261682	NM_021960	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Missense_Mutation	SNP	ENST00000369026.2	37	CCDS957.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917467	0.33815	.	.	ENSG00000143384	ENST00000369026;ENST00000439749	T	0.04603	3.59	4.77	1.08	0.20341	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	0.298701	0.31601	N	0.007374	T	0.00815	0.0027	N	0.11560	0.145	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.46965	-0.9153	10	0.33141	T	0.24	-5.5956	4.6041	0.12368	0.4735:0.2298:0.2967:0.0	.	246	Q07820	MCL1_HUMAN	V	246;175	ENSP00000358022:L246V	ENSP00000358022:L246V	L	-	1	2	MCL1	148817544	0.087000	0.21565	0.993000	0.49108	0.996000	0.88848	0.574000	0.23714	0.345000	0.23873	0.533000	0.62120	TTG	.	.	none		0.478	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960	
C6orf136	221545	hgsc.bcm.edu	37	6	30615413	30615413	+	Intron	SNP	T	T	C	rs146616682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30615413T>C	ENST00000376473.5	+	1	231				C6orf136_ENST00000376471.4_Intron|C6orf136_ENST00000493705.1_3'UTR|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000293604.6_Silent_p.I135I|C6orf136_ENST00000528347.2_5'Flank	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136							mitochondrion (GO:0005739)				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCCGAGAGATTCGTAGCCCTG	0.716													T|||	13	0.00259585	0.0	0.0072	5008	,	,		13756	0.001		0.007	False		,,,				2504	0.0				p.I135I		Atlas-SNP	.											.	C6orf136	31	.	0			c.T405C						PASS	.						5.0	7.0	7.0					6																	30615413		669	1552	2221	SO:0001627	intron_variant	221545	exon1			AGAGATTCGTAGC	BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.72+333T>C	6.37:g.30615413T>C		59.0	0.0	0		67.0	44.0	0.656716	NM_001161376	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Silent	SNP	ENST00000376473.5	37	CCDS43443.1																																																																																			T|0.994;C|0.006	0.006	strong		0.716	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029	
CFHR2	3080	hgsc.bcm.edu	37	1	196918741	196918741	+	Missense_Mutation	SNP	G	G	A	rs79351096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196918741G>A	ENST00000367415.5	+	2	315	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000476712.2_Missense_Mutation_p.C72Y|CFHR2_ENST00000367421.3_Missense_Mutation_p.C72Y	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	72	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGCATAACGTGCGCAGAAGAA	0.403													g|||	76	0.0151757	0.0015	0.0288	5008	,	,		18573	0.0		0.0189	False		,,,				2504	0.0358				p.C72Y		Atlas-SNP	.											CFHR2_ENST00000367415,NS,carcinoma,-1,1	CFHR2	73	1	0			c.G215A						PASS	.	G	TYR/CYS	30,4376		0,30,2173	101.0	89.0	93.0		215	3.3	0.0	1	dbSNP_133	93	220,8380		2,216,4082	no	missense	CFHR2	NM_005666.2	194	2,246,6255	AA,AG,GG		2.5581,0.6809,1.9222	probably-damaging	72/271	196918741	250,12756	2203	4300	6503	SO:0001583	missense	3080	exon2			TAACGTGCGCAGA	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.215G>A	1.37:g.196918741G>A	ENSP00000356385:p.Cys72Tyr	247.0	0.0	0		213.0	103.0	0.483568	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	33	0.01510989010989011	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	18	0.023746701846965697	.	13.46	2.242600	0.39598	0.006809	0.025581	ENSG00000080910	ENST00000367421;ENST00000367415	D;D	0.98090	-4.71;-4.71	3.33	3.33	0.38152	Complement control module (2);Sushi/SCR/CCP (2);	0.000000	0.36893	N	0.002344	D	0.94305	0.8170	M	0.84082	2.675	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86843	0.2018	10	0.87932	D	0	.	10.313	0.43721	0.0:0.0:1.0:0.0	.	72	P36980	FHR2_HUMAN	Y	72	ENSP00000356391:C72Y;ENSP00000356385:C72Y	ENSP00000356385:C72Y	C	+	2	0	CFHR2	195185364	0.417000	0.25432	0.004000	0.12327	0.001000	0.01503	3.949000	0.56668	1.825000	0.53177	0.508000	0.49915	TGC	G|0.983;A|0.017	0.017	strong		0.403	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666	
PTPN12	5782	hgsc.bcm.edu	37	7	77256150	77256150	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77256150A>G	ENST00000248594.6	+	13	1426	c.1154A>G	c.(1153-1155)gAt>gGt	p.D385G	PTPN12_ENST00000415482.2_Missense_Mutation_p.D266G|PTPN12_ENST00000435495.2_Missense_Mutation_p.D255G	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	385	Interaction with TGFB1I1. {ECO:0000250}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CAGGACAATGATAGATACCAT	0.458																																					p.D385G		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1154G						PASS	.						94.0	83.0	87.0					7																	77256150		2203	4300	6503	SO:0001583	missense	5782	exon13			ACAATGATAGATA		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1154A>G	7.37:g.77256150A>G	ENSP00000248594:p.Asp385Gly	189.0	0.0	0		178.0	37.0	0.207865	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974843	0.74360	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.51574	0.7;0.7;0.7	6.17	5.02	0.67125	.	0.043790	0.85682	N	0.000000	T	0.64627	0.2615	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.62144	-0.6916	10	0.24483	T	0.36	.	12.092	0.53733	0.9337:0.0:0.0663:0.0	.	385	Q05209	PTN12_HUMAN	G	385;266;266;255	ENSP00000248594:D385G;ENSP00000392429:D266G;ENSP00000397991:D255G	ENSP00000248594:D385G	D	+	2	0	PTPN12	77094086	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.871000	0.75531	1.160000	0.42584	0.533000	0.62120	GAT	.	.	none		0.458	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
SLIT2	9353	hgsc.bcm.edu	37	4	20493415	20493415	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20493415T>A	ENST00000504154.1	+	9	1059	c.807T>A	c.(805-807)agT>agA	p.S269R	SLIT2_ENST00000503823.1_Missense_Mutation_p.S269R|SLIT2_ENST00000503837.1_Missense_Mutation_p.S273R|SLIT2_ENST00000273739.5_Missense_Mutation_p.S273R	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	269	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CTTCTTGTAGTGTTTTGCACT	0.408																																					p.S269R		Atlas-SNP	.											.	SLIT2	290	.	0			c.T807A						PASS	.						132.0	132.0	132.0					4																	20493415		2203	4300	6503	SO:0001583	missense	9353	exon9			TTGTAGTGTTTTG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.807T>A	4.37:g.20493415T>A	ENSP00000422591:p.Ser269Arg	147.0	0.0	0		106.0	32.0	0.301887	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912535	0.72983	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81247	-1.45;-1.47;-1.38;-1.44	5.63	-10.6	0.00265	.	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	N	0.17764	0.52	0.54753	D	0.999988	P;D	0.55172	0.801;0.97	P;P	0.53912	0.578;0.737	D	0.85392	0.1126	10	0.48119	T	0.1	.	17.9392	0.89022	0.0:0.5825:0.0:0.4175	.	269;269	O94813-3;O94813	.;SLIT2_HUMAN	R	269;269;273;273;273	ENSP00000427548:S269R;ENSP00000422591:S269R;ENSP00000273739:S273R;ENSP00000422261:S273R	ENSP00000273739:S273R	S	+	3	2	SLIT2	20102513	0.076000	0.21285	0.120000	0.21714	0.952000	0.60782	-0.425000	0.07017	-2.280000	0.00675	-0.146000	0.13790	AGT	.	.	none		0.408	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
AGAP1	116987	hgsc.bcm.edu	37	2	236817442	236817442	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:236817442C>T	ENST00000304032.8	+	11	1796	c.1216C>T	c.(1216-1218)Cca>Tca	p.P406S	AGAP1_ENST00000409538.1_Missense_Mutation_p.P671S|AGAP1_ENST00000428334.2_Missense_Mutation_p.P245S|AGAP1_ENST00000336665.5_Missense_Mutation_p.P406S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	406	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGTGAAAGTCCCAGGGAAGAG	0.468																																					p.P406S		Atlas-SNP	.											.	AGAP1	95	.	0			c.C1216T						PASS	.						73.0	68.0	70.0					2																	236817442		2203	4300	6503	SO:0001583	missense	116987	exon11			AAAGTCCCAGGGA	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1216C>T	2.37:g.236817442C>T	ENSP00000307634:p.Pro406Ser	116.0	0.0	0		153.0	20.0	0.130719	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.116727|5.116727	0.94385|0.94385	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	.|T;T;T;T	.|0.75367	.|-0.93;-0.93;-0.93;-0.93	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Pleckstrin homology domain (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87350|0.87350	0.6155|0.6155	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.91635	.|0.948;0.999	D|D	0.88666|0.88666	0.3192|0.3192	6|10	.|0.56958	.|D	.|0.05	.|.	18.4385|18.4385	0.90654|0.90654	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|406;406	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	L|S	39|406;406;671;245	.|ENSP00000307634:P406S;ENSP00000338378:P406S;ENSP00000386897:P671S;ENSP00000411824:P245S	.|ENSP00000307634:P406S	P|P	+|+	2|1	0|0	AGAP1|AGAP1	236482181|236482181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.610000|7.610000	0.82949|0.82949	2.527000|2.527000	0.85204|0.85204	0.655000|0.655000	0.94253|0.94253	CCC|CCA	.	.	none		0.468	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
ZNF442	79973	hgsc.bcm.edu	37	19	12461745	12461745	+	Silent	SNP	A	A	G	rs117398535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12461745A>G	ENST00000242804.4	-	6	1236	c.654T>C	c.(652-654)ttT>ttC	p.F218F	ZNF442_ENST00000438182.1_Silent_p.F149F|CTD-3105H18.13_ENST00000563695.2_lincRNA	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	218					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TAGGCCAAAAAAAGGCTTTCC	0.403													A|||	10	0.00199681	0.0015	0.0014	5008	,	,		22597	0.0		0.007	False		,,,				2504	0.0				p.F218F		Atlas-SNP	.											ZNF442,middle_lobe,carcinoma,0,1	ZNF442	102	1	0			c.T654C						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	138.0	134.0	135.0		654	-1.5	0.0	19	dbSNP_132	135	56,8544	35.9+/-90.5	0,56,4244	no	coding-synonymous	ZNF442	NM_030824.2		0,60,6443	GG,GA,AA		0.6512,0.0908,0.4613		218/628	12461745	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79973	exon6			CCAAAAAAAGGCT	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.654T>C	19.37:g.12461745A>G		54.0	0.0	0		46.0	18.0	0.391304	NM_030824	B4DJ48	Silent	SNP	ENST00000242804.4	37	CCDS12271.1																																																																																			A|0.995;G|0.005	0.005	strong		0.403	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
PADI2	11240	hgsc.bcm.edu	37	1	17413152	17413152	+	Missense_Mutation	SNP	C	C	T	rs61749340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17413152C>T	ENST00000375486.4	-	7	761	c.698G>A	c.(697-699)cGg>cAg	p.R233Q	PADI2_ENST00000444885.2_Missense_Mutation_p.G152R|PADI2_ENST00000375481.1_Missense_Mutation_p.R233Q	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	233					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GTAGAGCTTCCGCCGGCCCAG	0.612													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17851	0.0		0.0119	False		,,,				2504	0.0031				p.R233Q		Atlas-SNP	.											.	PADI2	72	.	0			c.G698A						PASS	.	C	GLN/ARG	25,4381	31.7+/-61.6	1,23,2179	79.0	84.0	83.0		698	-0.0	1.0	1	dbSNP_129	83	86,8514	49.8+/-109.6	0,86,4214	yes	missense	PADI2	NM_007365.2	43	1,109,6393	TT,TC,CC		1.0,0.5674,0.8535	benign	233/666	17413152	111,12895	2203	4300	6503	SO:0001583	missense	11240	exon7			AGCTTCCGCCGGC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.698G>A	1.37:g.17413152C>T	ENSP00000364635:p.Arg233Gln	109.0	0.0	0		117.0	58.0	0.495726	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	6.143|6.143	0.394510|0.394510	0.11638|0.11638	0.005674|0.005674	0.01|0.01	ENSG00000117115|ENSG00000117115	ENST00000444885|ENST00000375486;ENST00000375481	T|T;T	0.06294|0.15834	3.32|2.39;2.39	4.71|4.71	-0.0409|-0.0409	0.13870|0.13870	.|Protein-arginine deiminase (PAD), central domain (2);	.|0.666471	.|0.15848	.|N	.|0.241686	T|T	0.03136|0.03136	0.0092|0.0092	N|N	0.02539|0.02539	-0.55|-0.55	0.22185|0.22185	N|N	0.999304|0.999304	B|B	0.06786|0.02656	0.001|0.0	B|B	0.01281|0.04013	0.0|0.001	T|T	0.42327|0.42327	-0.9458|-0.9458	9|10	0.20519|0.02654	T|T	0.43|1	-11.41|-11.41	8.498|8.498	0.33141|0.33141	0.0:0.3828:0.0:0.6172|0.0:0.3828:0.0:0.6172	rs61749340|rs61749340	152|233	B4DIU3|Q9Y2J8	.|PADI2_HUMAN	R|Q	152|233	ENSP00000405894:G152R|ENSP00000364635:R233Q;ENSP00000364630:R233Q	ENSP00000405894:G152R|ENSP00000364630:R233Q	G|R	-|-	1|2	0|0	PADI2|PADI2	17285739|17285739	0.001000|0.001000	0.12720|0.12720	0.981000|0.981000	0.43875|0.43875	0.988000|0.988000	0.76386|0.76386	-0.161000|-0.161000	0.10026|0.10026	0.067000|0.067000	0.16545|0.16545	0.460000|0.460000	0.39030|0.39030	GGA|CGG	C|0.994;T|0.006	0.006	strong		0.612	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
PCSK9	255738	hgsc.bcm.edu	37	1	55505679	55505679	+	Missense_Mutation	SNP	G	G	A	rs145886902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505679G>A	ENST00000302118.5	+	1	459	c.169G>A	c.(169-171)Gag>Aag	p.E57K	PCSK9_ENST00000452118.2_Missense_Mutation_p.E57K|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	57			E -> K. {ECO:0000269|PubMed:16465619}.		apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CGAAGCACCCGAGCACGGAAC	0.716													G|||	5	0.000998403	0.0038	0.0	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.E57K	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G169A	GRCh37	CM060421	PCSK9	M	rs145886902	PASS	.	G	LYS/GLU	11,4359		0,11,2174	29.0	24.0	26.0		169	-4.7	0.0	1	dbSNP_134	26	2,8534		0,2,4266	yes	missense	PCSK9	NM_174936.3	56	0,13,6440	AA,AG,GG		0.0234,0.2517,0.1007	benign	57/693	55505679	13,12893	2185	4268	6453	SO:0001583	missense	255738	exon1			GCACCCGAGCACG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.169G>A	1.37:g.55505679G>A	ENSP00000303208:p.Glu57Lys	87.0	0.0	0		106.0	22.0	0.207547	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	7.413	0.635044	0.14322	0.002517	2.34E-4	ENSG00000169174	ENST00000302118;ENST00000452118	T;T	0.71461	-0.51;-0.57	3.09	-4.71	0.03279	.	1.506200	0.05619	U	0.579657	T	0.45296	0.1335	N	0.14661	0.345	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.11794	T	0.64	3.2202	5.4094	0.16341	0.1325:0.2249:0.5426:0.1	.	57	Q8NBP7	PCSK9_HUMAN	K	57	ENSP00000303208:E57K;ENSP00000401598:E57K	ENSP00000303208:E57K	E	+	1	0	PCSK9	55278267	0.000000	0.05858	0.000000	0.03702	0.228000	0.25075	-0.351000	0.07711	-0.725000	0.04901	-0.802000	0.03209	GAG	G|0.999;A|0.001	0.001	strong		0.716	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
TLN2	83660	hgsc.bcm.edu	37	15	63125804	63125804	+	Silent	SNP	G	G	A	rs142793310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63125804G>A	ENST00000561311.1	+	54	7334	c.7104G>A	c.(7102-7104)caG>caA	p.Q2368Q	RP11-1069G10.1_ENST00000558888.1_RNA|TLN2_ENST00000306829.6_Silent_p.Q2368Q|RP11-1069G10.1_ENST00000558404.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2368	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CAGCAGCCCAGAGGGAGCTGG	0.577																																					p.Q2368Q		Atlas-SNP	.											.	TLN2	253	.	0			c.G7104A						PASS	.	G		0,4406		0,0,2203	77.0	77.0	77.0		7104	5.1	1.0	15	dbSNP_134	77	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	TLN2	NM_015059.2		0,7,6496	AA,AG,GG		0.0814,0.0,0.0538		2368/2543	63125804	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon52			AGCCCAGAGGGAG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7104G>A	15.37:g.63125804G>A		130.0	0.0	0		84.0	24.0	0.285714	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
MAP3K1	4214	hgsc.bcm.edu	37	5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	rs56069227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	snoU13_ENST00000459264.1_RNA|AC008937.2_ENST00000415589.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42.0	42.0	42.0		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	225.0	0.0	0		206.0	128.0	0.621359	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
KCNK12	56660	hgsc.bcm.edu	37	2	47748558	47748558	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47748558C>T	ENST00000327876.4	-	2	1388	c.781G>A	c.(781-783)Gac>Aac	p.D261N	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	261						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTCACCAGGTCCCCGAAGCCG	0.632																																					p.D261N		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.G781A						PASS	.						41.0	39.0	40.0					2																	47748558		2203	4299	6502	SO:0001583	missense	56660	exon2			CCAGGTCCCCGAA	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.781G>A	2.37:g.47748558C>T	ENSP00000327611:p.Asp261Asn	74.0	0.0	0		170.0	43.0	0.252941	NM_022055		Missense_Mutation	SNP	ENST00000327876.4	37	CCDS1835.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172527	0.78452	.	.	ENSG00000184261	ENST00000327876	T	0.41758	0.99	4.1	3.22	0.36961	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80885	-0.1182	10	0.87932	D	0	.	13.8032	0.63214	0.0:0.8451:0.1549:0.0	.	261	Q9HB15	KCNKC_HUMAN	N	261	ENSP00000327611:D261N	ENSP00000327611:D261N	D	-	1	0	KCNK12	47602062	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	5.915000	0.69973	0.922000	0.37019	0.305000	0.20034	GAC	.	.	none		0.632	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
GOLGB1	2804	hgsc.bcm.edu	37	3	121386377	121386377	+	Missense_Mutation	SNP	T	T	A	rs144495540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121386377T>A	ENST00000340645.5	-	20	9610	c.9485A>T	c.(9484-9486)gAc>gTc	p.D3162V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.D3172V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	3162					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CACTCTTTGGTCTCGTTCTTC	0.493																																					p.D3172V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A9515T						PASS	.	T	VAL/ASP	0,4406		0,0,2203	104.0	93.0	97.0		9485	5.5	1.0	3	dbSNP_134	97	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GOLGB1	NM_004487.3	152	0,7,6496	AA,AT,TT		0.0814,0.0,0.0538	probably-damaging	3162/3260	121386377	7,12999	2203	4300	6503	SO:0001583	missense	2804	exon20			CTTTGGTCTCGTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.9485A>T	3.37:g.121386377T>A	ENSP00000341848:p.Asp3162Val	264.0	1.0	0.00378788		248.0	115.0	0.46371	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.290072	0.59976	0.0	8.14E-4	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.16073	2.37;2.37	5.48	5.48	0.80851	.	0.090168	0.48767	D	0.000177	T	0.23451	0.0567	N	0.24115	0.695	0.54753	D	0.999989	D;D;P	0.55800	0.973;0.973;0.903	P;P;P	0.59546	0.859;0.859;0.65	T	0.01456	-1.1350	10	0.56958	D	0.05	.	11.8745	0.52539	0.0:0.0:0.0:1.0	.	3172;3172;3162	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	V	3162;3172	ENSP00000341848:D3162V;ENSP00000377275:D3172V	ENSP00000341848:D3162V	D	-	2	0	GOLGB1	122869067	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.287000	0.59001	2.302000	0.77476	0.528000	0.53228	GAC	T|0.999;A|0.001	0.001	strong		0.493	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
TTC3	7267	hgsc.bcm.edu	37	21	38572565	38572565	+	Silent	SNP	C	C	T	rs150750778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38572565C>T	ENST00000399017.2	+	45	8630	c.5883C>T	c.(5881-5883)caC>caT	p.H1961H	TTC3_ENST00000355666.1_Silent_p.H1961H|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Silent_p.H1961H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1961					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAATATGCCACGAGGTGTTCA	0.433													C|||	14	0.00279553	0.0083	0.0029	5008	,	,		17732	0.0		0.001	False		,,,				2504	0.0				p.H1961H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C5883T						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	85.0	74.0	78.0		5883,5883	-11.2	0.0	21	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	0,12,6491	TT,TC,CC		0.0,0.2724,0.0923	,	1961/2026,1961/2026	38572565	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	7267	exon45			ATGCCACGAGGTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5883C>T	21.37:g.38572565C>T		240.0	0.0	0		287.0	56.0	0.195122	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	C	5.526	0.282044	0.10458	0.002724	0.0	ENSG00000182670	ENST00000428693	.	.	.	5.58	-11.2	0.00127	.	.	.	.	.	.	.	.	.	.	.	0.22684	N	0.99886	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.0597	9.5757	0.39457	0.2457:0.4773:0.0:0.2771	.	.	.	.	X	253	.	.	R	+	1	2	TTC3	37494435	0.000000	0.05858	0.000000	0.03702	0.741000	0.42261	-3.228000	0.00549	-3.780000	0.00108	-1.090000	0.02178	CGA	C|0.998;T|0.002	0.002	strong		0.433	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
BCKDHB	594	hgsc.bcm.edu	37	6	80816415	80816415	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:80816415C>T	ENST00000320393.6	+	1	52	c.5C>T	c.(4-6)gCg>gTg	p.A2V	BCKDHB_ENST00000545529.1_Missense_Mutation_p.A2V|BCKDHB_ENST00000356489.5_Missense_Mutation_p.A2V|BCKDHB_ENST00000369760.4_Missense_Mutation_p.A2V	NM_183050.2	NP_898871.1	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1, beta polypeptide	2					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(1)	15		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		GCGGGGATGGCGGTTGTAGCG	0.726																																					p.A2V		Atlas-SNP	.											.	BCKDHB	36	.	0			c.C5T						PASS	.						5.0	6.0	5.0					6																	80816415		2025	3958	5983	SO:0001583	missense	594	exon1			GGATGGCGGTTGT	M55575	CCDS4994.1	6q14.1	2008-07-31	2008-07-31		ENSG00000083123	ENSG00000083123			987	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	248611					Standard	NM_183050		Approved		uc003pje.2	P21953	OTTHUMG00000016430	ENST00000320393.6:c.5C>T	6.37:g.80816415C>T	ENSP00000318351:p.Ala2Val	37.0	0.0	0		60.0	21.0	0.35	NM_000056	Q5T2J3|Q9BQL0	Missense_Mutation	SNP	ENST00000320393.6	37	CCDS4994.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837710	0.50951	.	.	ENSG00000083123	ENST00000369760;ENST00000320393;ENST00000356489;ENST00000545529	D;D;D;D	0.97232	-4.3;-4.22;-4.22;-4.3	5.35	4.46	0.54185	.	0.158692	0.53938	D	0.000046	D	0.87038	0.6078	N	0.08118	0	0.25088	N	0.990873	P	0.50943	0.94	B	0.40636	0.335	D	0.84007	0.0346	10	0.72032	D	0.01	-12.6247	11.7712	0.51960	0.0:0.8233:0.1767:0.0	.	2	P21953	ODBB_HUMAN	V	2	ENSP00000358775:A2V;ENSP00000318351:A2V;ENSP00000348880:A2V;ENSP00000443564:A2V	ENSP00000318351:A2V	A	+	2	0	BCKDHB	80873134	1.000000	0.71417	0.983000	0.44433	0.142000	0.21351	3.221000	0.51215	1.458000	0.47871	0.511000	0.50034	GCG	.	.	none		0.726	BCKDHB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043911.2	NM_000056	
ECT2L	345930	hgsc.bcm.edu	37	6	139223635	139223635	+	Splice_Site	SNP	A	A	T	rs200545869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139223635A>T	ENST00000423192.1	+	21	2748		c.e21-1		ECT2L_ENST00000541398.1_Splice_Site|ECT2L_ENST00000367682.2_Splice_Site			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like								Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						ATGCTTTTACAGATGTCAAGA	0.289			"""N, Splice, Mis"""		ETP ALL								A|||	1	0.000199681	0.0	0.0	5008	,	,		18297	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.2588-2A>T						PASS	.	A	,	2,3602		0,2,1800	75.0	71.0	72.0		,	5.6	1.0	6		72	5,8143		0,5,4069	yes	splice-3,splice-3	ECT2L	NM_001077706.2,NM_001195037.2	,	0,7,5869	TT,TA,AA		0.0614,0.0555,0.0596	,	,	139223635	7,11745	1802	4074	5876	SO:0001630	splice_region_variant	345930	exon21			TTTTACAGATGTC		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.2588-1A>T	6.37:g.139223635A>T		76.0	0.0	0		31.0	12.0	0.387097	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Splice_Site	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049498	0.75846	5.55E-4	6.14E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3602	0.60652	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ECT2L	139265328	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.636000	0.67848	2.145000	0.66743	0.533000	0.62120	.	A|0.999;T|0.001	0.001	weak		0.289	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	Intron
MUC4	4585	hgsc.bcm.edu	37	3	195505872	195505872	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505872A>C	ENST00000463781.3	-	2	13038	c.12579T>G	c.(12577-12579)ctT>ctG	p.L4193L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.L4193L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L4193L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGGTGACAGGAAGAGGGGTGG	0.602																																					p.L4193L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	1	Substitution - coding silent(1)	kidney(1)	c.T12579G						scavenged	.						21.0	15.0	17.0					3																	195505872		689	1579	2268	SO:0001819	synonymous_variant	4585	exon2			GACAGGAAGAGGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12579T>G	3.37:g.195505872A>C		66.0	0.0	0		85.0	5.0	0.0588235	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NPC1	4864	hgsc.bcm.edu	37	18	21140367	21140367	+	Missense_Mutation	SNP	G	G	A	rs80358251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21140367G>A	ENST00000269228.5	-	6	1263	c.709C>T	c.(709-711)Cca>Tca	p.P237S	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_5'Flank	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	237			P -> S (in NPC1; late infantile form; dbSNP:rs80358251). {ECO:0000269|PubMed:11182931, ECO:0000269|PubMed:11333381, ECO:0000269|PubMed:11349231, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:12955717}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CAGCTACATGGTGCTGTGACC	0.547													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		16533	0.0		0.0169	False		,,,				2504	0.002				p.P237S		Atlas-SNP	.											.	NPC1	114	.	0			c.C709T	GRCh37	CM990941	NPC1	M	rs80358251	PASS	.	G	SER/PRO	13,4393	20.2+/-43.8	0,13,2190	70.0	60.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	709	5.9	0.3	18	dbSNP_132	63	137,8463	68.7+/-131.2	1,135,4164	yes	missense	NPC1	NM_000271.4	74	1,148,6354	AA,AG,GG		1.593,0.2951,1.1533	benign	237/1279	21140367	150,12856	2203	4300	6503	SO:0001583	missense	4864	exon6			TACATGGTGCTGT	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.709C>T	18.37:g.21140367G>A	ENSP00000269228:p.Pro237Ser	113.0	0.0	0		71.0	70.0	0.985915	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	14	0.00641025641025641	1	0.0020325203252032522	0	0.0	0	0.0	13	0.017150395778364115	G	11.43	1.635647	0.29068	0.002951	0.01593	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.91011	-2.77	5.87	5.87	0.94306	.	0.052444	0.85682	D	0.000000	T	0.79811	0.4510	L	0.39147	1.195	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.78393	-0.2221	10	0.23891	T	0.37	-22.0744	20.206	0.98277	0.0:0.0:1.0:0.0	.	248;237	Q59GR1;O15118	.;NPC1_HUMAN	S	237;82	ENSP00000269228:P237S	ENSP00000269228:P237S	P	-	1	0	NPC1	19394365	1.000000	0.71417	0.333000	0.25482	0.084000	0.17831	8.061000	0.89467	2.785000	0.95823	0.655000	0.94253	CCA	G|0.991;A|0.009	0.009	strong		0.547	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
PANK1	53354	hgsc.bcm.edu	37	10	91359116	91359116	+	Silent	SNP	C	C	T	rs11592870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:91359116C>T	ENST00000307534.4	-	3	1358	c.1203G>A	c.(1201-1203)ccG>ccA	p.P401P	PANK1_ENST00000322191.6_Silent_p.P176P|PANK1_ENST00000342512.3_Silent_p.P176P|PANK1_ENST00000371774.2_Silent_p.P203P	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	401					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						CAAGGCAGTACGGCTTTTTTT	0.438													C|||	75	0.014976	0.0	0.013	5008	,	,		19072	0.0		0.0408	False		,,,				2504	0.0256				p.P401P		Atlas-SNP	.											PANK1,colon,carcinoma,0,1	PANK1	35	1	0			c.G1203A						scavenged	.	C	,,	30,4376	36.8+/-68.6	0,30,2173	236.0	213.0	221.0		528,1203,528	-4.7	1.0	10	dbSNP_120	221	250,8350	99.0+/-160.6	1,248,4051	no	coding-synonymous,coding-synonymous,coding-synonymous	PANK1	NM_138316.3,NM_148977.2,NM_148978.2	,,	1,278,6224	TT,TC,CC		2.907,0.6809,2.1529	,,	176/315,401/599,176/374	91359116	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	53354	exon3			GCAGTACGGCTTT	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.1203G>A	10.37:g.91359116C>T		177.0	1.0	0.00564972		149.0	74.0	0.496644	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			C|0.981;T|0.019	0.019	strong		0.438	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
FAM186A	121006	hgsc.bcm.edu	37	12	50744283	50744283	+	Missense_Mutation	SNP	G	G	A	rs372753266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:50744283G>A	ENST00000327337.5	-	4	6331	c.6332C>T	c.(6331-6333)gCt>gTt	p.A2111V	FAM186A_ENST00000543096.1_Missense_Mutation_p.A122V|FAM186A_ENST00000543111.1_Missense_Mutation_p.A2111V	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2111																	CTTCTTCTGAGCCTCCACATC	0.403													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20592	0.0		0.0	False		,,,				2504	0.0				p.A2111V	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6332T						PASS	.	G	VAL/ALA	2,1382		0,2,690	215.0	170.0	184.0		6332	1.6	1.0	12		184	0,3182		0,0,1591	no	missense	FAM186A	NM_001145475.1	64	0,2,2281	AA,AG,GG		0.0,0.1445,0.0438	probably-damaging	2111/2352	50744283	2,4564	692	1591	2283	SO:0001583	missense	121006	exon4			TTCTGAGCCTCCA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6332C>T	12.37:g.50744283G>A	ENSP00000329995:p.Ala2111Val	176.0	0.0	0		149.0	43.0	0.288591	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.449357	0.63178	0.001445	0.0	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.54279	0.58;0.58;0.58	3.7	1.56	0.23342	.	.	.	.	.	T	0.64271	0.2583	L	0.60455	1.87	0.25564	N	0.986965	D;D	0.76494	0.999;0.999	D;D	0.68943	0.961;0.961	T	0.52011	-0.8632	9	0.87932	D	0	.	9.1064	0.36701	0.0:0.4454:0.5546:0.0	.	2111;2111	F5GYN0;A6NE01	.;F186A_HUMAN	V	2111;122;2111	ENSP00000441337:A2111V;ENSP00000443703:A122V;ENSP00000329995:A2111V	ENSP00000329995:A2111V	A	-	2	0	FAM186A	49030550	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.034000	0.41145	0.848000	0.35191	0.462000	0.41574	GCT	.	.	weak		0.403	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
STK32C	282974	hgsc.bcm.edu	37	10	134038809	134038809	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134038809G>A	ENST00000368622.1	-	7	834	c.453C>T	c.(451-453)ggC>ggT	p.G151G	STK32C_ENST00000368625.4_Silent_p.G281G					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		AGCCGGTCCCGCCGTTGACAA	0.632																																					p.G268G		Atlas-SNP	.											.	STK32C	61	.	0			c.C804T						PASS	.						27.0	29.0	28.0					10																	134038809		2200	4296	6496	SO:0001819	synonymous_variant	282974	exon7			GGTCCCGCCGTTG	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.453C>T	10.37:g.134038809G>A		118.0	0.0	0		95.0	49.0	0.515789	NM_173575		Silent	SNP	ENST00000368622.1	37																																																																																				.	.	none		0.632	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
RYR3	6263	hgsc.bcm.edu	37	15	34130697	34130697	+	Silent	SNP	G	G	C	rs75286462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34130697G>C	ENST00000389232.4	+	89	12586	c.12516G>C	c.(12514-12516)gtG>gtC	p.V4172V	RYR3_ENST00000415757.3_Silent_p.V4167V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4172					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACAGGAACGTGAAAAAGATGA	0.512													G|||	81	0.0161741	0.0015	0.0216	5008	,	,		20602	0.0		0.0557	False		,,,				2504	0.0082				p.V4172V		Atlas-SNP	.											.	RYR3	760	.	0			c.G12516C						PASS	.	G		34,3884		0,34,1925	82.0	89.0	86.0		12516	1.6	1.0	15	dbSNP_132	86	326,7936		5,316,3810	no	coding-synonymous	RYR3	NM_001036.3		5,350,5735	CC,CG,GG		3.9458,0.8678,2.9557		4172/4871	34130697	360,11820	1959	4131	6090	SO:0001819	synonymous_variant	6263	exon89			GAACGTGAAAAAG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.12516G>C	15.37:g.34130697G>C		196.0	0.0	0		185.0	111.0	0.6	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.975;C|0.025	0.025	strong		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
EN1	2019	hgsc.bcm.edu	37	2	119600674	119600674	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:119600674A>C	ENST00000295206.6	-	2	1529	c.1019T>G	c.(1018-1020)cTc>cGc	p.L340R	EN1_ENST00000546667.1_5'Flank	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	340					anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						GTTGAGGCTGAGTTCCTGGGC	0.612																																					p.L340R		Atlas-SNP	.											.	EN1	33	.	0			c.T1019G						PASS	.						69.0	63.0	65.0					2																	119600674		2203	4300	6503	SO:0001583	missense	2019	exon2			AGGCTGAGTTCCT	L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064		"""Homeoboxes / ANTP class : NKL subclass"""	3342	protein-coding gene	gene with protein product		131290				8094370	Standard	NM_001426		Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.1019T>G	2.37:g.119600674A>C	ENSP00000295206:p.Leu340Arg	89.0	0.0	0		96.0	33.0	0.34375	NM_001426	Q4ZG44	Missense_Mutation	SNP	ENST00000295206.6	37	CCDS2123.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267128	0.80469	.	.	ENSG00000163064	ENST00000295206	D	0.98280	-4.84	4.89	4.89	0.63831	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99432	0.9799	H	0.99169	4.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98029	1.0375	10	0.87932	D	0	-14.1387	14.1743	0.65529	1.0:0.0:0.0:0.0	.	340	Q05925	HME1_HUMAN	R	340	ENSP00000295206:L340R	ENSP00000295206:L340R	L	-	2	0	EN1	119317144	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.330000	0.96422	1.831000	0.53308	0.454000	0.30748	CTC	.	.	none		0.612	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254191.3		
PGBD1	84547	hgsc.bcm.edu	37	6	28251890	28251890	+	Silent	SNP	C	C	T	rs527450661		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28251890C>T	ENST00000405948.2	+	2	720	c.300C>T	c.(298-300)ctC>ctT	p.L100L	PGBD1_ENST00000259883.3_Silent_p.L100L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	100	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.					membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						CCAAGGAGCTCCAGCCCTGTG	0.532													C|||	1	0.000199681	0.0	0.0	5008	,	,		18052	0.001		0.0	False		,,,				2504	0.0				p.L100L		Atlas-SNP	.											.	PGBD1	106	.	0			c.C300T						PASS	.						101.0	93.0	95.0					6																	28251890		2203	4300	6503	SO:0001819	synonymous_variant	84547	exon2			GGAGCTCCAGCCC	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.300C>T	6.37:g.28251890C>T		81.0	0.0	0		88.0	4.0	0.0454545	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	37	CCDS4648.1																																																																																			.	.	none		0.532	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
FAM120B	84498	hgsc.bcm.edu	37	6	170627266	170627266	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627266T>C	ENST00000476287.1	+	2	896	c.788T>C	c.(787-789)aTc>aCc	p.I263T	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000540480.1_Missense_Mutation_p.I275T|FAM120B_ENST00000537664.1_Missense_Mutation_p.I286T	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	263					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AAAGGTAACATCATATTAGCT	0.373																																					p.I263T		Atlas-SNP	.											.	FAM120B	108	.	0			c.T788C						PASS	.						76.0	82.0	80.0					6																	170627266		2203	4300	6503	SO:0001583	missense	84498	exon2			GTAACATCATATT	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.788T>C	6.37:g.170627266T>C	ENSP00000417970:p.Ile263Thr	55.0	0.0	0		39.0	15.0	0.384615	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	t	4.546	0.101307	0.08731	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08896	3.05;3.04;3.05	5.36	1.33	0.21861	.	1.307360	0.04590	N	0.396515	T	0.02610	0.0079	L	0.41236	1.265	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.44967	-0.9293	10	0.28530	T	0.3	-0.9253	9.4172	0.38528	0.0:0.263:0.0:0.737	.	263;263	Q96EK7;F2Z2E1	F120B_HUMAN;.	T	275;286;263	ENSP00000444125:I275T;ENSP00000440125:I286T;ENSP00000417970:I263T	ENSP00000436640:I263T	I	+	2	0	FAM120B	170469191	0.001000	0.12720	0.002000	0.10522	0.470000	0.32858	0.928000	0.28831	0.426000	0.26116	-0.266000	0.10368	ATC	.	.	none		0.373	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
CHRD	8646	hgsc.bcm.edu	37	3	184102814	184102814	+	Missense_Mutation	SNP	G	G	A	rs138882380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184102814G>A	ENST00000204604.1	+	14	1852	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_Missense_Mutation_p.V166M|CHRD_ENST00000348986.3_Missense_Mutation_p.V496M|CHRD_ENST00000450923.1_Missense_Mutation_p.V536M	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	536	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGCGCTGCCCGTGCCCCTAGC	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		16943	0.0		0.001	False		,,,				2504	0.0				p.V536M		Atlas-SNP	.											.	CHRD	149	.	0			c.G1606A						PASS	.	G	MET/VAL	0,4406		0,0,2203	106.0	112.0	110.0		1606	3.6	1.0	3	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	no	missense	CHRD	NM_003741.2	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	536/956	184102814	2,13004	2203	4300	6503	SO:0001583	missense	8646	exon14			CTGCCCGTGCCCC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1606G>A	3.37:g.184102814G>A	ENSP00000204604:p.Val536Met	84.0	0.0	0		71.0	40.0	0.56338	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.85	3.236050	0.58886	0.0	2.33E-4	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.38	3.59	0.41128	CHRD (3);	0.125547	0.52532	D	0.000071	T	0.58250	0.2109	M	0.66939	2.045	0.47183	D	0.99934	D;D;D;D	0.89917	0.999;1.0;0.989;1.0	D;D;P;D	0.76071	0.982;0.987;0.906;0.98	T	0.56153	-0.8026	10	0.45353	T	0.12	-20.6515	9.8593	0.41105	0.1666:0.0:0.8334:0.0	.	166;496;536;536	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	M	536;536;496;166;249	ENSP00000204604:V536M;ENSP00000408972:V536M;ENSP00000334036:V496M;ENSP00000442948:V166M	ENSP00000204604:V536M	V	+	1	0	CHRD	185585508	0.810000	0.29049	0.978000	0.43139	0.744000	0.42396	1.230000	0.32612	0.781000	0.33589	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.607	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632831	32632831	+	Missense_Mutation	SNP	G	G	C	rs111588946		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32632831G>C	ENST00000399084.1	-	3	301	c.123C>G	c.(121-123)ttC>ttG	p.F41L	HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.F41L|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	41	Beta-1.		Y -> F (in allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:10, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:29, allele DQB1*06:33 and allele DQB1*06:37; dbSNP:rs9274407).|Y -> L (in allele DQB1*06:01 and allele DQB1*06:35; requires 2 nucleotide substitutions).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CCTTAAACTGGAACACGAAAT	0.647									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.F41L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C123G						PASS	.						20.0	21.0	21.0					6																	32632831		2088	4185	6273	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AAACTGGAACACG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.123C>G	6.37:g.32632831G>C	ENSP00000382034:p.Phe41Leu	29.0	0.0	0		65.0	24.0	0.369231	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	6.750	0.507124	0.12883	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	4.13	3.23	0.37069	.	0.154608	0.26359	U	0.024831	T	0.01800	0.0057	L	0.52905	1.665	0.35375	D	0.789428	B;B;B	0.16166	0.016;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35773	-0.9775	10	0.19147	T	0.46	.	6.6967	0.23203	0.2157:0.0:0.7843:0.0	.	51;41;41	Q59F80;A2AAZ0;Q5Y7D6	.;.;.	L	41	ENSP00000382029:F41L;ENSP00000364080:F41L;ENSP00000407332:F41L;ENSP00000382034:F41L	ENSP00000364080:F41L	F	-	3	2	HLA-DQB1	32740809	0.000000	0.05858	0.071000	0.20095	0.019000	0.09904	0.055000	0.14229	2.161000	0.67846	0.305000	0.20034	TTC	T|1.000;|0.000	.	alt		0.647	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329496	59329496	+	Missense_Mutation	SNP	C	C	T	rs373559127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59329496C>T	ENST00000399598.2	+	2	294	c.172C>T	c.(172-174)Cgg>Tgg	p.R58W	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	58						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						CAAGAGCCCACGGACACCACC	0.333													C|||	2	0.000399361	0.0	0.0	5008	,	,		15290	0.0		0.0	False		,,,				2504	0.002				p.R58W		Atlas-SNP	.											UBXN2B,NS,carcinoma,-1,1	UBXN2B	36	1	0			c.C172T						PASS	.	C	TRP/ARG	0,3690		0,0,1845	87.0	75.0	79.0		172	2.4	1.0	8		79	1,8187		0,1,4093	no	missense	UBXN2B	NM_001077619.1	101	0,1,5938	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	58/332	59329496	1,11877	1845	4094	5939	SO:0001583	missense	137886	exon2			AGCCCACGGACAC	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.172C>T	8.37:g.59329496C>T	ENSP00000382507:p.Arg58Trp	33.0	0.0	0		41.0	14.0	0.341463	NM_001077619	B3KWZ3	Missense_Mutation	SNP	ENST00000399598.2	37	CCDS43741.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.635959|3.635959	0.67130|0.67130	0.0|0.0	1.22E-4|1.22E-4	ENSG00000215114|ENSG00000215114	ENST00000399598|ENST00000521796	T|.	0.48522|.	0.81|.	5.62|5.62	2.44|2.44	0.29823|0.29823	.|.	0.547615|.	0.14599|.	U|.	0.309721|.	T|T	0.49525|0.49525	0.1562|0.1562	L|L	0.54323|0.54323	1.7|1.7	0.29724|0.29724	N|N	0.838446|0.838446	D|.	0.71674|.	0.998|.	P|.	0.53185|.	0.72|.	T|T	0.47774|0.47774	-0.9091|-0.9091	10|5	0.72032|.	D|.	0.01|.	-12.2333|-12.2333	11.203|11.203	0.48751|0.48751	0.6042:0.3958:0.0:0.0|0.6042:0.3958:0.0:0.0	.|.	58|.	Q14CS0|.	UBX2B_HUMAN|.	W|M	58|3	ENSP00000382507:R58W|.	ENSP00000382507:R58W|.	R|T	+|+	1|2	2|0	UBXN2B|UBXN2B	59492050|59492050	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.995000|0.995000	0.86356|0.86356	0.723000|0.723000	0.25939|0.25939	0.670000|0.670000	0.31165|0.31165	0.563000|0.563000	0.77884|0.77884	CGG|ACG	.	.	weak		0.333	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
LY6K	54742	hgsc.bcm.edu	37	8	143783109	143783109	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:143783109A>G	ENST00000292430.6	+	2	612	c.195A>G	c.(193-195)ccA>ccG	p.P65P	LY6K_ENST00000518841.1_Silent_p.P65P|LY6K_ENST00000519390.1_3'UTR|LY6K_ENST00000519387.1_Silent_p.P65P|LY6K_ENST00000522591.1_Silent_p.P65P|CTD-2292P10.4_ENST00000520572.1_RNA|LY6K_ENST00000561179.1_Silent_p.P123P			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	65	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GGACAGAGCCATACTGCGTTA	0.502																																					p.P65P		Atlas-SNP	.											.	LY6K	23	.	0			c.A195G						PASS	.						139.0	130.0	133.0					8																	143783109		2203	4300	6503	SO:0001819	synonymous_variant	54742	exon2			AGAGCCATACTGC	AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886			24225	protein-coding gene	gene with protein product	"""cancer/testis antigen 97"""	615093				12516096	Standard	NM_017527		Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000292430.6:c.195A>G	8.37:g.143783109A>G		193.0	0.0	0		179.0	32.0	0.178771	NM_001160354	G3V116|O15227|Q9BVD7	Silent	SNP	ENST00000292430.6	37	CCDS6385.2	.	.	.	.	.	.	.	.	.	.	A	2.177	-0.388411	0.04932	.	.	ENSG00000160886	ENST00000522591	.	.	.	1.96	-3.92	0.04155	.	.	.	.	.	T	0.19406	0.0466	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.04029	-1.0983	4	.	.	.	.	2.3733	0.04336	0.2347:0.2455:0.4048:0.1149	.	.	.	.	R	84	.	.	H	+	2	0	LY6K	143780111	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.285000	0.00526	-4.514000	0.00045	-2.025000	0.00428	CAT	.	.	none		0.502	LY6K-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379893.2	NM_017527	
DOCK10	55619	hgsc.bcm.edu	37	2	225670845	225670845	+	Missense_Mutation	SNP	G	G	T	rs375740801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:225670845G>T	ENST00000258390.7	-	34	3879	c.3812C>A	c.(3811-3813)gCa>gAa	p.A1271E	DOCK10_ENST00000409592.3_Missense_Mutation_p.A1265E	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1271					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCAAGTACCTGCTATGGAATT	0.343																																					p.A1271E		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3812A						PASS	.	G	GLU/ALA	0,3708		0,0,1854	104.0	103.0	103.0		3812	6.0	1.0	2		103	3,8181		0,3,4089	no	missense	DOCK10	NM_014689.2	107	0,3,5943	TT,TG,GG		0.0367,0.0,0.0252	benign	1271/2187	225670845	3,11889	1854	4092	5946	SO:0001583	missense	55619	exon34			GTACCTGCTATGG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3812C>A	2.37:g.225670845G>T	ENSP00000258390:p.Ala1271Glu	76.0	0.0	0		99.0	46.0	0.464646	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.622605|4.622605	0.87460|0.87460	0.0|0.0	3.67E-4|3.67E-4	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390|ENST00000422684	T;T|.	0.21361|.	3.53;2.01|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.049031|.	0.85682|.	D|.	0.000000|.	T|T	0.72653|0.72653	0.3487|0.3487	L|L	0.53249|0.53249	1.67|1.67	0.58432|0.58432	D|D	0.999996|0.999996	D;P;P|.	0.59767|.	0.986;0.799;0.745|.	P;B;B|.	0.55455|.	0.776;0.343;0.276|.	T|T	0.67051|0.67051	-0.5768|-0.5768	10|5	0.45353|.	T|.	0.12|.	.|.	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1271;134;1265|.	Q96BY6;B4DF07;B3FL70|.	DOC10_HUMAN;.;.|.	E|K	1265;1271|162	ENSP00000386694:A1265E;ENSP00000258390:A1271E|.	ENSP00000258390:A1271E|.	A|Q	-|-	2|1	0|0	DOCK10|DOCK10	225379089|225379089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.442000|8.442000	0.90317|0.90317	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	weak		0.343	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
LRP3	4037	hgsc.bcm.edu	37	19	33696647	33696647	+	Missense_Mutation	SNP	C	C	T	rs368108554		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33696647C>T	ENST00000253193.7	+	5	1173	c.971C>T	c.(970-972)aCg>aTg	p.T324M	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	324	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CTGCTGCAGACGCTGTCCTAC	0.736																																					p.T324M		Atlas-SNP	.											.	LRP3	46	.	0			c.C971T						PASS	.	C	MET/THR	0,4284		0,0,2142	8.0	12.0	10.0		971	5.0	1.0	19		10	1,8407		0,1,4203	no	missense	LRP3	NM_002333.3	81	0,1,6345	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging	324/771	33696647	1,12691	2142	4204	6346	SO:0001583	missense	4037	exon5			TGCAGACGCTGTC	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.971C>T	19.37:g.33696647C>T	ENSP00000253193:p.Thr324Met	29.0	0.0	0		36.0	15.0	0.416667	NM_002333	B3KQD6|B4DKF2	Missense_Mutation	SNP	ENST00000253193.7	37	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972764	0.53614	0.0	1.19E-4	ENSG00000130881	ENST00000431491;ENST00000253193	D	0.87334	-2.24	5.02	5.02	0.67125	CUB (5);	0.218511	0.42548	D	0.000688	D	0.92113	0.7500	M	0.63843	1.955	0.40643	D	0.981969	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.70935	0.96;0.971;0.96	D	0.92597	0.6088	10	0.51188	T	0.08	-22.6449	17.3303	0.87261	0.0:1.0:0.0:0.0	.	198;324;242	C9J8W0;O75074;B7ZAJ9	.;LRP3_HUMAN;.	M	198;324	ENSP00000253193:T324M	ENSP00000253193:T324M	T	+	2	0	LRP3	38388487	0.906000	0.30813	0.994000	0.49952	0.732000	0.41865	2.288000	0.43514	2.341000	0.79615	0.313000	0.20887	ACG	.	.	weak		0.736	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
KDM4D	55693	hgsc.bcm.edu	37	11	94731905	94731905	+	Missense_Mutation	SNP	C	C	G	rs144086807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:94731905C>G	ENST00000335080.5	+	3	2201	c.1369C>G	c.(1369-1371)Cct>Gct	p.P457A	KDM4D_ENST00000536741.1_Missense_Mutation_p.P457A	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	457					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TGGTCGCCCTCCTCAGAAACT	0.597													.|||	5	0.000998403	0.0	0.0	5008	,	,		19936	0.0		0.003	False		,,,				2504	0.002				p.P457A		Atlas-SNP	.											.	KDM4D	58	.	0			c.C1369G						PASS	.	C	ALA/PRO	4,4398	8.1+/-20.4	0,4,2197	52.0	54.0	53.0		1369	1.6	0.0	11	dbSNP_134	53	46,8550	29.0+/-79.6	0,46,4252	yes	missense	KDM4D	NM_018039.2	27	0,50,6449	GG,GC,CC		0.5351,0.0909,0.3847	possibly-damaging	457/524	94731905	50,12948	2201	4298	6499	SO:0001583	missense	55693	exon3			CGCCCTCCTCAGA	AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"""Chromatin-modifying enzymes / K-demethylases"""	25498	protein-coding gene	gene with protein product		609766	"""jumonji domain containing 2D"""	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.1369C>G	11.37:g.94731905C>G	ENSP00000334181:p.Pro457Ala	80.0	0.0	0		59.0	48.0	0.813559	NM_018039	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Missense_Mutation	SNP	ENST00000335080.5	37	CCDS8302.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	10.19	1.281211	0.23392	9.09E-4	0.005351	ENSG00000186280	ENST00000335080	T	0.28666	1.6	3.52	1.58	0.23477	.	0.179179	0.35555	U	0.003127	T	0.11281	0.0275	L	0.32530	0.975	0.09310	N	1	P	0.48407	0.91	B	0.38106	0.265	T	0.13335	-1.0513	10	0.22109	T	0.4	-5.8535	4.7061	0.12849	0.0:0.6512:0.2251:0.1236	.	457	Q6B0I6	KDM4D_HUMAN	A	457	ENSP00000334181:P457A	ENSP00000334181:P457A	P	+	1	0	KDM4D	94371553	0.023000	0.18921	0.001000	0.08648	0.002000	0.02628	0.744000	0.26245	0.462000	0.27095	0.655000	0.94253	CCT	C|0.997;G|0.003	0.003	strong		0.597	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039	
DMGDH	29958	hgsc.bcm.edu	37	5	78326767	78326767	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:78326767C>T	ENST00000255189.3	-	10	1600	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	DMGDH_ENST00000540686.1_Silent_p.Q144Q|DMGDH_ENST00000380311.4_Silent_p.Q323Q	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	524					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TTTGCATAACCTGTTTATACT	0.423																																					p.Q524Q		Atlas-SNP	.											.	DMGDH	88	.	0			c.G1572A						PASS	.						115.0	109.0	111.0					5																	78326767		2203	4300	6503	SO:0001819	synonymous_variant	29958	exon10			CATAACCTGTTTA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1572G>A	5.37:g.78326767C>T		104.0	0.0	0		133.0	85.0	0.639098	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																			.	.	none		0.423	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
RAVER1	125950	hgsc.bcm.edu	37	19	10439540	10439540	+	Silent	SNP	A	A	G	rs3745262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439540A>G	ENST00000293677.6	-	3	666	c.585T>C	c.(583-585)gcT>gcC	p.A195A		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	178	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			TCATGTACTCAGCAAAGCCAT	0.642													G|||	135	0.0269569	0.0234	0.0058	5008	,	,		16733	0.0397		0.0328	False		,,,				2504	0.0276				p.A195A		Atlas-SNP	.											RAVER1_ENST00000293677,caecum,carcinoma,0,2	RAVER1	67	2	0			c.T585C						PASS	.	G		97,4143		0,97,2023	34.0	40.0	38.0		585	-10.1	0.4	19	dbSNP_107	38	274,8204		6,262,3971	yes	coding-synonymous	RAVER1	NM_133452.2		6,359,5994	GG,GA,AA		3.2319,2.2877,2.9171		195/757	10439540	371,12347	2120	4239	6359	SO:0001819	synonymous_variant	125950	exon3			GTACTCAGCAAAG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.585T>C	19.37:g.10439540A>G		181.0	0.0	0		131.0	50.0	0.381679	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			A|0.972;G|0.028	0.028	strong		0.642	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
NBPF3	84224	hgsc.bcm.edu	37	1	21797221	21797221	+	Missense_Mutation	SNP	A	A	G	rs145790279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21797221A>G	ENST00000318249.5	+	4	790	c.440A>G	c.(439-441)gAg>gGg	p.E147G	NBPF3_ENST00000342104.5_Missense_Mutation_p.E147G|NBPF3_ENST00000318220.6_Missense_Mutation_p.E91G|NBPF3_ENST00000454000.2_Missense_Mutation_p.E77G	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	147						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAAGCTGAGGAGCTCAGGTGA	0.552													.|||	22	0.00439297	0.0	0.0058	5008	,	,		17610	0.0		0.0129	False		,,,				2504	0.0051				p.T147R		Atlas-SNP	.											.	NBPF3	55	.	0			c.C440G						PASS	.	A	GLY/GLU	6,4400		0,6,2197	42.0	47.0	46.0		440	-2.5	0.0	1	dbSNP_134	46	108,8492		0,108,4192	yes	missense	NBPF3	NM_032264.2	98	0,114,6389	GG,GA,AA		1.2558,0.1362,0.8765	probably-damaging	147/634	21797221	114,12892	2203	4300	6503	SO:0001583	missense	84224	exon4			CTGAGGAGCTCAG	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.440A>G	1.37:g.21797221A>G	ENSP00000316782:p.Glu147Gly	106.0	0.0	0		115.0	63.0	0.547826	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	.	9.834	1.189143	0.21954	0.001362	0.012558	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T;T	0.03860	3.78;4.03;4.03;4.03;4.03	1.23	-2.46	0.06461	.	.	.	.	.	T	0.07188	0.0182	L	0.47716	1.5	0.09310	N	1	P;D;D	0.64830	0.862;0.994;0.976	B;D;P	0.64877	0.405;0.93;0.696	T	0.10917	-1.0609	9	0.56958	D	0.05	.	5.9408	0.19192	0.3793:0.0:0.6207:0.0	.	77;147;147	B4DSP2;Q9H094-3;Q9H094	.;.;NBPF3_HUMAN	G	77;91;147;91;147;91	ENSP00000415711:E77G;ENSP00000316739:E91G;ENSP00000316782:E147G;ENSP00000340336:E147G;ENSP00000391865:E91G	ENSP00000316739:E91G	E	+	2	0	NBPF3	21669808	0.096000	0.21769	0.001000	0.08648	0.076000	0.17211	-0.001000	0.12947	-0.972000	0.03559	0.327000	0.21459	GAG	A|0.992;G|0.008	0.008	strong		0.552	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
PPP1R3D	5509	hgsc.bcm.edu	37	20	58514312	58514312	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58514312C>A	ENST00000370996.3	-	1	1040	c.675G>T	c.(673-675)ggG>ggT	p.G225G	FAM217B_ENST00000358293.3_Intron|FAM217B_ENST00000360816.3_5'Flank	NM_006242.3	NP_006233.1	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	225	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				dephosphorylation (GO:0016311)|glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)	protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|urinary_tract(1)	13	all_lung(29;0.00391)		BRCA - Breast invasive adenocarcinoma(7;5.12e-09)			GGCCTGCGGGCCCGCGCCACC	0.697																																					p.G225G		Atlas-SNP	.											.	PPP1R3D	23	.	0			c.G675T						PASS	.						32.0	34.0	33.0					20																	58514312		2201	4299	6500	SO:0001819	synonymous_variant	5509	exon1			TGCGGGCCCGCGC	Y18206	CCDS13483.1	20q13.3	2012-04-17	2011-10-04	2001-08-01	ENSG00000132825	ENSG00000132825		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9294	protein-coding gene	gene with protein product		603326	"""protein phosphatase 1, regulatory (inhibitor) subunit 3D"""	PPP1R6		9414128, 9275233	Standard	NM_006242		Approved		uc002ybb.3	O95685	OTTHUMG00000032876	ENST00000370996.3:c.675G>T	20.37:g.58514312C>A		4.0	0.0	0		17.0	12.0	0.705882	NM_006242	Q6DK02	Silent	SNP	ENST00000370996.3	37	CCDS13483.1																																																																																			.	.	none		0.697	PPP1R3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079940.2	NM_006242	
CHMP6	79643	hgsc.bcm.edu	37	17	78972192	78972192	+	Silent	SNP	C	C	T	rs61752553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78972192C>T	ENST00000325167.5	+	7	600	c.522C>T	c.(520-522)ccC>ccT	p.P174P	CTD-2561B21.7_ENST00000577061.2_RNA|CTD-2561B21.7_ENST00000576215.1_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	174	Interaction with VPS4A.				endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CAGAGGTTCCCTCCGAGCCCC	0.522																																					p.P174P		Atlas-SNP	.											.	CHMP6	16	.	0			c.C522T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	108.0	110.0	109.0		522	-7.9	0.0	17	dbSNP_129	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CHMP6	NM_024591.4		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		174/202	78972192	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon7			GGTTCCCTCCGAG	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.522C>T	17.37:g.78972192C>T		137.0	0.0	0		125.0	5.0	0.04	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;T|0.001	0.001	strong		0.522	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
SUGP1	57794	hgsc.bcm.edu	37	19	19427402	19427402	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19427402C>T	ENST00000247001.5	-	2	382	c.35G>A	c.(34-36)gGa>gAa	p.G12E	SUGP1_ENST00000585763.1_5'UTR|SUGP1_ENST00000334782.5_Splice_Site_p.G12E	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	12					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						GTTAGCCTTTCCTGGGGAGGG	0.483																																					p.G12E		Atlas-SNP	.											.	SUGP1	63	.	0			c.G35A						PASS	.						61.0	55.0	57.0					19																	19427402		2203	4300	6503	SO:0001630	splice_region_variant	57794	exon2			GCCTTTCCTGGGG	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.35-1G>A	19.37:g.19427402C>T		141.0	0.0	0		91.0	4.0	0.043956	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894791	0.72639	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.35048	1.33	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	M	0.63843	1.955	0.51767	D	0.999935	D	0.89917	1.0	D	0.91635	0.999	T	0.62397	-0.6863	10	0.87932	D	0	.	16.9497	0.86242	0.0:1.0:0.0:0.0	.	12	Q8IWZ8	SUGP1_HUMAN	E	12	ENSP00000247001:G12E	ENSP00000247001:G12E	G	-	2	0	SUGP1	19288402	1.000000	0.71417	0.998000	0.56505	0.695000	0.40330	4.890000	0.63178	2.425000	0.82216	0.561000	0.74099	GGA	.	.	none		0.483	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	Missense_Mutation
GPR142	350383	hgsc.bcm.edu	37	17	72367973	72367973	+	Missense_Mutation	SNP	T	T	C	rs148514779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72367973T>C	ENST00000335666.4	+	4	671	c.623T>C	c.(622-624)gTg>gCg	p.V208A		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	208						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						ATCATCCAGGTGGTCATCGTG	0.657													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		18903	0.0		0.005	False		,,,				2504	0.0				p.V208A		Atlas-SNP	.											.	GPR142	74	.	0			c.T623C						PASS	.	T	ALA/VAL	5,4401	9.9+/-24.2	0,5,2198	84.0	68.0	74.0		623	5.0	1.0	17	dbSNP_134	74	46,8554	30.1+/-81.4	0,46,4254	yes	missense	GPR142	NM_181790.1	64	0,51,6452	CC,CT,TT		0.5349,0.1135,0.3921	probably-damaging	208/463	72367973	51,12955	2203	4300	6503	SO:0001583	missense	350383	exon4			TCCAGGTGGTCAT	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.623T>C	17.37:g.72367973T>C	ENSP00000335158:p.Val208Ala	75.0	0.0	0		65.0	39.0	0.6	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	37	CCDS11698.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	25.2	4.615913	0.87359	0.001135	0.005349	ENSG00000257008	ENST00000335666	T	0.38240	1.15	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.065348	0.64402	D	0.000007	T	0.43188	0.1236	L	0.47716	1.5	0.43007	D	0.994535	D;D	0.58620	0.977;0.983	P;D	0.65233	0.814;0.933	T	0.50734	-0.8793	10	0.72032	D	0.01	-25.2533	14.4349	0.67274	0.0:0.0:0.0:1.0	.	208;1170	Q7Z601;Q8NGB0	GP142_HUMAN;.	A	208	ENSP00000335158:V208A	ENSP00000335158:V208A	V	+	2	0	GPR142	69879568	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.848000	0.69458	2.188000	0.69820	0.529000	0.55759	GTG	T|0.997;C|0.003	0.003	strong		0.657	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
BARD1	580	hgsc.bcm.edu	37	2	215657089	215657089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:215657089C>T	ENST00000260947.4	-	3	430	c.296G>A	c.(295-297)aGa>aAa	p.R99K	BARD1_ENST00000449967.2_Intron|BARD1_ENST00000471787.1_Intron	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	99	Interaction with BRCA1.				cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTCCAGTTGTCTATTTATCTT	0.363									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R99K		Atlas-SNP	.											.	BARD1	138	.	0			c.G296A						PASS	.						139.0	137.0	138.0					2																	215657089		2203	4300	6503	SO:0001583	missense	580	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGTTGTCTATTTA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.296G>A	2.37:g.215657089C>T	ENSP00000260947:p.Arg99Lys	153.0	0.0	0		109.0	5.0	0.0458716	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.312107	0.60414	.	.	ENSG00000138376	ENST00000260947	T	0.75938	-0.98	5.29	4.42	0.53409	Zinc finger, RING/FYVE/PHD-type (1);	0.047598	0.85682	N	0.000000	T	0.70133	0.3189	L	0.53249	1.67	0.80722	D	1	B	0.25390	0.125	B	0.22152	0.038	T	0.70400	-0.4882	10	0.87932	D	0	-23.2173	14.0072	0.64470	0.0:0.9269:0.0:0.0731	.	99	Q99728	BARD1_HUMAN	K	99	ENSP00000260947:R99K	ENSP00000260947:R99K	R	-	2	0	BARD1	215365334	1.000000	0.71417	0.962000	0.40283	0.949000	0.60115	2.583000	0.46094	1.368000	0.46115	0.557000	0.71058	AGA	.	.	none		0.363	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
HERC4	26091	hgsc.bcm.edu	37	10	69695973	69695973	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695973C>T	ENST00000395198.3	-	23	2862	c.2615G>A	c.(2614-2616)gGt>gAt	p.G872D	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.G762D|HERC4_ENST00000412272.2_Missense_Mutation_p.G794D|HERC4_ENST00000373700.4_Missense_Mutation_p.G864D	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TTCTGTTGCACCAAAGTTTTC	0.313																																					p.G872D		Atlas-SNP	.											.	HERC4	78	.	0			c.G2615A						PASS	.						141.0	131.0	135.0					10																	69695973		2203	4300	6503	SO:0001583	missense	26091	exon23			GTTGCACCAAAGT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2615G>A	10.37:g.69695973C>T	ENSP00000378624:p.Gly872Asp	69.0	0.0	0		65.0	17.0	0.261538	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831789	0.91036	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.75391	0.3843	M	0.82323	2.585	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.992	T	0.75204	-0.3400	10	0.37606	T	0.19	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	D	762;794;872;864	ENSP00000277817:G762D;ENSP00000416504:G794D;ENSP00000378624:G872D;ENSP00000362804:G864D	ENSP00000277817:G762D	G	-	2	0	HERC4	69365979	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.313	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
WDR38	401551	hgsc.bcm.edu	37	9	127618775	127618775	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127618775C>T	ENST00000373574.1	+	6	570	c.514C>T	c.(514-516)Cac>Tac	p.H172Y		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	172			H -> R (in dbSNP:rs2274970). {ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CTCCACCGTACACATCTGGGA	0.637																																					p.H172Y		Atlas-SNP	.											.	WDR38	21	.	0			c.C514T						PASS	.						22.0	26.0	25.0					9																	127618775		2030	4179	6209	SO:0001583	missense	401551	exon6			ACCGTACACATCT		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.514C>T	9.37:g.127618775C>T	ENSP00000362677:p.His172Tyr	56.0	0.0	0		61.0	11.0	0.180328	NM_001045476	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	37	CCDS43876.1	.	.	.	.	.	.	.	.	.	.	C	9.880	1.201340	0.22121	.	.	ENSG00000136918	ENST00000373574	T	0.59906	0.23	4.68	1.78	0.24846	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.349118	0.25127	N	0.032940	T	0.34337	0.0894	N	0.12887	0.27	0.09310	N	1	B	0.25521	0.128	B	0.26310	0.068	T	0.25152	-1.0140	10	0.87932	D	0	.	5.2255	0.15391	0.165:0.6532:0.0:0.1818	.	172	Q5JTN6	WDR38_HUMAN	Y	172	ENSP00000362677:H172Y	ENSP00000362677:H172Y	H	+	1	0	WDR38	126658596	0.006000	0.16342	0.173000	0.22940	0.446000	0.32137	-0.009000	0.12765	0.193000	0.20303	0.561000	0.74099	CAC	.	.	none		0.637	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
BTG1	694	hgsc.bcm.edu	37	12	92538171	92538171	+	Nonsense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:92538171G>C	ENST00000256015.3	-	2	562	c.201C>G	c.(199-201)taC>taG	p.Y67*	C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	67					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.Y67Y(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAATACAACGGTAACCCGATC	0.458			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y67X		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C201G						PASS	.						131.0	131.0	131.0					12																	92538171		2203	4300	6503	SO:0001587	stop_gained	694	exon2			ACAACGGTAACCC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.201C>G	12.37:g.92538171G>C	ENSP00000256015:p.Tyr67*	125.0	0.0	0	1291	109.0	20.0	0.183486	NM_001731	P31607	Nonsense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	37	6.239268	0.97403	.	.	ENSG00000133639	ENST00000256015	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0719	13.2979	0.60307	0.072:0.0:0.928:0.0	.	.	.	.	X	67	.	ENSP00000256015:Y67X	Y	-	3	2	BTG1	91062302	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.401000	0.66326	2.738000	0.93877	0.655000	0.94253	TAC	.	.	none		0.458	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
IL5RA	3568	hgsc.bcm.edu	37	3	3146610	3146610	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3146610G>A	ENST00000446632.2	-	3	633	c.59C>T	c.(58-60)gCt>gTt	p.A20V	IL5RA_ENST00000311981.8_Missense_Mutation_p.A20V|SNORA43_ENST00000517240.1_RNA|IL5RA_ENST00000256452.3_Missense_Mutation_p.A20V|IL5RA_ENST00000430514.2_Missense_Mutation_p.A20V|IL5RA_ENST00000456302.1_Missense_Mutation_p.A20V|IL5RA_ENST00000445864.2_Missense_Mutation_p.A20V|IL5RA_ENST00000438560.1_Missense_Mutation_p.A20V|IL5RA_ENST00000418488.2_Missense_Mutation_p.A20V|IL5RA_ENST00000383846.1_Missense_Mutation_p.A20V	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	20					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		AAGTAAGTCAGCTTGCAGTAT	0.348																																					p.A20V	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											IL5RA,caecum,carcinoma,0,1	IL5RA	55	1	0			c.C59T						PASS	.						102.0	100.0	101.0					3																	3146610		2203	4300	6503	SO:0001583	missense	3568	exon3			AAGTCAGCTTGCA	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.59C>T	3.37:g.3146610G>A	ENSP00000412209:p.Ala20Val	186.0	0.0	0		178.0	44.0	0.247191	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853768	0.32791	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701;ENST00000427088	D;D;D;T;T;T;T;T;T;T	0.88664	-2.41;-2.31;-2.41;1.08;1.37;1.14;1.14;1.15;1.15;1.41	5.6	0.812	0.18744	.	0.640598	0.15081	N	0.281648	T	0.79695	0.4490	L	0.31926	0.97	0.09310	N	1	B;B;B;B;B;B	0.33637	0.028;0.047;0.047;0.028;0.42;0.084	B;B;B;B;B;B	0.28465	0.024;0.022;0.032;0.01;0.09;0.028	T	0.66594	-0.5884	10	0.44086	T	0.13	-6.1116	8.1152	0.30940	0.4066:0.0:0.5934:0.0	.	20;20;20;20;20;20	B4E2G0;Q01344-3;Q01344-2;Q01344;B3IU77;E7ERY4	.;.;.;IL5RA_HUMAN;.;.	V	20	ENSP00000412209:A20V;ENSP00000390753:A20V;ENSP00000256452:A20V;ENSP00000388858:A20V;ENSP00000402598:A20V;ENSP00000373358:A20V;ENSP00000309196:A20V;ENSP00000400400:A20V;ENSP00000392059:A20V;ENSP00000398117:A20V	ENSP00000256452:A20V	A	-	2	0	IL5RA	3121610	0.016000	0.18221	0.000000	0.03702	0.030000	0.12068	0.998000	0.29744	-0.062000	0.13088	0.650000	0.86243	GCT	.	.	none		0.348	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000589517.1_Silent_p.G41G|TYROBP_ENST00000585901.2_Silent_p.G41G|TYROBP_ENST00000424586.3_Silent_p.G30G	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	41					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGCCAGCACGCCCGGGCTCA	0.672													G|||	56	0.0111821	0.0008	0.0202	5008	,	,		16218	0.0		0.0348	False		,,,				2504	0.0061				p.G41G		Atlas-SNP	.											TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	0			c.C123G						PASS	.	G	,,,	36,4370	36.8+/-68.6	0,36,2167	36.0	38.0	37.0		90,90,123,123	-10.3	0.0	19	dbSNP_132	37	366,8234	115.9+/-175.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TYROBP	NM_001173514.1,NM_001173515.1,NM_003332.3,NM_198125.2	,,,	8,386,6109	CC,CG,GG		4.2558,0.8171,3.0909	,,,	30/103,30/102,41/114,41/113	36398454	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	7305	exon3			CAGCACGCCCGGG	AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"""killer activating receptor associated protein"", ""DNAX-activation protein 12"""	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.123C>G	19.37:g.36398454G>C		76.0	0.0	0		68.0	39.0	0.573529	NM_198125	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Silent	SNP	ENST00000262629.4	37	CCDS12482.1																																																																																			A|0.000;C|0.024;G|0.976	0.024	strong		0.672	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509078	195509078	+	Missense_Mutation	SNP	C	C	T	rs371017154|rs35479616		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509078C>T	ENST00000463781.3	-	2	9832	c.9373G>A	c.(9373-9375)Gac>Aac	p.D3125N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3125N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.587																																					p.D3125N		Atlas-SNP	.											.	MUC4	1505	.	0			c.G9373A						PASS	.						12.0	7.0	9.0					3																	195509078		654	1507	2161	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9373G>A	3.37:g.195509078C>T	ENSP00000417498:p.Asp3125Asn	46.0	0.0	0		34.0	5.0	0.147059	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	9.849	1.193221	0.22037	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	.	.	.	.	.	.	.	.	T	0.14700	0.0355	N	0.19112	0.55	0.20403	N	0.9999	B	0.12013	0.005	B	0.01281	0.0	T	0.27938	-1.0059	7	.	.	.	.	2.6652	0.05046	0.0:0.5:0.0:0.5	.	2997	E7ESK3	.	N	3125	ENSP00000417498:D3125N;ENSP00000420243:D3125N	.	D	-	1	0	MUC4	196993857	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.521000	0.06245	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LPIN1	23175	hgsc.bcm.edu	37	2	11943082	11943082	+	Missense_Mutation	SNP	C	C	T	rs4669781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11943082C>T	ENST00000256720.2	+	14	1921	c.1828C>T	c.(1828-1830)Cca>Tca	p.P610S	LPIN1_ENST00000425416.2_Missense_Mutation_p.P616S|LPIN1_ENST00000396097.1_Missense_Mutation_p.P340S|LPIN1_ENST00000396099.1_Missense_Mutation_p.P652S|LPIN1_ENST00000449576.2_Missense_Mutation_p.P695S|LPIN1_ENST00000404113.2_Missense_Mutation_p.P111S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	610			P -> S (in dbSNP:rs4669781). {ECO:0000269|PubMed:12111372}.		cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AGCTGCCAAGCCATCAAACGC	0.537													C|||	140	0.0279553	0.0008	0.0476	5008	,	,		20971	0.0		0.0378	False		,,,				2504	0.0695				p.P695S		Atlas-SNP	.											LPIN1_ENST00000404113,NS,carcinoma,-2,3	LPIN1	99	3	0			c.C2083T						PASS	.	C	SER/PRO	53,4353	51.6+/-87.1	0,53,2150	182.0	160.0	167.0		1828	4.6	1.0	2	dbSNP_111	167	460,8140	137.5+/-194.4	15,430,3855	yes	missense	LPIN1	NM_145693.1	74	15,483,6005	TT,TC,CC		5.3488,1.2029,3.9443	benign	610/891	11943082	513,12493	2203	4300	6503	SO:0001583	missense	23175	exon16			GCCAAGCCATCAA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1828C>T	2.37:g.11943082C>T	ENSP00000256720:p.Pro610Ser	63.0	0.0	0		44.0	17.0	0.386364	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	49	0.022435897435897436	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	29	0.03825857519788918	C	7.475	0.647393	0.14516	0.012029	0.053488	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	T;T;T;T;T;T;T	0.80480	-1.38;-1.37;-1.36;-1.35;-1.19;-0.35;0.53	4.56	4.56	0.56223	.	0.053133	0.85682	D	0.000000	T	0.24736	0.0600	N	0.17312	0.475	0.36110	D	0.844742	B;B;B	0.31705	0.0;0.336;0.002	B;B;B	0.33454	0.003;0.164;0.008	T	0.57100	-0.7869	10	0.07175	T	0.84	-19.8574	13.5335	0.61635	0.1567:0.8433:0.0:0.0	rs4669781;rs4669781	111;695;610	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	S	695;652;616;610;340;111;137	ENSP00000397908:P695S;ENSP00000379406:P652S;ENSP00000401522:P616S;ENSP00000256720:P610S;ENSP00000379404:P340S;ENSP00000386120:P111S;ENSP00000413714:P137S	ENSP00000256720:P610S	P	+	1	0	LPIN1	11860533	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	2.155000	0.42301	2.240000	0.73641	0.462000	0.41574	CCA	C|0.968;T|0.032	0.032	strong		0.537	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
MIA3	375056	hgsc.bcm.edu	37	1	222823669	222823669	+	Missense_Mutation	SNP	A	A	G	rs201134844		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222823669A>G	ENST00000344922.5	+	9	3692	c.3667A>G	c.(3667-3669)Atc>Gtc	p.I1223V	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Missense_Mutation_p.I101V|MIA3_ENST00000344441.6_Missense_Mutation_p.I1223V	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1223					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GTTGAAGACTATCATGAAAGA	0.274																																					p.I1223V		Atlas-SNP	.											.	MIA3	167	.	0			c.A3667G						PASS	.	A	VAL/ILE	0,3618		0,0,1809	33.0	34.0	34.0		3667	-6.1	0.0	1		34	7,8113		0,7,4053	yes	missense	MIA3	NM_198551.2	29	0,7,5862	GG,GA,AA		0.0862,0.0,0.0596	possibly-damaging	1223/1908	222823669	7,11731	1809	4060	5869	SO:0001583	missense	375056	exon9			AAGACTATCATGA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3667A>G	1.37:g.222823669A>G	ENSP00000340900:p.Ile1223Val	152.0	0.0	0		102.0	48.0	0.470588	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.974|8.974	0.973738|0.973738	0.18736|0.18736	0.0|0.0	8.62E-4|8.62E-4	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471|ENST00000354906	T;T;T|.	0.28666|.	1.6;1.6;1.6|.	5.75|5.75	-6.14|-6.14	0.02111|0.02111	.|.	.|.	.|.	.|.	.|.	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.31294|0.31294	0.92|0.92	0.09310|0.09310	N|N	1|1	P;B;B|.	0.39022|.	0.655;0.012;0.081|.	B;B;B|.	0.35039|.	0.194;0.015;0.017|.	T|T	0.36311|0.36311	-0.9753|-0.9753	9|5	0.49607|.	T|.	0.09|.	.|.	7.868|7.868	0.29549|0.29549	0.1682:0.4854:0.0:0.3464|0.1682:0.4854:0.0:0.3464	.|.	1223;101;1223|.	Q5JRA6-2;Q5JRA6-4;Q5JRA6|.	.;.;MIA3_HUMAN|.	V|C	1223;1223;1223;101;101|805	ENSP00000340900:I1223V;ENSP00000340587:I1223V;ENSP00000345866:I101V|.	ENSP00000284471:I101V|.	I|Y	+|+	1|2	0|0	MIA3|MIA3	220890292|220890292	0.177000|0.177000	0.23109|0.23109	0.000000|0.000000	0.03702|0.03702	0.048000|0.048000	0.14542|0.14542	1.442000|1.442000	0.35046|0.35046	-0.870000|-0.870000	0.04047|0.04047	0.482000|0.482000	0.46254|0.46254	ATC|TAT	A|0.999;G|0.001	0.001	weak		0.274	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
ABCB9	23457	hgsc.bcm.edu	37	12	123444265	123444265	+	Missense_Mutation	SNP	G	G	A	rs114398803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123444265G>A	ENST00000542678.1	-	2	3356	c.518C>T	c.(517-519)aCg>aTg	p.T173M	ABCB9_ENST00000392439.3_Missense_Mutation_p.T173M|ABCB9_ENST00000346530.5_Missense_Mutation_p.T173M|ABCB9_ENST00000344275.7_Missense_Mutation_p.T173M|ABCB9_ENST00000280560.8_Missense_Mutation_p.T173M|ABCB9_ENST00000442833.2_Missense_Mutation_p.T173M|ABCB9_ENST00000540285.1_Missense_Mutation_p.T173M|ABCB9_ENST00000442028.2_Missense_Mutation_p.T173M			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	173					peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CTTCTGCAGCGTGGCCCCAGA	0.706													G|||	2	0.000399361	0.0008	0.0	5008	,	,		11470	0.0		0.001	False		,,,				2504	0.0				p.T173M	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ABCB9	50	.	0			c.C518T						PASS	.	G	MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	37.0	37.0	37.0		518,518,518	5.3	1.0	12	dbSNP_132	37	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	ABCB9	NM_019624.3,NM_019625.3,NM_203444.3	81,81,81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	173/724,173/767,173/767	123444265	1,13001	2203	4298	6501	SO:0001583	missense	23457	exon2			TGCAGCGTGGCCC	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.518C>T	12.37:g.123444265G>A	ENSP00000440288:p.Thr173Met	35.0	0.0	0		26.0	10.0	0.384615	NM_019625	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.27	3.076558	0.55753	0.0	1.16E-4	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028	D;D;D;D;D;D	0.90732	-2.39;-2.72;-2.61;-2.39;-2.39;-2.37	5.3	5.3	0.74995	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	L	0.55481	1.735	0.50467	D	0.999878	P;D;B;D	0.76494	0.48;0.999;0.287;0.999	B;D;B;P	0.68039	0.079;0.955;0.109;0.875	D	0.92663	0.6143	10	0.48119	T	0.1	-32.5478	14.1825	0.65583	0.0:0.0:0.8504:0.1496	.	173;173;173;173	B4E2J0;Q9NP78-3;Q9NP78-2;Q9NP78	.;.;.;ABCB9_HUMAN	M	173	ENSP00000280560:T173M;ENSP00000441734:T173M;ENSP00000280559:T173M;ENSP00000376234:T173M;ENSP00000440288:T173M;ENSP00000394898:T173M	ENSP00000280560:T173M	T	-	2	0	ABCB9	122010218	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	6.425000	0.73370	2.653000	0.90120	0.561000	0.74099	ACG	G|0.999;A|0.001	0.001	strong		0.706	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
OR51B5	282763	hgsc.bcm.edu	37	11	5364640	5364640	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5364640C>T	ENST00000300773.2	-	1	169	c.115G>A	c.(115-117)Ggc>Agc	p.G39S	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	39					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGCCATTGCCAAAAAGGATG	0.478																																					p.G39S		Atlas-SNP	.											.	OR51B5	60	.	0			c.G115A						PASS	.						62.0	66.0	65.0					11																	5364640		2201	4297	6498	SO:0001583	missense	282763	exon5			CATTGCCAAAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.115G>A	11.37:g.5364640C>T	ENSP00000300773:p.Gly39Ser	63.0	0.0	0		67.0	52.0	0.776119	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145360	0.57044	.	.	ENSG00000242180	ENST00000300773	T	0.00530	6.77	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40064	N	0.001186	T	0.01156	0.0038	M	0.90870	3.155	0.38694	D	0.952823	P	0.37398	0.593	B	0.37550	0.253	T	0.50118	-0.8865	10	0.72032	D	0.01	.	16.5938	0.84789	0.0:1.0:0.0:0.0	.	39	Q9H339	O51B5_HUMAN	S	39	ENSP00000300773:G39S	ENSP00000300773:G39S	G	-	1	0	OR51B5	5321216	0.190000	0.23276	0.966000	0.40874	0.675000	0.39556	2.218000	0.42889	2.482000	0.83794	0.650000	0.86243	GGC	.	.	none		0.478	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
RAB5B	5869	hgsc.bcm.edu	37	12	56383858	56383858	+	Silent	SNP	C	C	T	rs141101772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:56383858C>T	ENST00000360299.5	+	3	512	c.291C>T	c.(289-291)atC>atT	p.I97I	RAB5B_ENST00000448789.2_Silent_p.I97I|RAB5B_ENST00000553116.1_Silent_p.I97I	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	97					antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			AAGCTGCAATCGTGGTTTACG	0.488													C|||	2	0.000399361	0.0	0.0014	5008	,	,		23495	0.0		0.001	False		,,,				2504	0.0				p.I97I		Atlas-SNP	.											RAB5B,NS,lymphoid_neoplasm,+2,1	RAB5B	22	1	0			c.C291T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	100.0	79.0	86.0		291	-4.7	0.9	12	dbSNP_134	86	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	RAB5B	NM_002868.2		0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923		97/216	56383858	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5869	exon3			TGCAATCGTGGTT		CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"""RAB, member RAS oncogene"""	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.291C>T	12.37:g.56383858C>T		181.0	0.0	0		150.0	67.0	0.446667	NM_002868	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Silent	SNP	ENST00000360299.5	37	CCDS8900.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.22	1.290646	0.23564	6.81E-4	0.001047	ENSG00000111540	ENST00000549218	.	.	.	4.81	-4.69	0.03299	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48692	-0.9013	4	.	.	.	-8.259	7.6574	0.28383	0.0:0.2762:0.1073:0.6166	.	.	.	.	C	17	.	.	R	+	1	0	RAB5B	54670125	0.398000	0.25279	0.865000	0.33974	0.959000	0.62525	-0.395000	0.07287	-0.990000	0.03481	-1.329000	0.01275	CGT	C|0.999;T|0.001	0.001	strong		0.488	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1		
OR5K2	402135	hgsc.bcm.edu	37	3	98216586	98216586	+	Missense_Mutation	SNP	C	C	G	rs143260385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98216586C>G	ENST00000427338.1	+	1	139	c.62C>G	c.(61-63)cCt>cGt	p.P21R		NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P21L(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACAGATCACCCTGAGCTGAAG	0.413													C|||	16	0.00319489	0.0008	0.0	5008	,	,		20316	0.0		0.0149	False		,,,				2504	0.0				p.P21R		Atlas-SNP	.											OR5K2,bladder,carcinoma,0,1	OR5K2	56	1	1	Substitution - Missense(1)	urinary_tract(1)	c.C62G						PASS	.	C	ARG/PRO	15,4391	22.3+/-47.3	0,15,2188	94.0	95.0	95.0		62	2.9	0.9	3	dbSNP_134	95	60,8534	36.9+/-92.0	0,60,4237	no	missense	OR5K2	NM_001004737.1	103	0,75,6425	GG,GC,CC		0.6982,0.3404,0.5769	probably-damaging	21/317	98216586	75,12925	2203	4297	6500	SO:0001583	missense	402135	exon1			ATCACCCTGAGCT	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"""GPCR / Class A : Olfactory receptors"""	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.62C>G	3.37:g.98216586C>G	ENSP00000393889:p.Pro21Arg	349.0	0.0	0		361.0	170.0	0.470914	NM_001004737	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	16	0.007326007326007326	0	0.0	0	0.0	0	0.0	16	0.021108179419525065	C	11.04	1.521543	0.27211	0.003404	0.006982	ENSG00000231861	ENST00000427338	T	0.20332	2.08	2.91	2.91	0.33838	.	0.000000	0.41294	D	0.000912	T	0.18257	0.0438	M	0.69523	2.12	0.23896	N	0.99653	P	0.45396	0.857	P	0.49637	0.617	T	0.04360	-1.0957	10	0.66056	D	0.02	-9.1222	12.101	0.53783	0.0:1.0:0.0:0.0	.	21	Q8NHB8	OR5K2_HUMAN	R	21	ENSP00000393889:P21R	ENSP00000393889:P21R	P	+	2	0	OR5K2	99699276	0.000000	0.05858	0.913000	0.36048	0.263000	0.26337	0.179000	0.16840	1.940000	0.56252	0.298000	0.19748	CCT	C|0.994;G|0.006	0.006	strong		0.413	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2		
MTX2	10651	hgsc.bcm.edu	37	2	177194090	177194090	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:177194090A>G	ENST00000249442.6	+	8	690	c.479A>G	c.(478-480)cAa>cGa	p.Q160R	MTX2_ENST00000443241.1_Missense_Mutation_p.Q104R|MTX2_ENST00000392529.2_Missense_Mutation_p.Q150R	NM_006554.4	NP_006545.1	O75431	MTX2_HUMAN	metaxin 2	160					cellular protein metabolic process (GO:0044267)|mitochondrial transport (GO:0006839)|protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)			TTGGCCTATCAAAAACAGTGG	0.403																																					p.Q160R		Atlas-SNP	.											.	MTX2	25	.	0			c.A479G						PASS	.						110.0	109.0	110.0					2																	177194090		2203	4300	6503	SO:0001583	missense	10651	exon8			CCTATCAAAAACA	AF053551	CCDS2272.1	2q31.1	2012-02-07			ENSG00000128654	ENSG00000128654			7506	protein-coding gene	gene with protein product		608555				10381257, 17624330	Standard	NM_006554		Approved		uc002ukx.3	O75431	OTTHUMG00000132514	ENST00000249442.6:c.479A>G	2.37:g.177194090A>G	ENSP00000249442:p.Gln160Arg	219.0	0.0	0		222.0	111.0	0.5	NM_006554	A8JZZ4|Q53S50|Q53SQ2|Q5M7Z6|Q8IZ68	Missense_Mutation	SNP	ENST00000249442.6	37	CCDS2272.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.456513	0.26161	.	.	ENSG00000128654	ENST00000249442;ENST00000392529;ENST00000443241	T;T;T	0.41758	0.99;0.99;0.99	5.19	5.19	0.71726	Glutathione S-transferase, C-terminal-like (1);	0.059658	0.64402	D	0.000001	T	0.26376	0.0644	N	0.17594	0.5	0.58432	D	0.999999	B;B	0.14012	0.002;0.009	B;B	0.09377	0.004;0.003	T	0.08700	-1.0709	10	0.09843	T	0.71	-0.1211	15.031	0.71708	1.0:0.0:0.0:0.0	.	160;150	O75431;Q8IZ68	MTX2_HUMAN;.	R	160;150;104	ENSP00000249442:Q160R;ENSP00000376314:Q150R;ENSP00000414176:Q104R	ENSP00000249442:Q160R	Q	+	2	0	MTX2	176902336	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.172000	0.94808	1.948000	0.56530	0.455000	0.32223	CAA	.	.	none		0.403	MTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255695.4	NM_006554	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987921	60987921	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60987921C>T	ENST00000252998.1	-	12	1867	c.1711G>A	c.(1711-1713)Gac>Aac	p.D571N		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	571						extracellular space (GO:0005615)											TCCAGTTCGTCGGACTCTGGT	0.657																																					p.D571N		Atlas-SNP	.											.	.	.	.	0			c.G1711A						PASS	.						129.0	106.0	114.0					20																	60987921		2203	4300	6503	SO:0001583	missense	140893	exon12			GTTCGTCGGACTC	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1711G>A	20.37:g.60987921C>T	ENSP00000252998:p.Asp571Asn	110.0	0.0	0		81.0	31.0	0.382716	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846159	0.51164	.	.	ENSG00000130701	ENST00000252998	T	0.20598	2.06	3.52	2.56	0.30785	.	0.908502	0.09136	N	0.843633	T	0.19765	0.0475	L	0.46157	1.445	0.09310	N	1	D	0.61080	0.989	P	0.44447	0.45	T	0.12218	-1.0556	10	0.18276	T	0.48	-0.964	8.456	0.32899	0.0:0.8818:0.0:0.1182	.	571	Q8NC74	CT151_HUMAN	N	571	ENSP00000252998:D571N	ENSP00000252998:D571N	D	-	1	0	C20orf151	60421316	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	1.089000	0.30890	0.783000	0.33636	-0.339000	0.08088	GAC	.	.	none		0.657	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124805	26124805	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124805G>A	ENST00000602637.1	+	1	375	c.345G>A	c.(343-345)gtG>gtA	p.V115V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.V115V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	115						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						TCCAGGCCGTGCTTCTGCCTA	0.562																																					p.V115V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G345A						PASS	.						82.0	82.0	82.0					6																	26124805		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGCCGTGCTTCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.345G>A	6.37:g.26124805G>A		134.0	0.0	0		128.0	40.0	0.3125	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.562	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
SLC41A3	54946	hgsc.bcm.edu	37	3	125726062	125726062	+	Missense_Mutation	SNP	T	T	C	rs79696429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:125726062T>C	ENST00000315891.6	-	11	1499	c.1261A>G	c.(1261-1263)Atc>Gtc	p.I421V	SLC41A3_ENST00000383598.2_Missense_Mutation_p.I395V|SLC41A3_ENST00000360370.4_Missense_Mutation_p.I421V|SLC41A3_ENST00000346785.5_Missense_Mutation_p.I385V|SLC41A3_ENST00000508835.1_Missense_Mutation_p.I304V	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	421						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		TACAGCAGGATTGTCACCTGT	0.537													T|||	99	0.0197684	0.056	0.0072	5008	,	,		21514	0.0		0.007	False		,,,				2504	0.0133				p.I421V		Atlas-SNP	.											.	SLC41A3	80	.	0			c.A1261G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	242,4164	140.0+/-175.5	8,226,1969	56.0	52.0	53.0		1261,1153,1183,910,1261	4.4	0.8	3	dbSNP_132	53	63,8537	39.3+/-95.6	1,61,4238	yes	missense,missense,missense,missense,missense	SLC41A3	NM_001008485.1,NM_001008486.1,NM_001008487.1,NM_001164475.1,NM_017836.3	29,29,29,29,29	9,287,6207	CC,CT,TT		0.7326,5.4925,2.3451	benign,benign,benign,benign,benign	421/508,385/472,395/462,304/371,421/488	125726062	305,12701	2203	4300	6503	SO:0001583	missense	54946	exon11			GCAGGATTGTCAC		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1261A>G	3.37:g.125726062T>C	ENSP00000326070:p.Ile421Val	85.0	0.0	0		70.0	27.0	0.385714	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	37	0.01694139194139194	27	0.054878048780487805	5	0.013812154696132596	0	0.0	5	0.006596306068601583	T	10.45	1.353842	0.24512	0.054925	0.007326	ENSG00000114544	ENST00000360370;ENST00000346785;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000508835	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.52	4.37	0.52481	MgtE magnesium transporter, integral membrane (1);	0.088897	0.85682	N	0.000000	T	0.04272	0.0118	L	0.35249	1.045	0.45150	D	0.998169	B;B;B;B;B	0.30439	0.031;0.279;0.236;0.279;0.144	B;B;B;B;B	0.36092	0.058;0.217;0.138;0.217;0.084	T	0.02574	-1.1139	10	0.38643	T	0.18	0.3499	9.4473	0.38706	0.0:0.0848:0.0:0.9152	.	304;421;385;421;395	B7Z4Y2;E7ENY4;Q96GZ6-3;Q96GZ6;Q96GZ6-7	.;.;.;S41A3_HUMAN;.	V	421;385;395;412;421;304	ENSP00000353533:I421V;ENSP00000264471:I385V;ENSP00000373092:I395V;ENSP00000326070:I421V;ENSP00000427409:I304V	ENSP00000326070:I421V	I	-	1	0	SLC41A3	127208752	0.388000	0.25197	0.794000	0.32065	0.903000	0.53119	0.596000	0.24044	0.939000	0.37446	0.482000	0.46254	ATC	T|0.980;C|0.020	0.020	strong		0.537	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
ZFP42	132625	hgsc.bcm.edu	37	4	188924230	188924230	+	Missense_Mutation	SNP	C	C	T	rs149675060		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924230C>T	ENST00000326866.4	+	4	677	c.269C>T	c.(268-270)tCa>tTa	p.S90L	ZFP42_ENST00000509524.1_Missense_Mutation_p.S90L	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	90					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		GAAGAGGACTCACTTTTTGAG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20567	0.0		0.001	False		,,,				2504	0.0				p.S90L		Atlas-SNP	.											.	ZFP42	87	.	0			c.C269T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	83.0	85.0	85.0		269	-1.7	0.0	4	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZFP42	NM_174900.3	145	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	benign	90/311	188924230	8,12998	2203	4300	6503	SO:0001583	missense	132625	exon4			AGGACTCACTTTT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.269C>T	4.37:g.188924230C>T	ENSP00000317686:p.Ser90Leu	64.0	0.0	0		89.0	44.0	0.494382	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.005	-2.129602	0.00338	4.54E-4	6.98E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.62788	0.0;0.0	4.49	-1.68	0.08212	.	0.950524	0.08730	N	0.902147	T	0.42314	0.1197	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27806	-1.0063	10	0.39692	T	0.17	.	10.2546	0.43390	0.0:0.717:0.0:0.283	.	90	Q96MM3	ZFP42_HUMAN	L	90	ENSP00000317686:S90L;ENSP00000424662:S90L	ENSP00000317686:S90L	S	+	2	0	ZFP42	189161224	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.552000	0.06020	-0.188000	0.10499	0.655000	0.94253	TCA	C|0.999;T|0.001	0.001	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
NUDT12	83594	hgsc.bcm.edu	37	5	102895169	102895169	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:102895169C>T	ENST00000230792.2	-	3	303	c.207G>A	c.(205-207)ggG>ggA	p.G69G	NUDT12_ENST00000507423.1_Splice_Site_p.M51I	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	69					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		ATCTGTCACACCTATAGATGG	0.323																																					p.G69G		Atlas-SNP	.											.	NUDT12	27	.	0			c.G207A						PASS	.						34.0	34.0	34.0					5																	102895169		2037	4218	6255	SO:0001630	splice_region_variant	83594	exon3			GTCACACCTATAG	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.207-1G>A	5.37:g.102895169C>T		122.0	0.0	0		74.0	18.0	0.243243	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	37	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333868	0.24253	.	.	ENSG00000112874	ENST00000507423	T	0.34072	1.38	5.9	3.17	0.36434	.	.	.	.	.	T	0.29749	0.0743	.	.	.	0.19945	N	0.999946	B	0.09022	0.002	B	0.12837	0.008	T	0.24190	-1.0167	8	0.62326	D	0.03	.	10.3521	0.43943	0.0:0.7281:0.0:0.2719	.	51	E7EM93	.	I	51	ENSP00000424521:M51I	ENSP00000424521:M51I	M	-	3	0	NUDT12	102923068	1.000000	0.71417	0.998000	0.56505	0.533000	0.34776	1.488000	0.35551	0.399000	0.25367	-0.142000	0.14014	ATG	.	.	none		0.323	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	Silent
ZNF474	133923	hgsc.bcm.edu	37	5	121487969	121487969	+	Missense_Mutation	SNP	G	G	A	rs72786994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:121487969G>A	ENST00000296600.4	+	2	667	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	95							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		CCTGGATTCCGGGTATGCTAT	0.502													G|||	52	0.0103834	0.0008	0.0086	5008	,	,		17148	0.0		0.0179	False		,,,				2504	0.0276				p.R95Q		Atlas-SNP	.											.	ZNF474	43	.	0			c.G284A						PASS	.	G	GLN/ARG	15,4391	23.3+/-48.9	0,15,2188	74.0	81.0	79.0		284	-1.7	0.1	5	dbSNP_130	79	171,8429	78.6+/-141.3	1,169,4130	yes	missense	ZNF474	NM_207317.1	43	1,184,6318	AA,AG,GG		1.9884,0.3404,1.4301	probably-damaging	95/365	121487969	186,12820	2203	4300	6503	SO:0001583	missense	133923	exon2			GATTCCGGGTATG	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.284G>A	5.37:g.121487969G>A	ENSP00000296600:p.Arg95Gln	104.0	0.0	0		91.0	43.0	0.472527	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	G	10.15	1.271155	0.23221	0.003404	0.019884	ENSG00000164185	ENST00000296600	T	0.51325	0.71	5.58	-1.72	0.08107	.	3.416030	0.00792	N	0.001340	T	0.30230	0.0758	L	0.52011	1.625	0.19775	N	0.999959	P	0.51147	0.942	P	0.47470	0.548	T	0.34551	-0.9824	10	0.27082	T	0.32	1.9702	6.2544	0.20865	0.5859:0.0:0.2818:0.1323	.	95	Q6S9Z5	ZN474_HUMAN	Q	95	ENSP00000296600:R95Q	ENSP00000296600:R95Q	R	+	2	0	ZNF474	121515868	0.019000	0.18553	0.146000	0.22360	0.062000	0.15995	-0.172000	0.09868	-0.163000	0.10946	-0.123000	0.14984	CGG	G|0.988;A|0.012	0.012	strong		0.502	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
ZBP1	81030	hgsc.bcm.edu	37	20	56189956	56189956	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:56189956C>T	ENST00000371173.3	-	4	666	c.489G>A	c.(487-489)acG>acA	p.T163T	ZBP1_ENST00000541799.1_Silent_p.T163T|ZBP1_ENST00000343535.4_Silent_p.T163T|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000395822.3_Silent_p.T88T|ZBP1_ENST00000340462.4_Silent_p.T140T	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	163					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			GGCGGTAAATCGTCCATGCTT	0.552																																					p.T163T		Atlas-SNP	.											ZBP1,NS,carcinoma,0,1	ZBP1	65	1	0			c.G489A						PASS	.						161.0	127.0	139.0					20																	56189956		2203	4300	6503	SO:0001819	synonymous_variant	81030	exon4			GTAAATCGTCCAT	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.489G>A	20.37:g.56189956C>T		187.0	0.0	0		135.0	28.0	0.207407	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			.	.	none		0.552	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21.0	26.0	24.0		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	116.0	0.0	0		124.0	27.0	0.217742	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092920	1092920	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092920C>A	ENST00000441003.2	+	30	4766	c.4739C>A	c.(4738-4740)aCc>aAc	p.T1580N	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1581N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ggcacacagaccccaacatcg	0.632																																					p.T1580N		Atlas-SNP	.											.	MUC2	614	.	0			c.C4739A						PASS	.						74.0	113.0	100.0					11																	1092920		1924	3573	5497	SO:0001583	missense	4583	exon30			CACAGACCCCAAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4739C>A	11.37:g.1092920C>A	ENSP00000415183:p.Thr1580Asn	46.0	0.0	0		72.0	4.0	0.0555556	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.897	-0.228278	0.06022	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15952	2.38;2.53	1.75	-3.51	0.04696	.	7739.210000	0.00597	U	0.000365	T	0.08492	0.0211	.	.	.	0.09310	N	1	B	0.28026	0.198	B	0.17098	0.017	T	0.10776	-1.0615	9	0.27082	T	0.32	.	2.0197	0.03506	0.1703:0.3607:0.3305:0.1386	.	1580	E7EUV1	.	N	1580;1581	ENSP00000415183:T1580N;ENSP00000351956:T1581N	ENSP00000351956:T1581N	T	+	2	0	MUC2	1082920	0.001000	0.12720	0.000000	0.03702	0.071000	0.16799	1.304000	0.33482	-1.223000	0.02584	0.121000	0.15741	ACC	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
LRP1	4035	hgsc.bcm.edu	37	12	57587437	57587437	+	Silent	SNP	T	T	C	rs34456957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587437T>C	ENST00000243077.3	+	47	8239	c.7773T>C	c.(7771-7773)tgT>tgC	p.C2591C	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2591	LDL-receptor class A 12. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGACGACTGTGGGGATGGCT	0.602													T|||	7	0.00139776	0.0	0.0029	5008	,	,		21660	0.0		0.005	False		,,,				2504	0.0				p.C2591C		Atlas-SNP	.											.	LRP1	428	.	0			c.T7773C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	94.0	84.0	87.0		7773	-8.4	0.8	12	dbSNP_126	87	63,8537	39.3+/-95.6	0,63,4237	no	coding-synonymous	LRP1	NM_002332.2		0,69,6434	CC,CT,TT		0.7326,0.1362,0.5305		2591/4545	57587437	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon47			CGACTGTGGGGAT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7773T>C	12.37:g.57587437T>C		71.0	0.0	0		64.0	29.0	0.453125	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			T|0.996;C|0.004	0.004	strong		0.602	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
NAPB	63908	hgsc.bcm.edu	37	20	23377815	23377815	+	Silent	SNP	G	G	A	rs17750862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23377815G>A	ENST00000377026.4	-	3	274	c.189C>T	c.(187-189)aaC>aaT	p.N63N	NAPB_ENST00000398425.3_De_novo_Start_InFrame|NAPB_ENST00000432543.2_Intron|NAPB_ENST00000472855.1_Intron	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	63					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					GACAAAATGCGTTTCCTGCAG	0.478													G|||	110	0.0219649	0.0015	0.0231	5008	,	,		17642	0.001		0.0537	False		,,,				2504	0.0378				p.N63N		Atlas-SNP	.											.	NAPB	22	.	0			c.C189T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	71.0	59.0	63.0		189	-2.1	1.0	20	dbSNP_123	63	440,8160	134.7+/-192.1	18,404,3878	no	coding-synonymous	NAPB	NM_022080.2		18,451,6034	AA,AG,GG		5.1163,1.0667,3.7444		63/299	23377815	487,12519	2203	4300	6503	SO:0001819	synonymous_variant	63908	exon3			AAATGCGTTTCCT	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.189C>T	20.37:g.23377815G>A		84.0	0.0	0		62.0	24.0	0.387097	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Silent	SNP	ENST00000377026.4	37	CCDS13152.1																																																																																			G|0.966;A|0.034	0.034	strong		0.478	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080	
CATSPERB	79820	hgsc.bcm.edu	37	14	92102819	92102819	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:92102819G>A	ENST00000256343.3	-	17	1848	c.1692C>T	c.(1690-1692)atC>atT	p.I564I		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	564					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TCTTGCTGTAGATCGTTTCCT	0.408																																					p.I564I		Atlas-SNP	.											.	CATSPERB	114	.	0			c.C1692T						PASS	.						174.0	157.0	163.0					14																	92102819		2203	4300	6503	SO:0001819	synonymous_variant	79820	exon17			GCTGTAGATCGTT	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"""chromosome 14 open reading frame 161"", ""cation channel, sperm-associated, beta"""	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1692C>T	14.37:g.92102819G>A		212.0	0.0	0		180.0	39.0	0.216667	NM_024764	A0AV51	Silent	SNP	ENST00000256343.3	37	CCDS32142.1																																																																																			.	.	none		0.408	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
LACTB	114294	hgsc.bcm.edu	37	15	63419223	63419223	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63419223C>T	ENST00000261893.4	+	3	662	c.590C>T	c.(589-591)cCa>cTa	p.P197L	LACTB_ENST00000413507.2_Missense_Mutation_p.P197L|RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	197						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CCCGAATTCCCAGAAAAAGAA	0.363																																					p.P197L	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.C590T						PASS	.						67.0	58.0	61.0					15																	63419223		2203	4300	6503	SO:0001583	missense	114294	exon3			AATTCCCAGAAAA	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.590C>T	15.37:g.63419223C>T	ENSP00000261893:p.Pro197Leu	138.0	0.0	0		155.0	28.0	0.180645	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588482	0.86851	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	T;T	0.47177	0.85;0.85	5.5	5.5	0.81552	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	M	0.70108	2.13	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71059	-0.4702	10	0.62326	D	0.03	-9.8513	18.3852	0.90464	0.0:1.0:0.0:0.0	.	197	P83111	LACTB_HUMAN	L	197	ENSP00000261893:P197L;ENSP00000392956:P197L	ENSP00000261893:P197L	P	+	2	0	LACTB	61206276	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.616000	0.83018	2.585000	0.87301	0.563000	0.77884	CCA	.	.	none		0.363	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
PDGFRB	5159	hgsc.bcm.edu	37	5	149509446	149509446	+	Missense_Mutation	SNP	C	C	T	rs41287110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149509446C>T	ENST00000261799.4	-	10	1922	c.1453G>A	c.(1453-1455)Gag>Aag	p.E485K		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	485	Ig-like C2-type 5.		E -> K (in dbSNP:rs41287110). {ECO:0000269|PubMed:17344846}.		adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCCTGCTCCTCCTCCCAGTAC	0.647			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	54	0.0107827	0.0015	0.0216	5008	,	,		23425	0.0		0.0328	False		,,,				2504	0.0041				p.E485K		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.G1453A						PASS	.	C	LYS/GLU	21,4385	29.0+/-57.7	0,21,2182	186.0	118.0	141.0		1453	3.7	1.0	5	dbSNP_127	141	224,8376	93.3+/-155.3	4,216,4080	yes	missense	PDGFRB	NM_002609.3	56	4,237,6262	TT,TC,CC		2.6047,0.4766,1.8837	benign	485/1107	149509446	245,12761	2203	4300	6503	SO:0001583	missense	5159	exon10			GCTCCTCCTCCCA	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1453G>A	5.37:g.149509446C>T	ENSP00000261799:p.Glu485Lys	175.0	0.0	0	1725	123.0	62.0	0.504065	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	39	0.017857142857142856	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	27	0.03562005277044855	C	13.36	2.214386	0.39102	0.004766	0.026047	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.75938	-0.98	4.64	3.73	0.42828	.	0.108236	0.40554	N	0.001077	T	0.25754	0.0627	N	0.22421	0.69	0.38651	D	0.951848	B;B	0.25441	0.126;0.126	B;B	0.21360	0.034;0.034	T	0.46219	-0.9207	10	0.23302	T	0.38	.	12.5115	0.56007	0.0:0.8166:0.1834:0.0	rs41287110;rs62620662	485;485	A8KAM8;P09619	.;PGFRB_HUMAN	K	485;155	ENSP00000261799:E485K	ENSP00000261799:E485K	E	-	1	0	PDGFRB	149489639	0.920000	0.31207	0.958000	0.39756	0.940000	0.58332	1.826000	0.39092	2.409000	0.81822	0.462000	0.41574	GAG	C|0.980;T|0.020	0.020	strong		0.647	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
AGL	178	hgsc.bcm.edu	37	1	100340286	100340286	+	Silent	SNP	G	G	A	rs369218410		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100340286G>A	ENST00000294724.4	+	8	1480	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	AGL_ENST00000370163.3_Silent_p.T334T|AGL_ENST00000361302.3_Silent_p.T318T|AGL_ENST00000361915.3_Silent_p.T334T|AGL_ENST00000477753.1_3'UTR|AGL_ENST00000361522.4_Silent_p.T317T|AGL_ENST00000370161.2_Silent_p.T318T|AGL_ENST00000370165.3_Silent_p.T334T	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	334					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AACACCTTACGATTATTCAAG	0.343																																					p.T334T		Atlas-SNP	.											.	AGL	137	.	0			c.G1002A						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	127.0	111.0	116.0		1002,1002,1002,1002,951,954	1.8	1.0	1		116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	334/1533,334/1533,334/1533,334/1533,317/1516,318/1517	100340286	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	178	exon8			CCTTACGATTATT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1002G>A	1.37:g.100340286G>A		78.0	0.0	0		75.0	4.0	0.0533333	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			.	.	none		0.343	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
MUC4	4585	hgsc.bcm.edu	37	3	195512480	195512480	+	Missense_Mutation	SNP	A	A	G	rs200533337	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512480A>G	ENST00000463781.3	-	2	6430	c.5971T>C	c.(5971-5973)Tcc>Ccc	p.S1991P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1991P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACACTGAGGAAGCGTCGGTG	0.602													.|||	91	0.0181709	0.0068	0.0418	5008	,	,		25743	0.0		0.0507	False		,,,				2504	0.002				p.S1991P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.T5971C						PASS	.						43.0	40.0	41.0					3																	195512480		691	1590	2281	SO:0001583	missense	4585	exon2			CTGAGGAAGCGTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5971T>C	3.37:g.195512480A>G	ENSP00000417498:p.Ser1991Pro	73.0	0.0	0		129.0	31.0	0.24031	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	3.721	-0.057533	0.07317	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.46	.	.	.	.	.	.	.	.	T	0.14399	0.0348	N	0.19112	0.55	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.27400	-1.0075	7	.	.	.	.	3.355	0.07165	0.649:0.0:1.0E-4:0.3509	.	1991	E7ESK3	.	P	1991	ENSP00000417498:S1991P;ENSP00000420243:S1991P	.	S	-	1	0	MUC4	196996875	0.997000	0.39634	0.003000	0.11579	0.158000	0.22134	0.513000	0.22770	-0.876000	0.04017	0.055000	0.15244	TCC	A|0.973;G|0.027	0.027	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AOC2	314	hgsc.bcm.edu	37	17	40997461	40997461	+	Missense_Mutation	SNP	G	G	A	rs35508987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40997461G>A	ENST00000253799.3	+	1	845	c.818G>A	c.(817-819)cGg>cAg	p.R273Q	AOC2_ENST00000452774.2_Missense_Mutation_p.R273Q	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	273			R -> Q (in dbSNP:rs35508987). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CAGTTGGAACGGGAGTTTAAG	0.572													G|||	14	0.00279553	0.0	0.0029	5008	,	,		18840	0.0		0.0099	False		,,,				2504	0.002				p.R273Q		Atlas-SNP	.											.	AOC2	61	.	0			c.G818A						PASS	.	G	GLN/ARG,GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	81.0	80.0	81.0		818,818	1.0	0.8	17	dbSNP_126	81	79,8521	47.2+/-106.3	0,79,4221	yes	missense,missense	AOC2	NM_001158.3,NM_009590.2	43,43	0,92,6411	AA,AG,GG		0.9186,0.2951,0.7074	benign,benign	273/730,273/757	40997461	92,12914	2203	4300	6503	SO:0001583	missense	314	exon1			TGGAACGGGAGTT	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.818G>A	17.37:g.40997461G>A	ENSP00000253799:p.Arg273Gln	141.0	0.0	0		116.0	60.0	0.517241	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.383	0.255861	0.10185	0.002951	0.009186	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.15603	2.41;2.41	5.75	1.03	0.20045	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	1.003210	0.08026	N	0.992717	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.007;0.012	B;B	0.10450	0.002;0.005	T	0.42275	-0.9461	10	0.12766	T	0.61	-24.7701	6.4476	0.21885	0.3468:0.0:0.5339:0.1193	rs35508987	273;273	O75106;O75106-2	AOC2_HUMAN;.	Q	273	ENSP00000253799:R273Q;ENSP00000406134:R273Q	ENSP00000253799:R273Q	R	+	2	0	AOC2	38250987	0.000000	0.05858	0.837000	0.33122	0.916000	0.54674	0.563000	0.23547	0.366000	0.24427	-0.254000	0.11334	CGG	G|0.993;A|0.007	0.007	strong		0.572	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122384	100122384	+	Splice_Site	SNP	G	G	A	rs376419121		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:100122384G>A	ENST00000357054.1	+	37	4463		c.e37+1		RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Splice_Site|CCDC180_ENST00000529487.1_Splice_Site|CCDC180_ENST00000395220.1_Splice_Site			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.?(1)									GGTCTTTACCGTAAGGAATGG	0.547																																					.		Atlas-SNP	.											KIAA1529,mouth,carcinoma,0,1	.	.	1	1	Unknown(1)	upper_aerodigestive_tract(1)	c.3615+1G>A						PASS	.	G		0,4406		0,0,2203	100.0	95.0	97.0			3.5	0.9	9		97	1,8599	1.2+/-3.3	0,1,4299	no	splice-5	C9orf174	NM_020893.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			100122384	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	0	exon26			TTTACCGTAAGGA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3528+1G>A	9.37:g.100122384G>A		92.0	0.0	0		67.0	17.0	0.253731	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Splice_Site	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	G	12.90	2.075193	0.36662	0.0	1.16E-4	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	.	.	.	5.31	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3386	0.26623	0.1896:0.0:0.8104:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C9orf174	99162205	0.974000	0.33945	0.889000	0.34880	0.044000	0.14063	1.890000	0.39728	1.571000	0.49722	0.561000	0.74099	.	.	.	weak		0.547	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	Intron
OXGR1	27199	hgsc.bcm.edu	37	13	97639021	97639021	+	Silent	SNP	A	A	G	rs9584456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639021A>G	ENST00000298440.1	-	4	1236	c.993T>C	c.(991-993)atT>atC	p.I331I	OXGR1_ENST00000543457.1_Silent_p.I331I	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	331					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTGAGTAACTAATTTTCTTTG	0.398													G|||	319	0.0636981	0.2118	0.0288	5008	,	,		21899	0.0		0.0179	False		,,,				2504	0.001				p.I331I		Atlas-SNP	.											.	OXGR1	46	.	0			c.T993C						PASS	.	G		814,3592	740.9+/-411.2	74,666,1463	104.0	107.0	106.0		993	2.4	0.0	13	dbSNP_119	106	83,8517	814.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,749,5680	GG,GA,AA		0.9651,18.4748,6.8968		331/338	97639021	897,12109	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			GTAACTAATTTTC	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"""GPCR / Class A : Orphans"""	4531	protein-coding gene	gene with protein product	"""2-oxoglutarate receptor 1"", ""alpha-ketoglutarate receptor 1"""	606922	"""G protein-coupled receptor 80"""	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.993T>C	13.37:g.97639021A>G		53.0	0.0	0		34.0	13.0	0.382353	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			A|0.933;G|0.067	0.067	strong		0.398	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818	
CHD6	84181	hgsc.bcm.edu	37	20	40049579	40049579	+	Missense_Mutation	SNP	T	T	A	rs55864139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:40049579T>A	ENST00000373233.3	-	31	5873	c.5696A>T	c.(5695-5697)aAc>aTc	p.N1899I		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1899					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTTGAGATGTTAGTAGTGGG	0.517													T|||	32	0.00638978	0.0008	0.0216	5008	,	,		18821	0.0		0.0159	False		,,,				2504	0.0				p.N1899I		Atlas-SNP	.											.	CHD6	312	.	0			c.A5696T						PASS	.	T	ILE/ASN	18,4388	24.3+/-50.5	0,18,2185	140.0	139.0	139.0		5696	-6.9	0.0	20	dbSNP_129	139	125,8475	63.9+/-126.0	1,123,4176	yes	missense	CHD6	NM_032221.3	149	1,141,6361	AA,AT,TT		1.4535,0.4085,1.0995	benign	1899/2716	40049579	143,12863	2203	4300	6503	SO:0001583	missense	84181	exon31			GAGATGTTAGTAG	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.5696A>T	20.37:g.40049579T>A	ENSP00000362330:p.Asn1899Ile	281.0	0.0	0		252.0	125.0	0.496032	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	T	3.272	-0.148971	0.06585	0.004085	0.014535	ENSG00000124177	ENST00000373233	D	0.85702	-2.02	5.86	-6.91	0.01649	.	1.661450	0.02896	N	0.134718	T	0.58221	0.2107	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52895	-0.8514	10	0.34782	T	0.22	-0.042	4.3803	0.11290	0.0875:0.369:0.3003:0.2432	rs55864139;rs61752059	1899	Q8TD26	CHD6_HUMAN	I	1899	ENSP00000362330:N1899I	ENSP00000362330:N1899I	N	-	2	0	CHD6	39482993	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.483000	0.06536	-0.683000	0.05190	0.533000	0.62120	AAC	T|0.991;A|0.009	0.009	strong		0.517	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
KCNN1	3780	hgsc.bcm.edu	37	19	18096220	18096220	+	Silent	SNP	C	C	T	rs76273600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18096220C>T	ENST00000222249.9	+	6	1336	c.1017C>T	c.(1015-1017)caC>caT	p.H339H		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	339					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	TGGTGCCCCACACCTACTGCG	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		21197	0.0		0.001	False		,,,				2504	0.0				p.H339H		Atlas-SNP	.											.	KCNN1	74	.	0			c.C1017T						PASS	.	C		0,4346		0,0,2173	91.0	98.0	96.0		1017	2.7	1.0	19	dbSNP_131	96	5,8567	4.3+/-15.6	0,5,4281	no	coding-synonymous	KCNN1	NM_002248.3		0,5,6454	TT,TC,CC		0.0583,0.0,0.0387		339/544	18096220	5,12913	2173	4286	6459	SO:0001819	synonymous_variant	3780	exon6			GCCCCACACCTAC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1017C>T	19.37:g.18096220C>T		143.0	0.0	0		187.0	104.0	0.55615	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.998;T|0.002	0.002	weak		0.597	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
USP43	124739	hgsc.bcm.edu	37	17	9604775	9604775	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9604775A>G	ENST00000285199.7	+	12	1865	c.1769A>G	c.(1768-1770)aAa>aGa	p.K590R	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.K590R	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	590	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						ATCCACCTCAAAAGGTTCTGC	0.567																																					p.K590R		Atlas-SNP	.											.	USP43	65	.	0			c.A1769G						PASS	.						34.0	36.0	36.0					17																	9604775		2123	4249	6372	SO:0001583	missense	124739	exon12			ACCTCAAAAGGTT	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1769A>G	17.37:g.9604775A>G	ENSP00000285199:p.Lys590Arg	76.0	0.0	0		44.0	7.0	0.159091	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284577	0.80803	.	.	ENSG00000154914	ENST00000285199	T	0.39229	1.09	5.12	5.12	0.69794	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	H	0.94964	3.605	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	T	0.81026	-0.1119	10	0.87932	D	0	-15.7098	13.1508	0.59488	1.0:0.0:0.0:0.0	.	590;279;590;102	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	R	590	ENSP00000285199:K590R	ENSP00000285199:K590R	K	+	2	0	USP43	9545500	1.000000	0.71417	0.691000	0.30163	0.845000	0.48019	8.748000	0.91615	2.040000	0.60383	0.460000	0.39030	AAA	.	.	none		0.567	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
KLB	152831	hgsc.bcm.edu	37	4	39436192	39436192	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:39436192A>C	ENST00000257408.4	+	2	1285	c.1188A>C	c.(1186-1188)ttA>ttC	p.L396F		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	396	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						CACTTAATTTAAGAGAAGCGC	0.418																																					p.L396F		Atlas-SNP	.											.	KLB	95	.	0			c.A1188C						PASS	.						105.0	105.0	105.0					4																	39436192		2203	4300	6503	SO:0001583	missense	152831	exon2			TAATTTAAGAGAA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1188A>C	4.37:g.39436192A>C	ENSP00000257408:p.Leu396Phe	81.0	0.0	0		43.0	12.0	0.27907	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.283680	0.40394	.	.	ENSG00000134962	ENST00000257408	T	0.44482	0.92	6.06	-0.216	0.13153	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000001	T	0.52581	0.1743	L	0.49699	1.58	0.42547	D	0.993094	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.50030	-0.8875	10	0.56958	D	0.05	-15.1023	10.3696	0.44046	0.412:0.0:0.588:0.0	.	396;396	B7ZL50;Q86Z14	.;KLOTB_HUMAN	F	396	ENSP00000257408:L396F	ENSP00000257408:L396F	L	+	3	2	KLB	39112587	1.000000	0.71417	0.945000	0.38365	0.055000	0.15305	1.488000	0.35551	-0.025000	0.13918	-0.250000	0.11733	TTA	.	.	none		0.418	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
FNIP2	57600	hgsc.bcm.edu	37	4	159780274	159780274	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:159780274G>A	ENST00000264433.6	+	9	998	c.923G>A	c.(922-924)aGg>aAg	p.R308K	FNIP2_ENST00000379346.3_Missense_Mutation_p.R331K	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	308					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ATGGTTAGGAGGAAGAAAATT	0.403																																					p.R308K		Atlas-SNP	.											.	FNIP2	90	.	0			c.G923A						PASS	.						80.0	78.0	78.0					4																	159780274		1843	4097	5940	SO:0001583	missense	57600	exon9			TTAGGAGGAAGAA	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.923G>A	4.37:g.159780274G>A	ENSP00000264433:p.Arg308Lys	345.0	0.0	0		339.0	77.0	0.227139	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774472	0.49786	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346;ENST00000504715	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.51	5.51	0.81932	.	.	.	.	.	T	0.25382	0.0617	L	0.34521	1.04	0.53688	D	0.999978	B	0.29162	0.235	B	0.33890	0.172	T	0.03443	-1.1036	8	.	.	.	.	19.4099	0.94667	0.0:0.0:1.0:0.0	.	308	Q9P278	FNIP2_HUMAN	K	308;331;331;173	ENSP00000264433:R308K;ENSP00000421488:R331K;ENSP00000368651:R331K;ENSP00000420841:R173K	.	R	+	2	0	FNIP2	159999724	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.620000	0.61226	2.582000	0.87167	0.655000	0.94253	AGG	.	.	none		0.403	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
TBATA	219793	hgsc.bcm.edu	37	10	72534090	72534090	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72534090G>T	ENST00000299290.1	-	9	1185	c.796C>A	c.(796-798)Ctg>Atg	p.L266M	TBATA_ENST00000394982.2_5'Flank|TBATA_ENST00000456372.2_Silent_p.S238S	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	266					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											GCTGTCTGCAGGAGTCCCAGA	0.612																																					p.L266M		Atlas-SNP	.											.	.	.	.	0			c.C796A						PASS	.						47.0	46.0	46.0					10																	72534090		2203	4300	6503	SO:0001583	missense	219793	exon9			TCTGCAGGAGTCC	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"""chromosome 10 open reading frame 27"""	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.796C>A	10.37:g.72534090G>T	ENSP00000299290:p.Leu266Met	84.0	0.0	0		77.0	16.0	0.207792	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	37	CCDS7308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.85|14.85	2.659135|2.659135	0.47467|0.47467	.|.	.|.	ENSG00000166220|ENSG00000166220	ENST00000299290|ENST00000536955	T|.	0.24151|.	1.87|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.52532|.	D|.	0.000080|.	T|T	0.74635|0.74635	0.3742|0.3742	M|M	0.75447|0.75447	2.3|2.3	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.78290|0.78290	-0.2261|-0.2261	10|6	0.72032|0.87932	D|D	0.01|0	-13.863|-13.863	13.674|13.674	0.62443|0.62443	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265;267;266|.	B7ZMN4;B7ZMN5;Q96M53|.	.;.;SPATL_HUMAN|.	M|H	266|288	ENSP00000299290:L266M|.	ENSP00000299290:L266M|ENSP00000438618:P288H	L|P	-|-	1|2	2|0	C10orf27|C10orf27	72204096|72204096	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.193000|0.193000	0.23685|0.23685	3.298000|3.298000	0.51818|0.51818	2.298000|2.298000	0.77334|0.77334	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.	none		0.612	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710	
ATG4C	84938	hgsc.bcm.edu	37	1	63284834	63284834	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:63284834T>A	ENST00000317868.4	+	5	760	c.553T>A	c.(553-555)Tat>Aat	p.Y185N	ATG4C_ENST00000371120.3_Missense_Mutation_p.Y185N	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	185					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						AATTGGGAAATATTCTGATGA	0.363																																					p.Y185N		Atlas-SNP	.											.	ATG4C	96	.	0			c.T553A						PASS	.						106.0	113.0	111.0					1																	63284834		2203	4300	6503	SO:0001583	missense	84938	exon5			GGGAAATATTCTG	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.553T>A	1.37:g.63284834T>A	ENSP00000322159:p.Tyr185Asn	162.0	0.0	0		114.0	26.0	0.22807	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	T	10.07	1.249108	0.22880	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000371118	.	.	.	5.92	-1.03	0.10102	.	1.091040	0.06854	N	0.797869	T	0.09862	0.0242	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.26121	-1.0112	9	0.28530	T	0.3	-1.3461	1.7001	0.02870	0.1081:0.2507:0.2521:0.3891	.	185	Q96DT6	ATG4C_HUMAN	N	185	.	ENSP00000322159:Y185N	Y	+	1	0	ATG4C	63057422	0.000000	0.05858	0.003000	0.11579	0.952000	0.60782	0.067000	0.14510	0.136000	0.18733	0.528000	0.53228	TAT	.	.	none		0.363	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
GOLGA4	2803	hgsc.bcm.edu	37	3	37368710	37368710	+	Missense_Mutation	SNP	T	T	A	rs144205536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:37368710T>A	ENST00000361924.2	+	14	5707	c.5333T>A	c.(5332-5334)aTa>aAa	p.I1778K	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.I1800K	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1778	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GAGCGCTTAATAAAGCTAGAA	0.373													T|||	2	0.000399361	0.0	0.0	5008	,	,		20680	0.0		0.002	False		,,,				2504	0.0				p.I1800K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T5399A						PASS	.	T	LYS/ILE,LYS/ILE	1,4405	2.1+/-5.4	0,1,2202	98.0	100.0	99.0		5399,5333	-4.5	0.0	3	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	102,102	0,4,6499	AA,AT,TT		0.0349,0.0227,0.0308	benign,benign	1800/2244,1778/2231	37368710	4,13002	2203	4300	6503	SO:0001583	missense	2803	exon15			GCTTAATAAAGCT	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5333T>A	3.37:g.37368710T>A	ENSP00000354486:p.Ile1778Lys	150.0	0.0	0		106.0	52.0	0.490566	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	4.803	0.149256	0.09185	2.27E-4	3.49E-4	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.20332	2.08;2.08;2.08	4.59	-4.53	0.03462	.	0.710473	0.11563	N	0.551556	T	0.06917	0.0176	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.39840	-0.9594	10	0.06099	T	0.92	.	1.6064	0.02684	0.1664:0.2826:0.3456:0.2054	.	1778;1778;1800;1778	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	1778;1800;1649	ENSP00000354486:I1778K;ENSP00000349305:I1800K;ENSP00000405842:I1649K	ENSP00000349305:I1800K	I	+	2	0	GOLGA4	37343714	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	-0.047000	0.11963	-0.318000	0.08665	0.459000	0.35465	ATA	T|0.999;A|0.001	0.001	strong		0.373	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
PPP1R12A	4659	hgsc.bcm.edu	37	12	80199958	80199958	+	Missense_Mutation	SNP	C	C	G	rs61756418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:80199958C>G	ENST00000450142.2	-	13	2077	c.1811G>C	c.(1810-1812)gGc>gCc	p.G604A	PPP1R12A_ENST00000546369.1_Missense_Mutation_p.G517A|PPP1R12A_ENST00000550107.1_Intron|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.G604A|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.G604A|AC073569.1_ENST00000598624.1_Intron	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	604	Ser/Thr-rich.				centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						GCTTTGTGTGCCTGCTGAGGA	0.458													C|||	12	0.00239617	0.0008	0.0058	5008	,	,		18491	0.0		0.007	False		,,,				2504	0.0				p.G604A		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.G1811C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	3,3917		0,3,1957	290.0	274.0	279.0		1811,1550,1811	5.6	1.0	12	dbSNP_129	279	61,8257		0,61,4098	yes	missense,missense,missense	PPP1R12A	NM_001143885.1,NM_001143886.1,NM_002480.2	60,60,60	0,64,6055	GG,GC,CC		0.7333,0.0765,0.523	possibly-damaging,possibly-damaging,possibly-damaging	604/1031,517/944,604/1031	80199958	64,12174	1960	4159	6119	SO:0001583	missense	4659	exon13			TGTGTGCCTGCTG	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7618	protein-coding gene	gene with protein product	"""myosin phosphatase-targeting subunit 1"", ""myosin binding subunit"""	602021	"""protein phosphatase 1, regulatory (inhibitor) subunit 12A"""	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.1811G>C	12.37:g.80199958C>G	ENSP00000389168:p.Gly604Ala	91.0	0.0	0		118.0	51.0	0.432203	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	15.42|15.42	2.827657|2.827657	0.50845|0.50845	7.65E-4|7.65E-4	0.007333|0.007333	ENSG00000058272|ENSG00000058272	ENST00000553081|ENST00000261207;ENST00000546189;ENST00000360825;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000547330	.|T;T;T;T;T	.|0.36340	.|1.33;1.33;1.37;1.36;1.26	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.151958	.|0.64402	.|D	.|0.000009	T|T	0.33585|0.33585	0.0868|0.0868	L|L	0.31065|0.31065	0.9|0.9	0.44871|0.44871	D|D	0.997885|0.997885	.|P;D;P	.|0.56035	.|0.93;0.974;0.956	.|P;P;P	.|0.54499	.|0.459;0.754;0.572	T|T	0.03112|0.03112	-1.1071|-1.1071	5|10	.|0.20046	.|T	.|0.44	.|.	19.6432|19.6432	0.95764|0.95764	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61756418|rs61756418	.|604;604;604	.|F8W8Q6;O14974-2;O14974	.|.;.;MYPT1_HUMAN	P|A	196|604;604;604;604;604;604;517;604	.|ENSP00000261207:G604A;ENSP00000389168:G604A;ENSP00000416769:G604A;ENSP00000449514:G517A;ENSP00000446816:G604A	.|ENSP00000261207:G604A	A|G	-|-	1|2	0|0	PPP1R12A|PPP1R12A	78724089|78724089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.058000|3.058000	0.49939|0.49939	2.641000|2.641000	0.89580|0.89580	0.591000|0.591000	0.81541|0.81541	GCA|GGC	C|0.996;G|0.004	0.004	strong		0.458	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480	
SCRIB	23513	hgsc.bcm.edu	37	8	144875168	144875168	+	Missense_Mutation	SNP	G	G	A	rs202137464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144875168G>A	ENST00000320476.3	-	29	4001	c.3995C>T	c.(3994-3996)cCg>cTg	p.P1332L	SCRIB_ENST00000546337.1_5'UTR|RP11-429J17.8_ENST00000534089.1_RNA|SCRIB_ENST00000377533.3_Missense_Mutation_p.P1251L|SCRIB_ENST00000356994.2_Missense_Mutation_p.P1332L|RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000527139.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1332	Pro-rich.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-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;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ATCCTCAGGCGGGTGAGAAGT	0.716													G|||	10	0.00199681	0.0	0.0	5008	,	,		12252	0.0		0.008	False		,,,				2504	0.002				p.P1332L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3995T						PASS	.	G	LEU/PRO,LEU/PRO	9,4275		0,9,2133	15.0	16.0	15.0		3995,3995	2.2	0.0	8		15	62,8392		0,62,4165	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	98,98	0,71,6298	AA,AG,GG		0.7334,0.2101,0.5574	possibly-damaging,possibly-damaging	1332/1631,1332/1656	144875168	71,12667	2142	4227	6369	SO:0001583	missense	23513	exon29			TCAGGCGGGTGAG	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3995C>T	8.37:g.144875168G>A	ENSP00000322938:p.Pro1332Leu	100.0	0.0	0		110.0	83.0	0.754545	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	14.28	2.488712	0.44249	0.002101	0.007334	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.37411	1.41;1.36;1.2	4.17	2.25	0.28309	.	.	.	.	.	T	0.41442	0.1159	L	0.56769	1.78	0.09310	N	1	D;D;D	0.89917	0.998;0.999;1.0	P;P;D	0.91635	0.688;0.904;0.999	T	0.16719	-1.0393	9	0.42905	T	0.14	.	5.165	0.15081	0.1014:0.0:0.5328:0.3658	.	1332;1332;1251	Q14160;Q14160-3;Q14160-2	SCRIB_HUMAN;.;.	L	1332;1332;1251;701	ENSP00000349486:P1332L;ENSP00000322938:P1332L;ENSP00000366756:P1251L	ENSP00000322938:P1332L	P	-	2	0	SCRIB	144947156	0.955000	0.32602	0.040000	0.18447	0.028000	0.11728	1.498000	0.35660	0.693000	0.31634	0.195000	0.17529	CCG	G|0.998;A|0.002	0.002	strong		0.716	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
ZFP36L1	677	hgsc.bcm.edu	37	14	69256848	69256848	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69256848C>A	ENST00000439696.2	-	2	720	c.419G>T	c.(418-420)gGc>gTc	p.G140V	ZFP36L1_ENST00000555997.1_3'UTR|ZFP36L1_ENST00000336440.3_Missense_Mutation_p.G140V	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	140					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CTCGTGGATGCCGTGTGCGAA	0.647											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G209V		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G626T						PASS	.						96.0	91.0	93.0					14																	69256848		2203	4300	6503	SO:0001583	missense	677	exon3			TGGATGCCGTGTG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.419G>T	14.37:g.69256848C>A	ENSP00000388402:p.Gly140Val	158.0	0.0	0	1113	155.0	27.0	0.174194	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090153	0.76756	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000557086;ENST00000557022	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	4.69	4.69	0.59074	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.79209	0.4407	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86683	0.1918	10	0.87932	D	0	0.0068	17.8126	0.88620	0.0:1.0:0.0:0.0	.	140	Q07352	TISB_HUMAN	V	140;140;123;146;118	ENSP00000388402:G140V;ENSP00000337386:G140V;ENSP00000450784:G146V;ENSP00000450600:G118V	ENSP00000337386:G140V	G	-	2	0	ZFP36L1	68326601	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.563000	0.82314	2.423000	0.82170	0.585000	0.79938	GGC	.	.	none		0.647	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
DNAH17	8632	hgsc.bcm.edu	37	17	76490894	76490894	+	Silent	SNP	G	G	A	rs372912923		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76490894G>A	ENST00000585328.1	-	40	6160	c.6036C>T	c.(6034-6036)taC>taT	p.Y2012Y	DNAH17_ENST00000389840.5_Silent_p.Y2003Y|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2003	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GGCCCCAGTCGTAATGATCCT	0.672																																					p.Y2017Y		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6051T						PASS	.	G		0,4330		0,0,2165	18.0	21.0	20.0		6051	-2.0	0.9	17		20	9,8557		0,9,4274	no	coding-synonymous	DNAH17	NM_173628.3		0,9,6439	AA,AG,GG		0.1051,0.0,0.0698		2017/4463	76490894	9,12887	2165	4283	6448	SO:0001819	synonymous_variant	8632	exon40			CCAGTCGTAATGA	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6036C>T	17.37:g.76490894G>A		73.0	0.0	0		85.0	42.0	0.494118	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	weak		0.672	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
ITSN1	6453	hgsc.bcm.edu	37	21	35147359	35147359	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35147359A>C	ENST00000381318.3	+	14	1831	c.1543A>C	c.(1543-1545)Aaa>Caa	p.K515Q	ITSN1_ENST00000399353.1_Missense_Mutation_p.K478Q|ITSN1_ENST00000399352.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000379960.5_Missense_Mutation_p.K515Q|ITSN1_ENST00000399367.3_Missense_Mutation_p.K515Q|ITSN1_ENST00000399349.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000381291.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000437442.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399338.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000399355.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399326.3_Missense_Mutation_p.K515Q|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381285.4_Missense_Mutation_p.K515Q	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	515	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GAGCACAAACAAATCTAGAGA	0.368																																					p.K515Q		Atlas-SNP	.											.	ITSN1	166	.	0			c.A1543C						PASS	.						100.0	103.0	102.0					21																	35147359		2203	4300	6503	SO:0001583	missense	6453	exon14			ACAAACAAATCTA	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1543A>C	21.37:g.35147359A>C	ENSP00000370719:p.Lys515Gln	214.0	0.0	0		198.0	106.0	0.535354	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560779	0.45590	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.44881	1.53;0.93;1.0;0.93;1.53;1.53;1.0;1.53;1.53;1.53;1.53;0.91	5.07	5.07	0.68467	.	0.114374	0.56097	D	0.000026	T	0.38825	0.1055	L	0.27053	0.805	0.43936	D	0.996595	P;B;B;B;P;B;B;B;P;B	0.39352	0.539;0.397;0.068;0.264;0.669;0.296;0.245;0.245;0.542;0.397	B;B;B;B;B;B;B;B;P;B	0.45794	0.281;0.209;0.019;0.17;0.19;0.046;0.077;0.077;0.493;0.209	T	0.16660	-1.0395	10	0.31617	T	0.26	.	14.8326	0.70159	1.0:0.0:0.0:0.0	.	478;478;478;515;515;515;515;515;515;478	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	Q	478;515;515;515;515;515;515;515;515;515;515;515;515;515	ENSP00000382290:K478Q;ENSP00000370719:K515Q;ENSP00000370691:K515Q;ENSP00000370685:K515Q;ENSP00000382301:K515Q;ENSP00000382289:K515Q;ENSP00000382292:K515Q;ENSP00000382286:K515Q;ENSP00000382275:K515Q;ENSP00000387377:K515Q;ENSP00000382265:K515Q;ENSP00000369294:K515Q	ENSP00000369294:K515Q	K	+	1	0	ITSN1	34069229	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.956000	0.76013	1.910000	0.55303	0.482000	0.46254	AAA	.	.	none		0.368	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
FAM160A2	84067	hgsc.bcm.edu	37	11	6245256	6245256	+	Missense_Mutation	SNP	C	C	T	rs200289464		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6245256C>T	ENST00000449352.2	-	3	624	c.361G>A	c.(361-363)Gat>Aat	p.D121N	FAM160A2_ENST00000265978.4_Missense_Mutation_p.D121N|FAM160A2_ENST00000524416.1_Missense_Mutation_p.D121N			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	121					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCGACCCCATCCCCAAGCTCA	0.607																																					p.D121N		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G361A						PASS	.	C	ASN/ASP,ASN/ASP	0,4402		0,0,2201	54.0	46.0	48.0		361,361	4.1	1.0	11		48	3,8589	3.0+/-9.4	0,3,4293	yes	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	23,23	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	121/973,121/987	6245256	3,12991	2201	4296	6497	SO:0001583	missense	84067	exon3			CCCCATCCCCAAG		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.361G>A	11.37:g.6245256C>T	ENSP00000416918:p.Asp121Asn	77.0	0.0	0		97.0	17.0	0.175258	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392996	0.62066	0.0	3.49E-4	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.34472	1.36;1.36;1.36	5.05	4.14	0.48551	.	0.244954	0.28914	N	0.013721	T	0.35508	0.0934	N	0.14661	0.345	0.36163	D	0.84822	D;P;P	0.67145	0.996;0.611;0.557	D;B;B	0.66716	0.946;0.257;0.167	T	0.43877	-0.9364	10	0.48119	T	0.1	-17.8004	6.1565	0.20340	0.1851:0.7216:0.0:0.0933	.	121;121;121	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	N	121;46;121;121	ENSP00000416918:D121N;ENSP00000265978:D121N;ENSP00000431773:D121N	ENSP00000265978:D121N	D	-	1	0	FAM160A2	6201832	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.975000	0.49281	1.364000	0.46038	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	weak		0.607	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
RNF213	57674	hgsc.bcm.edu	37	17	78237572	78237572	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78237572T>C	ENST00000582970.1	+	2	235	c.92T>C	c.(91-93)aTa>aCa	p.I31T	RNF213_ENST00000508628.2_Missense_Mutation_p.I31T|RNF213_ENST00000456466.1_Missense_Mutation_p.I31T|RNF213_ENST00000319921.4_Missense_Mutation_p.I31T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	31					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCAGCCCCCATAGCAGGTGAG	0.642																																					p.I31T		Atlas-SNP	.											.	RNF213	766	.	0			c.T92C						PASS	.						39.0	41.0	40.0					17																	78237572		2203	4300	6503	SO:0001583	missense	57674	exon2			CCCCCATAGCAGG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.92T>C	17.37:g.78237572T>C	ENSP00000464087:p.Ile31Thr	98.0	0.0	0		90.0	4.0	0.0444444	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	8.002	0.755608	0.15846	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T	0.22743	1.94	3.71	-6.01	0.02199	.	.	.	.	.	T	0.07188	0.0182	N	0.08118	0	0.09310	N	0.999995	B	0.21452	0.056	B	0.18263	0.021	T	0.28202	-1.0051	9	0.46703	T	0.11	.	0.4433	0.00489	0.2848:0.2872:0.1455:0.2825	.	31	Q9HCF4-2	.	T	31	ENSP00000425956:I31T	ENSP00000324392:I31T	I	+	2	0	RNF213	75852167	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-3.408000	0.00481	-1.514000	0.01786	0.460000	0.39030	ATA	.	.	none		0.642	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
MYBL2	4605	hgsc.bcm.edu	37	20	42338621	42338621	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42338621G>C	ENST00000217026.4	+	10	1651	c.1524G>C	c.(1522-1524)caG>caC	p.Q508H	MYBL2_ENST00000396863.4_Missense_Mutation_p.Q484H	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	508					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCCCAGATCAGAAGTACTCCA	0.622																																					p.Q508H		Atlas-SNP	.											.	MYBL2	82	.	0			c.G1524C						PASS	.						211.0	213.0	212.0					20																	42338621		2203	4300	6503	SO:0001583	missense	4605	exon10			AGATCAGAAGTAC		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1524G>C	20.37:g.42338621G>C	ENSP00000217026:p.Gln508His	85.0	0.0	0		63.0	25.0	0.396825	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289002	0.40494	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.28069	1.63;1.63	4.86	4.86	0.63082	C-myb, C-terminal (1);	0.198115	0.46442	D	0.000282	T	0.09774	0.0240	N	0.00926	-1.1	0.40656	D	0.982083	B;B	0.33637	0.287;0.42	B;B	0.31686	0.078;0.134	T	0.30707	-0.9969	10	0.11794	T	0.64	-30.2082	12.2911	0.54819	0.0:0.0:0.8302:0.1697	.	484;508	F8W6N6;P10244	.;MYBB_HUMAN	H	484;508	ENSP00000380072:Q484H;ENSP00000217026:Q508H	ENSP00000217026:Q508H	Q	+	3	2	MYBL2	41772035	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.551000	0.60740	2.427000	0.82271	0.467000	0.42956	CAG	.	.	none		0.622	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
UFC1	51506	hgsc.bcm.edu	37	1	161123901	161123901	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161123901C>G	ENST00000368003.5	+	1	360	c.114C>G	c.(112-114)tcC>tcG	p.S38S	UFC1_ENST00000473766.1_3'UTR|RP11-297K8.2_ENST00000420498.1_RNA	NM_016406.3	NP_057490.2	Q9Y3C8	UFC1_HUMAN	ubiquitin-fold modifier conjugating enzyme 1	38					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	extracellular vesicular exosome (GO:0070062)	UFM1 conjugating enzyme activity (GO:0071568)			endometrium(1)|lung(9)	10	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AATATCAGTCCCTTATCCGGG	0.537																																					p.S38S		Atlas-SNP	.											.	UFC1	16	.	0			c.C114G						PASS	.						179.0	157.0	165.0					1																	161123901		2203	4300	6503	SO:0001819	synonymous_variant	51506	exon1			TCAGTCCCTTATC	AF161504	CCDS1220.1	1q23.3	2008-02-05			ENSG00000143222	ENSG00000143222			26941	protein-coding gene	gene with protein product		610554				15071506, 11042152	Standard	NM_016406		Approved	HSPC155	uc001fyd.4	Q9Y3C8	OTTHUMG00000033155	ENST00000368003.5:c.114C>G	1.37:g.161123901C>G		123.0	0.0	0		96.0	11.0	0.114583	NM_016406	A8K9R1|D3DVF9|Q549X0|Q5VTX1|Q9BS96|Q9P009	Silent	SNP	ENST00000368003.5	37	CCDS1220.1																																																																																			.	.	none		0.537	UFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080810.1	NM_016406	
ARSF	416	hgsc.bcm.edu	37	X	3021870	3021870	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:3021870G>T	ENST00000381127.1	+	9	1391	c.1170G>T	c.(1168-1170)aaG>aaT	p.K390N	ARSF_ENST00000359361.2_Missense_Mutation_p.K390N|ARSF_ENST00000537104.1_Missense_Mutation_p.K390N	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	390					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCCTGGAAAGGTACCAGCTG	0.473																																					p.K390N		Atlas-SNP	.											.	ARSF	97	.	0			c.G1170T						PASS	.						101.0	92.0	95.0					X																	3021870		2203	4300	6503	SO:0001583	missense	416	exon9			TGGAAAGGTACCA	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1170G>T	X.37:g.3021870G>T	ENSP00000370519:p.Lys390Asn	248.0	0.0	0		152.0	152.0	1	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268921	0.23221	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.98684	-5.07;-5.07;-5.07	3.4	-1.61	0.08399	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.484707	0.19510	U	0.112538	D	0.96414	0.8830	L	0.61387	1.9	0.09310	N	1	B	0.20671	0.047	B	0.32090	0.14	D	0.89916	0.4055	10	0.16896	T	0.51	.	6.4355	0.21821	0.2735:0.1278:0.5988:0.0	.	390	P54793	ARSF_HUMAN	N	390	ENSP00000370519:K390N;ENSP00000445594:K390N;ENSP00000352319:K390N	ENSP00000352319:K390N	K	+	3	2	ARSF	3031870	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-1.019000	0.03622	-0.569000	0.06030	0.279000	0.19357	AAG	.	.	none		0.473	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
C2orf16	84226	hgsc.bcm.edu	37	2	27804547	27804547	+	Missense_Mutation	SNP	G	G	A	rs201164610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27804547G>A	ENST00000408964.2	+	1	5159	c.5108G>A	c.(5107-5109)cGt>cAt	p.R1703H	ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000416005.2_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1703	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGGAGCCATCGTGGTCCCTCT	0.587													g|||	16	0.00319489	0.0	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0164				p.R1703H		Atlas-SNP	.											.	C2orf16	357	.	0			c.G5108A						PASS	.						156.0	159.0	158.0					2																	27804547		1929	4134	6063	SO:0001583	missense	84226	exon1			GCCATCGTGGTCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5108G>A	2.37:g.27804547G>A	ENSP00000386190:p.Arg1703His	65.0	0.0	0		72.0	24.0	0.333333	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	g	8.649	0.897869	0.17686	.	.	ENSG00000221843	ENST00000408964	T	0.05447	3.44	3.34	-4.16	0.03869	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.09310	N	1	B	0.32800	0.385	B	0.21708	0.036	T	0.39921	-0.9590	9	0.33940	T	0.23	.	0.1461	0.00088	0.2733:0.2564:0.2106:0.2596	.	1703	Q68DN1	CB016_HUMAN	H	1703	ENSP00000386190:R1703H	ENSP00000386190:R1703H	R	+	2	0	C2orf16	27658051	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.454000	0.01004	-1.009000	0.03400	-1.402000	0.01139	CGT	G|0.999;A|0.001	0.001	weak		0.587	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
ZNF189	7743	hgsc.bcm.edu	37	9	104170796	104170796	+	Missense_Mutation	SNP	A	A	T	rs370077009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104170796A>T	ENST00000339664.2	+	3	875	c.746A>T	c.(745-747)aAa>aTa	p.K249I	ZNF189_ENST00000259395.4_Missense_Mutation_p.K207I|ZNF189_ENST00000374861.3_Missense_Mutation_p.K235I	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	249					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AGCCTTGTTAAACATCAAAGG	0.423																																					p.K249I		Atlas-SNP	.											.	ZNF189	79	.	0			c.A746T						PASS	.	A	ILE/LYS,ILE/LYS	0,4406		0,0,2203	183.0	188.0	186.0		746,620	4.7	1.0	9		186	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ZNF189	NM_003452.2,NM_197977.1	102,102	0,2,6501	TT,TA,AA		0.0233,0.0,0.0154	benign,benign	249/627,207/585	104170796	2,13004	2203	4300	6503	SO:0001583	missense	7743	exon3			TTGTTAAACATCA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.746A>T	9.37:g.104170796A>T	ENSP00000342019:p.Lys249Ile	65.0	0.0	0		46.0	27.0	0.586957	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	8.404	0.842724	0.16963	0.0	2.33E-4	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.20598	2.06;2.06;2.06	4.67	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000079	T	0.12689	0.0308	L	0.28649	0.875	0.31428	N	0.67353	P;B;P	0.43314	0.803;0.136;0.507	B;B;B	0.37304	0.246;0.032;0.205	T	0.06917	-1.0800	10	0.30078	T	0.28	.	7.1431	0.25566	0.9035:0.0:0.0965:0.0	.	234;235;249	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	I	235;249;207	ENSP00000363995:K235I;ENSP00000342019:K249I;ENSP00000259395:K207I	ENSP00000259395:K207I	K	+	2	0	ZNF189	103210617	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-2.494000	0.00972	2.324000	0.78689	0.533000	0.62120	AAA	.	.	weak		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
ZMIZ1	57178	hgsc.bcm.edu	37	10	81053248	81053248	+	Silent	SNP	G	G	A	rs146995829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:81053248G>A	ENST00000334512.5	+	12	1640	c.1068G>A	c.(1066-1068)acG>acA	p.T356T	ZMIZ1_ENST00000478357.1_3'UTR	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	356	Pro-rich.				artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CTGGCATGACGCCCTCGGGGA	0.701													G|||	26	0.00519169	0.0	0.0029	5008	,	,		10851	0.0		0.0129	False		,,,				2504	0.0112				p.T356T		Atlas-SNP	.											ZMIZ1,NS,carcinoma,+1,1	ZMIZ1	101	1	0			c.G1068A						PASS	.	G		9,4379		0,9,2185	31.0	41.0	38.0		1068	-9.8	0.9	10	dbSNP_134	38	88,8482		0,88,4197	no	coding-synonymous	ZMIZ1	NM_020338.3		0,97,6382	AA,AG,GG		1.0268,0.2051,0.7486		356/1068	81053248	97,12861	2194	4285	6479	SO:0001819	synonymous_variant	57178	exon12			CATGACGCCCTCG	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1068G>A	10.37:g.81053248G>A		29.0	0.0	0		32.0	13.0	0.40625	NM_020338	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
REV3L	5980	hgsc.bcm.edu	37	6	111631254	111631254	+	Silent	SNP	T	T	C	rs150392515		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:111631254T>C	ENST00000358835.3	-	31	9298	c.8844A>G	c.(8842-8844)cgA>cgG	p.R2948R	RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000435970.1_Silent_p.R2870R|REV3L_ENST00000368805.1_Silent_p.R2948R|REV3L_ENST00000368802.3_Silent_p.R2948R|REV3L_ENST00000462119.1_5'UTR			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2948					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CGTATGGCACTCGCTCCCCAA	0.498								DNA polymerases (catalytic subunits)																													p.R2948R		Atlas-SNP	.											REV3L,NS,carcinoma,-2,1	REV3L	386	1	0			c.A8844G						PASS	.	T		0,4406		0,0,2203	74.0	76.0	75.0		8844	0.2	1.0	6	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	REV3L	NM_002912.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		2948/3131	111631254	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon30			TGGCACTCGCTCC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8844A>G	6.37:g.111631254T>C		40.0	0.0	0		31.0	15.0	0.483871	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			T|1.000;C|0.000	0.000	weak		0.498	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
UNC45A	55898	hgsc.bcm.edu	37	15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	rs149872991		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	RCCD1_ENST00000394258.2_5'Flank|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000556618.1_5'Flank|RCCD1_ENST00000555155.1_5'Flank|AC068831.6_ENST00000553321.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83.0	62.0	69.0		2333,2378	4.9	1.0	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	73.0	0.0	0		74.0	48.0	0.648649	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
HLA-A	3105	hgsc.bcm.edu	37	6	29910551	29910551	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910551T>G	ENST00000396634.1	+	4	432	c.91T>G	c.(91-93)Tat>Gat	p.Y31D	HLA-A_ENST00000376802.2_Missense_Mutation_p.Y31D|HLA-A_ENST00000376809.5_Missense_Mutation_p.Y31D|HLA-A_ENST00000376806.5_Missense_Mutation_p.Y31D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	31	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CTCCATGAGGTATTTCTTCAC	0.726									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.Y31D		Atlas-SNP	.											.	HLA-A	89	.	0			c.T91G						PASS	.						15.0	14.0	15.0					6																	29910551		2179	4262	6441	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATGAGGTATTTCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.91T>G	6.37:g.29910551T>G	ENSP00000379873:p.Tyr31Asp	25.0	0.0	0		33.0	15.0	0.454545	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.530	1.110553	0.20714	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	3.72	2.49	0.30216	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.275088	0.19018	U	0.124883	T	0.19087	0.0458	H	0.99999	5.785	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.48115	-0.9063	10	0.87932	D	0	.	6.2298	0.20728	0.2235:0.0:0.0:0.7765	.	31;31;31;31;31	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	D	31	ENSP00000379873:Y31D;ENSP00000366002:Y31D;ENSP00000366005:Y31D;ENSP00000365998:Y31D	ENSP00000348012:Y31D	Y	+	1	0	HLA-A	30018530	0.000000	0.05858	0.020000	0.16555	0.261000	0.26267	0.438000	0.21559	0.583000	0.29574	0.391000	0.25812	TAT	.	.	none		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SLC29A4	222962	hgsc.bcm.edu	37	7	5339049	5339049	+	Silent	SNP	C	C	T	rs142638970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:5339049C>T	ENST00000396872.3	+	9	1361	c.1200C>T	c.(1198-1200)ttC>ttT	p.F400F	SLC29A4_ENST00000439491.2_3'UTR|SLC29A4_ENST00000406453.3_Silent_p.F386F|SLC29A4_ENST00000297195.4_Silent_p.F400F			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	400					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	TGTCAGACTTCGTGGGCAAGG	0.657													C|||	3	0.000599042	0.0015	0.0	5008	,	,		18164	0.0		0.001	False		,,,				2504	0.0				p.F400F		Atlas-SNP	.											.	SLC29A4	52	.	0			c.C1200T						PASS	.	C	,	4,4402		0,4,2199	49.0	37.0	41.0		1200,1200	0.2	1.0	7	dbSNP_134	41	53,8543		0,53,4245	no	coding-synonymous,coding-synonymous	SLC29A4	NM_001040661.1,NM_153247.2	,	0,57,6444	TT,TC,CC		0.6166,0.0908,0.4384	,	400/531,400/531	5339049	57,12945	2203	4298	6501	SO:0001819	synonymous_variant	222962	exon9			AGACTTCGTGGGC	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"""Solute carriers"""	23097	protein-coding gene	gene with protein product		609149	"""solute carrier family 29 (nucleoside transporters), member 4"""			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.1200C>T	7.37:g.5339049C>T		138.0	0.0	0		124.0	99.0	0.798387	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	CCDS5340.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247	
SLC25A13	10165	hgsc.bcm.edu	37	7	95761057	95761057	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95761057G>A	ENST00000265631.5	-	15	1725	c.1589C>T	c.(1588-1590)gCt>gTt	p.A530V	SLC25A13_ENST00000416240.2_Missense_Mutation_p.A531V|SLC25A13_ENST00000542654.1_Missense_Mutation_p.A422V			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	530					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	ACACTCACCAGCTATGGCACC	0.507																																					p.A531V		Atlas-SNP	.											.	SLC25A13	131	.	0			c.C1592T						PASS	.						76.0	68.0	70.0					7																	95761057		2203	4300	6503	SO:0001583	missense	10165	exon15			TCACCAGCTATGG	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1589C>T	7.37:g.95761057G>A	ENSP00000265631:p.Ala530Val	123.0	0.0	0		104.0	49.0	0.471154	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127249	0.94473	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	D;D;D	0.87256	-2.23;-2.23;-2.23	4.65	4.65	0.58169	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94719	0.8296	M	0.90252	3.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.95624	0.8683	10	0.87932	D	0	-12.4191	18.1095	0.89530	0.0:0.0:1.0:0.0	.	422;531;530	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	V	530;531;422	ENSP00000265631:A530V;ENSP00000400101:A531V;ENSP00000440484:A422V	ENSP00000265631:A530V	A	-	2	0	SLC25A13	95598993	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.657000	0.98554	2.599000	0.87857	0.655000	0.94253	GCT	.	.	none		0.507	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
NEK3	4752	hgsc.bcm.edu	37	13	52710320	52710320	+	Missense_Mutation	SNP	T	T	C	rs371075629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52710320T>C	ENST00000400357.2	-	11	2348	c.1055A>G	c.(1054-1056)aAt>aGt	p.N352S	NEK3_ENST00000452082.2_Missense_Mutation_p.N373S|NEK3_ENST00000339406.3_Missense_Mutation_p.N369S|NEK3_ENST00000378101.2_Missense_Mutation_p.N369S			P51956	NEK3_HUMAN	NIMA-related kinase 3	369					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		AAGAGCTGTATTGGGTACATT	0.378																																					p.N369S		Atlas-SNP	.											.	NEK3	41	.	0			c.A1106G						PASS	.	T	SER/ASN,SER/ASN	0,3738		0,0,1869	160.0	153.0	156.0		1055,1105	-11.1	0.0	13		156	1,8193		0,1,4096	no	missense,missense	NEK3	NM_001146099.1,NM_152720.2	46,46	0,1,5965	CC,CT,TT		0.0122,0.0,0.0084	benign,benign	352/490,369/507	52710320	1,11931	1869	4097	5966	SO:0001583	missense	4752	exon13			GCTGTATTGGGTA	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1055A>G	13.37:g.52710320T>C	ENSP00000383210:p.Asn352Ser	232.0	0.0	0		230.0	97.0	0.421739	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	T	2.579	-0.297749	0.05532	0.0	1.22E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.70631	-0.34;-0.34;-0.5;-0.36;-0.34	5.57	-11.1	0.00147	.	0.832180	0.11642	N	0.543642	T	0.32882	0.0844	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.31110	-0.9955	10	0.07175	T	0.84	.	9.6098	0.39657	0.0:0.2182:0.255:0.5268	.	369;373;346	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	S	369;369;352;373;346	ENSP00000339429:N369S;ENSP00000367341:N369S;ENSP00000383210:N352S;ENSP00000404197:N373S;ENSP00000448716:N346S	ENSP00000339429:N369S	N	-	2	0	NEK3	51608321	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.293000	0.01145	-2.658000	0.00420	-0.290000	0.09829	AAT	.	.	weak		0.378	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
UBR4	23352	hgsc.bcm.edu	37	1	19447882	19447882	+	Silent	SNP	G	G	A	rs34710232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19447882G>A	ENST00000375254.3	-	68	9969	c.9942C>T	c.(9940-9942)ggC>ggT	p.G3314G	UBR4_ENST00000375267.2_Silent_p.G3314G|UBR4_ENST00000375226.2_Silent_p.G3290G|UBR4_ENST00000375218.3_5'Flank|UBR4_ENST00000375217.2_Silent_p.G3307G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3314					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CTGGGGACACGCCCTCATCCA	0.592													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		15686	0.0		0.0159	False		,,,				2504	0.0031				p.G3314G		Atlas-SNP	.											UBR4,right_upper_lobe,carcinoma,-1,1	UBR4	415	1	0			c.C9942T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	73.0	66.0	68.0		9942	-6.2	0.9	1	dbSNP_126	68	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	UBR4	NM_020765.2		0,71,6432	AA,AG,GG		0.7442,0.1589,0.5459		3314/5184	19447882	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon68			GGACACGCCCTCA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.9942C>T	1.37:g.19447882G>A		360.0	1.0	0.00277778		329.0	175.0	0.531915	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.996;A|0.004	0.004	strong		0.592	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ENG	2022	hgsc.bcm.edu	37	9	130586661	130586661	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130586661C>T	ENST00000373203.4	-	8	1456	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	RP11-228B15.4_ENST00000425991.1_RNA|ENG_ENST00000344849.3_Silent_p.P352P|ENG_ENST00000480266.1_5'UTR|RP11-228B15.4_ENST00000439298.1_RNA	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	352	Ser/Thr-rich.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)	p.P352P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						TGAGCAGCTCCGGGCTACAAG	0.597									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.P352P		Atlas-SNP	.											ENG,NS,carcinoma,0,1	ENG	44	1	1	Substitution - coding silent(1)	lung(1)	c.G1056A						scavenged	.						142.0	116.0	125.0					9																	130586661		2203	4300	6503	SO:0001819	synonymous_variant	2022	exon8	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	CAGCTCCGGGCTA	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.1056G>A	9.37:g.130586661C>T		154.0	1.0	0.00649351		116.0	56.0	0.482759	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																			.	.	none		0.597	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
GABRG3	2567	hgsc.bcm.edu	37	15	27765249	27765249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27765249A>G	ENST00000333743.6	+	7	1098	c.844A>G	c.(844-846)Acg>Gcg	p.T282A	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	282					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAAAGATGCTACGCCAGCAAG	0.348																																					p.T282A	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A844G						PASS	.						63.0	59.0	60.0					15																	27765249		1840	4106	5946	SO:0001583	missense	2567	exon7			GATGCTACGCCAG		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.844A>G	15.37:g.27765249A>G	ENSP00000331912:p.Thr282Ala	102.0	0.0	0		99.0	4.0	0.040404	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.264631	0.40095	.	.	ENSG00000182256	ENST00000333743;ENST00000554696	D;D	0.86097	-2.07;-2.07	5.39	5.39	0.77823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.101026	0.64402	D	0.000002	T	0.72946	0.3524	N	0.13168	0.305	0.80722	D	1	B	0.20780	0.048	B	0.28305	0.088	T	0.67448	-0.5668	10	0.25751	T	0.34	.	9.2407	0.37495	0.9204:0.0:0.0795:0.0	.	282	Q99928	GBRG3_HUMAN	A	282;224	ENSP00000331912:T282A;ENSP00000451862:T224A	ENSP00000331912:T282A	T	+	1	0	GABRG3	25438844	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.888000	0.63164	2.260000	0.74910	0.528000	0.53228	ACG	.	.	none		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
NUTM1	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K|NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76.0	61.0	66.0		3043	4.3	1.0	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	55.0	0.0	0		52.0	27.0	0.519231	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
BSN	8927	hgsc.bcm.edu	37	3	49693972	49693972	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49693972C>T	ENST00000296452.4	+	5	7097	c.6983C>T	c.(6982-6984)cCt>cTt	p.P2328L		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2328					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCCCCAGCTCCTGCCCCACTA	0.652																																					p.P2328L		Atlas-SNP	.											.	BSN	272	.	0			c.C6983T						PASS	.						8.0	9.0	9.0					3																	49693972		2177	4270	6447	SO:0001583	missense	8927	exon5			CAGCTCCTGCCCC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.6983C>T	3.37:g.49693972C>T	ENSP00000296452:p.Pro2328Leu	62.0	0.0	0		45.0	18.0	0.4	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	3.630	-0.075656	0.07184	.	.	ENSG00000164061	ENST00000296452	T	0.17370	2.28	5.38	5.38	0.77491	.	0.902375	0.09734	N	0.762721	T	0.14013	0.0339	N	0.24115	0.695	0.53688	D	0.999974	B	0.27559	0.181	B	0.21708	0.036	T	0.11348	-1.0591	10	0.30854	T	0.27	-0.369	14.5099	0.67776	0.0:1.0:0.0:0.0	.	2328	Q9UPA5	BSN_HUMAN	L	2328	ENSP00000296452:P2328L	ENSP00000296452:P2328L	P	+	2	0	BSN	49668976	0.002000	0.14202	0.055000	0.19348	0.331000	0.28603	1.786000	0.38694	2.813000	0.96785	0.655000	0.94253	CCT	.	.	none		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
PRR21	643905	hgsc.bcm.edu	37	2	240982379	240982379	+	Silent	SNP	T	T	C	rs138056768		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982379T>C	ENST00000408934.1	-	1	20	c.21A>G	c.(19-21)acA>acG	p.T7T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	7										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GATGAAGAGCTGTGGATGAAC	0.572																																					p.T7T		Atlas-SNP	.											.	PRR21	53	.	0			c.A21G						PASS	.						78.0	66.0	70.0					2																	240982379		2185	4279	6464	SO:0001819	synonymous_variant	643905	exon1			AAGAGCTGTGGAT	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.21A>G	2.37:g.240982379T>C		33.0	0.0	0		18.0	9.0	0.5	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			T|0.989;C|0.011	0.011	strong		0.572	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617472	28617472	+	Missense_Mutation	SNP	G	G	A	rs150459557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28617472G>A	ENST00000395607.1	-	7	953	c.680C>T	c.(679-681)aCg>aTg	p.T227M	SULT1A1_ENST00000314752.7_Missense_Mutation_p.T227M|SULT1A1_ENST00000395609.1_Missense_Mutation_p.T227M|SULT1A1_ENST00000350842.4_Missense_Mutation_p.T149M|SULT1A1_ENST00000569554.1_Missense_Mutation_p.T227M	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	227					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.T149M(1)|p.T227M(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	CTTGAACGACGTGTGCTGAAC	0.557													.|||	6	0.00119808	0.0	0.0014	5008	,	,		16587	0.0		0.005	False		,,,				2504	0.0				p.T227M		Atlas-SNP	.											SULT1A1,NS,carcinoma,0,1	SULT1A1	53	1	2	Substitution - Missense(2)	endometrium(2)	c.C680T						scavenged	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	3,4391	4.2+/-10.8	0,3,2194	119.0	64.0	82.0		680,680,680,680,446	2.2	0.1	16	dbSNP_134	82	35,8559	21.6+/-65.8	0,35,4262	no	missense,missense,missense,missense,missense	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	81,81,81,81,81	0,38,6456	AA,AG,GG		0.4073,0.0683,0.2926	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	227/296,227/296,227/296,227/296,149/218	28617472	38,12950	2197	4297	6494	SO:0001583	missense	6817	exon6			AACGACGTGTGCT	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.680C>T	16.37:g.28617472G>A	ENSP00000378971:p.Thr227Met	277.0	2.0	0.00722022		456.0	114.0	0.25	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	g	9.434	1.086340	0.20390	6.83E-4	0.004073	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64	2.18	2.18	0.27775	Sulfotransferase domain (1);	0.080875	0.51477	D	0.000090	D	0.91355	0.7273	M	0.91920	3.255	0.24615	N	0.993706	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.82684	-0.0335	10	0.87932	D	0	.	10.4847	0.44715	0.0:0.0:1.0:0.0	.	179;149;227	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	M	227;149;227;227	ENSP00000321988:T227M;ENSP00000329399:T149M;ENSP00000378972:T227M;ENSP00000378971:T227M	ENSP00000321988:T227M	T	-	2	0	SULT1A1	28524973	0.991000	0.36638	0.060000	0.19600	0.064000	0.16182	2.688000	0.46984	1.559000	0.49555	0.306000	0.20318	ACG	G|0.998;A|0.002	0.002	strong		0.557	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
CST4	1472	hgsc.bcm.edu	37	20	23667738	23667738	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23667738G>C	ENST00000217423.3	-	2	399	c.329C>G	c.(328-330)cCa>cGa	p.P110R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	110					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CTGCAGTTCTGGCTGTTCATG	0.572																																					p.P110R		Atlas-SNP	.											.	CST4	37	.	0			c.C329G						PASS	.						207.0	168.0	181.0					20																	23667738		2203	4300	6503	SO:0001583	missense	1472	exon2			AGTTCTGGCTGTT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.329C>G	20.37:g.23667738G>C	ENSP00000217423:p.Pro110Arg	242.0	0.0	0		194.0	37.0	0.190722	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165362	0.38217	.	.	ENSG00000101441	ENST00000217423	T	0.14516	2.5	1.51	0.516	0.17019	Proteinase inhibitor I25, cystatin (2);	0.298786	0.30959	U	0.008521	T	0.33118	0.0852	M	0.87682	2.9	0.09310	N	0.999999	D	0.69078	0.997	D	0.80764	0.994	T	0.08617	-1.0713	10	0.87932	D	0	.	3.9044	0.09176	0.2423:0.0:0.7577:0.0	.	110	P01036	CYTS_HUMAN	R	110	ENSP00000217423:P110R	ENSP00000217423:P110R	P	-	2	0	CST4	23615738	0.017000	0.18338	0.006000	0.13384	0.644000	0.38419	-0.007000	0.12810	0.190000	0.20209	0.205000	0.17691	CCA	.	.	none		0.572	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
SLC5A9	200010	hgsc.bcm.edu	37	1	48705066	48705066	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:48705066G>A	ENST00000438567.2	+	12	1586	c.1534G>A	c.(1534-1536)Gcg>Acg	p.A512T	SLC5A9_ENST00000236495.5_Missense_Mutation_p.A537T|SLC5A9_ENST00000533824.1_Missense_Mutation_p.A533T	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	512					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CTCATACCCAGCGCCAGCCTG	0.597																																					p.A537T		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1609A						PASS	.						172.0	163.0	166.0					1																	48705066		2203	4300	6503	SO:0001583	missense	200010	exon13			TACCCAGCGCCAG	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1534G>A	1.37:g.48705066G>A	ENSP00000401730:p.Ala512Thr	230.0	1.0	0.00434783		194.0	87.0	0.448454	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320633	0.23994	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.63096	-0.02;-0.02;-0.02	5.18	5.18	0.71444	.	0.458166	0.26086	N	0.026430	T	0.41488	0.1161	N	0.11673	0.155	0.29064	N	0.883691	B;B;B	0.19445	0.036;0.005;0.009	B;B;B	0.13407	0.007;0.009;0.009	T	0.07520	-1.0768	10	0.06757	T	0.87	.	17.85	0.88744	0.0:0.0:1.0:0.0	.	533;512;537	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	T	533;512;537	ENSP00000431900:A533T;ENSP00000401730:A512T;ENSP00000236495:A537T	ENSP00000236495:A537T	A	+	1	0	SLC5A9	48477653	0.000000	0.05858	0.855000	0.33649	0.575000	0.36095	0.380000	0.20602	2.682000	0.91365	0.650000	0.86243	GCG	.	.	none		0.597	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
CD200R1	131450	hgsc.bcm.edu	37	3	112648107	112648107	+	Silent	SNP	G	G	A	rs373257099		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112648107G>A	ENST00000471858.1	-	3	613	c.381C>T	c.(379-381)gaC>gaT	p.D127D	CD200R1_ENST00000308611.3_Silent_p.D150D|CD200R1_ENST00000440122.2_Silent_p.D150D|CD200R1_ENST00000490004.1_Silent_p.D127D|CD200R1_ENST00000295863.4_Silent_p.D105D	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	127	Ig-like V-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTAATACCCGTCATGAGTGA	0.443													g|||	1	0.000199681	0.0	0.0	5008	,	,		20605	0.0		0.0	False		,,,				2504	0.001				p.D150D		Atlas-SNP	.											CD200R1_ENST00000440122,NS,carcinoma,0,2	CD200R1	91	2	0			c.C450T						PASS	.	A	,,,	0,4406		0,0,2203	164.0	156.0	159.0		450,450,381,381	-10.9	0.2	3		159	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	150/349,150/189,127/166,127/326	112648107	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon4			ATACCCGTCATGA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.381C>T	3.37:g.112648107G>A		302.0	0.0	0		244.0	108.0	0.442623	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			.	.	weak		0.443	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100465824G>A	ENST00000200457.4	+	3	692	c.332G>A	c.(331-333)cGg>cAg	p.R111Q		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	111			R -> Q (in dbSNP:rs2437100). {ECO:0000269|PubMed:15489334}.		focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					AATGGGGGTCGGGGTCATGCG	0.672													G|||	32	0.00638978	0.0008	0.0058	5008	,	,		14361	0.0		0.0268	False		,,,				2504	0.0				p.R111Q		Atlas-SNP	.											.	TRIP6	45	.	0			c.G332A						PASS	.	G	GLN/ARG	21,4385	29.0+/-57.7	0,21,2182	41.0	41.0	41.0		332	4.5	0.8	7	dbSNP_100	41	176,8424	80.6+/-143.3	1,174,4125	yes	missense	TRIP6	NM_003302.2	43	1,195,6307	AA,AG,GG		2.0465,0.4766,1.5147	probably-damaging	111/477	100465824	197,12809	2203	4300	6503	SO:0001583	missense	7205	exon3			GGGGTCGGGGTCA	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.332G>A	7.37:g.100465824G>A	ENSP00000200457:p.Arg111Gln	55.0	0.0	0		50.0	22.0	0.44	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	26	0.011904761904761904	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	23	0.030343007915567283	G	18.42	3.619897	0.66787	0.004766	0.020465	ENSG00000087077	ENST00000200457	T	0.59502	0.26	4.53	4.53	0.55603	.	0.374538	0.26931	N	0.021774	T	0.33089	0.0851	L	0.47716	1.5	0.28405	N	0.918477	D	0.69078	0.997	P	0.53518	0.728	T	0.40646	-0.9552	10	0.11794	T	0.64	.	12.7393	0.57241	0.0:0.0:1.0:0.0	rs2437100	111	Q15654	TRIP6_HUMAN	Q	111	ENSP00000200457:R111Q	ENSP00000200457:R111Q	R	+	2	0	TRIP6	100303760	0.997000	0.39634	0.757000	0.31301	0.054000	0.15201	3.870000	0.56070	2.074000	0.62210	0.455000	0.32223	CGG	G|0.985;A|0.015	0.015	strong		0.672	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
HNRNPA1L2	144983	hgsc.bcm.edu	37	13	53216666	53216666	+	Silent	SNP	G	G	A	rs113869751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:53216666G>A	ENST00000357495.2	+	1	99	c.39G>A	c.(37-39)ctG>ctA	p.L13L	HNRNPA1L2_ENST00000398039.1_Silent_p.L13L|HNRNPA1L2_ENST00000342657.3_Silent_p.L13L			Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like 2	13	Globular A domain.				alternative mRNA splicing, via spliceosome (GO:0000380)|mRNA transport (GO:0051028)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			cervix(1)|large_intestine(1)|lung(5)	7						CCGAACAGCTGAGGAAGCTCT	0.502													-|||	54	0.0107827	0.0015	0.0144	5008	,	,		19278	0.0		0.0348	False		,,,				2504	0.0072				p.L13L		Atlas-SNP	.											.	HNRNPA1L2	20	.	0			c.G39A						PASS	.	G	,	19,4387	25.3+/-52.1	0,19,2184	68.0	71.0	70.0		39,39	0.3	0.9	13	dbSNP_132	70	266,8334	101.2+/-162.5	5,256,4039	no	coding-synonymous,coding-synonymous	HNRNPA1L2	NM_001011724.1,NM_001011725.1	,	5,275,6223	AA,AG,GG		3.093,0.4312,2.1913	,	13/321,13/321	53216666	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	144983	exon7			ACAGCTGAGGAAG		CCDS31980.1	13q14.3	2013-02-12			ENSG00000139675	ENSG00000139675		"""RNA binding motif (RRM) containing"""	27067	protein-coding gene	gene with protein product						12477932	Standard	NM_001011724		Approved	LOC144983	uc001vgy.1	Q32P51	OTTHUMG00000016972	ENST00000357495.2:c.39G>A	13.37:g.53216666G>A		63.0	0.0	0		54.0	26.0	0.481481	NM_001011724	Q5TBS2	Silent	SNP	ENST00000357495.2	37	CCDS31980.1																																																																																			G|0.980;A|0.020	0.020	strong		0.502	HNRNPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045098.1	NM_001011724	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68930465	68930465	+	Missense_Mutation	SNP	G	G	A	rs143544573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68930465G>A	ENST00000356291.2	-	8	1012	c.953C>T	c.(952-954)tCt>tTt	p.S318F	RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	318	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.S318F(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						CAACTTTATAGATGAGTCTGG	0.388													G|||	13	0.00259585	0.0	0.0029	5008	,	,		16858	0.0		0.0109	False		,,,				2504	0.0				p.S318F		Atlas-SNP	.											TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	79	1	1	Substitution - Missense(1)	prostate(1)	c.C953T						PASS	.	G	PHE/SER	6,4400	12.9+/-30.5	0,6,2197	68.0	68.0	68.0		953	4.0	1.0	4	dbSNP_134	68	101,8499	55.6+/-116.7	1,99,4200	yes	missense	TMPRSS11F	NM_207407.2	155	1,105,6397	AA,AG,GG		1.1744,0.1362,0.8227	possibly-damaging	318/439	68930465	107,12899	2203	4300	6503	SO:0001583	missense	389208	exon8			TTTATAGATGAGT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.953C>T	4.37:g.68930465G>A	ENSP00000348639:p.Ser318Phe	102.0	0.0	0		87.0	51.0	0.586207	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	14.79	2.641763	0.47153	0.001362	0.011744	ENSG00000198092	ENST00000356291	D	0.89681	-2.55	5.92	4.0	0.46444	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.207319	0.34652	N	0.003800	T	0.78457	0.4286	L	0.28192	0.835	0.42271	D	0.992056	P	0.49090	0.919	B	0.43082	0.407	T	0.83214	-0.0072	10	0.72032	D	0.01	.	12.357	0.55182	0.0:0.0:0.6819:0.3181	.	318	Q6ZWK6	TM11F_HUMAN	F	318	ENSP00000348639:S318F	ENSP00000348639:S318F	S	-	2	0	TMPRSS11F	68613060	0.983000	0.35010	1.000000	0.80357	0.595000	0.36748	1.369000	0.34227	1.488000	0.48433	0.650000	0.86243	TCT	G|0.994;A|0.006	0.006	strong		0.388	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
DGKH	160851	hgsc.bcm.edu	37	13	42729463	42729463	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42729463G>A	ENST00000337343.4	+	4	442	c.421G>A	c.(421-423)Gag>Aag	p.E141K	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_5'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.E5K|DGKH_ENST00000540693.1_Missense_Mutation_p.E141K|DGKH_ENST00000261491.5_Missense_Mutation_p.E141K|DGKH_ENST00000379274.2_Missense_Mutation_p.E5K	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		GCTGTGTGCTGAGAACAGAAA	0.398																																					p.E141K		Atlas-SNP	.											.	DGKH	106	.	0			c.G421A						PASS	.						157.0	152.0	154.0					13																	42729463		2203	4300	6503	SO:0001583	missense	160851	exon5			TGTGCTGAGAACA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.421G>A	13.37:g.42729463G>A	ENSP00000337572:p.Glu141Lys	205.0	0.0	0		206.0	42.0	0.203883	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.196603	0.79015	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	6.04	5.2	0.72013	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.454524	0.24815	N	0.035363	T	0.42720	0.1215	L	0.59967	1.855	0.80722	D	1	B;B	0.26845	0.161;0.065	B;B	0.35607	0.079;0.206	T	0.36040	-0.9764	10	0.52906	T	0.07	.	15.3721	0.74573	0.0664:0.0:0.9336:0.0	.	141;141	Q86XP1-2;Q86XP1	.;DGKH_HUMAN	K	141;141;141;5;5	ENSP00000440823:E141K;ENSP00000337572:E141K;ENSP00000261491:E141K;ENSP00000368576:E5K;ENSP00000445114:E5K	ENSP00000261491:E141K	E	+	1	0	DGKH	41627463	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.837000	0.99465	1.591000	0.50007	-0.236000	0.12185	GAG	.	.	none		0.398	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
FBXO40	51725	hgsc.bcm.edu	37	3	121341019	121341019	+	Missense_Mutation	SNP	A	A	T	rs142436040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121341019A>T	ENST00000338040.4	+	3	1157	c.743A>T	c.(742-744)aAa>aTa	p.K248I		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	248					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		GACTCCGAGAAAGAACAGATT	0.468													A|||	10	0.00199681	0.0	0.0043	5008	,	,		22737	0.0		0.007	False		,,,				2504	0.0				p.K248I		Atlas-SNP	.											.	FBXO40	108	.	0			c.A743T						PASS	.	A	ILE/LYS	4,4402	8.1+/-20.4	1,2,2200	64.0	69.0	67.0		743	0.2	0.0	3	dbSNP_134	67	34,8566	23.4+/-69.3	0,34,4266	yes	missense	FBXO40	NM_016298.3	102	1,36,6466	TT,TA,AA		0.3953,0.0908,0.2922	possibly-damaging	248/710	121341019	38,12968	2203	4300	6503	SO:0001583	missense	51725	exon3			CCGAGAAAGAACA	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"""F-boxes /  ""other"""""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.743A>T	3.37:g.121341019A>T	ENSP00000337510:p.Lys248Ile	61.0	0.0	0		47.0	28.0	0.595745	NM_016298	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	8.429	0.848116	0.17034	9.08E-4	0.003953	ENSG00000163833	ENST00000338040	T	0.49139	0.79	5.51	0.213	0.15244	.	0.880954	0.10192	N	0.704471	T	0.29716	0.0742	L	0.47716	1.5	0.23036	N	0.998398	P	0.42620	0.785	B	0.40940	0.344	T	0.15983	-1.0418	10	0.44086	T	0.13	-7.038	5.3399	0.15979	0.6143:0.1385:0.2472:0.0	.	248	Q9UH90	FBX40_HUMAN	I	248	ENSP00000337510:K248I	ENSP00000337510:K248I	K	+	2	0	FBXO40	122823709	0.008000	0.16893	0.009000	0.14445	0.009000	0.06853	0.391000	0.20784	0.058000	0.16222	0.402000	0.26972	AAA	A|0.997;T|0.003	0.003	strong		0.468	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298	
ZNF804A	91752	hgsc.bcm.edu	37	2	185800768	185800768	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185800768T>C	ENST00000302277.6	+	4	1239	c.645T>C	c.(643-645)tcT>tcC	p.S215S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	215							metal ion binding (GO:0046872)	p.S215S(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TCGGCTTTTCTTTTGCATTTC	0.433																																					p.S215S		Atlas-SNP	.											ZNF804A,colon,carcinoma,0,1	ZNF804A	322	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T645C						PASS	.						66.0	67.0	66.0					2																	185800768		2203	4300	6503	SO:0001819	synonymous_variant	91752	exon4			CTTTTCTTTTGCA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.645T>C	2.37:g.185800768T>C		106.0	0.0	0		71.0	20.0	0.28169	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.	.	none		0.433	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157219	26157219	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26157219C>T	ENST00000304218.3	+	1	661	c.601C>T	c.(601-603)Cca>Tca	p.P201S	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	201					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GGCGGCTAAACCAAAGACCGC	0.527																																					p.P201S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C601T						PASS	.						32.0	34.0	33.0					6																	26157219		2202	4299	6501	SO:0001583	missense	3008	exon1			GCTAAACCAAAGA	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.601C>T	6.37:g.26157219C>T	ENSP00000307705:p.Pro201Ser	98.0	0.0	0		71.0	10.0	0.140845	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	11.35	1.612147	0.28712	.	.	ENSG00000168298	ENST00000304218	T	0.12672	2.66	5.48	4.56	0.56223	.	0.130977	0.52532	D	0.000076	T	0.07007	0.0178	L	0.59912	1.85	0.37467	D	0.915446	B	0.20261	0.043	B	0.14578	0.011	T	0.06427	-1.0827	10	0.31617	T	0.26	-1.4746	11.1455	0.48428	0.1401:0.7241:0.1358:0.0	.	201	P10412	H14_HUMAN	S	201	ENSP00000307705:P201S	ENSP00000307705:P201S	P	+	1	0	HIST1H1E	26265198	1.000000	0.71417	0.284000	0.24805	0.975000	0.68041	2.111000	0.41883	2.717000	0.92951	0.655000	0.94253	CCA	.	.	none		0.527	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
ITPR3	3710	hgsc.bcm.edu	37	6	33658780	33658780	+	Silent	SNP	C	C	T	rs35506178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33658780C>T	ENST00000374316.5	+	53	8179	c.7119C>T	c.(7117-7119)gcC>gcT	p.A2373A	ITPR3_ENST00000605930.1_Silent_p.A2373A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2373					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGCTGACAGCCCTGCTGGCCC	0.577													C|||	89	0.0177716	0.003	0.013	5008	,	,		21516	0.0119		0.0517	False		,,,				2504	0.0123				p.A2373A		Atlas-SNP	.											.	ITPR3	409	.	0			c.C7119T						PASS	.	C		58,4348	55.5+/-91.7	1,56,2146	150.0	122.0	131.0		7119	1.8	1.0	6	dbSNP_126	131	431,8169	132.8+/-190.4	10,411,3879	no	coding-synonymous	ITPR3	NM_002224.3		11,467,6025	TT,TC,CC		5.0116,1.3164,3.7598		2373/2672	33658780	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon52			GACAGCCCTGCTG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7119C>T	6.37:g.33658780C>T		172.0	0.0	0		162.0	81.0	0.5	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.966;T|0.034	0.034	strong		0.577	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230407	23230407	+	Missense_Mutation	SNP	C	C	G	rs538609996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230407C>G	ENST00000526893.1	+	1	448	c.174C>G	c.(172-174)agC>agG	p.S58R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S58R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S58R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	58						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CAGTTGGAAGCAGCCGATCCA	0.662																																					p.S58R		Atlas-SNP	.											.	IGLL5	26	.	0			c.C174G						PASS	.																																			SO:0001583	missense	100423062	exon1			TGGAAGCAGCCGA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.174C>G	22.37:g.23230407C>G	ENSP00000431254:p.Ser58Arg	122.0	0.0	0		110.0	22.0	0.2	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505085	0.26949	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00585	6.4;6.39	3.92	0.621	0.17643	.	.	.	.	.	T	0.00524	0.0017	L	0.32530	0.975	0.09310	N	1	B	0.21225	0.053	B	0.19148	0.024	T	0.46555	-0.9183	9	0.72032	D	0.01	.	4.068	0.09869	0.0:0.5528:0.224:0.2232	.	58	B9A064	IGLL5_HUMAN	R	58	ENSP00000436353:S58R;ENSP00000431254:S58R	ENSP00000431254:S58R	S	+	3	2	IGLL5	21560407	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	0.487000	0.22356	0.228000	0.21019	-0.152000	0.13540	AGC	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
C5	727	hgsc.bcm.edu	37	9	123776220	123776220	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123776220C>T	ENST00000223642.1	-	17	2217	c.2188G>A	c.(2188-2190)Gaa>Aaa	p.E730K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	730	Anaphylatoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00022}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	ACACAACATTCAGTGAAAGCT	0.438																																					p.E730K		Atlas-SNP	.											.	C5	124	.	0			c.G2188A						PASS	.						170.0	145.0	154.0					9																	123776220		2203	4300	6503	SO:0001583	missense	727	exon17			AACATTCAGTGAA	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.2188G>A	9.37:g.123776220C>T	ENSP00000223642:p.Glu730Lys	153.0	0.0	0		131.0	42.0	0.320611	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829145	0.32329	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.24151	1.87	6.06	0.0997	0.14504	Complement C3a/C4a/C5a anaphylatoxin (1);Anaphylatoxin (2);Anaphylatoxin/fibulin (4);	1.861730	0.01962	N	0.043417	T	0.17662	0.0424	L	0.35593	1.075	0.09310	N	1	B	0.30563	0.285	B	0.28916	0.096	T	0.10291	-1.0636	10	0.15952	T	0.53	.	3.2397	0.06777	0.1112:0.4786:0.1091:0.3011	.	730	P01031	CO5_HUMAN	K	730;801	ENSP00000223642:E730K	ENSP00000223642:E730K	E	-	1	0	C5	122816041	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.178000	0.09782	0.088000	0.17205	0.650000	0.86243	GAA	.	.	none		0.438	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230317	23230317	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230317G>A	ENST00000526893.1	+	1	358	c.84G>A	c.(82-84)ctG>ctA	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|IGLL5_ENST00000532223.2_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCTGCTGCTGCTGGGTCTGG	0.657																																					p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G84A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCTGCTGCTGGGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.84G>A	22.37:g.23230317G>A		153.0	0.0	0		158.0	33.0	0.208861	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
JARID2	3720	hgsc.bcm.edu	37	6	15512616	15512616	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:15512616G>A	ENST00000341776.2	+	14	3374	c.3130G>A	c.(3130-3132)Gcc>Acc	p.A1044T	JARID2_ENST00000397311.3_Missense_Mutation_p.A872T	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1044	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				CTTTGAGACCGCCAAGGTGAG	0.607																																					p.A1044T		Atlas-SNP	.											.	JARID2	135	.	0			c.G3130A						PASS	.						139.0	133.0	135.0					6																	15512616		2203	4300	6503	SO:0001583	missense	3720	exon14			GAGACCGCCAAGG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.3130G>A	6.37:g.15512616G>A	ENSP00000341280:p.Ala1044Thr	59.0	0.0	0		44.0	13.0	0.295455	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520516	0.85495	.	.	ENSG00000008083	ENST00000341776;ENST00000397311	T;T	0.70282	-0.47;-0.47	5.02	4.15	0.48705	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	L	0.35542	1.07	0.80722	D	1	D	0.67145	0.996	P	0.50136	0.632	T	0.60632	-0.7225	10	0.46703	T	0.11	-15.1615	13.6151	0.62103	0.0757:0.0:0.9243:0.0	.	1044	Q92833	JARD2_HUMAN	T	1044;872	ENSP00000341280:A1044T;ENSP00000380478:A872T	ENSP00000341280:A1044T	A	+	1	0	JARID2	15620595	1.000000	0.71417	0.991000	0.47740	0.956000	0.61745	9.796000	0.99103	1.238000	0.43771	0.609000	0.83330	GCC	.	.	none		0.607	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
INTS3	65123	hgsc.bcm.edu	37	1	153701188	153701188	+	Silent	SNP	G	G	A	rs150819290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153701188G>A	ENST00000318967.2	+	1	646	c.78G>A	c.(76-78)gcG>gcA	p.A26A	Y_RNA_ENST00000362695.1_RNA|INTS3_ENST00000456435.1_5'UTR|INTS3_ENST00000435409.2_Silent_p.A26A	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	0	Ala/Gly-rich.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			gaggaggagcgggagcaggag	0.627													G|||	17	0.00339457	0.0	0.0043	5008	,	,		11478	0.0		0.0139	False		,,,				2504	0.0				p.A26A		Atlas-SNP	.											.	INTS3	83	.	0			c.G78A						PASS	.	G		7,4393		0,7,2193	34.0	45.0	41.0		78	4.1	1.0	1	dbSNP_134	41	106,8494		0,106,4194	no	coding-synonymous	INTS3	NM_023015.3		0,113,6387	AA,AG,GG		1.2326,0.1591,0.8692		26/1043	153701188	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	65123	exon1			AGGAGCGGGAGCA	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.78G>A	1.37:g.153701188G>A		151.0	0.0	0		137.0	70.0	0.510949	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			G|0.994;A|0.006	0.006	strong		0.627	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
DHX9	1660	hgsc.bcm.edu	37	1	182850520	182850520	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:182850520G>A	ENST00000367549.3	+	23	2856	c.2746G>A	c.(2746-2748)Gta>Ata	p.V916I	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	916					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTCTGATCACGTAGCCCTTTT	0.433																																					p.V916I	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G2746A						PASS	.						149.0	140.0	143.0					1																	182850520		1865	4107	5972	SO:0001583	missense	1660	exon23			GATCACGTAGCCC	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.2746G>A	1.37:g.182850520G>A	ENSP00000356520:p.Val916Ile	134.0	0.0	0		117.0	62.0	0.529915	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082905	0.94050	.	.	ENSG00000135829	ENST00000367549	T	0.27557	1.66	5.76	5.76	0.90799	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.36580	0.0972	N	0.17379	0.485	0.80722	D	1	D;D	0.60575	0.969;0.988	P;P	0.58077	0.572;0.832	T	0.07028	-1.0794	10	0.30854	T	0.27	.	19.5961	0.95538	0.0:0.0:1.0:0.0	.	195;916	B3KU66;Q08211	.;DHX9_HUMAN	I	916	ENSP00000356520:V916I	ENSP00000356520:V916I	V	+	1	0	DHX9	181117143	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	7.251000	0.78297	2.706000	0.92434	0.655000	0.94253	GTA	.	.	none		0.433	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
SLC8A1	6546	hgsc.bcm.edu	37	2	40656756	40656756	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:40656756A>T	ENST00000403092.1	-	2	698	c.665T>A	c.(664-666)tTg>tAg	p.L222*	SLC8A1_ENST00000406785.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000408028.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000402441.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405901.3_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000332839.4_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000406391.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542756.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542024.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405269.1_Nonsense_Mutation_p.L222*			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	222					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TATGACAGACAAAATAATGTA	0.473																																					p.L222X		Atlas-SNP	.											.	SLC8A1	221	.	0			c.T665A						PASS	.						52.0	56.0	55.0					2																	40656756		2203	4300	6503	SO:0001587	stop_gained	6546	exon1			ACAGACAAAATAA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.665T>A	2.37:g.40656756A>T	ENSP00000384763:p.Leu222*	54.0	0.0	0		100.0	15.0	0.15	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Nonsense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631169	0.87660	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4743	0.61299	1.0:0.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000332931:L222X	L	-	2	0	SLC8A1	40510260	1.000000	0.71417	0.954000	0.39281	0.928000	0.56348	9.151000	0.94674	2.076000	0.62316	0.460000	0.39030	TTG	.	.	none		0.473	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134503415	134503415	+	Silent	SNP	C	C	T	rs371503343		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134503415C>T	ENST00000372189.3	-	9	1158	c.1035G>A	c.(1033-1035)tcG>tcA	p.S345S	RAPGEF1_ENST00000372190.3_Silent_p.S363S|RAPGEF1_ENST00000481260.1_5'UTR|RAPGEF1_ENST00000372195.1_Silent_p.S362S	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	345					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		AGAGGCGGGGCGACTCTCCAC	0.547																																					p.S363S		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1089A						PASS	.	C	,	0,4264		0,0,2132	28.0	31.0	30.0		1035,1089	-3.3	0.9	9		30	2,8484		0,2,4241	no	coding-synonymous,coding-synonymous	RAPGEF1	NM_005312.2,NM_198679.1	,	0,2,6373	TT,TC,CC		0.0236,0.0,0.0157	,	345/1078,363/1096	134503415	2,12748	2132	4243	6375	SO:0001819	synonymous_variant	2889	exon9			GCGGGGCGACTCT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1035G>A	9.37:g.134503415C>T		46.0	0.0	0		45.0	23.0	0.511111	NM_198679	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1																																																																																			.	.	weak		0.547	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
VPS18	57617	hgsc.bcm.edu	37	15	41191184	41191184	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41191184C>T	ENST00000220509.5	+	3	652	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	VPS18_ENST00000558474.1_Missense_Mutation_p.L105F	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	105					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CAAGATGTTCCTTGACCATAC	0.567																																					p.L105F		Atlas-SNP	.											.	VPS18	67	.	0			c.C313T						PASS	.						117.0	97.0	104.0					15																	41191184		2203	4300	6503	SO:0001583	missense	57617	exon3			ATGTTCCTTGACC	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.313C>T	15.37:g.41191184C>T	ENSP00000220509:p.Leu105Phe	70.0	0.0	0		46.0	24.0	0.521739	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	37	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824795	0.50739	.	.	ENSG00000104142	ENST00000220509	T	0.55234	0.53	4.77	3.73	0.42828	.	0.000000	0.64402	D	0.000001	T	0.67832	0.2935	M	0.81682	2.555	0.54753	D	0.999982	D	0.71674	0.998	D	0.72338	0.977	T	0.67925	-0.5544	10	0.56958	D	0.05	-14.8434	5.7082	0.17921	0.0:0.6252:0.0:0.3748	.	105	Q9P253	VPS18_HUMAN	F	105	ENSP00000220509:L105F	ENSP00000220509:L105F	L	+	1	0	VPS18	38978476	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.289000	0.33307	1.063000	0.40649	0.455000	0.32223	CTT	.	.	none		0.567	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
MACF1	23499	hgsc.bcm.edu	37	1	39816626	39816626	+	Missense_Mutation	SNP	C	C	A	rs116162513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39816626C>A	ENST00000372915.3	+	42	11237	c.11150C>A	c.(11149-11151)aCa>aAa	p.T3717K	MACF1_ENST00000545844.1_Missense_Mutation_p.T1650K|MACF1_ENST00000567887.1_Missense_Mutation_p.T3749K|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Missense_Mutation_p.T1650K|MACF1_ENST00000361689.2_Missense_Mutation_p.T1650K|MACF1_ENST00000564288.1_Missense_Mutation_p.T3712K|MACF1_ENST00000317713.7_Missense_Mutation_p.T1650K|MACF1_ENST00000289893.4_Missense_Mutation_p.T2152K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3717					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGGAAGAGACACGTGTGGCC	0.493																																					p.T1650K		Atlas-SNP	.											.	MACF1	909	.	0			c.C4949A						PASS	.						72.0	70.0	71.0					1																	39816626		2203	4300	6503	SO:0001583	missense	23499	exon39			AAGAGACACGTGT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11150C>A	1.37:g.39816626C>A	ENSP00000362006:p.Thr3717Lys	80.0	0.0	0		57.0	14.0	0.245614	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.97|18.97	3.735836|3.735836	0.69189|0.69189	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	.|T;T;T;T;T;T;T	.|0.62232	.|1.27;0.04;1.27;1.27;1.27;1.27;1.07	6.06|6.06	5.15|5.15	0.70609|0.70609	.|.	.|0.190098	.|0.37012	.|N	.|0.002284	T|T	0.70150|0.70150	0.3191|0.3191	L|L	0.60455|0.60455	1.87|1.87	0.44843|0.44843	D|D	0.997855|0.997855	.|B;P;D;B	.|0.54772	.|0.433;0.864;0.968;0.225	.|B;P;P;B	.|0.56343	.|0.375;0.669;0.796;0.155	T|T	0.73075|0.73075	-0.4097|-0.4097	5|10	.|0.66056	.|D	.|0.02	.|.	12.0779|12.0779	0.53655|0.53655	0.0:0.8611:0.0:0.1389|0.0:0.8611:0.0:0.1389	.|.	.|3717;1650;1650;1615	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	E|K	783|1650;3717;1650;1650;1650;1799;2152	.|ENSP00000439537:T1650K;ENSP00000362006:T3717K;ENSP00000354573:T1650K;ENSP00000313438:T1650K;ENSP00000444364:T1650K;ENSP00000437059:T1799K;ENSP00000289893:T2152K	.|ENSP00000289893:T2152K	D|T	+|+	3|2	2|0	MACF1|MACF1	39589213|39589213	0.985000|0.985000	0.35326|0.35326	0.012000|0.012000	0.15200|0.15200	0.872000|0.872000	0.50106|0.50106	3.723000|3.723000	0.54955|0.54955	1.584000|1.584000	0.49913|0.49913	0.650000|0.650000	0.86243|0.86243	GAC|ACA	C|0.999;T|0.001	.	alt		0.493	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
C7	730	hgsc.bcm.edu	37	5	40934471	40934471	+	Silent	SNP	G	G	A	rs34196526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:40934471G>A	ENST00000313164.9	+	4	542	c.183G>A	c.(181-183)caG>caA	p.Q61Q		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	61	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				ATGGAGGCCAGCCTTGTGTTG	0.458													G|||	35	0.00698882	0.0008	0.0058	5008	,	,		16468	0.0		0.008	False		,,,				2504	0.0225				p.Q61Q		Atlas-SNP	.											.	C7	136	.	0			c.G183A						PASS	.	G		9,3901		0,9,1946	160.0	165.0	163.0		183	-11.8	0.0	5	dbSNP_126	163	197,8095		3,191,3952	no	coding-synonymous	C7	NM_000587.2		3,200,5898	AA,AG,GG		2.3758,0.2302,1.6882		61/844	40934471	206,11996	1955	4146	6101	SO:0001819	synonymous_variant	730	exon4			AGGCCAGCCTTGT	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.183G>A	5.37:g.40934471G>A		266.0	0.0	0		268.0	162.0	0.604478	NM_000587	Q6P3T5|Q92489	Silent	SNP	ENST00000313164.9	37	CCDS47201.1																																																																																			G|0.992;A|0.008	0.008	strong		0.458	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
PDE4A	5141	hgsc.bcm.edu	37	19	10572271	10572271	+	Missense_Mutation	SNP	A	A	G	rs141379029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10572271A>G	ENST00000352831.6	+	12	1645	c.1535A>G	c.(1534-1536)aAg>aGg	p.K512R	PDE4A_ENST00000380702.2_Missense_Mutation_p.K490R|PDE4A_ENST00000592685.1_Missense_Mutation_p.K490R|PDE4A_ENST00000440014.2_Missense_Mutation_p.K451R|PDE4A_ENST00000344979.3_Missense_Mutation_p.K273R|PDE4A_ENST00000293683.5_Missense_Mutation_p.K486R	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	512	Catalytic.				cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	GTGGGCTTCAAGCTGCTGCAG	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		10749	0.0		0.001	False		,,,				2504	0.0				p.K512R		Atlas-SNP	.											.	PDE4A	236	.	0			c.A1535G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	0,4406		0,0,2203	77.0	69.0	72.0		1535,1457,1352,818	3.9	1.0	19	dbSNP_134	72	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense	PDE4A	NM_001111307.1,NM_001111308.1,NM_001111309.1,NM_006202.2	26,26,26,26	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign,benign,benign,benign	512/887,486/861,451/826,273/648	10572271	3,13003	2203	4300	6503	SO:0001583	missense	5141	exon12			GCTTCAAGCTGCT		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.1535A>G	19.37:g.10572271A>G	ENSP00000270474:p.Lys512Arg	154.0	0.0	0		105.0	52.0	0.495238	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	18.40	3.614645	0.66672	0.0	3.49E-4	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	3.92	3.92	0.45320	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.053169	0.64402	D	0.000001	D	0.84433	0.5471	L	0.43701	1.375	0.58432	D	0.999995	B;D;D;D;D	0.64830	0.081;0.994;0.992;0.971;0.989	B;D;D;P;D	0.83275	0.073;0.996;0.988;0.906;0.943	D	0.85413	0.1138	10	0.87932	D	0	.	10.7358	0.46124	1.0:0.0:0.0:0.0	.	178;273;451;486;512	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	R	490;512;486;451;273;178	ENSP00000370078:K490R;ENSP00000270474:K512R;ENSP00000293683:K486R;ENSP00000394754:K451R;ENSP00000341007:K273R	ENSP00000293683:K486R	K	+	2	0	PDE4A	10433271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.022000	0.93678	1.652000	0.50683	0.477000	0.44152	AAG	A|1.000;G|0.000	0.000	strong		0.632	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		121.0	0.0	0		125.0	56.0	0.448	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
ULBP3	79465	hgsc.bcm.edu	37	6	150386752	150386752	+	Missense_Mutation	SNP	C	C	T	rs34547018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:150386752C>T	ENST00000367339.2	-	3	438	c.410G>A	c.(409-411)cGt>cAt	p.R137H	ULBP3_ENST00000438272.2_Missense_Mutation_p.R137H			Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3	137	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)|viral process (GO:0016032)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			central_nervous_system(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	9		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)		CCAAGATCCACGGATGTATCC	0.517													C|||	25	0.00499201	0.0091	0.0029	5008	,	,		22692	0.0		0.008	False		,,,				2504	0.0031				p.R137H		Atlas-SNP	.											.	ULBP3	22	.	0			c.G410A						PASS	.	C	HIS/ARG	26,4380	32.6+/-62.9	0,26,2177	128.0	119.0	122.0		410	-6.7	0.0	6	dbSNP_126	122	22,8578	15.3+/-51.7	0,22,4278	yes	missense	ULBP3	NM_024518.1	29	0,48,6455	TT,TC,CC		0.2558,0.5901,0.3691	benign	137/245	150386752	48,12958	2203	4300	6503	SO:0001583	missense	79465	exon3			GATCCACGGATGT	AF304379	CCDS5225.1	6q25	2008-04-11			ENSG00000131019	ENSG00000131019			14895	protein-coding gene	gene with protein product		605699				11239445, 11827464	Standard	NM_024518		Approved	RAET1N	uc003qns.3	Q9BZM4	OTTHUMG00000015811	ENST00000367339.2:c.410G>A	6.37:g.150386752C>T	ENSP00000356308:p.Arg137His	105.0	0.0	0		69.0	19.0	0.275362	NM_024518	Q5VY82|Q8IZX5|Q8TE75	Missense_Mutation	SNP	ENST00000367339.2	37	CCDS5225.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	1.414	-0.574714	0.03882	0.005901	0.002558	ENSG00000131019	ENST00000399812;ENST00000253335;ENST00000367339;ENST00000438272	T;T	0.08102	3.13;3.13	3.34	-6.69	0.01772	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.01765	0.0056	M	0.71581	2.175	0.09310	N	1	B;B	0.25206	0.12;0.12	B;B	0.11329	0.006;0.006	T	0.24333	-1.0163	9	0.39692	T	0.17	1.34	0.3216	0.00304	0.3017:0.137:0.2037:0.3577	rs34547018	137;137	Q5VY82;Q9BZM4	.;N2DL3_HUMAN	H	88;137;137;137	ENSP00000356308:R137H;ENSP00000403562:R137H	ENSP00000253335:R137H	R	-	2	0	ULBP3	150428445	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.449000	0.01008	-3.228000	0.00210	-1.434000	0.01081	CGT	C|0.997;T|0.003	0.003	strong		0.517	ULBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042678.2		
RAD51AP2	729475	hgsc.bcm.edu	37	2	17697635	17697635	+	Missense_Mutation	SNP	T	T	C	rs181531922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:17697635T>C	ENST00000399080.2	-	1	2071	c.2048A>G	c.(2047-2049)gAa>gGa	p.E683G		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	683										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCATATGTTTCAAAAATCGG	0.289													T|||	13	0.00259585	0.0008	0.0043	5008	,	,		17559	0.0		0.0089	False		,,,				2504	0.0				p.E683G		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.A2048G						PASS	.	T	GLY/GLU	10,3590		0,10,1790	38.0	36.0	37.0		2048	4.6	0.0	2		37	115,7961		0,115,3923	yes	missense	RAD51AP2	NM_001099218.2	98	0,125,5713	CC,CT,TT		1.424,0.2778,1.0706	possibly-damaging	683/1160	17697635	125,11551	1800	4038	5838	SO:0001583	missense	729475	exon1			TATGTTTCAAAAA	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.2048A>G	2.37:g.17697635T>C	ENSP00000382030:p.Glu683Gly	113.0	0.0	0		84.0	50.0	0.595238	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	5.534	0.283387	0.10458	0.002778	0.01424	ENSG00000214842	ENST00000399080	T	0.25250	1.81	4.62	4.62	0.57501	.	.	.	.	.	T	0.15089	0.0364	N	0.14661	0.345	0.09310	N	1	P	0.44429	0.835	P	0.47645	0.553	T	0.05801	-1.0863	9	0.66056	D	0.02	-0.2662	8.6213	0.33861	0.0:0.0886:0.0:0.9114	.	683	Q09MP3	R51A2_HUMAN	G	683	ENSP00000382030:E683G	ENSP00000382030:E683G	E	-	2	0	RAD51AP2	17561116	0.532000	0.26346	0.003000	0.11579	0.009000	0.06853	2.814000	0.48010	2.012000	0.59069	0.482000	0.46254	GAA	T|0.994;C|0.006	0.006	strong		0.289	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
ZNF91	7644	hgsc.bcm.edu	37	19	23542626	23542626	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23542626C>T	ENST00000300619.7	-	4	3360	c.3155G>A	c.(3154-3156)tGt>tAt	p.C1052Y	ZNF91_ENST00000397082.2_Missense_Mutation_p.C1020Y|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1052					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ACATTCTTCACACTTGTAAGG	0.358																																					p.C1052Y		Atlas-SNP	.											.	ZNF91	349	.	0			c.G3155A						PASS	.						65.0	70.0	68.0					19																	23542626		2185	4292	6477	SO:0001583	missense	7644	exon4			TCTTCACACTTGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3155G>A	19.37:g.23542626C>T	ENSP00000300619:p.Cys1052Tyr	34.0	0.0	0		25.0	12.0	0.48	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.889340	0.33348	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	D;D	0.85088	-1.94;-1.94	1.31	-0.339	0.12647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94032	0.8088	H	0.97962	4.115	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83578	0.0116	9	0.87932	D	0	.	7.5061	0.27545	0.2521:0.7479:0.0:0.0	.	1020;1052	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	1052;1020	ENSP00000300619:C1052Y;ENSP00000380272:C1020Y	ENSP00000300619:C1052Y	C	-	2	0	ZNF91	23334466	0.951000	0.32395	0.119000	0.21687	0.692000	0.40212	2.703000	0.47110	0.676000	0.31285	0.196000	0.17591	TGT	.	.	none		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
C6	729	hgsc.bcm.edu	37	5	41155088	41155088	+	Missense_Mutation	SNP	T	T	C	rs41271067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41155088T>C	ENST00000263413.3	-	14	2351	c.2087A>G	c.(2086-2088)gAt>gGt	p.D696G	C6_ENST00000337836.5_Missense_Mutation_p.D696G	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	696	C5b-binding domain.|CCP 2.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GCATTCCACATCCCCTTGTCT	0.413													T|||	17	0.00339457	0.0	0.0086	5008	,	,		19476	0.001		0.008	False		,,,				2504	0.002				p.D696G		Atlas-SNP	.											.	C6	197	.	0			c.A2087G						PASS	.	T	GLY/ASP,GLY/ASP	8,4398	14.3+/-33.2	0,8,2195	148.0	138.0	142.0		2087,2087	3.5	1.0	5	dbSNP_127	142	115,8485	60.6+/-122.4	1,113,4186	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	94,94	1,121,6381	CC,CT,TT		1.3372,0.1816,0.9457	benign,benign	696/935,696/935	41155088	123,12883	2203	4300	6503	SO:0001583	missense	729	exon14			TCCACATCCCCTT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2087A>G	5.37:g.41155088T>C	ENSP00000263413:p.Asp696Gly	95.0	0.0	0		107.0	38.0	0.35514	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	13.64	2.298824	0.40694	0.001816	0.013372	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.41758	0.99;0.99	5.82	3.51	0.40186	Complement control module (2);Sushi/SCR/CCP (2);	0.475155	0.24788	N	0.035595	T	0.26048	0.0635	L	0.47190	1.495	0.34230	D	0.676444	B	0.17852	0.024	B	0.25759	0.063	T	0.36939	-0.9727	10	0.36615	T	0.2	-24.0381	7.4848	0.27425	0.0:0.1133:0.1879:0.6988	rs41271067;rs61733157	696	P13671	CO6_HUMAN	G	696	ENSP00000338861:D696G;ENSP00000263413:D696G	ENSP00000263413:D696G	D	-	2	0	C6	41190845	0.576000	0.26700	0.999000	0.59377	0.992000	0.81027	0.724000	0.25954	2.232000	0.73038	0.528000	0.53228	GAT	T|0.992;C|0.008	0.008	strong		0.413	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10469292	10469292	+	Silent	SNP	C	C	T	rs62490857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50.0	57.0	55.0		2316	-10.2	0.0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2316G>A	8.37:g.10469292C>T		81.0	0.0	0		97.0	74.0	0.762887	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
NCAN	1463	hgsc.bcm.edu	37	19	19335135	19335135	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19335135G>A	ENST00000252575.6	+	5	770	c.671G>A	c.(670-672)cGt>cAt	p.R224H	NCAN_ENST00000538881.1_5'Flank	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	224	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACCCAGTCCCGTCCTGGTTGC	0.587																																					p.R224H		Atlas-SNP	.											.	NCAN	277	.	0			c.G671A						PASS	.						157.0	140.0	146.0					19																	19335135		2203	4300	6503	SO:0001583	missense	1463	exon5			AGTCCCGTCCTGG	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.671G>A	19.37:g.19335135G>A	ENSP00000252575:p.Arg224His	111.0	0.0	0		88.0	20.0	0.227273	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996086	0.93167	.	.	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.13657	2.57	4.83	4.83	0.62350	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.000000	0.34853	N	0.003626	T	0.49338	0.1551	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65026	-0.6268	10	0.87932	D	0	-14.3002	15.4278	0.75069	0.0:0.0:1.0:0.0	.	224	O14594	NCAN_HUMAN	H	238;224	ENSP00000252575:R224H	ENSP00000252575:R224H	R	+	2	0	NCAN	19196135	0.943000	0.32029	0.642000	0.29436	0.926000	0.56050	4.868000	0.63021	2.240000	0.73641	0.561000	0.74099	CGT	.	.	none		0.587	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
TBX5	6910	hgsc.bcm.edu	37	12	114793414	114793414	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:114793414G>A	ENST00000310346.4	-	9	2146	c.1480C>T	c.(1480-1482)Cca>Tca	p.P494S	TBX5_ENST00000349716.5_Missense_Mutation_p.P444S|TBX5_ENST00000405440.2_Missense_Mutation_p.P494S	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	494				PRTLSPHQYHSVHGVGMVPEWSDNS -> QGLYPLISTTLC TELAWCRVERQ (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		AGAGTCCTTGGCACGCCATGA	0.597																																					p.P494S	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C1480T						PASS	.						57.0	55.0	56.0					12																	114793414		2203	4300	6503	SO:0001583	missense	6910	exon9			TCCTTGGCACGCC	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1480C>T	12.37:g.114793414G>A	ENSP00000309913:p.Pro494Ser	90.0	0.0	0		87.0	42.0	0.482759	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	3.093	-0.186357	0.06340	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000405440	D;D;D	0.86694	-2.15;-2.16;-2.16	5.42	3.6	0.41247	.	0.168870	0.53938	N	0.000057	T	0.76586	0.4008	L	0.31664	0.95	0.49130	D	0.999753	B	0.12013	0.005	B	0.10450	0.005	T	0.64935	-0.6290	10	0.06757	T	0.87	.	11.3993	0.49860	0.145:0.0:0.855:0.0	.	494	Q99593	TBX5_HUMAN	S	444;494;494	ENSP00000337723:P444S;ENSP00000309913:P494S;ENSP00000384152:P494S	ENSP00000309913:P494S	P	-	1	0	TBX5	113277797	1.000000	0.71417	0.916000	0.36221	0.860000	0.49131	5.471000	0.66762	0.667000	0.31107	0.655000	0.94253	CCA	.	.	none		0.597	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717	
KDR	3791	hgsc.bcm.edu	37	4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	rs1870377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Q472H(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79.0	82.0	81.0		1416	-1.8	0.0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	164.0	0.0	0		139.0	66.0	0.47482	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17306074G>A	ENST00000594824.1	+	22	3985	c.3838G>A	c.(3838-3840)Ggc>Agc	p.G1280S	MYO9B_ENST00000595618.1_Missense_Mutation_p.G1280S|MYO9B_ENST00000397274.2_Missense_Mutation_p.G1280S			Q13459	MYO9B_HUMAN	myosin IXB	1280	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAAACCATGTGGCAGCCCAAG	0.701													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		13079	0.0		0.0129	False		,,,				2504	0.0031				p.G1280S		Atlas-SNP	.											MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	0			c.G3838A						PASS	.	G	SER/GLY,SER/GLY	11,3783		0,11,1886	20.0	27.0	25.0		3838,3838	-3.2	0.0	19	dbSNP_132	25	119,8027		0,119,3954	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	56,56	0,130,5840	AA,AG,GG		1.4608,0.2899,1.0888	benign,benign	1280/2023,1280/2158	17306074	130,11810	1897	4073	5970	SO:0001583	missense	4650	exon22			CCATGTGGCAGCC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3838G>A	19.37:g.17306074G>A	ENSP00000471367:p.Gly1280Ser	38.0	0.0	0		57.0	29.0	0.508772	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	5.753	0.323409	0.10900	0.002899	0.014608	ENSG00000099331	ENST00000397274	D	0.83673	-1.75	5.28	-3.16	0.05217	.	1.740110	0.03022	N	0.150866	T	0.65123	0.2661	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.56932	-0.7897	10	0.07030	T	0.85	.	10.5091	0.44851	0.645:0.0:0.355:0.0	.	1280;1280;1286	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	S	1280	ENSP00000380444:G1280S	ENSP00000380444:G1280S	G	+	1	0	MYO9B	17167074	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.479000	0.06567	-0.339000	0.08401	-0.367000	0.07326	GGC	G|0.994;A|0.006	0.006	strong		0.701	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ATP2B4	493	hgsc.bcm.edu	37	1	203669371	203669371	+	Silent	SNP	G	G	A	rs2228446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203669371G>A	ENST00000357681.5	+	5	1810	c.687G>A	c.(685-687)ggG>ggA	p.G229G	ATP2B4_ENST00000391954.2_Silent_p.G229G|ATP2B4_ENST00000367219.3_Silent_p.G229G|ATP2B4_ENST00000367218.3_Silent_p.G229G|ATP2B4_ENST00000341360.2_Silent_p.G229G	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	229					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGATCCAAGGGAATGATCTGA	0.517													G|||	25	0.00499201	0.0008	0.0072	5008	,	,		20092	0.0		0.0139	False		,,,				2504	0.0051				p.G229G		Atlas-SNP	.											.	ATP2B4	226	.	0			c.G687A						PASS	.	G	,	12,4394	19.1+/-41.9	0,12,2191	114.0	110.0	112.0		687,687	-9.8	0.8	1	dbSNP_98	112	171,8429	78.6+/-141.3	0,171,4129	no	coding-synonymous,coding-synonymous	ATP2B4	NM_001001396.2,NM_001684.4	,	0,183,6320	AA,AG,GG		1.9884,0.2724,1.407	,	229/1171,229/1206	203669371	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	493	exon5			CCAAGGGAATGAT	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"""ATPases / P-type"""	817	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 4"""	108732	"""matrix-remodelling associated 1"""	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.687G>A	1.37:g.203669371G>A		108.0	0.0	0		97.0	49.0	0.505155	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Silent	SNP	ENST00000357681.5	37	CCDS1440.1																																																																																			G|0.987;A|0.013	0.013	strong		0.517	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396	
CD22	933	hgsc.bcm.edu	37	19	35831986	35831986	+	Silent	SNP	C	C	T	rs25677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35831986C>T	ENST00000085219.5	+	7	1518	c.1452C>T	c.(1450-1452)tgC>tgT	p.C484C	CD22_ENST00000341773.6_Silent_p.C307C|CD22_ENST00000544992.2_Silent_p.C484C|CD22_ENST00000536635.2_Silent_p.C396C|CD22_ENST00000270311.6_Silent_p.C364C|CD22_ENST00000419549.2_Silent_p.C312C|CD22_ENST00000594250.1_Silent_p.C307C	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	484	Ig-like C2-type 4.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCATCGCCTGCGCAGCTTGTA	0.607													C|||	294	0.0587061	0.1936	0.0403	5008	,	,		17505	0.0		0.0099	False		,,,				2504	0.0				p.C484C	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.C1452T						PASS	.	C	,,,	761,3645	308.0+/-290.3	67,627,1509	95.0	84.0	88.0		1188,1452,921,1452	-2.3	0.0	19	dbSNP_72	88	105,8495	56.8+/-118.0	1,103,4196	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	68,730,5705	TT,TC,CC		1.2209,17.2719,6.6585	,,,	396/760,484/752,307/671,484/848	35831986	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	933	exon7			CGCCTGCGCAGCT	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1452C>T	19.37:g.35831986C>T		138.0	0.0	0		126.0	64.0	0.507937	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			A|0.015;C|0.932;T|0.053	0.053	strong		0.607	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
OR2AG2	338755	hgsc.bcm.edu	37	11	6789492	6789492	+	Missense_Mutation	SNP	C	C	T	rs143018775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6789492C>T	ENST00000338569.2	-	1	794	c.697G>A	c.(697-699)Ggg>Agg	p.G233R		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTCTTCCTCCCCTCATTTGAT	0.502													C|||	8	0.00159744	0.0	0.0086	5008	,	,		19208	0.0		0.002	False		,,,				2504	0.0				p.G233R		Atlas-SNP	.											.	OR2AG2	55	.	0			c.G697A						PASS	.	C	ARG/GLY	2,4400	4.2+/-10.8	0,2,2199	110.0	95.0	100.0		697	3.5	0.1	11	dbSNP_134	100	19,8573	14.0+/-48.4	0,19,4277	yes	missense	OR2AG2	NM_001004490.1	125	0,21,6476	TT,TC,CC		0.2211,0.0454,0.1616	probably-damaging	233/317	6789492	21,12973	2201	4296	6497	SO:0001583	missense	338755	exon1			TCCTCCCCTCATT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.697G>A	11.37:g.6789492C>T	ENSP00000342697:p.Gly233Arg	199.0	0.0	0		179.0	145.0	0.810056	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.95	2.092121	0.36952	4.54E-4	0.002211	ENSG00000188124	ENST00000338569	T	0.00295	8.25	4.47	3.55	0.40652	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000084	T	0.00496	0.0016	M	0.85197	2.74	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28554	-1.0040	10	0.87932	D	0	.	10.7934	0.46447	0.0:0.9061:0.0:0.0939	.	233	A6NM03	O2AG2_HUMAN	R	233	ENSP00000342697:G233R	ENSP00000342697:G233R	G	-	1	0	OR2AG2	6746068	0.000000	0.05858	0.111000	0.21465	0.605000	0.37080	0.158000	0.16422	1.480000	0.48289	0.655000	0.94253	GGG	C|0.999;T|0.001	0.001	strong		0.502	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
CCDC64B	146439	hgsc.bcm.edu	37	16	3085326	3085326	+	Missense_Mutation	SNP	C	C	T	rs71386699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3085326C>T	ENST00000572449.1	-	2	234	c.172G>A	c.(172-174)Gag>Aag	p.E58K	RP11-473M20.5_ENST00000382225.3_RNA|CCDC64B_ENST00000573514.1_5'Flank|CCDC64B_ENST00000389347.4_Missense_Mutation_p.E58K			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	58										breast(1)|endometrium(2)|large_intestine(1)	4						AGGTCTTTCTCCTTCTGCTGC	0.647													C|||	45	0.00898562	0.0023	0.0173	5008	,	,		11912	0.0		0.0258	False		,,,				2504	0.0041				p.E58K		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G172A						PASS	.	C	LYS/GLU	12,3838		0,12,1913	10.0	11.0	11.0		172	5.1	1.0	16	dbSNP_130	11	204,8038		3,198,3920	yes	missense	CCDC64B	NM_001103175.1	56	3,210,5833	TT,TC,CC		2.4751,0.3117,1.7863	benign	58/509	3085326	216,11876	1925	4121	6046	SO:0001583	missense	146439	exon1			CTTTCTCCTTCTG	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.172G>A	16.37:g.3085326C>T	ENSP00000459043:p.Glu58Lys	132.0	0.0	0		132.0	17.0	0.128788	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	21.5	4.163784	0.78226	0.003117	0.024751	ENSG00000162069	ENST00000389347	T	0.05513	3.43	5.08	5.08	0.68730	.	0.063133	0.64402	D	0.000009	T	0.08088	0.0202	M	0.71036	2.16	0.50813	D	0.999892	D	0.64830	0.994	D	0.63488	0.915	T	0.00044	-1.2219	10	0.62326	D	0.03	-26.8836	15.9724	0.80031	0.0:1.0:0.0:0.0	.	58	A1A5D9	BICR2_HUMAN	K	58	ENSP00000373998:E58K	ENSP00000373998:E58K	E	-	1	0	CCDC64B	3025327	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.271000	0.72569	2.361000	0.80049	0.457000	0.33378	GAG	C|0.985;T|0.015	0.015	strong		0.647	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
TET1	80312	hgsc.bcm.edu	37	10	70332312	70332312	+	Missense_Mutation	SNP	C	C	T	rs138684329		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70332312C>T	ENST00000373644.4	+	2	426	c.217C>T	c.(217-219)Ctt>Ttt	p.L73F		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	73					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AGTCAGAAGCCTTCTGACAAG	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.L73F		Atlas-SNP	.											.	TET1	255	.	0			c.C217T						PASS	.	C	PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	71.0	77.0	75.0		217	4.3	1.0	10	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TET1	NM_030625.2	22	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	73/2137	70332312	3,13003	2203	4300	6503	SO:0001583	missense	80312	exon2			AGAAGCCTTCTGA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.217C>T	10.37:g.70332312C>T	ENSP00000362748:p.Leu73Phe	100.0	0.0	0		97.0	43.0	0.443299	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.23	2.472520	0.43942	2.27E-4	2.33E-4	ENSG00000138336	ENST00000373644	T	0.08984	3.03	5.24	4.32	0.51571	.	0.000000	0.44902	D	0.000417	T	0.05135	0.0137	N	0.19112	0.55	0.24628	N	0.993634	B	0.33748	0.423	B	0.31751	0.135	T	0.37865	-0.9687	10	0.27082	T	0.32	.	7.5134	0.27587	0.2035:0.7101:0.0:0.0864	.	73	Q8NFU7	TET1_HUMAN	F	73	ENSP00000362748:L73F	ENSP00000362748:L73F	L	+	1	0	TET1	70002318	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.411000	0.44600	1.168000	0.42723	0.563000	0.77884	CTT	C|1.000;T|0.000	0.000	strong		0.423	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
PDCD11	22984	hgsc.bcm.edu	37	10	105205260	105205260	+	Missense_Mutation	SNP	A	A	G	rs151054853		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:105205260A>G	ENST00000369797.3	+	36	5664	c.5570A>G	c.(5569-5571)aAg>aGg	p.K1857R		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1857					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GTCAAGGCCAAGGCCCTGGAG	0.587													A|||	1	0.000199681	0.0	0.0	5008	,	,		19265	0.0		0.001	False		,,,				2504	0.0				p.K1857R		Atlas-SNP	.											.	PDCD11	160	.	0			c.A5570G						PASS	.	A	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	115.0	96.0	102.0		5570	5.6	1.0	10	dbSNP_134	102	31,8569	19.8+/-62.0	0,31,4269	yes	missense	PDCD11	NM_014976.1	26	0,32,6471	GG,GA,AA		0.3605,0.0227,0.246	probably-damaging	1857/1872	105205260	32,12974	2203	4300	6503	SO:0001583	missense	22984	exon36			AGGCCAAGGCCCT	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5570A>G	10.37:g.105205260A>G	ENSP00000358812:p.Lys1857Arg	177.0	0.0	0		134.0	78.0	0.58209	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.812885	0.70912	2.27E-4	0.003605	ENSG00000148843	ENST00000369797	T	0.22743	1.94	5.6	5.6	0.85130	Suppressor of forked (1);	0.087859	0.85682	D	0.000000	T	0.34077	0.0885	L	0.41027	1.25	0.58432	D	0.999993	D	0.89917	1.0	D	0.77557	0.99	T	0.03739	-1.1008	10	0.23302	T	0.38	-26.404	12.0882	0.53710	0.8159:0.1841:0.0:0.0	.	1857	Q14690	RRP5_HUMAN	R	1857	ENSP00000358812:K1857R	ENSP00000358812:K1857R	K	+	2	0	PDCD11	105195250	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.030000	0.76484	2.143000	0.66587	0.459000	0.35465	AAG	A|0.998;G|0.002	0.002	strong		0.587	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
ABHD4	63874	hgsc.bcm.edu	37	14	23072905	23072905	+	Silent	SNP	C	C	G	rs540141952		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23072905C>G	ENST00000428304.2	+	4	631	c.561C>G	c.(559-561)ccC>ccG	p.P187P	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	187					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		TCCGTGCACCCCCAGCCTGGG	0.557																																					p.P187P		Atlas-SNP	.											.	ABHD4	30	.	0			c.C561G						PASS	.						109.0	102.0	105.0					14																	23072905		2203	4300	6503	SO:0001819	synonymous_variant	63874	exon4			TGCACCCCCAGCC	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"""Abhydrolase domain containing"""	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.561C>G	14.37:g.23072905C>G		198.0	0.0	0		183.0	91.0	0.497268	NM_022060	B4DDH7|Q9H9E0	Silent	SNP	ENST00000428304.2	37	CCDS9572.1																																																																																			.	.	none		0.557	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3		
GMIP	51291	hgsc.bcm.edu	37	19	19745962	19745962	+	Missense_Mutation	SNP	G	G	A	rs372547969		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19745962G>A	ENST00000203556.4	-	16	1758	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W	GMIP_ENST00000586269.1_5'UTR|GMIP_ENST00000445806.2_Missense_Mutation_p.R512W|GMIP_ENST00000587238.1_Missense_Mutation_p.R515W	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	541					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GCTGGGAGCCGCCTGTGTCCA	0.607																																					p.R541W		Atlas-SNP	.											.	GMIP	55	.	0			c.C1621T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	29.0	31.0	30.0		1621	1.2	0.8	19		30	1,8599	1.2+/-3.3	0,1,4299	no	missense	GMIP	NM_016573.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	541/971	19745962	1,13005	2203	4300	6503	SO:0001583	missense	51291	exon16			GGAGCCGCCTGTG	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"""Rho GTPase activating proteins"""	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.1621C>T	19.37:g.19745962G>A	ENSP00000203556:p.Arg541Trp	122.0	0.0	0		94.0	6.0	0.0638298	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	37	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086928	0.55861	0.0	1.16E-4	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.23147	1.93;1.92	4.93	1.24	0.21308	.	0.558941	0.13840	N	0.359079	T	0.25901	0.0631	N	0.14661	0.345	0.35031	D	0.758787	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.56648	0.803;0.702;0.803	T	0.41787	-0.9489	10	0.87932	D	0	-14.6413	11.5425	0.50675	0.0:0.0:0.2902:0.7098	.	512;515;541	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	W	541;512	ENSP00000203556:R541W;ENSP00000397075:R512W	ENSP00000203556:R541W	R	-	1	2	GMIP	19606962	1.000000	0.71417	0.752000	0.31206	0.569000	0.35902	4.044000	0.57361	0.419000	0.25927	0.462000	0.41574	CGG	.	.	weak		0.607	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573	
PDE11A	50940	hgsc.bcm.edu	37	2	178528641	178528641	+	Missense_Mutation	SNP	G	G	C	rs61306957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178528641G>C	ENST00000286063.6	-	19	2916	c.2599C>G	c.(2599-2601)Cgg>Ggg	p.R867G	PDE11A_ENST00000450799.2_Missense_Mutation_p.R58G|PDE11A_ENST00000358450.4_Missense_Mutation_p.R617G|PDE11A_ENST00000389683.3_Missense_Mutation_p.R423G|PDE11A_ENST00000409504.1_Missense_Mutation_p.R509G|PDE11A_ENST00000449286.2_Missense_Mutation_p.R509G	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	867	Catalytic. {ECO:0000250}.		R -> G (in dbSNP:rs61306957). {ECO:0000269|PubMed:16767104}.		blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	AGTTGCAACCGAGGCAGTTCA	0.453									Primary Pigmented Nodular Adrenocortical Disease, Familial				G|||	160	0.0319489	0.0393	0.0115	5008	,	,		18868	0.0109		0.0199	False		,,,				2504	0.0706				p.R867G		Atlas-SNP	.											.	PDE11A	283	.	0			c.C2599G	GRCh37	CM067442	PDE11A	M	rs61306957	PASS	.	G	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	190,4216	122.1+/-159.5	5,180,2018	114.0	100.0	104.0		1267,1849,1525,2599	4.1	1.0	2	dbSNP_129	104	149,8451	72.3+/-134.9	2,145,4153	yes	missense,missense,missense,missense	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	125,125,125,125	7,325,6171	CC,CG,GG		1.7326,4.3123,2.6065	benign,benign,benign,benign	423/490,617/684,509/576,867/934	178528641	339,12667	2203	4300	6503	SO:0001583	missense	50940	exon19	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	GCAACCGAGGCAG	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2599C>G	2.37:g.178528641G>C	ENSP00000286063:p.Arg867Gly	111.0	0.0	0		70.0	34.0	0.485714	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	38|38	0.0173992673992674|0.0173992673992674	14|14	0.028455284552845527|0.028455284552845527	5|5	0.013812154696132596|0.013812154696132596	5|5	0.008741258741258742|0.008741258741258742	14|14	0.018469656992084433|0.018469656992084433	G|G	10.44|10.44	1.352134|1.352134	0.24512|0.24512	0.043123|0.043123	0.017326|0.017326	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000436700	T;T;T;T;T;T|.	0.76578|.	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03|.	6.07|6.07	4.14|4.14	0.48551|0.48551	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.11836|0.11836	0.0288|0.0288	N|N	0.12569|0.12569	0.235|0.235	0.41027|0.41027	D|D	0.985121|0.985121	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.08055|.	0.001;0.003|.	T|T	0.05767|0.05767	-1.0865|-1.0865	10|5	0.23302|.	T|.	0.38|.	.|.	11.939|11.939	0.52890|0.52890	0.0:0.1083:0.6827:0.2089|0.0:0.1083:0.6827:0.2089	rs61306957|rs61306957	617;867|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	G|W	867;617;58;509;423;509|69	ENSP00000286063:R867G;ENSP00000351232:R617G;ENSP00000387964:R58G;ENSP00000386539:R509G;ENSP00000374333:R423G;ENSP00000390599:R509G|.	ENSP00000286063:R867G|.	R|S	-|-	1|2	2|0	PDE11A|PDE11A	178236887|178236887	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.923000|2.923000	0.48868|0.48868	1.529000|1.529000	0.49120|0.49120	0.655000|0.655000	0.94253|0.94253	CGG|TCG	G|0.975;C|0.025	0.025	strong		0.453	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
BCS1L	617	hgsc.bcm.edu	37	2	219527857	219527857	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219527857G>A	ENST00000431802.1	+	8	1707	c.1008G>A	c.(1006-1008)agG>agA	p.R336R	BCS1L_ENST00000439945.1_Splice_Site_p.R336R|BCS1L_ENST00000392110.2_Splice_Site_p.R336R|BCS1L_ENST00000465706.1_3'UTR|BCS1L_ENST00000392109.1_Splice_Site_p.R336R|BCS1L_ENST00000392111.2_Splice_Site_p.R336R|BCS1L_ENST00000359273.3_Splice_Site_p.R336R|BCS1L_ENST00000412366.1_Splice_Site_p.R336R			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	336					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTCTCTCAGGCTGGACCCTG	0.602																																					p.R336R		Atlas-SNP	.											.	BCS1L	22	.	0			c.G1008A						PASS	.						73.0	76.0	75.0					2																	219527857		2203	4300	6503	SO:0001630	splice_region_variant	617	exon9			TCTCAGGCTGGAC	AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"""ATPases / AAA-type"", ""Mitochondrial respiratory chain complex assembly factors"""	1020	protein-coding gene	gene with protein product	"""GRACILE syndrome"", ""Bjornstad syndrome"""	603647	"""BCS1 (yeast homolog)-like"", ""BCS1-like (yeast)"", ""BCS1-like (S. cerevisiae)"""			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.1008-1G>A	2.37:g.219527857G>A		184.0	0.0	0		146.0	39.0	0.267123	NM_001257343	B3KTW9|Q7Z2V7	Silent	SNP	ENST00000431802.1	37	CCDS2419.1	.	.	.	.	.	.	.	.	.	.	G	4.628	0.116645	0.08881	.	.	ENSG00000074582	ENST00000426649	.	.	.	5.12	2.05	0.26809	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49542	-0.8929	4	.	.	.	.	8.9926	0.36033	0.2679:0.0:0.7321:0.0	.	.	.	.	T	118	.	.	A	+	1	0	BCS1L	219236101	1.000000	0.71417	0.998000	0.56505	0.156000	0.22039	3.543000	0.53633	0.207000	0.20607	-0.291000	0.09656	GCT	.	.	none		0.602	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	Silent
BTG2	7832	hgsc.bcm.edu	37	1	203274826	203274826	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203274826G>A	ENST00000290551.4	+	1	163	c.92G>A	c.(91-93)aGc>aAc	p.S31N	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	31					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GGCTGCGTGAGCGAGCAGAGG	0.711																																					p.S31N		Atlas-SNP	.											.	BTG2	16	.	0			c.G92A						PASS	.						16.0	16.0	16.0					1																	203274826		2157	4238	6395	SO:0001583	missense	7832	exon1			GCGTGAGCGAGCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.92G>A	1.37:g.203274826G>A	ENSP00000290551:p.Ser31Asn	132.0	0.0	0		165.0	44.0	0.266667	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	9.276	1.046979	0.19748	.	.	ENSG00000159388	ENST00000290551	T	0.22539	1.95	4.66	3.75	0.43078	Anti-proliferative protein (3);	0.175253	0.47455	N	0.000221	T	0.11324	0.0276	N	0.17800	0.525	0.32144	N	0.585114	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	10	0.14656	T	0.56	-0.1987	8.0794	0.30735	0.1867:0.0:0.8133:0.0	.	31	P78543	BTG2_HUMAN	N	31	ENSP00000290551:S31N	ENSP00000290551:S31N	S	+	2	0	BTG2	201541449	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.876000	0.48498	1.194000	0.43101	0.478000	0.44815	AGC	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
CEACAM19	56971	hgsc.bcm.edu	37	19	45176003	45176003	+	Missense_Mutation	SNP	A	A	G	rs201929208		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45176003A>G	ENST00000403660.3	+	2	401	c.191A>G	c.(190-192)aAc>aGc	p.N64S	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM19_ENST00000480278.1_3'UTR|CEACAM19_ENST00000358777.4_Missense_Mutation_p.N64S			Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 19	64						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	11	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				CAGGACTTCAACTGGTACCTG	0.567																																					p.N64S		Atlas-SNP	.											.	CEACAM19	27	.	0			c.A191G						PASS	.						103.0	75.0	84.0					19																	45176003		2203	4300	6503	SO:0001583	missense	56971	exon2			ACTTCAACTGGTA	AF406955	CCDS12641.1, CCDS46108.1	19q13.31	2013-01-11			ENSG00000186567	ENSG00000186567		"""Immunoglobulin superfamily / V-set domain containing"""	31951	protein-coding gene	gene with protein product		606691					Standard	NM_020219		Approved	CEAL1	uc002ozo.4	Q7Z692	OTTHUMG00000151528	ENST00000403660.3:c.191A>G	19.37:g.45176003A>G	ENSP00000384887:p.Asn64Ser	124.0	0.0	0		151.0	76.0	0.503311	NM_001127893	Q5XJ15|Q7Z693	Missense_Mutation	SNP	ENST00000403660.3	37	CCDS12641.1	.	.	.	.	.	.	.	.	.	.	A	6.496	0.459717	0.12342	.	.	ENSG00000186567	ENST00000358777;ENST00000403660	T;T	0.62941	-0.01;-0.01	4.18	-0.79	0.10932	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.319679	0.22466	N	0.059684	T	0.34774	0.0909	N	0.17764	0.52	0.21386	N	0.999705	B;B	0.17268	0.021;0.021	B;B	0.18871	0.023;0.023	T	0.08932	-1.0698	10	0.21014	T	0.42	-5.3844	1.0166	0.01509	0.296:0.1476:0.1065:0.4499	.	64;64	Q5XJ15;Q7Z692	.;CEA19_HUMAN	S	64	ENSP00000351627:N64S;ENSP00000384887:N64S	ENSP00000351627:N64S	N	+	2	0	CEACAM19	49867843	0.003000	0.15002	0.944000	0.38274	0.969000	0.65631	-0.536000	0.06135	-0.547000	0.06207	0.454000	0.30748	AAC	.	.	weak		0.567	CEACAM19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323022.1	NM_020219	
DCLK2	166614	hgsc.bcm.edu	37	4	151141918	151141918	+	Missense_Mutation	SNP	A	A	C	rs148315360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:151141918A>C	ENST00000296550.7	+	6	1874	c.1120A>C	c.(1120-1122)Ata>Cta	p.I374L	DCLK2_ENST00000302176.8_Missense_Mutation_p.I391L|DCLK2_ENST00000506325.1_Missense_Mutation_p.I373L	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	374					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TGACCGTTGCATAAGTCCTGA	0.413													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19679	0.0		0.002	False		,,,				2504	0.0				p.I391L	GBM(195;186 2215 13375 16801 37459)	Atlas-SNP	.											.	DCLK2	168	.	0			c.A1171C						PASS	.	A	LEU/ILE,LEU/ILE	4,4402	8.1+/-20.4	0,4,2199	131.0	105.0	114.0		1120,1171	-6.0	1.0	4	dbSNP_134	114	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	DCLK2	NM_001040260.3,NM_001040261.4	5,5	0,22,6481	CC,CA,AA		0.2093,0.0908,0.1692	benign,benign	374/767,391/784	151141918	22,12984	2203	4300	6503	SO:0001583	missense	166614	exon7			CGTTGCATAAGTC	BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1120A>C	4.37:g.151141918A>C	ENSP00000296550:p.Ile374Leu	215.0	0.0	0		134.0	71.0	0.529851	NM_001040261	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.88	1.475306	0.26511	9.08E-4	0.002093	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.63913	0.94;0.94;-0.07	5.49	-5.99	0.02213	.	0.793091	0.12274	N	0.483509	T	0.19327	0.0464	N	0.03608	-0.345	0.09310	N	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.39742	-0.9599	10	0.06494	T	0.89	.	8.557	0.33487	0.1693:0.6518:0.08:0.0989	.	391;373;374	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	L	374;373;391	ENSP00000296550:I374L;ENSP00000427235:I373L;ENSP00000303887:I391L	ENSP00000296550:I374L	I	+	1	0	DCLK2	151361368	0.004000	0.15560	0.970000	0.41538	0.777000	0.43975	-1.810000	0.01729	-0.498000	0.06632	0.533000	0.62120	ATA	A|0.998;C|0.002	0.002	strong		0.413	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	
ULK1	8408	hgsc.bcm.edu	37	12	132401058	132401058	+	Missense_Mutation	SNP	C	C	T	rs55815560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132401058C>T	ENST00000321867.4	+	20	2345	c.1994C>T	c.(1993-1995)tCg>tTg	p.S665L	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	665			S -> L (in dbSNP:rs55815560). {ECO:0000269|PubMed:17344846}.		autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CCCGACCTCTCGGAGGTGGGA	0.697													C|||	5	0.000998403	0.0	0.0	5008	,	,		15038	0.001		0.003	False		,,,				2504	0.001				p.S665L		Atlas-SNP	.											.	ULK1	92	.	0			c.C1994T						PASS	.	C	LEU/SER	1,4397	2.1+/-5.4	0,1,2198	37.0	43.0	41.0		1994	3.8	0.9	12	dbSNP_129	41	22,8572	16.6+/-54.9	0,22,4275	yes	missense	ULK1	NM_003565.2	145	0,23,6473	TT,TC,CC		0.256,0.0227,0.177	benign	665/1051	132401058	23,12969	2199	4297	6496	SO:0001583	missense	8408	exon20			ACCTCTCGGAGGT	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.1994C>T	12.37:g.132401058C>T	ENSP00000324560:p.Ser665Leu	60.0	0.0	0		61.0	30.0	0.491803	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	11.31	1.599607	0.28534	2.27E-4	0.00256	ENSG00000177169	ENST00000321867;ENST00000541761	T;T	0.29397	1.57;2.5	5.69	3.79	0.43588	.	1.033790	0.07680	N	0.936898	T	0.19685	0.0473	L	0.44542	1.39	0.20873	N	0.999836	B	0.09022	0.002	B	0.04013	0.001	T	0.04165	-1.0972	10	0.35671	T	0.21	-11.4096	7.8361	0.29371	0.365:0.5069:0.1281:0.0	rs55815560	665	O75385	ULK1_HUMAN	L	665;13	ENSP00000324560:S665L;ENSP00000444298:S13L	ENSP00000324560:S665L	S	+	2	0	ULK1	130967011	0.866000	0.29940	0.897000	0.35233	0.013000	0.08279	2.057000	0.41365	2.684000	0.91462	0.655000	0.94253	TCG	C|0.998;T|0.002	0.002	strong		0.697	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
ANKRD30A	91074	hgsc.bcm.edu	37	10	37486235	37486235	+	Missense_Mutation	SNP	G	G	A	rs201775035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37486235G>A	ENST00000602533.1	+	28	2572	c.2473G>A	c.(2473-2475)Gag>Aag	p.E825K	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E944K|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E825K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	881					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						ATCTGCCTTCGAGGTATTTAG	0.333													.|||	4	0.000798722	0.0	0.0	5008	,	,		18178	0.003		0.001	False		,,,				2504	0.0				p.E825K		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G2473A						scavenged	.	G	LYS/GLU	1,3605		0,1,1802	164.0	139.0	147.0		2473	-2.7	0.0	10		147	3,8151		0,3,4074	no	missense	ANKRD30A	NM_052997.2	56	0,4,5876	AA,AG,GG		0.0368,0.0277,0.034	possibly-damaging	825/1342	37486235	4,11756	1803	4077	5880	SO:0001583	missense	91074	exon28			GCCTTCGAGGTAT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2473G>A	10.37:g.37486235G>A	ENSP00000473551:p.Glu825Lys	328.0	1.0	0.00304878		292.0	18.0	0.0616438	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.726410	0.00694	2.77E-4	3.68E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.07114	3.22;3.22	1.36	-2.73	0.05950	.	.	.	.	.	T	0.02929	0.0087	N	0.01576	-0.805	0.09310	N	1	P	0.50272	0.933	P	0.52189	0.692	T	0.15838	-1.0423	9	0.02654	T	1	.	2.1426	0.03778	0.4051:0.3297:0.2652:0.0	.	881	Q9BXX3	AN30A_HUMAN	K	825;944	ENSP00000354432:E825K;ENSP00000363792:E944K	ENSP00000354432:E825K	E	+	1	0	ANKRD30A	37526241	0.016000	0.18221	0.008000	0.14137	0.002000	0.02628	-0.757000	0.04772	-0.171000	0.10797	-0.482000	0.04802	GAG	.	.	weak		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
PCCB	5096	hgsc.bcm.edu	37	3	136012637	136012637	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:136012637A>T	ENST00000251654.4	+	7	764	c.694A>T	c.(694-696)Aag>Tag	p.K232*	PCCB_ENST00000469217.1_Nonsense_Mutation_p.K252*|PCCB_ENST00000468777.1_Nonsense_Mutation_p.K263*|PCCB_ENST00000483687.1_Nonsense_Mutation_p.K213*|PCCB_ENST00000490504.1_Nonsense_Mutation_p.K175*|PCCB_ENST00000482086.1_Nonsense_Mutation_p.K116*|PCCB_ENST00000474833.1_3'UTR|PCCB_ENST00000478469.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000466072.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000462637.1_Nonsense_Mutation_p.K209*|PCCB_ENST00000471595.1_Nonsense_Mutation_p.K232*	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	232	Carboxyltransferase.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	TGATGTTGTGAAGTCTGTCAC	0.507																																					p.K252X		Atlas-SNP	.											.	PCCB	52	.	0			c.A754T						PASS	.						216.0	204.0	208.0					3																	136012637		2203	4300	6503	SO:0001587	stop_gained	5096	exon8			GTTGTGAAGTCTG		CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"""propionyl Coenzyme A carboxylase, beta polypeptide"""			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	ENST00000251654.4:c.694A>T	3.37:g.136012637A>T	ENSP00000251654:p.Lys232*	83.0	0.0	0		58.0	17.0	0.293103	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Nonsense_Mutation	SNP	ENST00000251654.4	37	CCDS3089.1	.	.	.	.	.	.	.	.	.	.	A	36	5.673289	0.96754	.	.	ENSG00000114054	ENST00000251654;ENST00000490504;ENST00000483687;ENST00000468777;ENST00000462637;ENST00000466072;ENST00000482086;ENST00000471595;ENST00000469217;ENST00000478469	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7115	0.69235	1.0:0.0:0.0:0.0	.	.	.	.	X	232;175;213;263;209;232;116;232;252;232	.	ENSP00000251654:K232X	K	+	1	0	PCCB	137495327	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.520000	0.90566	2.009000	0.58944	0.528000	0.53228	AAG	.	.	none		0.507	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1		
TMC6	11322	hgsc.bcm.edu	37	17	76117136	76117136	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76117136G>A	ENST00000590602.1	-	12	1652	c.1493C>T	c.(1492-1494)cCg>cTg	p.P498L	TMC6_ENST00000592076.1_Intron|TMC6_ENST00000322914.3_Missense_Mutation_p.P498L|TMC6_ENST00000591436.1_Missense_Mutation_p.P137L|TMC6_ENST00000322933.4_Missense_Mutation_p.P137L|TMC6_ENST00000392467.3_Missense_Mutation_p.P498L|TMC6_ENST00000589553.1_Missense_Mutation_p.P271L|TMC6_ENST00000306591.7_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	498					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGAGTCATGCGGCTCCAGGGC	0.632																																					p.P498L		Atlas-SNP	.											.	TMC6	42	.	0			c.C1493T						PASS	.						40.0	39.0	39.0					17																	76117136		2203	4300	6503	SO:0001583	missense	11322	exon12			TCATGCGGCTCCA	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.1493C>T	17.37:g.76117136G>A	ENSP00000465261:p.Pro498Leu	117.0	0.0	0		129.0	71.0	0.550388	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	4.500	0.092789	0.08632	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933	T;T;T	0.70399	-0.1;-0.1;-0.48	3.93	0.273	0.15650	.	0.837178	0.10830	N	0.629444	T	0.44414	0.1292	N	0.19112	0.55	0.33151	D	0.545754	B;P;B;B	0.39094	0.099;0.659;0.09;0.259	B;B;B;B	0.24848	0.033;0.056;0.005;0.027	T	0.48080	-0.9066	10	0.42905	T	0.14	-12.4351	4.296	0.10901	0.0:0.191:0.2303:0.5788	.	271;498;498;137	Q7Z403-4;B3KTU5;Q7Z403;Q7Z403-3	.;.;TMC6_HUMAN;.	L	498;498;137	ENSP00000313408:P498L;ENSP00000376260:P498L;ENSP00000313479:P137L	ENSP00000313408:P498L	P	-	2	0	TMC6	73628731	0.022000	0.18835	0.402000	0.26371	0.729000	0.41735	-0.010000	0.12743	-0.092000	0.12417	0.462000	0.41574	CCG	.	.	none		0.632	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1		
NFATC4	4776	hgsc.bcm.edu	37	14	24838953	24838953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24838953C>T	ENST00000250373.4	+	2	490	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	NFATC4_ENST00000539237.2_Missense_Mutation_p.R149C|NFATC4_ENST00000553469.1_Missense_Mutation_p.R149C|NFATC4_ENST00000556169.1_Missense_Mutation_p.R105C|NFATC4_ENST00000554050.1_Missense_Mutation_p.R117C|NFATC4_ENST00000557451.1_Missense_Mutation_p.R47C|NFATC4_ENST00000554344.1_Missense_Mutation_p.R47C|NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000553879.1_Missense_Mutation_p.R47C|NFATC4_ENST00000413692.2_Missense_Mutation_p.R180C|NFATC4_ENST00000554591.1_Missense_Mutation_p.R180C|NFATC4_ENST00000554661.1_Missense_Mutation_p.R47C|NFATC4_ENST00000556279.1_Missense_Mutation_p.R149C|NFATC4_ENST00000424781.2_Missense_Mutation_p.R130C|NFATC4_ENST00000554966.1_Missense_Mutation_p.R130C|NFATC4_ENST00000555590.1_Missense_Mutation_p.R130C|NFATC4_ENST00000555453.1_Missense_Mutation_p.R105C|NFATC4_ENST00000422617.3_Missense_Mutation_p.R105C|NFATC4_ENST00000553708.1_Missense_Mutation_p.R117C	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	117	Calcineurin-binding.|Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		TCCCAGCATCCGCATCACCTC	0.687																																					p.R180C		Atlas-SNP	.											.	NFATC4	115	.	0			c.C538T						PASS	.						12.0	14.0	13.0					14																	24838953		2190	4254	6444	SO:0001583	missense	4776	exon3			AGCATCCGCATCA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.349C>T	14.37:g.24838953C>T	ENSP00000250373:p.Arg117Cys	65.0	0.0	0		70.0	4.0	0.0571429	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491135	0.84962	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000554903;ENST00000250373;ENST00000553708;ENST00000557674;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35	3.76	3.76	0.43208	.	0.096786	0.44097	D	0.000481	T	0.27384	0.0672	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;P	0.67725	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.953;0.953;0.93;0.953;0.93;0.93;0.853	T	0.04579	-1.0941	10	0.87932	D	0	-5.8251	13.1624	0.59552	0.0:1.0:0.0:0.0	.	105;105;149;149;130;130;130;180;180;105;149;94;180;117	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	C	180;180;130;130;130;149;149;149;117;117;117;117;94;47;47;47;105;47;105;105	ENSP00000388910:R180C;ENSP00000452039:R180C;ENSP00000451224:R130C;ENSP00000450644:R130C;ENSP00000388668:R130C;ENSP00000439350:R149C;ENSP00000452270:R149C;ENSP00000451502:R149C;ENSP00000451151:R117C;ENSP00000451853:R117C;ENSP00000250373:R117C;ENSP00000450590:R117C;ENSP00000452352:R94C;ENSP00000452349:R47C;ENSP00000450469:R47C;ENSP00000450733:R47C;ENSP00000451454:R105C;ENSP00000451284:R47C;ENSP00000396788:R105C;ENSP00000450686:R105C	ENSP00000250373:R117C	R	+	1	0	NFATC4	23908793	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.890000	0.75633	1.943000	0.56356	0.558000	0.71614	CGC	.	.	none		0.687	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
MUC16	94025	hgsc.bcm.edu	37	19	9013905	9013905	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9013905C>G	ENST00000397910.4	-	33	38688	c.38485G>C	c.(38485-38487)Ggg>Cgg	p.G12829R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12831				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGAGGTCCCAGGAGCTGAA	0.502																																					p.G12829R		Atlas-SNP	.											.	MUC16	4315	.	0			c.G38485C						PASS	.						68.0	61.0	63.0					19																	9013905		1920	4127	6047	SO:0001583	missense	94025	exon33			AGGTCCCAGGAGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38485G>C	19.37:g.9013905C>G	ENSP00000381008:p.Gly12829Arg	103.0	0.0	0		83.0	18.0	0.216867	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.580	1.123389	0.20959	.	.	ENSG00000181143	ENST00000397910	T	0.01918	4.56	1.48	1.48	0.22813	.	.	.	.	.	T	0.07458	0.0188	M	0.73962	2.25	.	.	.	D	0.71674	0.998	P	0.58520	0.84	T	0.10730	-1.0617	8	0.87932	D	0	.	6.367	0.21461	0.0:1.0:0.0:0.0	.	12829	B5ME49	.	R	12829	ENSP00000381008:G12829R	ENSP00000381008:G12829R	G	-	1	0	MUC16	8874905	0.000000	0.05858	0.075000	0.20258	0.028000	0.11728	-0.025000	0.12413	1.121000	0.41925	0.484000	0.47621	GGG	.	.	none		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KANK2	25959	hgsc.bcm.edu	37	19	11303618	11303618	+	Missense_Mutation	SNP	G	G	A	rs144821191		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11303618G>A	ENST00000586659.1	-	4	1452	c.1138C>T	c.(1138-1140)Cgc>Tgc	p.R380C	KANK2_ENST00000589359.1_Missense_Mutation_p.R380C|KANK2_ENST00000432929.2_Missense_Mutation_p.R380C|KANK2_ENST00000589894.1_Missense_Mutation_p.R380C|KANK2_ENST00000355150.5_Missense_Mutation_p.R380C			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	380					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCCTGGCTGCGGAACACAGGT	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16197	0.0		0.001	False		,,,				2504	0.0				p.R380C		Atlas-SNP	.											.	KANK2	47	.	0			c.C1138T						PASS	.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	70.0	74.0	72.0		1138,1138	0.2	1.0	19	dbSNP_134	72	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	180,180	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	benign,benign	380/852,380/860	11303618	11,12995	2203	4300	6503	SO:0001583	missense	25959	exon2			GGCTGCGGAACAC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1138C>T	19.37:g.11303618G>A	ENSP00000465650:p.Arg380Cys	165.0	0.0	0		131.0	65.0	0.496183	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.976	0.550018	0.13374	2.27E-4	0.001163	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37235	1.21;1.21	4.11	0.147	0.14838	.	0.085848	0.43747	D	0.000540	T	0.24774	0.0601	L	0.45581	1.43	0.33354	D	0.571462	B;B;B	0.13145	0.001;0.001;0.007	B;B;B	0.06405	0.002;0.0;0.002	T	0.10474	-1.0628	10	0.37606	T	0.19	-34.2083	5.155	0.15031	0.305:0.0:0.546:0.149	.	380;380;380	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	C	380	ENSP00000395650:R380C;ENSP00000347276:R380C	ENSP00000347276:R380C	R	-	1	0	KANK2	11164618	0.023000	0.18921	0.998000	0.56505	0.366000	0.29705	0.248000	0.18198	0.224000	0.20940	-0.448000	0.05591	CGC	G|0.999;A|0.001	0.001	strong		0.642	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
RFTN2	130132	hgsc.bcm.edu	37	2	198460748	198460748	+	Silent	SNP	T	T	G	rs77442629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198460748T>G	ENST00000295049.4	-	8	1736	c.1200A>C	c.(1198-1200)ccA>ccC	p.P400P		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	400					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TCCACATAACTGGCCTCTGAA	0.328													T|||	12	0.00239617	0.0008	0.0	5008	,	,		17368	0.0		0.0109	False		,,,				2504	0.0				p.P400P		Atlas-SNP	.											.	RFTN2	68	.	0			c.A1200C						PASS	.	T		5,4401	9.9+/-24.2	0,5,2198	100.0	90.0	93.0		1200	-4.7	0.0	2	dbSNP_132	93	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	RFTN2	NM_144629.2		0,69,6434	GG,GT,TT		0.7442,0.1135,0.5305		400/502	198460748	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	130132	exon8			CATAACTGGCCTC	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 11"""	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.1200A>C	2.37:g.198460748T>G		83.0	0.0	0		65.0	30.0	0.461538	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Silent	SNP	ENST00000295049.4	37	CCDS2323.1																																																																																			T|0.995;G|0.005	0.005	strong		0.328	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629	
ZNF416	55659	hgsc.bcm.edu	37	19	58084605	58084605	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58084605C>G	ENST00000196489.3	-	4	889	c.667G>C	c.(667-669)Gag>Cag	p.E223Q		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		TGGCTGGACTCTCTCCTGCAT	0.438																																					p.E223Q		Atlas-SNP	.											.	ZNF416	50	.	0			c.G667C						PASS	.						140.0	142.0	141.0					19																	58084605		2203	4300	6503	SO:0001583	missense	55659	exon4			TGGACTCTCTCCT	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.667G>C	19.37:g.58084605C>G	ENSP00000196489:p.Glu223Gln	178.0	0.0	0		174.0	108.0	0.62069	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	C	8.461	0.855209	0.17106	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.07444	3.19	3.65	1.43	0.22495	.	.	.	.	.	T	0.05502	0.0145	L	0.27053	0.805	0.09310	N	1	B	0.30361	0.277	B	0.25759	0.063	T	0.36720	-0.9736	9	0.66056	D	0.02	.	4.8172	0.13372	0.1732:0.6307:0.0:0.1961	.	223	Q9BWM5	ZN416_HUMAN	Q	223;209;203	ENSP00000196489:E223Q	ENSP00000196489:E223Q	E	-	1	0	ZNF416	62776417	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-0.488000	0.06497	0.334000	0.23590	0.655000	0.94253	GAG	.	.	none		0.438	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
DNA2	1763	hgsc.bcm.edu	37	10	70191970	70191970	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70191970A>G	ENST00000358410.3	-	12	1916	c.1866T>C	c.(1864-1866)atT>atC	p.I622I	DNA2_ENST00000399180.2_Silent_p.I708I|DNA2_ENST00000399179.2_Silent_p.I622I	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	622	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TACCCTTTAGAATGCAGGCAA	0.323																																					p.I622I		Atlas-SNP	.											.	DNA2	76	.	0			c.T1866C						PASS	.						132.0	126.0	128.0					10																	70191970		1836	4087	5923	SO:0001819	synonymous_variant	1763	exon12			CTTTAGAATGCAG	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1866T>C	10.37:g.70191970A>G		177.0	0.0	0		150.0	6.0	0.04	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
IGSF8	93185	hgsc.bcm.edu	37	1	160064697	160064697	+	Missense_Mutation	SNP	C	C	T	rs200550632		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160064697C>T	ENST00000368086.1	-	2	620	c.404G>A	c.(403-405)cGc>cAc	p.R135H	IGSF8_ENST00000460351.1_5'UTR|IGSF8_ENST00000314485.7_Missense_Mutation_p.R135H			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	135	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GCCCAGGTAGCGGGTATCAGT	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		18151	0.0		0.001	False		,,,				2504	0.0				p.R135H		Atlas-SNP	.											.	IGSF8	59	.	0			c.G404A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	34.0	37.0	36.0		404,404	-1.3	0.9	1		36	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IGSF8	NM_001206665.2,NM_052868.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	135/614,135/614	160064697	1,13005	2203	4300	6503	SO:0001583	missense	93185	exon2			AGGTAGCGGGTAT	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.404G>A	1.37:g.160064697C>T	ENSP00000357065:p.Arg135His	69.0	0.0	0		86.0	54.0	0.627907	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	37	CCDS1195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.12	3.552769	0.65425	0.0	1.16E-4	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417	T;T;T	0.10382	3.47;3.47;2.88	4.89	-1.29	0.09288	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.619503	0.14945	N	0.289261	T	0.03390	0.0098	L	0.42245	1.32	0.26281	N	0.978279	P	0.48694	0.914	B	0.43251	0.413	T	0.35101	-0.9802	10	0.56958	D	0.05	-5.5588	6.2467	0.20823	0.0:0.2743:0.1448:0.5809	.	135	Q969P0	IGSF8_HUMAN	H	135	ENSP00000316664:R135H;ENSP00000357065:R135H;ENSP00000397464:R135H	ENSP00000316664:R135H	R	-	2	0	IGSF8	158331321	0.085000	0.21516	0.917000	0.36280	0.965000	0.64279	-0.605000	0.05661	-0.104000	0.12154	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	strong		0.627	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68765205C>T	ENST00000303795.4	+	7	1177	c.1006C>T	c.(1006-1008)Ctt>Ttt	p.L336F	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	336			L -> F (in dbSNP:rs13404469).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGGCGACTCACTTCAGGATGA	0.423													T|||	395	0.0788738	0.1483	0.0735	5008	,	,		18007	0.005		0.0726	False		,,,				2504	0.0716				p.L336F		Atlas-SNP	.											.	APLF	69	.	0			c.C1006T						PASS	.	T	PHE/LEU	637,3769		51,535,1617	92.0	86.0	88.0		1006	4.0	0.0	2	dbSNP_121	88	695,7905		33,629,3638	yes	missense	APLF	NM_173545.2	22	84,1164,5255	TT,TC,CC		8.0814,14.4576,10.2414	benign	336/512	68765205	1332,11674	2203	4300	6503	SO:0001583	missense	200558	exon7			GACTCACTTCAGG	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1006C>T	2.37:g.68765205C>T	ENSP00000307004:p.Leu336Phe	203.0	1.0	0.00492611		187.0	94.0	0.502674	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	151	0.06913919413919414	62	0.12601626016260162	28	0.07734806629834254	4	0.006993006993006993	57	0.07519788918205805	.	0.181	-1.061812	0.01950	0.144576	0.080814	ENSG00000169621	ENST00000303795	T	0.23950	1.88	5.19	4.0	0.46444	.	1.310930	0.04804	N	0.434102	T	0.00073	0.0002	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.26408	T	0.33	.	8.0877	0.30782	0.0:0.1667:0.0:0.8333	rs13404469;rs52799369;rs13404469	336	Q8IW19	APLF_HUMAN	F	336	ENSP00000307004:L336F	ENSP00000307004:L336F	L	+	1	0	APLF	68618709	0.006000	0.16342	0.002000	0.10522	0.063000	0.16089	0.651000	0.24873	0.274000	0.22072	-0.381000	0.06696	CTT	C|0.910;T|0.090	0.090	strong		0.423	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
E2F1	1869	hgsc.bcm.edu	37	20	32266134	32266134	+	Missense_Mutation	SNP	C	C	T	rs35385772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:32266134C>T	ENST00000343380.5	-	4	737	c.598G>A	c.(598-600)Ggc>Agc	p.G200S	RP1-63M2.5_ENST00000606866.1_RNA	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	200	Dimerization. {ECO:0000255}.|Required for interaction with TRIM28.		G -> S (in dbSNP:rs35385772).		anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						AGCCGTCCGCCGACGCCCACT	0.652													C|||	64	0.0127796	0.0015	0.0274	5008	,	,		18426	0.0		0.0408	False		,,,				2504	0.002				p.G200S		Atlas-SNP	.											.	E2F1	41	.	0			c.G598A						PASS	.	C	SER/GLY	30,4376	36.0+/-67.5	0,30,2173	36.0	34.0	34.0		598	-3.4	0.0	20	dbSNP_126	34	224,8374	91.4+/-153.5	0,224,4075	yes	missense	E2F1	NM_005225.2	56	0,254,6248	TT,TC,CC		2.6053,0.6809,1.9532	benign	200/438	32266134	254,12750	2203	4299	6502	SO:0001583	missense	1869	exon4			GTCCGCCGACGCC		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.598G>A	20.37:g.32266134C>T	ENSP00000345571:p.Gly200Ser	115.0	0.0	0		98.0	45.0	0.459184	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	37	CCDS13224.1	41	0.018772893772893772	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	0.011	-1.707208	0.00719	0.006809	0.026053	ENSG00000101412	ENST00000343380	T	0.07908	3.15	5.16	-3.42	0.04825	.	1.060050	0.07264	N	0.867922	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.46133	-0.9213	10	0.07644	T	0.81	-2.1827	9.5138	0.39093	0.0:0.2833:0.1035:0.6132	rs35385772;rs61752051	200	Q01094	E2F1_HUMAN	S	200	ENSP00000345571:G200S	ENSP00000345571:G200S	G	-	1	0	E2F1	31729795	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.376000	0.07465	-0.774000	0.04590	-1.945000	0.00491	GGC	C|0.980;T|0.020	0.020	strong		0.652	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2		
PPP1R21	129285	hgsc.bcm.edu	37	2	48687054	48687054	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48687054A>C	ENST00000294952.8	+	5	694	c.537A>C	c.(535-537)ctA>ctC	p.L179L	PPP1R21_ENST00000281394.4_Silent_p.L179L|PPP1R21_ENST00000449090.2_Silent_p.L179L	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	179						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						AGGCTAAACTAGAAGTAAGCC	0.433																																					p.L179L		Atlas-SNP	.											.	PPP1R21	47	.	0			c.A537C						PASS	.						59.0	56.0	57.0					2																	48687054		2203	4300	6503	SO:0001819	synonymous_variant	129285	exon5			TAAACTAGAAGTA	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30595	protein-coding gene	gene with protein product			"""coiled-coil domain containing 128"", ""KLRAQ motif containing 1"""	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.537A>C	2.37:g.48687054A>C		166.0	0.0	0		334.0	33.0	0.0988024	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			.	.	none		0.433	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994	
FBN3	84467	hgsc.bcm.edu	37	19	8145928	8145928	+	Missense_Mutation	SNP	C	C	T	rs3848570|rs398088717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8145928C>T	ENST00000600128.1	-	59	7826	c.7412G>A	c.(7411-7413)cGc>cAc	p.R2471H	FBN3_ENST00000270509.2_Missense_Mutation_p.R2471H|FBN3_ENST00000601739.1_Missense_Mutation_p.R2471H			Q75N90	FBN3_HUMAN	fibrillin 3	2471	EGF-like 40; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		R -> H (in dbSNP:rs3848570).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GGGCGGACAGCGGCAGGTGAA	0.622													C|||	111	0.0221645	0.0083	0.0403	5008	,	,		17290	0.0		0.0467	False		,,,				2504	0.0256				p.R2471H		Atlas-SNP	.											.	FBN3	300	.	0			c.G7412A						PASS	.	C	HIS/ARG	55,4351	51.6+/-87.1	1,53,2149	60.0	55.0	56.0		7412	0.9	1.0	19	dbSNP_108	56	406,8194	126.0+/-184.5	7,392,3901	yes	missense	FBN3	NM_032447.3	29	8,445,6050	TT,TC,CC		4.7209,1.2483,3.5445	benign	2471/2810	8145928	461,12545	2203	4300	6503	SO:0001583	missense	84467	exon58			GGACAGCGGCAGG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.7412G>A	19.37:g.8145928C>T	ENSP00000470498:p.Arg2471His	28.0	0.0	0		23.0	9.0	0.391304	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	55	0.025183150183150184	3	0.006097560975609756	14	0.03867403314917127	0	0.0	38	0.05013192612137203	C	12.22	1.871409	0.33069	0.012483	0.047209	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.92545	-3.06	4.06	0.915	0.19366	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.310571	0.28436	N	0.015342	T	0.47691	0.1459	N	0.17312	0.475	0.27752	N	0.944128	B;B	0.21452	0.032;0.056	B;B	0.22753	0.041;0.027	T	0.62492	-0.6843	10	0.41790	T	0.15	.	5.5084	0.16866	0.0:0.3205:0.0:0.6795	rs3848570;rs3848570	2471;577	Q75N90;Q6ZNB8	FBN3_HUMAN;.	H	2471;577	ENSP00000270509:R2471H	ENSP00000270509:R2471H	R	-	2	0	FBN3	8051928	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	3.177000	0.50871	0.551000	0.29008	0.297000	0.19635	CGC	C|0.971;T|0.029	0.029	strong		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
TLN2	83660	hgsc.bcm.edu	37	15	63102153	63102153	+	Silent	SNP	C	C	T	rs150114385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63102153C>T	ENST00000561311.1	+	51	6923	c.6693C>T	c.(6691-6693)gaC>gaT	p.D2231D	TLN2_ENST00000306829.6_Silent_p.D2231D			Q9Y4G6	TLN2_HUMAN	talin 2	2231					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						ATGTCAGTGACGAGGTGAGAA	0.547													C|||	3	0.000599042	0.0015	0.0	5008	,	,		22983	0.0		0.001	False		,,,				2504	0.0				p.D2231D		Atlas-SNP	.											.	TLN2	253	.	0			c.C6693T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	128.0	94.0	106.0		6693	-4.9	0.9	15	dbSNP_134	106	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	TLN2	NM_015059.2		0,32,6471	TT,TC,CC		0.3372,0.0681,0.246		2231/2543	63102153	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon49			CAGTGACGAGGTG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6693C>T	15.37:g.63102153C>T		180.0	0.0	0		201.0	123.0	0.61194	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
ZNF426	79088	hgsc.bcm.edu	37	19	9641722	9641722	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9641722G>A	ENST00000535489.1	-	5	683	c.347C>T	c.(346-348)aCc>aTc	p.T116I	ZNF426_ENST00000253115.2_Missense_Mutation_p.T116I|ZNF426_ENST00000593003.1_Missense_Mutation_p.T78I|ZNF426_ENST00000589289.1_Intron			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						AGACCACTGGGTTTCAAGTCG	0.418																																					p.T116I		Atlas-SNP	.											.	ZNF426	56	.	0			c.C347T						PASS	.						110.0	104.0	106.0					19																	9641722		2203	4300	6503	SO:0001583	missense	79088	exon7			CACTGGGTTTCAA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.347C>T	19.37:g.9641722G>A	ENSP00000439017:p.Thr116Ile	113.0	0.0	0		111.0	27.0	0.243243	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	5.359	0.251581	0.10185	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.06608	3.28;3.28	1.53	0.414	0.16406	.	.	.	.	.	T	0.04679	0.0127	L	0.29908	0.895	0.09310	N	1	B;B	0.21688	0.059;0.017	B;B	0.14023	0.01;0.006	T	0.39881	-0.9592	9	0.41790	T	0.15	.	5.6008	0.17353	0.0:0.3499:0.6501:0.0	.	103;116	Q59EH4;Q9BUY5	.;ZN426_HUMAN	I	103;116;116	ENSP00000253115:T116I;ENSP00000439017:T116I	ENSP00000253115:T116I	T	-	2	0	ZNF426	9502722	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.134000	0.10436	0.183000	0.20059	0.460000	0.39030	ACC	.	.	none		0.418	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
CHRNA9	55584	hgsc.bcm.edu	37	4	40339250	40339250	+	Silent	SNP	T	T	C	rs55998310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:40339250T>C	ENST00000310169.2	+	3	373	c.234T>C	c.(232-234)acT>acC	p.T78T		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	78					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	AAATTCTGACTGCTTATTTGT	0.468													T|||	20	0.00399361	0.0008	0.0014	5008	,	,		20941	0.0		0.0149	False		,,,				2504	0.0031				p.T78T	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.T234C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	103.0	80.0	88.0		234	-11.7	0.0	4	dbSNP_129	88	93,8507	51.9+/-112.3	0,93,4207	no	coding-synonymous	CHRNA9	NM_017581.2		0,96,6407	CC,CT,TT		1.0814,0.0681,0.7381		78/480	40339250	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	55584	exon3			TCTGACTGCTTAT	AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	14079	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 9 (neuronal)"""	605116	"""cholinergic receptor, nicotinic, alpha polypeptide 9"""				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.234T>C	4.37:g.40339250T>C		137.0	0.0	0		156.0	70.0	0.448718	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																			T|0.993;C|0.007	0.007	strong		0.468	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1		
CTDP1	9150	hgsc.bcm.edu	37	18	77455227	77455227	+	Missense_Mutation	SNP	C	C	T	rs115044443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77455227C>T	ENST00000299543.7	+	2	464	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CTDP1_ENST00000075430.7_Missense_Mutation_p.A106V	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	106					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TTTTGTAGAGCGGTTCTGGTG	0.438													C|||	99	0.0197684	0.0613	0.0072	5008	,	,		16271	0.0		0.0119	False		,,,				2504	0.001				p.A106V		Atlas-SNP	.											.	CTDP1	67	.	0			c.C317T						PASS	.	C	,VAL/ALA,VAL/ALA	222,4184	135.7+/-171.8	5,212,1986	121.0	109.0	113.0		,317,317	3.9	0.0	18	dbSNP_132	113	125,8475	64.2+/-126.4	0,125,4175	yes	utr-5,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,64,64	5,337,6161	TT,TC,CC		1.4535,5.0386,2.668	,benign,benign	,106/962,106/868	77455227	347,12659	2203	4300	6503	SO:0001583	missense	9150	exon2			GTAGAGCGGTTCT	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.317C>T	18.37:g.77455227C>T	ENSP00000299543:p.Ala106Val	193.0	0.0	0		119.0	40.0	0.336134	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	43	0.019688644688644688	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	14.60	2.584590	0.46110	0.050386	0.014535	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.10382	2.9;2.88	4.8	3.86	0.44501	.	0.283877	0.39615	N	0.001318	T	0.01254	0.0041	M	0.65975	2.015	0.21256	N	0.999743	D;P	0.53312	0.959;0.931	B;B	0.40165	0.321;0.171	T	0.20075	-1.0286	10	0.27785	T	0.31	-21.0839	14.1115	0.65123	0.0:0.6821:0.3179:0.0	.	106;106	Q9Y5B0-4;Q9Y5B0	.;CTDP1_HUMAN	V	106	ENSP00000299543:A106V;ENSP00000075430:A106V	ENSP00000075430:A106V	A	+	2	0	CTDP1	75556215	0.964000	0.33143	0.008000	0.14137	0.004000	0.04260	2.608000	0.46308	2.376000	0.81061	0.655000	0.94253	GCG	C|0.977;T|0.023	0.023	strong		0.438	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
MISP	126353	hgsc.bcm.edu	37	19	757234	757234	+	Silent	SNP	C	C	T	rs34384654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:757234C>T	ENST00000215582.6	+	2	391	c.288C>T	c.(286-288)cgC>cgT	p.R96R		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	96					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGTTTACCGCCTGGGCGCCA	0.667													C|||	41	0.0081869	0.0008	0.0043	5008	,	,		17750	0.0		0.0328	False		,,,				2504	0.0041				p.R96R		Atlas-SNP	.											C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	0			c.C288T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	60.0	53.0	55.0		288	1.2	0.0	19	dbSNP_126	55	188,8412	82.9+/-145.4	2,184,4114	no	coding-synonymous	C19orf21	NM_173481.2		2,198,6303	TT,TC,CC		2.186,0.3177,1.5531		96/680	757234	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TTACCGCCTGGGC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.288C>T	19.37:g.757234C>T		111.0	0.0	0		63.0	31.0	0.492063	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			C|0.986;T|0.014	0.014	strong		0.667	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
CCDC168	643677	hgsc.bcm.edu	37	13	103390322	103390322	+	5'Flank	SNP	T	T	C	rs112442443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103390322T>C	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		tttctgttgctcttcaacttc	0.438													T|||	10	0.00199681	0.0	0.0029	5008	,	,		21687	0.0		0.006	False		,,,				2504	0.002				p.E4242G		Atlas-SNP	.											.	.	.	.	0			c.A12725G						PASS	.	T	GLY/GLU	2,1382		0,2,690	140.0	111.0	120.0		12725	-0.2	0.0	13	dbSNP_132	120	24,3158		0,24,1567	yes	missense	CCDC168	NM_001146197.1	98	0,26,2257	CC,CT,TT		0.7542,0.1445,0.5694		4242/7082	103390322	26,4540	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			TGTTGCTCTTCAA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103390322T>C	Exception_encountered	301.0	1.0	0.00332226		245.0	124.0	0.506122	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				T|0.995;C|0.005	0.005	strong		0.438	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
F2R	2149	hgsc.bcm.edu	37	5	76028669	76028669	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:76028669C>T	ENST00000319211.4	+	2	884	c.619C>T	c.(619-621)Ccc>Tcc	p.P207S		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	207					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	TGTGGTGTATCCCATGCAGTC	0.527																																					p.P207S		Atlas-SNP	.											.	F2R	58	.	0			c.C619T						PASS	.						184.0	181.0	182.0					5																	76028669		2203	4300	6503	SO:0001583	missense	2149	exon2			GTGTATCCCATGC	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"""GPCR / Class A : Protease activated receptors"""	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.619C>T	5.37:g.76028669C>T	ENSP00000321326:p.Pro207Ser	249.0	0.0	0		250.0	49.0	0.196	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Missense_Mutation	SNP	ENST00000319211.4	37	CCDS4032.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913750	0.92178	.	.	ENSG00000181104	ENST00000319211	T	0.60920	0.15	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80849	0.4702	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84195	0.0447	10	0.87932	D	0	-44.8056	19.0012	0.92834	0.0:1.0:0.0:0.0	.	207	P25116	PAR1_HUMAN	S	207	ENSP00000321326:P207S	ENSP00000321326:P207S	P	+	1	0	F2R	76064425	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.502000	0.81614	2.786000	0.95864	0.561000	0.74099	CCC	.	.	none		0.527	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2		
KLHL1	57626	hgsc.bcm.edu	37	13	70293616	70293616	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:70293616A>T	ENST00000377844.4	-	9	2659	c.1900T>A	c.(1900-1902)Tgt>Agt	p.C634S	KLHL1_ENST00000545028.1_Missense_Mutation_p.C441S	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	634					actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		CTCCTCTTACACATGGGAGCA	0.458																																					p.C634S		Atlas-SNP	.											.	KLHL1	164	.	0			c.T1900A						PASS	.						124.0	107.0	113.0					13																	70293616		2203	4300	6503	SO:0001583	missense	57626	exon9			TCTTACACATGGG	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"""Kelch-like"", ""BTB/POZ domain containing"""	6352	protein-coding gene	gene with protein product	"""Kelch-like protein 1"", ""Mayven-related protein 2"""	605332	"""kelch (Drosophila)-like 1"", ""kelch-like 1 (Drosophila)"""			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.1900T>A	13.37:g.70293616A>T	ENSP00000367075:p.Cys634Ser	106.0	0.0	0		82.0	15.0	0.182927	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	A	6.361	0.434642	0.12045	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.64991	-0.13;-0.13	5.82	5.82	0.92795	Galactose oxidase, beta-propeller (1);	0.082942	0.52532	D	0.000067	T	0.24236	0.0587	N	0.00178	-1.915	0.45261	D	0.998261	B;B	0.09022	0.002;0.002	B;B	0.15052	0.012;0.012	T	0.49688	-0.8913	10	0.02654	T	1	.	16.171	0.81817	1.0:0.0:0.0:0.0	.	634;634	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	S	634;441	ENSP00000367075:C634S;ENSP00000439602:C441S	ENSP00000367075:C634S	C	-	1	0	KLHL1	69191617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.228000	0.51270	2.211000	0.71520	0.533000	0.62120	TGT	.	.	none		0.458	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866	
LRRK2	120892	hgsc.bcm.edu	37	12	40677936	40677936	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:40677936G>A	ENST00000298910.7	+	19	2558		c.e19+1		LRRK2_ENST00000343742.2_Splice_Site	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AAACAAACAAGTAAGTAACAA	0.308																																					.		Atlas-SNP	.											.	LRRK2	763	.	0			c.2500+1G>A						PASS	.						65.0	71.0	69.0					12																	40677936		2202	4300	6502	SO:0001630	splice_region_variant	120892	exon19			AAACAAGTAAGTA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2500+1G>A	12.37:g.40677936G>A		39.0	0.0	0		43.0	13.0	0.302326	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Splice_Site	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510681	0.64522	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7573	0.91837	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRK2	38964203	1.000000	0.71417	0.993000	0.49108	0.716000	0.41182	5.970000	0.70431	2.498000	0.84270	0.591000	0.81541	.	.	.	none		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Intron
CHST10	9486	hgsc.bcm.edu	37	2	101009869	101009869	+	Silent	SNP	C	C	T	rs148920749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:101009869C>T	ENST00000264249.3	-	7	1294	c.909G>A	c.(907-909)gtG>gtA	p.V303V	CHST10_ENST00000542617.1_Silent_p.V351V|CHST10_ENST00000409701.1_Silent_p.V303V	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	303					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						TCGGGTATGACACCAGGTGGT	0.522													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17713	0.0		0.0099	False		,,,				2504	0.0051				p.V303V		Atlas-SNP	.											.	CHST10	42	.	0			c.G909A						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	174.0	143.0	154.0		909	1.6	1.0	2	dbSNP_134	154	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous	CHST10	NM_004854.4		0,102,6401	TT,TC,CC		1.1047,0.1589,0.7843		303/357	101009869	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	9486	exon7			GTATGACACCAGG	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"""Sulfotransferases, membrane-bound"""	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.909G>A	2.37:g.101009869C>T		296.0	0.0	0		249.0	117.0	0.46988	NM_004854	Q53T18	Silent	SNP	ENST00000264249.3	37	CCDS2047.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854	
RFX3	5991	hgsc.bcm.edu	37	9	3247895	3247895	+	Intron	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:3247895A>G	ENST00000382004.3	-	16	2280				RFX3_ENST00000302303.1_Missense_Mutation_p.V702A|RFX3_ENST00000358730.2_Missense_Mutation_p.V702A	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)						cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		tcttgcaataactccacagtc	0.348																																					p.V702A		Atlas-SNP	.											.	RFX3	156	.	0			c.T2105C						PASS	.						79.0	80.0	79.0					9																	3247895		2203	4300	6503	SO:0001627	intron_variant	5991	exon16			GCAATAACTCCAC	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1968+136T>C	9.37:g.3247895A>G		25.0	0.0	0		22.0	13.0	0.590909	NM_002919	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415133	0.25552	.	.	ENSG00000080298	ENST00000358730;ENST00000302303	T;T	0.59502	0.26;0.26	3.82	-0.0572	0.13802	.	.	.	.	.	T	0.42787	0.1218	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.37957	-0.9683	8	0.87932	D	0	.	5.4108	0.16346	0.5649:0.3387:0.0964:0.0	.	702	P48380-2	.	A	702	ENSP00000351574:V702A;ENSP00000303847:V702A	ENSP00000303847:V702A	V	-	2	0	RFX3	3237895	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.141000	0.10327	-0.009000	0.14296	-0.435000	0.05868	GTT	.	.	none		0.348	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919	
NOTCH1	4851	hgsc.bcm.edu	37	9	139407932	139407932	+	Silent	SNP	A	A	G	rs2229971|rs587778559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATTCACACTCATTGTTGTTGA	0.602			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109.0	123.0	118.0		2265	-2.3	0.0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2265T>C	9.37:g.139407932A>G		129.0	0.0	0		113.0	51.0	0.451327	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
FMNL2	114793	hgsc.bcm.edu	37	2	153378487	153378487	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:153378487A>T	ENST00000288670.9	+	2	515	c.148A>T	c.(148-150)Agg>Tgg	p.R50W		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	50	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TGACAAAGCCAGGTTACTGCG	0.363																																					p.R50W		Atlas-SNP	.											.	FMNL2	75	.	0			c.A148T						PASS	.						84.0	80.0	81.0					2																	153378487		1847	4093	5940	SO:0001583	missense	114793	exon2			AAAGCCAGGTTAC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.148A>T	2.37:g.153378487A>T	ENSP00000288670:p.Arg50Trp	127.0	0.0	0		107.0	21.0	0.196262	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.402207	0.62288	.	.	ENSG00000157827	ENST00000288670	D	0.90261	-2.64	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95337	0.8435	10	0.87932	D	0	.	15.3697	0.74554	1.0:0.0:0.0:0.0	.	50	Q96PY5-3	.	W	50	ENSP00000288670:R50W	ENSP00000288670:R50W	R	+	1	2	FMNL2	153086733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.999000	0.57031	2.270000	0.75569	0.482000	0.46254	AGG	.	.	none		0.363	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
PDGFRB	5159	hgsc.bcm.edu	37	5	149511636	149511636	+	Silent	SNP	C	C	G	rs2228439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149511636C>G	ENST00000261799.4	-	8	1618	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	383	Ig-like C2-type 4.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCACGCGAACCAGTGTCAGCT	0.557			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	24	0.00479233	0.0	0.0115	5008	,	,		20833	0.0		0.0159	False		,,,				2504	0.0				p.L383L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.G1149C						PASS	.	C		9,4397	14.3+/-33.2	0,9,2194	93.0	80.0	84.0		1149	1.1	0.9	5	dbSNP_98	84	100,8500	54.4+/-115.2	0,100,4200	no	coding-synonymous	PDGFRB	NM_002609.3		0,109,6394	GG,GC,CC		1.1628,0.2043,0.8381		383/1107	149511636	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon8			GCGAACCAGTGTC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1149G>C	5.37:g.149511636C>G		153.0	0.0	0		151.0	68.0	0.450331	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			C|0.992;G|0.008	0.008	strong		0.557	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
SGK1	6446	hgsc.bcm.edu	37	6	134495159	134495159	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495159G>C	ENST00000237305.7	-	3	300	c.212C>G	c.(211-213)gCc>gGc	p.A71G	SGK1_ENST00000528577.1_Missense_Mutation_p.A99G|SGK1_ENST00000413996.3_Missense_Mutation_p.A85G|SGK1_ENST00000367857.5_Missense_Mutation_p.A61G|SGK1_ENST00000367858.5_Missense_Mutation_p.A166G|SGK1_ENST00000475719.2_Missense_Mutation_p.A71G|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	71					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGAAGGGTTGGCATTCATAAG	0.453																																					p.A166G		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	0			c.C497G						PASS	.						152.0	146.0	148.0					6																	134495159		2203	4300	6503	SO:0001583	missense	6446	exon5			GGGTTGGCATTCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.212C>G	6.37:g.134495159G>C	ENSP00000237305:p.Ala71Gly	82.0	0.0	0		58.0	15.0	0.258621	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107682	0.37242	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72942	-0.69;-0.69;-0.69;-0.67;-0.68;-0.7	5.99	5.12	0.69794	.	0.399737	0.30076	N	0.010479	T	0.40171	0.1106	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.27559	0.001;0.0;0.0;0.019;0.181;0.0	B;B;B;B;B;B	0.26693	0.005;0.001;0.001;0.039;0.072;0.001	T	0.36625	-0.9740	10	0.20519	T	0.43	.	14.2908	0.66275	0.0:0.0:0.7295:0.2705	.	99;85;71;61;166;71	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	G	166;85;71;61;99;71;135	ENSP00000356832:A166G;ENSP00000396242:A85G;ENSP00000237305:A71G;ENSP00000356831:A61G;ENSP00000434450:A99G;ENSP00000434302:A71G	ENSP00000237305:A71G	A	-	2	0	SGK1	134536852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.654000	0.54453	1.523000	0.49018	0.655000	0.94253	GCC	.	.	none		0.453	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
ALPI	248	hgsc.bcm.edu	37	2	233322286	233322286	+	Silent	SNP	C	C	T	rs139371546		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233322286C>T	ENST00000295463.3	+	6	737	c.660C>T	c.(658-660)ggC>ggT	p.G220G		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	220					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGATCCTTGGCGGAGGCCGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19244	0.0		0.0	False		,,,				2504	0.0				p.G220G		Atlas-SNP	.											.	ALPI	64	.	0			c.C660T						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	56.0	59.0	58.0		660	-11.2	0.0	2	dbSNP_134	58	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	ALPI	NM_001631.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		220/529	233322286	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	248	exon6			CCTTGGCGGAGGC	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.660C>T	2.37:g.233322286C>T		240.0	1.0	0.00416667		228.0	129.0	0.565789	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
MOCS1	4337	hgsc.bcm.edu	37	6	39881568	39881568	+	Missense_Mutation	SNP	C	C	A	rs377241570		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39881568C>A	ENST00000340692.5	-	5	598	c.595G>T	c.(595-597)Gtc>Ttc	p.V199F	MOCS1_ENST00000373195.3_Missense_Mutation_p.V112F|MOCS1_ENST00000373188.2_Missense_Mutation_p.V199F|MOCS1_ENST00000425303.2_Missense_Mutation_p.V199F|MOCS1_ENST00000373186.4_Missense_Mutation_p.V199F|MOCS1_ENST00000308559.7_Missense_Mutation_p.V199F|MOCS1_ENST00000432280.2_Missense_Mutation_p.V170F|MOCS1_ENST00000373175.4_Missense_Mutation_p.V170F			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	199	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCCTCCATGACCTTGTGGAAG	0.592																																					p.V199F	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.G595T						PASS	.						120.0	101.0	107.0					6																	39881568		2203	4300	6503	SO:0001583	missense	4337	exon4			CCATGACCTTGTG	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.595G>T	6.37:g.39881568C>A	ENSP00000344794:p.Val199Phe	96.0	0.0	0		66.0	16.0	0.242424	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	37		.	.	.	.	.	.	.	.	.	.	C	27.2	4.806025	0.90623	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	4.84	4.84	0.62591	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.99357	4.53	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.995;0.999;0.999;0.995	D	0.96772	0.9569	9	.	.	.	-19.377	17.5587	0.87900	0.0:1.0:0.0:0.0	.	199;199;199;199;199	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	F	199;199;170;199;112;199;199;170	ENSP00000362282:V199F;ENSP00000309843:V199F;ENSP00000362270:V170F;ENSP00000362284:V199F;ENSP00000362291:V112F;ENSP00000344794:V199F;ENSP00000416478:V199F;ENSP00000410809:V170F	.	V	-	1	0	MOCS1	39989546	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.601000	0.82783	2.245000	0.73994	0.655000	0.94253	GTC	.	.	alt		0.592	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943	
LY75	4065	hgsc.bcm.edu	37	2	160732019	160732019	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160732019G>C	ENST00000263636.4	-	12	1937	c.1910C>G	c.(1909-1911)cCt>cGt	p.P637R	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.P637R|LY75_ENST00000554112.1_Missense_Mutation_p.P637R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.P637R|LY75_ENST00000553424.1_Missense_Mutation_p.P637R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	637					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		ATCAGGCTTAGGGGATGCTTC	0.463																																					p.P637R		Atlas-SNP	.											.	LY75	151	.	0			c.C1910G						PASS	.						119.0	126.0	123.0					2																	160732019		2203	4300	6503	SO:0001583	missense	4065	exon12			GGCTTAGGGGATG	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1910C>G	2.37:g.160732019G>C	ENSP00000263636:p.Pro637Arg	123.0	0.0	0		99.0	58.0	0.585859	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529779	0.64860	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	4.77	4.77	0.60923	C-type lectin-like (1);	0.000000	0.34959	N	0.003545	T	0.27384	0.0672	M	0.64630	1.985	0.80722	D	1	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	D;D;D;D	0.97110	0.928;1.0;0.999;0.999	T	0.01033	-1.1474	10	0.66056	D	0.02	-9.9671	16.9332	0.86196	0.0:0.0:1.0:0.0	.	255;637;637;637	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	R	637	ENSP00000451511:P637R;ENSP00000451446:P637R;ENSP00000263636:P637R;ENSP00000423463:P637R;ENSP00000421035:P637R	ENSP00000423463:P637R	P	-	2	0	LY75;LY75-CD302	160440265	1.000000	0.71417	0.987000	0.45799	0.952000	0.60782	4.393000	0.59665	2.356000	0.79943	0.455000	0.32223	CCT	.	.	none		0.463	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44137400	44137400	+	Missense_Mutation	SNP	C	C	T	rs118174674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44137400C>T	ENST00000398722.4	-	14	2434	c.2435G>A	c.(2434-2436)cGg>cAg	p.R812Q	LOXHD1_ENST00000536736.1_Missense_Mutation_p.R1090Q|LOXHD1_ENST00000441893.2_Missense_Mutation_p.R23Q|LOXHD1_ENST00000441551.2_Missense_Mutation_p.R884Q|LOXHD1_ENST00000300591.6_5'UTR|LOXHD1_ENST00000582408.1_5'UTR|LOXHD1_ENST00000579038.1_5'Flank			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	812	PLAT 6. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GTGGCGAATCCGAATCTTGGT	0.562													C|||	36	0.0071885	0.0008	0.0173	5008	,	,		19065	0.0		0.0229	False		,,,				2504	0.0				p.R1090Q		Atlas-SNP	.											LOXHD1_ENST00000398722,NS,carcinoma,-1,2	LOXHD1	367	2	0			c.G3269A						PASS	.	C	GLN/ARG,	0,1384		0,0,692	244.0	220.0	227.0		3269,	5.2	1.0	18	dbSNP_132	227	61,3121		0,61,1530	yes	missense,utr-5	LOXHD1	NM_144612.6,NM_001145472.2	43,	0,61,2222	TT,TC,CC		1.917,0.0,1.336	probably-damaging,	1090/2212,	44137400	61,4505	692	1591	2283	SO:0001583	missense	125336	exon21			CGAATCCGAATCT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.2435G>A	18.37:g.44137400C>T	ENSP00000381707:p.Arg812Gln	377.0	1.0	0.00265252		344.0	174.0	0.505814	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		26	0.011904761904761904	0	0.0	8	0.022099447513812154	0	0.0	18	0.023746701846965697	C	17.58	3.424203	0.62733	0.0	0.01917	ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730	T;T;T	0.66099	-0.19;-0.19;-0.19	5.21	5.21	0.72293	.	0.058685	0.64402	D	0.000005	T	0.61874	0.2382	L	0.58583	1.82	0.44754	D	0.997757	D;D;D	0.76494	0.999;0.998;0.995	D;D;P	0.76575	0.96;0.988;0.891	T	0.68205	-0.5470	10	0.34782	T	0.22	.	16.5328	0.84366	0.0:1.0:0.0:0.0	.	1090;23;812	F5GZB4;F8WA52;Q8IVV2-2	.;.;.	Q	812;1090;23;812	ENSP00000381707:R812Q;ENSP00000444586:R1090Q;ENSP00000409062:R23Q	ENSP00000338222:R812Q	R	-	2	0	LOXHD1	42391398	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.902000	0.63266	2.440000	0.82611	0.491000	0.48974	CGG	C|0.986;T|0.014	0.014	strong		0.562	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
AFF2	2334	hgsc.bcm.edu	37	X	148048494	148048494	+	Missense_Mutation	SNP	A	A	C	rs149653283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:148048494A>C	ENST00000370460.2	+	14	3567	c.3088A>C	c.(3088-3090)Atc>Ctc	p.I1030L	AFF2_ENST00000286437.5_Missense_Mutation_p.I671L|AFF2_ENST00000342251.3_Missense_Mutation_p.I997L|AFF2_ENST00000370457.5_Missense_Mutation_p.I995L	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1030					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					cacctctaccatcactacTGG	0.567													A|||	2	0.000529801	0.0	0.0014	3775	,	,		13632	0.0		0.001	False		,,,				2504	0.0				p.I1030L		Atlas-SNP	.											.	AFF2	679	.	0			c.A3088C						PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	1,3834		0,0,1,1632,570	380.0	264.0	304.0		2983,3058,2983,2971,2011,3088	4.2	1.0	X	dbSNP_134	304	5,6723		0,4,1,2424,1871	yes	missense,missense,missense,missense,missense,missense	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	5,5,5,5,5,5	0,4,2,4056,2441	CC,CA,C,AA,A		0.0743,0.0261,0.0568	benign,benign,benign,benign,benign,benign	995/1277,1020/1302,995/1277,991/1273,671/953,1030/1312	148048494	6,10557	2203	4300	6503	SO:0001583	missense	2334	exon14			TCTACCATCACTA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3088A>C	X.37:g.148048494A>C	ENSP00000359489:p.Ile1030Leu	147.0	0.0	0		91.0	89.0	0.978022	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	14.61	2.587998	0.46110	2.61E-4	7.43E-4	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.71934	-0.01;-0.27;-0.27;-0.61	4.18	4.18	0.49190	.	0.089728	0.42053	D	0.000773	T	0.47710	0.1460	N	0.08118	0	0.24214	N	0.995466	P;P;P;P;P;P	0.38473	0.633;0.579;0.579;0.579;0.579;0.633	B;B;B;B;B;B	0.40782	0.34;0.23;0.23;0.23;0.23;0.34	T	0.32851	-0.9891	10	0.27785	T	0.31	.	5.4451	0.16531	0.8777:0.0:0.1223:0.0	.	671;995;995;991;1020;1030	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	L	1030;995;997;671	ENSP00000359489:I1030L;ENSP00000359486:I995L;ENSP00000345459:I997L;ENSP00000286437:I671L	ENSP00000286437:I671L	I	+	1	0	AFF2	147856188	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.240000	0.51368	1.860000	0.53959	0.417000	0.27973	ATC	A|1.000;C|0.000	0.000	strong		0.567	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
DCC	1630	hgsc.bcm.edu	37	18	49867246	49867246	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:49867246C>T	ENST00000442544.2	+	1	705	c.89C>T	c.(88-90)aCc>aTc	p.T30I	RP11-25O3.1_ENST00000582700.1_lincRNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	30	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTTCAAGTAACCGGTAAGTGG	0.493																																					p.T30I		Atlas-SNP	.											.	DCC	360	.	0			c.C89T						PASS	.						180.0	160.0	167.0					18																	49867246		2203	4300	6503	SO:0001583	missense	1630	exon1			AAGTAACCGGTAA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.89C>T	18.37:g.49867246C>T	ENSP00000389140:p.Thr30Ile	247.0	0.0	0		190.0	37.0	0.194737	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964768	0.34659	.	.	ENSG00000187323	ENST00000442544	T	0.50548	0.74	5.73	5.73	0.89815	Immunoglobulin-like (1);	1.199860	0.05969	N	0.642001	T	0.42630	0.1211	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.03910	-1.0993	10	0.22706	T	0.39	.	18.6711	0.91512	0.0:1.0:0.0:0.0	.	30	P43146	DCC_HUMAN	I	30	ENSP00000389140:T30I	ENSP00000389140:T30I	T	+	2	0	DCC	48121244	0.992000	0.36948	1.000000	0.80357	0.965000	0.64279	2.219000	0.42899	2.709000	0.92574	0.561000	0.74099	ACC	.	.	none		0.493	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
TTN	7273	hgsc.bcm.edu	37	2	179396573	179396573	+	Silent	SNP	T	T	G	rs56375087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179396573T>G	ENST00000591111.1	-	308	100070	c.99846A>C	c.(99844-99846)acA>acC	p.T33282T	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Silent_p.T32355T|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000460472.2_Silent_p.T25858T|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000589042.1_Silent_p.T34923T|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Silent_p.T25983T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Silent_p.T26050T|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33282					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCTTTCTGATGTCTTCTGAG	0.458													T|||	19	0.00379393	0.0	0.0043	5008	,	,		21340	0.0		0.0159	False		,,,				2504	0.0				p.T34923T		Atlas-SNP	.											.	TTN	18412	.	0			c.A104769C						PASS	.	T	,,,	2,3864		0,2,1931	51.0	49.0	50.0		77574,97065,77949,78150	-2.6	1.0	2	dbSNP_129	50	56,8214		1,54,4080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,56,6011	GG,GT,TT		0.6771,0.0517,0.4779	,,,	25858/26927,32355/33424,25983/27052,26050/27119	179396573	58,12078	1933	4135	6068	SO:0001819	synonymous_variant	7273	exon358			TTCTGATGTCTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.99846A>C	2.37:g.179396573T>G		143.0	0.0	0		126.0	57.0	0.452381	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.993;G|0.007	0.007	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205337	73205337	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:73205337C>A	ENST00000426542.2	+	33	4282	c.4262C>A	c.(4261-4263)cCc>cAc	p.P1421H	ARHGEF28_ENST00000513042.2_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.P341H|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.P1377H|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.P1108H			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1421					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										CGAGGCGGCCCCTTGCAGGAC	0.642																																					p.P1421H		Atlas-SNP	.											.	.	.	.	0			c.C4262A						PASS	.						17.0	20.0	19.0					5																	73205337		2040	4194	6234	SO:0001583	missense	64283	exon34			GCGGCCCCTTGCA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.4262C>A	5.37:g.73205337C>A	ENSP00000412175:p.Pro1421His	198.0	0.0	0		270.0	108.0	0.4	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	4.756	0.140576	0.09083	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0	5.34	1.35	0.21983	.	0.670385	0.11270	U	0.581554	T	0.26011	0.0634	L	0.54323	1.7	0.09310	N	1	D;P;P;D;P	0.54047	0.964;0.836;0.836;0.963;0.898	P;P;P;P;P	0.52424	0.619;0.497;0.497;0.698;0.694	T	0.14008	-1.0488	10	0.56958	D	0.05	.	2.765	0.05317	0.2109:0.2926:0.0:0.4965	.	1108;1421;1421;341;1421	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	H	1421;1421;1421;1377;1421;1421;1108;341	ENSP00000296794:P1421H;ENSP00000441913:P1421H;ENSP00000441436:P1421H;ENSP00000287898:P1377H;ENSP00000411459:P1421H;ENSP00000412175:P1421H;ENSP00000296799:P1108H;ENSP00000421081:P341H	ENSP00000287898:P1377H	P	+	2	0	RP11-428C6.1	73241093	0.038000	0.19896	0.001000	0.08648	0.010000	0.07245	1.372000	0.34261	0.246000	0.21394	-0.324000	0.08512	CCC	.	.	none		0.642	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
OPLAH	26873	hgsc.bcm.edu	37	8	145107915	145107915	+	Missense_Mutation	SNP	G	G	A	rs200620019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145107915G>A	ENST00000426825.1	-	21	3070	c.2989C>T	c.(2989-2991)Cgc>Tgc	p.R997C	OPLAH_ENST00000534424.1_5'UTR|CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	997					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACACGGAGGCGGATGGGGGAA	0.687													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		14517	0.0		0.002	False		,,,				2504	0.001				p.R997C		Atlas-SNP	.											.	OPLAH	78	.	0			c.C2989T						PASS	.	G	CYS/ARG	1,4293		0,1,2146	19.0	23.0	22.0		2989	0.7	0.9	8		22	8,8440		0,8,4216	yes	missense	OPLAH	NM_017570.3	180	0,9,6362	AA,AG,GG		0.0947,0.0233,0.0706	benign	997/1289	145107915	9,12733	2147	4224	6371	SO:0001583	missense	26873	exon21			GGAGGCGGATGGG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.2989C>T	8.37:g.145107915G>A	ENSP00000475943:p.Arg997Cys	129.0	0.0	0		103.0	26.0	0.252427	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	G	3.876	-0.026921	0.07589	2.33E-4	9.47E-4	ENSG00000178814	ENST00000426825	.	.	.	4.68	0.665	0.17896	.	0.224693	0.42682	N	0.000665	T	0.28034	0.0691	.	.	.	0.37399	D	0.912761	B	0.06786	0.001	B	0.01281	0.0	T	0.08953	-1.0697	7	0.33940	T	0.23	.	3.9788	0.09486	0.387:0.0:0.4565:0.1565	.	997	O14841	OPLA_HUMAN	C	997	.	ENSP00000412071:R997C	R	-	1	0	OPLAH	145179903	0.886000	0.30341	0.905000	0.35620	0.031000	0.12232	1.258000	0.32944	0.058000	0.16222	-0.480000	0.04831	CGC	.	.	weak		0.687	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
SCARF1	8578	hgsc.bcm.edu	37	17	1538714	1538714	+	Missense_Mutation	SNP	T	T	G	rs61738531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1538714T>G	ENST00000263071.4	-	11	1880	c.1831A>C	c.(1831-1833)Agc>Cgc	p.S611R	SCARF1_ENST00000571272.1_3'UTR|SCARF1_ENST00000348987.3_Missense_Mutation_p.S525R	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	611	Pro/Ser-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGGAGCGGGCTGGAGAGCTCC	0.677													T|||	55	0.0109824	0.0008	0.0101	5008	,	,		15189	0.001		0.0149	False		,,,				2504	0.0317				p.S611R		Atlas-SNP	.											.	SCARF1	46	.	0			c.A1831C						PASS	.	T	ARG/SER,,ARG/SER	21,4385	27.2+/-55.0	0,21,2182	51.0	55.0	53.0		1831,,1573	5.2	1.0	17	dbSNP_129	53	214,8386	89.2+/-151.4	3,208,4089	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	110,,110	3,229,6271	GG,GT,TT		2.4884,0.4766,1.8069	probably-damaging,,probably-damaging	611/831,,525/745	1538714	235,12771	2203	4300	6503	SO:0001583	missense	8578	exon11			GCGGGCTGGAGAG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1831A>C	17.37:g.1538714T>G	ENSP00000263071:p.Ser611Arg	88.0	0.0	0		77.0	22.0	0.285714	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	T	22.4	4.289498	0.80914	0.004766	0.024884	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.37411	1.2;1.2	5.21	5.21	0.72293	.	0.124140	0.36628	N	0.002484	T	0.35364	0.0929	M	0.63428	1.95	0.27223	N	0.959619	D;P	0.63046	0.992;0.947	P;P	0.56648	0.803;0.622	T	0.43669	-0.9377	10	0.72032	D	0.01	-22.476	15.1104	0.72351	0.0:0.0:0.0:1.0	.	525;611	Q14162-2;Q14162	.;SREC_HUMAN	R	611;525	ENSP00000263071:S611R;ENSP00000323964:S525R	ENSP00000263071:S611R	S	-	1	0	SCARF1	1485464	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.194000	0.58393	1.965000	0.57142	0.454000	0.30748	AGC	T|0.984;G|0.016	0.016	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
UMODL1	89766	hgsc.bcm.edu	37	21	43543098	43543098	+	Silent	SNP	C	C	T	rs58867895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43543098C>T	ENST00000408910.2	+	17	2985	c.2985C>T	c.(2983-2985)atC>atT	p.I995I	UMODL1_ENST00000400427.1_Silent_p.I1051I|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Silent_p.I923I|UMODL1_ENST00000408989.2_Silent_p.I1123I	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	995	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TCTGTGAGATCGAGAAGGTGG	0.632													C|||	142	0.0283546	0.1006	0.0086	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.0				p.I1123I	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C3369T						PASS	.	C	,,,	370,3912		11,348,1782	75.0	80.0	78.0		2985,3153,2769,3369	-6.2	0.9	21	dbSNP_129	78	6,8496		0,6,4245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	11,354,6027	TT,TC,CC		0.0706,8.6408,2.9412	,,,	995/1319,1051/1375,923/1247,1123/1447	43543098	376,12408	2141	4251	6392	SO:0001819	synonymous_variant	89766	exon16			TGAGATCGAGAAG		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.2985C>T	21.37:g.43543098C>T		95.0	0.0	0		93.0	35.0	0.376344	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.985;T|0.015	0.015	strong		0.632	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
SLC20A2	6575	hgsc.bcm.edu	37	8	42294592	42294592	+	Missense_Mutation	SNP	C	C	T	rs79577461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:42294592C>T	ENST00000342228.3	-	8	1807	c.1438G>A	c.(1438-1440)Gca>Aca	p.A480T	SLC20A2_ENST00000520179.1_Missense_Mutation_p.A480T|SLC20A2_ENST00000520262.1_Missense_Mutation_p.A480T	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	480					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)			breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ACCTCGGGTGCGTCCTTCTCC	0.637													C|||	29	0.00579073	0.0008	0.013	5008	,	,		16739	0.0		0.0159	False		,,,				2504	0.0031				p.A480T		Atlas-SNP	.											.	SLC20A2	64	.	0			c.G1438A						PASS	.	C	THR/ALA	26,4380	32.6+/-62.9	0,26,2177	89.0	58.0	69.0		1438	-4.0	0.0	8	dbSNP_132	69	187,8413	83.7+/-146.2	3,181,4116	yes	missense	SLC20A2	NM_006749.3	58	3,207,6293	TT,TC,CC		2.1744,0.5901,1.6377	benign	480/653	42294592	213,12793	2203	4300	6503	SO:0001583	missense	6575	exon8			CGGGTGCGTCCTT		CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"""Solute carriers"""	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1438G>A	8.37:g.42294592C>T	ENSP00000340465:p.Ala480Thr	32.0	0.0	0		17.0	4.0	0.235294	NM_001257181		Missense_Mutation	SNP	ENST00000342228.3	37	CCDS6132.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	4.778	0.144587	0.09134	0.005901	0.021744	ENSG00000168575	ENST00000342228;ENST00000520262;ENST00000520179	D;D;D	0.89746	-2.56;-2.56;-2.56	5.63	-4.0	0.04057	.	0.358640	0.34828	N	0.003654	T	0.44871	0.1314	N	0.01438	-0.865	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.59118	-0.7514	10	0.11485	T	0.65	-2.0977	4.5824	0.12266	0.2622:0.3593:0.0:0.3785	.	480	Q08357	S20A2_HUMAN	T	480	ENSP00000340465:A480T;ENSP00000429754:A480T;ENSP00000429712:A480T	ENSP00000340465:A480T	A	-	1	0	SLC20A2	42413749	0.999000	0.42202	0.015000	0.15790	0.157000	0.22087	0.734000	0.26101	-1.008000	0.03404	-0.482000	0.04802	GCA	C|0.985;T|0.015	0.015	strong		0.637	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1		
ALOX15B	247	hgsc.bcm.edu	37	17	7950009	7950009	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7950009C>G	ENST00000380183.4	+	9	1363	c.1224C>G	c.(1222-1224)taC>taG	p.Y408*	ALOX15B_ENST00000380173.2_Intron|ALOX15B_ENST00000573359.1_Intron|ALOX15B_ENST00000572022.1_Nonsense_Mutation_p.Y408*	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	408	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						ACACCCGATACACCCTGCACA	0.627																																					p.Y408X		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1224G						PASS	.						64.0	54.0	57.0					17																	7950009		2203	4300	6503	SO:0001587	stop_gained	247	exon9			CCGATACACCCTG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1224C>G	17.37:g.7950009C>G	ENSP00000369530:p.Tyr408*	86.0	0.0	0		61.0	31.0	0.508197	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Nonsense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025494	0.54683	.	.	ENSG00000179593	ENST00000380183	.	.	.	4.99	-2.88	0.05682	.	0.264891	0.39020	N	0.001493	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1679	11.9463	0.52930	0.0:0.5497:0.0:0.4503	.	.	.	.	X	408	.	ENSP00000369530:Y408X	Y	+	3	2	ALOX15B	7890734	0.222000	0.23652	0.004000	0.12327	0.007000	0.05969	0.543000	0.23237	-0.334000	0.08463	-0.140000	0.14226	TAC	.	.	none		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
CNOT4	4850	hgsc.bcm.edu	37	7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	rs17480616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G|CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67.0	63.0	65.0		20,20,20,20,20,20	1.5	1.0	7	dbSNP_123	65	228,7992		4,220,3886	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	163.0	0.0	0		98.0	39.0	0.397959	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
SLC35E2	9906	hgsc.bcm.edu	37	1	1663960	1663960	+	Silent	SNP	G	G	A	rs147265331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1663960G>A	ENST00000246421.4	-	6	1150	c.735C>T	c.(733-735)gtC>gtT	p.V245V	SLC35E2_ENST00000475229.1_5'UTR|RP1-283E3.8_ENST00000598846.1_RNA|RP1-283E3.4_ENST00000417099.1_RNA|SLC35E2_ENST00000355439.2_Intron|SLC35E2_ENST00000400924.1_Intron	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	245						integral component of membrane (GO:0016021)				endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGGCCTGCGGGACCTGCAGGT	0.607													-|||	25	0.00499201	0.0015	0.0086	5008	,	,		16644	0.0		0.0099	False		,,,				2504	0.0072				p.V245V		Atlas-SNP	.											.	SLC35E2	13	.	0			c.C735T						PASS	.		,	16,4378	23.3+/-48.9	1,14,2182	41.0	37.0	38.0		,735	-2.3	0.0	1	dbSNP_134	38	168,8396	71.0+/-133.6	5,158,4119	no	intron,coding-synonymous	SLC35E2	NM_001199787.1,NM_182838.2	,	6,172,6301	AA,AG,GG		1.9617,0.3641,1.42	,	,245/267	1663960	184,12774	2197	4282	6479	SO:0001819	synonymous_variant	9906	exon6			CTGCGGGACCTGC	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"""Solute carriers"""	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.735C>T	1.37:g.1663960G>A		147.0	0.0	0		82.0	61.0	0.743902	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Silent	SNP	ENST00000246421.4	37	CCDS33.1																																																																																			G|0.987;A|0.013	0.013	strong		0.607	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733	
DTX1	1840	hgsc.bcm.edu	37	12	113496182	113496182	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496182T>G	ENST00000257600.3	+	1	688	c.185T>G	c.(184-186)cTg>cGg	p.L62R		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	62	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TCCGTGGTCCTGGGGCAGGTG	0.637																																					p.L62R		Atlas-SNP	.											.	DTX1	83	.	0			c.T185G						PASS	.						123.0	112.0	116.0					12																	113496182		2203	4300	6503	SO:0001583	missense	1840	exon1			TGGTCCTGGGGCA	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.185T>G	12.37:g.113496182T>G	ENSP00000257600:p.Leu62Arg	59.0	0.0	0		58.0	12.0	0.206897	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436253	0.83885	.	.	ENSG00000135144	ENST00000257600	T	0.64438	-0.1	4.05	4.05	0.47172	WWE domain (2);WWE domain, subgroup (1);	0.000000	0.56097	D	0.000033	T	0.81288	0.4791	M	0.89840	3.065	0.47862	D	0.999538	D	0.76494	0.999	D	0.87578	0.998	D	0.85075	0.0942	10	0.87932	D	0	-9.9988	12.1675	0.54138	0.0:0.0:0.0:1.0	.	62	Q86Y01	DTX1_HUMAN	R	62	ENSP00000257600:L62R	ENSP00000257600:L62R	L	+	2	0	DTX1	111980565	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.286000	0.78671	1.710000	0.51325	0.454000	0.30748	CTG	.	.	none		0.637	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
GABRB3	2562	hgsc.bcm.edu	37	15	26806154	26806154	+	Silent	SNP	G	G	A	rs74907974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26806154G>A	ENST00000311550.5	-	8	1116	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	GABRB3_ENST00000545868.1_Silent_p.G250G|GABRB3_ENST00000299267.4_Silent_p.G335G|GABRB3_ENST00000541819.2_Silent_p.G391G|GABRB3_ENST00000400188.3_Silent_p.G264G	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	335					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCCTTTGAGGGCCTCTTCCAA	0.493													G|||	55	0.0109824	0.034	0.0115	5008	,	,		18829	0.0		0.002	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											GABRB3_ENST00000541819,right_upper_lobe,carcinoma,-2,6	GABRB3	338	6	0			c.C1005T						PASS	.	G	,,,	122,4284	90.6+/-129.3	1,120,2082	156.0	163.0	161.0		1005,750,792,1005	2.1	1.0	15	dbSNP_131	161	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	1,136,6366	AA,AG,GG		0.186,2.769,1.061	,,,	335/474,250/389,264/403,335/474	26806154	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon8			TTGAGGGCCTCTT		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1005C>T	15.37:g.26806154G>A		159.0	0.0	0		129.0	53.0	0.410853	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
PPM1E	22843	hgsc.bcm.edu	37	17	56833612	56833612	+	Missense_Mutation	SNP	C	C	G	rs116991234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56833612C>G	ENST00000308249.2	+	1	383	c.254C>G	c.(253-255)cCg>cGg	p.P85R		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			gagcaagacccggagcccgag	0.756													c|||	23	0.00459265	0.0	0.0101	5008	,	,		8364	0.0		0.0129	False		,,,				2504	0.0031				p.P85R		Atlas-SNP	.											.	PPM1E	97	.	0			c.C254G						PASS	.		ARG/PRO	4,3962		0,4,1979	8.0	7.0	7.0		254	2.4	1.0	17	dbSNP_132	7	43,7859		0,43,3908	no	missense	PPM1E	NM_014906.3	103	0,47,5887	GG,GC,CC		0.5442,0.1009,0.396	benign	85/756	56833612	47,11821	1983	3951	5934	SO:0001583	missense	22843	exon1			AAGACCCGGAGCC	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19322	protein-coding gene	gene with protein product	"""partner of PIX 1"", ""nuclear calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1E (PP2C domain containing)"""			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.254C>G	17.37:g.56833612C>G	ENSP00000312411:p.Pro85Arg	46.0	0.0	0		57.0	25.0	0.438596	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	c	11.88	1.770544	0.31320	0.001009	0.005442	ENSG00000175175	ENST00000308249	T	0.27256	1.68	3.53	2.43	0.29744	.	.	.	.	.	T	0.11750	0.0286	N	0.19112	0.55	0.20638	N	0.999879	B	0.26775	0.159	B	0.31614	0.133	T	0.18335	-1.0340	9	0.34782	T	0.22	-3.1579	7.5016	0.27522	0.2562:0.7438:0.0:0.0	.	85	Q8WY54-2	.	R	85	ENSP00000312411:P85R	ENSP00000312411:P85R	P	+	2	0	PPM1E	54188611	.	.	0.997000	0.53966	0.470000	0.32858	.	.	1.690000	0.51089	0.457000	0.33378	CCG	C|0.993;G|0.007	0.007	strong		0.756	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906	
MTA1	9112	hgsc.bcm.edu	37	14	105936204	105936204	+	Silent	SNP	C	C	T	rs373034822		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105936204C>T	ENST00000331320.7	+	20	2086	c.1872C>T	c.(1870-1872)aaC>aaT	p.N624N	MTA1_ENST00000406191.1_Silent_p.N612N|MTA1_ENST00000405646.1_Silent_p.N607N|MTA1_ENST00000435036.2_Silent_p.N164N|RP11-521B24.5_ENST00000552675.1_RNA	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	624					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		TCCTGCTCAACGGGAAGTCCT	0.682																																					p.N624N		Atlas-SNP	.											.	MTA1	61	.	0			c.C1872T						PASS	.	C	,	0,4384		0,0,2192	27.0	26.0	27.0		,1872	-6.0	0.9	14		27	1,8585		0,1,4292	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	0,1,6484	TT,TC,CC		0.0116,0.0,0.0077	,	,624/716	105936204	1,12969	2192	4293	6485	SO:0001819	synonymous_variant	9112	exon20			GCTCAACGGGAAG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1872C>T	14.37:g.105936204C>T		102.0	0.0	0		97.0	53.0	0.546392	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	9.588	1.125368	0.20959	0.0	1.16E-4	ENSG00000182979	ENST00000494981	.	.	.	5.27	-6.01	0.02199	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55231	-0.8173	4	.	.	.	-33.3685	10.6162	0.45451	0.0:0.1432:0.115:0.7418	.	.	.	.	W	51	.	.	R	+	1	2	MTA1	105007249	0.007000	0.16637	0.911000	0.35937	0.890000	0.51754	-1.491000	0.02302	-1.078000	0.03117	-0.350000	0.07774	CGG	.	.	weak		0.682	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
WNK1	65125	hgsc.bcm.edu	37	12	999632	999632	+	Missense_Mutation	SNP	C	C	A	rs371264719		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:999632C>A	ENST00000315939.6	+	22	6105	c.5462C>A	c.(5461-5463)gCg>gAg	p.A1821E	WNK1_ENST00000530271.2_Missense_Mutation_p.A2319E|WNK1_ENST00000537687.1_Missense_Mutation_p.A2081E|WNK1_ENST00000535572.1_Missense_Mutation_p.A1574E|WNK1_ENST00000340908.4_Missense_Mutation_p.A1414E	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1821					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTGTCCATGGCGGCTCCAACA	0.463																																					p.A2081E	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C6242A						PASS	.						137.0	125.0	129.0					12																	999632		2203	4300	6503	SO:0001583	missense	65125	exon22			CCATGGCGGCTCC	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.5462C>A	12.37:g.999632C>A	ENSP00000313059:p.Ala1821Glu	312.0	0.0	0		249.0	55.0	0.220884	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	8.007	0.756729	0.15846	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.06	1.3	0.21679	.	0.576229	0.16749	N	0.201105	T	0.13756	0.0333	N	0.14661	0.345	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.23084	-1.0198	10	0.23891	T	0.37	0.0017	3.5613	0.07884	0.1573:0.2635:0.0:0.5792	.	1574;1574;1821	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	E	1574;1821;2081;994;2319;1414	ENSP00000441972:A1574E;ENSP00000313059:A1821E;ENSP00000444465:A2081E;ENSP00000433548:A2319E;ENSP00000341292:A1414E	ENSP00000252477:A994E	A	+	2	0	WNK1	869893	0.996000	0.38824	0.746000	0.31095	0.091000	0.18340	0.353000	0.20130	-0.096000	0.12329	-0.254000	0.11334	GCG	.	.	alt		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
TSEN54	283989	hgsc.bcm.edu	37	17	73520435	73520435	+	Missense_Mutation	SNP	G	G	A	rs200275380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73520435G>A	ENST00000333213.6	+	11	1559	c.1523G>A	c.(1522-1524)gGt>gAt	p.G508D	LLGL2_ENST00000578363.1_5'Flank|LLGL2_ENST00000375227.4_5'Flank|LLGL2_ENST00000167462.5_5'Flank|LLGL2_ENST00000392550.3_5'Flank	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	508					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTGGATCATGGTGACATCTCC	0.582																																					p.G508D		Atlas-SNP	.											.	TSEN54	27	.	0			c.G1523A						PASS	.						178.0	144.0	155.0					17																	73520435		2203	4300	6503	SO:0001583	missense	283989	exon11			ATCATGGTGACAT	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.1523G>A	17.37:g.73520435G>A	ENSP00000327487:p.Gly508Asp	180.0	0.0	0		150.0	83.0	0.553333	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	.	.	.	.	.	.	.	.	.	.	G	35	5.485368	0.96323	.	.	ENSG00000182173	ENST00000333213	T	0.60424	0.19	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79179	-0.1910	10	0.72032	D	0.01	-14.4051	19.6034	0.95572	0.0:0.0:1.0:0.0	.	508	Q7Z6J9	SEN54_HUMAN	D	508	ENSP00000327487:G508D	ENSP00000327487:G508D	G	+	2	0	TSEN54	71032030	1.000000	0.71417	0.970000	0.41538	0.988000	0.76386	9.171000	0.94802	2.637000	0.89404	0.561000	0.74099	GGT	G|0.999;A|0.001	0.001	weak		0.582	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
LCA5L	150082	hgsc.bcm.edu	37	21	40800368	40800368	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40800368C>T	ENST00000358268.2	-	4	580	c.52G>A	c.(52-54)Gtg>Atg	p.V18M	LCA5L_ENST00000380671.2_Missense_Mutation_p.V18M|LCA5L_ENST00000485895.2_Missense_Mutation_p.V18M|LCA5L_ENST00000288350.3_Missense_Mutation_p.V18M			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	18										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				TCTAATGCCACGCCGAAGAAA	0.368																																					p.V18M		Atlas-SNP	.											.	LCA5L	57	.	0			c.G52A						PASS	.						112.0	109.0	110.0					21																	40800368		2203	4300	6503	SO:0001583	missense	150082	exon4			ATGCCACGCCGAA	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.52G>A	21.37:g.40800368C>T	ENSP00000351008:p.Val18Met	89.0	0.0	0		124.0	23.0	0.185484	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	c	14.53	2.562098	0.45590	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.66099	0.19;0.19;0.19;0.62;0.58;0.57;0.56;0.56;0.47;0.42;-0.19	5.65	1.67	0.24075	.	1.008340	0.07969	N	0.983624	T	0.65852	0.2731	L	0.47716	1.5	0.09310	N	1	D;D	0.67145	0.993;0.996	P;P	0.61397	0.743;0.888	T	0.51132	-0.8744	10	0.72032	D	0.01	-2.9629	1.7285	0.02927	0.2757:0.4233:0.1428:0.1582	.	18;18	C9JFB6;O95447	.;LCA5L_HUMAN	M	18	ENSP00000288350:V18M;ENSP00000370046:V18M;ENSP00000351008:V18M;ENSP00000404521:V18M;ENSP00000405598:V18M;ENSP00000400086:V18M;ENSP00000405130:V18M;ENSP00000412691:V18M;ENSP00000395593:V18M;ENSP00000414784:V18M;ENSP00000407065:V18M	ENSP00000288350:V18M	V	-	1	0	LCA5L	39722238	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.181000	0.09740	0.032000	0.15435	-0.119000	0.15052	GTG	.	.	none		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
PKHD1	5314	hgsc.bcm.edu	37	6	51524681	51524681	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51524681G>A	ENST00000371117.3	-	61	10518	c.10243C>T	c.(10243-10245)Ctt>Ttt	p.L3415F		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3415					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.L3415F(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCGCTATCAAGAATTAGGACC	0.368																																					p.L3415F		Atlas-SNP	.											PKHD1,NS,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	lung(1)	c.C10243T						PASS	.						74.0	66.0	69.0					6																	51524681		2203	4300	6503	SO:0001583	missense	5314	exon61			TATCAAGAATTAG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10243C>T	6.37:g.51524681G>A	ENSP00000360158:p.Leu3415Phe	189.0	0.0	0		167.0	42.0	0.251497	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226393	0.39300	.	.	ENSG00000170927	ENST00000371117	D	0.86497	-2.13	5.48	4.6	0.57074	.	0.000000	0.56097	D	0.000021	D	0.85669	0.5750	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84345	0.0529	10	0.34782	T	0.22	.	11.1417	0.48406	0.1436:0.0:0.8564:0.0	.	3415	P08F94	PKHD1_HUMAN	F	3415	ENSP00000360158:L3415F	ENSP00000360158:L3415F	L	-	1	0	PKHD1	51632640	1.000000	0.71417	1.000000	0.80357	0.192000	0.23643	1.690000	0.37711	2.580000	0.87095	0.655000	0.94253	CTT	.	.	none		0.368	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
SLC35A1	10559	hgsc.bcm.edu	37	6	88218282	88218282	+	Missense_Mutation	SNP	A	A	G	rs188216651		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:88218282A>G	ENST00000369552.4	+	6	746	c.719A>G	c.(718-720)tAt>tGt	p.Y240C	C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000369556.3_Intron|SLC35A1_ENST00000544441.1_Missense_Mutation_p.Y106C|SLC35A1_ENST00000464978.1_3'UTR|SLC35A1_ENST00000369557.5_Intron	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	240					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|CMP-N-acetylneuraminate transport (GO:0015782)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456)|sugar:proton symporter activity (GO:0005351)			breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		GGATTTTTCTATGGTTACACA	0.323																																					p.Y240C	NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)	Atlas-SNP	.											.	SLC35A1	29	.	0			c.A719G						PASS	.						89.0	92.0	91.0					6																	88218282		2203	4298	6501	SO:0001583	missense	10559	exon6			TTTTCTATGGTTA	D87969	CCDS5010.1, CCDS55043.1	6q15	2013-05-22			ENSG00000164414	ENSG00000164414		"""Solute carriers"""	11021	protein-coding gene	gene with protein product		605634	"""solute carrier family 35 (UDP-galactose transporter), member 1"""			9010752, 9644260	Standard	NM_006416		Approved	CMPST, hCST	uc011dzj.2	P78382	OTTHUMG00000015177	ENST00000369552.4:c.719A>G	6.37:g.88218282A>G	ENSP00000358565:p.Tyr240Cys	59.0	0.0	0		52.0	31.0	0.596154	NM_006416	Q5W1L8	Missense_Mutation	SNP	ENST00000369552.4	37	CCDS5010.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.17|15.17	2.754984|2.754984	0.49362|0.49362	.|.	.|.	ENSG00000164414|ENSG00000164414	ENST00000429605|ENST00000544441;ENST00000369552	.|T;T	.|0.44881	.|0.91;0.91	5.64|5.64	3.21|3.21	0.36854|0.36854	.|.	.|0.214545	.|0.40908	.|U	.|0.000998	T|T	0.42585|0.42585	0.1209|0.1209	M|M	0.68593|0.68593	2.085|2.085	0.48901|0.48901	D|D	0.99972|0.99972	.|D;D	.|0.62365	.|0.991;0.978	.|P;P	.|0.62089	.|0.898;0.762	T|T	0.39800|0.39800	-0.9596|-0.9596	6|10	0.30078|0.54805	T|T	0.28|0.06	-56.8193|-56.8193	7.7786|7.7786	0.29051|0.29051	0.8085:0.0:0.0674:0.1241|0.8085:0.0:0.0674:0.1241	.|.	.|240;106	.|P78382;B4DEM1	.|S35A1_HUMAN;.	V|C	150|106;240	.|ENSP00000438603:Y106C;ENSP00000358565:Y240C	ENSP00000413148:M150V|ENSP00000358565:Y240C	M|Y	+|+	1|2	0|0	SLC35A1|SLC35A1	88275001|88275001	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.961000|2.961000	0.49168|0.49168	0.412000|0.412000	0.25729|0.25729	0.459000|0.459000	0.35465|0.35465	ATG|TAT	A|1.000;G|0.000	0.000	strong		0.323	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1		
CWF19L2	143884	hgsc.bcm.edu	37	11	107224415	107224415	+	Silent	SNP	A	A	G	rs35543671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:107224415A>G	ENST00000282251.5	-	13	1947	c.1920T>C	c.(1918-1920)ttT>ttC	p.F640F	CWF19L2_ENST00000433523.1_Silent_p.F640F	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	640							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CTTTGGAGACAAACATGTCAT	0.393													A|||	67	0.0133786	0.0023	0.0331	5008	,	,		17536	0.002		0.0278	False		,,,				2504	0.0112				p.F640F		Atlas-SNP	.											.	CWF19L2	135	.	0			c.T1920C						PASS	.	A		17,4385	25.3+/-52.1	0,17,2184	99.0	97.0	98.0		1920	2.4	1.0	11	dbSNP_126	98	217,8379	89.4+/-151.6	3,211,4084	no	coding-synonymous	CWF19L2	NM_152434.2		3,228,6268	GG,GA,AA		2.5244,0.3862,1.8003		640/895	107224415	234,12764	2201	4298	6499	SO:0001819	synonymous_variant	143884	exon13			GGAGACAAACATG	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1920T>C	11.37:g.107224415A>G		90.0	0.0	0		100.0	27.0	0.27	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	37	CCDS8336.2																																																																																			A|0.983;G|0.017	0.017	strong		0.393	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
TRPM1	4308	hgsc.bcm.edu	37	15	31327779	31327779	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31327779G>A	ENST00000256552.6	-	21	2817	c.2670C>T	c.(2668-2670)atC>atT	p.I890I	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.I868I|TRPM1_ENST00000542188.1_Silent_p.I907I	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CCAGGCTCACGATGTAGGAGA	0.542																																					p.I907I		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2721T						PASS	.						87.0	89.0	88.0					15																	31327779		2054	4193	6247	SO:0001819	synonymous_variant	4308	exon20			GCTCACGATGTAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2670C>T	15.37:g.31327779G>A		89.0	0.0	0		93.0	5.0	0.0537634	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
GCNT2	2651	hgsc.bcm.edu	37	6	10586727	10586727	+	Intron	SNP	G	G	A	rs56106312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:10586727G>A	ENST00000379597.3	+	2	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.A169T			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		CAGACTCCAGGCTGACCTGAA	0.483													G|||	12	0.00239617	0.0008	0.0058	5008	,	,		19773	0.0		0.006	False		,,,				2504	0.001				p.A169T		Atlas-SNP	.											.	GCNT2	123	.	0			c.G505A						PASS	.	G	,,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	127.0	123.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,505	5.6	1.0	6	dbSNP_129	124	45,8555	30.1+/-81.4	0,45,4255	yes	intron,intron,missense	GCNT2	NM_001491.2,NM_145649.4,NM_145655.3	,,58	0,48,6455	AA,AG,GG		0.5233,0.0681,0.3691	,,probably-damaging	,,169/403	10586727	48,12958	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			CTCCAGGCTGACC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34857G>A	6.37:g.10586727G>A		165.0	0.0	0		163.0	111.0	0.680982	NM_145655		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	18.84	3.709073	0.68615	6.81E-4	0.005233	ENSG00000111846	ENST00000265012	T	0.20332	2.08	5.58	5.58	0.84498	.	.	.	.	.	T	0.45836	0.1362	M	0.88842	2.985	0.58432	D	0.999996	D	0.76494	0.999	D	0.77557	0.99	T	0.53920	-0.8370	9	0.87932	D	0	.	14.7518	0.69530	0.0709:0.0:0.9291:0.0	rs56106312	169	Q8NFS9	GNT2C_HUMAN	T	169	ENSP00000265012:A169T	ENSP00000265012:A169T	A	+	1	0	GCNT2	10694713	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	6.558000	0.73942	2.624000	0.88883	0.655000	0.94253	GCT	G|0.996;A|0.004	0.004	strong		0.483	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
PAMR1	25891	hgsc.bcm.edu	37	11	35463043	35463043	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:35463043G>A	ENST00000378880.2	-	7	1464	c.1019C>T	c.(1018-1020)cCc>cTc	p.P340L	PAMR1_ENST00000532848.1_Missense_Mutation_p.P300L|PAMR1_ENST00000378878.3_Missense_Mutation_p.P229L|PAMR1_ENST00000278360.3_Missense_Mutation_p.P357L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	340	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TATGCAGATGGGCTGTTTCCC	0.418																																					p.P357L		Atlas-SNP	.											.	PAMR1	85	.	0			c.C1070T						PASS	.						195.0	189.0	191.0					11																	35463043		2202	4298	6500	SO:0001583	missense	25891	exon8			CAGATGGGCTGTT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1019C>T	11.37:g.35463043G>A	ENSP00000368158:p.Pro340Leu	129.0	0.0	0		129.0	65.0	0.503876	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031221	0.93575	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.84	5.84	0.93424	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.92306	0.7559	H	0.95187	3.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.93784	0.7086	10	0.87932	D	0	.	20.139	0.98050	0.0:0.0:1.0:0.0	.	229;340;357	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	L	357;340;229;300;317	ENSP00000278360:P357L;ENSP00000368158:P340L;ENSP00000368156:P229L;ENSP00000433868:P300L;ENSP00000432591:P317L	ENSP00000278360:P357L	P	-	2	0	PAMR1	35419619	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	8.755000	0.91646	2.764000	0.94973	0.655000	0.94253	CCC	.	.	none		0.418	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
FREM1	158326	hgsc.bcm.edu	37	9	14801725	14801725	+	Missense_Mutation	SNP	C	C	G	rs61744094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14801725C>G	ENST00000380880.3	-	20	4402	c.3619G>C	c.(3619-3621)Gag>Cag	p.E1207Q	FREM1_ENST00000380881.4_Missense_Mutation_p.E1208Q|FREM1_ENST00000422223.2_Missense_Mutation_p.E1207Q			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1207					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TGCTTATTCTCAGAGAAGTCT	0.512																																					p.E1207Q		Atlas-SNP	.											.	FREM1	261	.	0			c.G3619C						PASS	.	C	GLN/GLU	1,3989		0,1,1994	147.0	145.0	145.0		3619	1.5	0.0	9	dbSNP_129	145	2,8356		0,2,4177	no	missense	FREM1	NM_144966.5	29	0,3,6171	GG,GC,CC		0.0239,0.0251,0.0243	benign	1207/2180	14801725	3,12345	1995	4179	6174	SO:0001583	missense	158326	exon21			TATTCTCAGAGAA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3619G>C	9.37:g.14801725C>G	ENSP00000370262:p.Glu1207Gln	238.0	0.0	0		221.0	97.0	0.438914	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	0.332	-0.955355	0.02267	2.51E-4	2.39E-4	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51574	0.7;0.7;0.7	5.51	1.53	0.23141	.	0.815509	0.11476	N	0.560211	T	0.12902	0.0313	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31166	-0.9953	10	0.11794	T	0.64	0.2002	5.6173	0.17438	0.072:0.2719:0.5253:0.1308	rs61744094	1207	Q5H8C1	FREM1_HUMAN	Q	1208;1207;1207	ENSP00000370263:E1208Q;ENSP00000412940:E1207Q;ENSP00000370262:E1207Q	ENSP00000370257:E1210Q	E	-	1	0	FREM1	14791725	0.011000	0.17503	0.001000	0.08648	0.053000	0.15095	1.753000	0.38359	0.262000	0.21774	-0.340000	0.08031	GAG	C|0.889;G|0.111	0.111	strong		0.512	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
ZFHX3	463	hgsc.bcm.edu	37	16	72993397	72993397	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72993397C>T	ENST00000268489.5	-	2	1320	c.648G>A	c.(646-648)ccG>ccA	p.P216P	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	216					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTGAGGTATTCGGGAAAGCCT	0.572																																					p.P216P		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G648A						PASS	.						85.0	86.0	85.0					16																	72993397		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GGTATTCGGGAAA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.648G>A	16.37:g.72993397C>T		96.0	0.0	0		100.0	38.0	0.38	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
C1S	716	hgsc.bcm.edu	37	12	7175762	7175762	+	Missense_Mutation	SNP	G	G	C	rs150549869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7175762G>C	ENST00000406697.1	+	14	1826	c.1198G>C	c.(1198-1200)Gag>Cag	p.E400Q	C1S_ENST00000360817.5_Missense_Mutation_p.E400Q|C1S_ENST00000495061.1_3'UTR|C1S_ENST00000328916.3_Missense_Mutation_p.E400Q|C1S_ENST00000402681.3_Missense_Mutation_p.E233Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	400	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	TATTCCAGGGGAGTATCACTG	0.587																																					p.E400Q	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G1198C						PASS	.	G	GLN/GLU,GLN/GLU	0,4406		0,0,2203	246.0	189.0	208.0		1198,1198	4.4	0.7	12	dbSNP_134	208	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	benign,benign	400/689,400/689	7175762	5,13001	2203	4300	6503	SO:0001583	missense	716	exon11			CCAGGGGAGTATC		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1198G>C	12.37:g.7175762G>C	ENSP00000385035:p.Glu400Gln	137.0	0.0	0		120.0	56.0	0.466667	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	2.603	-0.292472	0.05568	0.0	5.81E-4	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.28	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.768045	0.11079	N	0.601989	T	0.57651	0.2068	L	0.55834	1.745	0.09310	N	1	B	0.23650	0.089	B	0.24974	0.057	T	0.47209	-0.9135	10	0.32370	T	0.25	.	10.104	0.42521	0.1176:0.1284:0.7539:0.0	.	400	P09871	C1S_HUMAN	Q	400;400;400;394;233	ENSP00000385035:E400Q;ENSP00000328173:E400Q;ENSP00000354057:E400Q;ENSP00000384171:E233Q	ENSP00000328173:E400Q	E	+	1	0	C1S	7046023	0.001000	0.12720	0.664000	0.29753	0.013000	0.08279	0.933000	0.28897	0.617000	0.30160	-2.178000	0.00318	GAG	G|1.000;C|0.000	0.000	strong		0.587	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
OR5T2	219464	hgsc.bcm.edu	37	11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	rs77295387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193.0	169.0	177.0		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	264.0	0.0	0		207.0	157.0	0.758454	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ALB	213	hgsc.bcm.edu	37	4	74285263	74285263	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74285263A>G	ENST00000503124.1	+	11	1449	c.1242A>G	c.(1240-1242)acA>acG	p.T414T	ALB_ENST00000401494.3_Silent_p.T449T|ALB_ENST00000509063.1_Silent_p.T564T|ALB_ENST00000295897.4_Silent_p.T564T|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Silent_p.T372T			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCAAGGCAACAAAAGAGCAAC	0.408																																					p.T564T		Atlas-SNP	.											.	ALB	132	.	0			c.A1692G						PASS	.						93.0	89.0	90.0					4																	74285263		2203	4300	6503	SO:0001819	synonymous_variant	213	exon13			GGCAACAAAAGAG	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1242A>G	4.37:g.74285263A>G		91.0	0.0	0		101.0	22.0	0.217822	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	A	10.22	1.290736	0.23564	.	.	ENSG00000163631	ENST00000511370	.	.	.	6.06	-2.4	0.06583	.	.	.	.	.	T	0.21801	0.0525	.	.	.	0.25935	N	0.982943	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	-29.7385	4.5011	0.11865	0.4432:0.0:0.2016:0.3552	.	.	.	.	E	409	.	.	K	+	1	0	ALB	74504127	0.001000	0.12720	0.046000	0.18839	0.538000	0.34931	-0.230000	0.09083	-0.111000	0.12001	0.533000	0.62120	AAA	.	.	none		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
KRT14	3861	hgsc.bcm.edu	37	17	39742921	39742921	+	Missense_Mutation	SNP	G	G	A	rs117484558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39742921G>A	ENST00000167586.6	-	1	252	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	56	Head.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				GAGGAGAAGCGGGAGGATGAG	0.706													G|||	31	0.0061901	0.0008	0.0043	5008	,	,		13635	0.0		0.0149	False		,,,				2504	0.0123				p.R56C		Atlas-SNP	.											KRT14,NS,carcinoma,+1,1	KRT14	65	1	0			c.C166T						PASS	.	G	CYS/ARG	8,4356		0,8,2174	25.0	30.0	28.0		166	3.4	1.0	17	dbSNP_132	28	57,8505		0,57,4224	no	missense	KRT14	NM_000526.4	180	0,65,6398	AA,AG,GG		0.6657,0.1833,0.5029	benign	56/473	39742921	65,12861	2182	4281	6463	SO:0001583	missense	3861	exon1			AGAAGCGGGAGGA	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.166C>T	17.37:g.39742921G>A	ENSP00000167586:p.Arg56Cys	22.0	0.0	0		25.0	10.0	0.4	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	0	0.0	12	0.0158311345646438	G	7.992	0.753456	0.15778	0.001833	0.006657	ENSG00000186847	ENST00000167586	D	0.84070	-1.8	4.37	3.4	0.38934	.	0.000000	0.53938	D	0.000053	T	0.61726	0.2370	L	0.47716	1.5	0.53005	D	0.999962	B	0.02656	0.0	B	0.01281	0.0	T	0.65623	-0.6123	10	0.36615	T	0.2	.	9.0759	0.36522	0.1706:0.0:0.8294:0.0	.	56	P02533	K1C14_HUMAN	C	56	ENSP00000167586:R56C	ENSP00000167586:R56C	R	-	1	0	KRT14	36996447	0.997000	0.39634	1.000000	0.80357	0.012000	0.07955	0.082000	0.14847	1.210000	0.43336	-0.235000	0.12190	CGC	G|0.994;A|0.006	0.006	strong		0.706	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
MUC4	4585	hgsc.bcm.edu	37	3	195505874	195505874	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505874G>C	ENST00000463781.3	-	2	13036	c.12577C>G	c.(12577-12579)Ctt>Gtt	p.L4193V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4193V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L4193V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGACAGGAAGAGGGGTGGTG	0.602																																					p.L4193V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C12577G						scavenged	.						21.0	15.0	17.0					3																	195505874		689	1580	2269	SO:0001583	missense	4585	exon2			CAGGAAGAGGGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12577C>G	3.37:g.195505874G>C	ENSP00000417498:p.Leu4193Val	64.0	1.0	0.015625		84.0	6.0	0.0714286	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	0.230	-1.021560	0.02061	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.42;1.39	.	.	.	.	.	.	.	.	T	0.26629	0.0651	N	0.19112	0.55	0.09310	N	1	P	0.43973	0.823	P	0.48952	0.596	T	0.10245	-1.0638	7	.	.	.	.	3.3879	0.07278	1.0E-4:1.0E-4:0.5468:0.453	.	4065	E7ESK3	.	V	4193	ENSP00000417498:L4193V;ENSP00000420243:L4193V	.	L	-	1	0	MUC4	196990653	0.000000	0.05858	0.128000	0.21923	0.050000	0.14768	-0.106000	0.10890	0.452000	0.26830	0.074000	0.15403	CTT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CPSF1	29894	hgsc.bcm.edu	37	8	145624578	145624578	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145624578G>A	ENST00000349769.3	-	15	1501	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	469					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CAATGTTCAGGATGCTGTCAC	0.672																																					p.I469I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1407T						PASS	.						11.0	12.0	12.0					8																	145624578		2196	4290	6486	SO:0001819	synonymous_variant	29894	exon15			GTTCAGGATGCTG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1407C>T	8.37:g.145624578G>A		95.0	0.0	0		89.0	40.0	0.449438	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			.	.	none		0.672	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
PTPRR	5801	hgsc.bcm.edu	37	12	71286606	71286606	+	Silent	SNP	G	G	A	rs149684669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:71286606G>A	ENST00000283228.2	-	2	662	c.210C>T	c.(208-210)tcC>tcT	p.S70S		NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	70					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		CTTGAGCTTCGGAAGAGGAAT	0.458													G|||	10	0.00199681	0.0	0.0014	5008	,	,		18216	0.0		0.006	False		,,,				2504	0.0031				p.S70S		Atlas-SNP	.											.	PTPRR	109	.	0			c.C210T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	230.0	233.0	232.0		210	-3.7	0.0	12	dbSNP_134	232	32,8568	22.8+/-68.1	0,32,4268	no	coding-synonymous	PTPRR	NM_002849.3		0,38,6465	AA,AG,GG		0.3721,0.1362,0.2922		70/658	71286606	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	5801	exon2			AGCTTCGGAAGAG	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.210C>T	12.37:g.71286606G>A		371.0	0.0	0		295.0	139.0	0.471186	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	37	CCDS8998.1																																																																																			G|0.997;A|0.003	0.003	strong		0.458	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
ATG13	9776	hgsc.bcm.edu	37	11	46690413	46690413	+	Missense_Mutation	SNP	G	G	A	rs35619591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:46690413G>A	ENST00000434074.1	+	15	1989	c.1300G>A	c.(1300-1302)Ggg>Agg	p.G434R	ATG13_ENST00000451945.1_Missense_Mutation_p.G397R|ATG13_ENST00000526508.1_Missense_Mutation_p.G434R|ATG13_ENST00000524625.1_Missense_Mutation_p.G397R|ATG13_ENST00000312040.4_Missense_Mutation_p.G434R|ATG13_ENST00000530500.1_Missense_Mutation_p.G318R|ATG13_ENST00000528494.1_Missense_Mutation_p.G467R|ATG13_ENST00000359513.4_Missense_Mutation_p.G434R|ATG13_ENST00000529655.1_Missense_Mutation_p.G397R	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	434					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TGGCTCCAGCGGGGGCAGCAG	0.532													G|||	40	0.00798722	0.0	0.0014	5008	,	,		19713	0.001		0.0109	False		,,,				2504	0.0276				p.G467R		Atlas-SNP	.											.	ATG13	60	.	0			c.G1399A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	6,4396	11.4+/-27.6	0,6,2195	136.0	122.0	127.0		1300,1399,1300,1189,952,1189	4.9	0.8	11	dbSNP_126	127	67,8531	41.7+/-99.0	1,65,4233	yes	missense,missense,missense,missense,missense,missense	ATG13	NM_001142673.2,NM_001205119.1,NM_001205120.1,NM_001205121.1,NM_001205122.1,NM_014741.4	125,125,125,125,125,125	1,71,6428	AA,AG,GG		0.7793,0.1363,0.5615	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	434/518,467/551,434/518,397/481,318/402,397/481	46690413	73,12927	2201	4299	6500	SO:0001583	missense	9776	exon16			TCCAGCGGGGGCA	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"""KIAA0652"", ""ATG13 autophagy related 13 homolog (S. cerevisiae)"""	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.1300G>A	11.37:g.46690413G>A	ENSP00000400642:p.Gly434Arg	26.0	0.0	0		24.0	19.0	0.791667	NM_001205119	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	37	CCDS44582.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	15.32	2.797457	0.50208	0.001363	0.007793	ENSG00000175224	ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000525009	.	.	.	5.8	4.88	0.63580	.	0.345068	0.38111	N	0.001815	T	0.33962	0.0881	L	0.29908	0.895	0.41529	D	0.988441	B;B;B;B	0.25390	0.047;0.003;0.014;0.125	B;B;B;B	0.19148	0.005;0.002;0.003;0.024	T	0.23833	-1.0177	9	0.30854	T	0.27	-14.1572	9.9398	0.41574	0.0698:0.0:0.7929:0.1373	rs35619591;rs35619591	318;434;467;397	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	R	434;434;397;397;318;434;397;434;467;166	.	ENSP00000310321:G434R	G	+	1	0	ATG13	46646989	1.000000	0.71417	0.765000	0.31456	0.721000	0.41392	4.226000	0.58606	1.452000	0.47756	0.655000	0.94253	GGG	G|0.994;A|0.006	0.006	strong		0.532	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741	
CUX1	1523	hgsc.bcm.edu	37	7	101921292	101921292	+	Missense_Mutation	SNP	A	A	C	rs118010189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:101921292A>C	ENST00000437600.4	+	18	1982	c.1630A>C	c.(1630-1632)Aag>Cag	p.K544Q	CUX1_ENST00000547394.2_Missense_Mutation_p.K530Q|CUX1_ENST00000425244.2_Missense_Mutation_p.K500Q|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000292538.4_Missense_Mutation_p.K546Q|CUX1_ENST00000393824.3_Missense_Mutation_p.K507Q	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	353					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CGACAACATCAAGCTCTTTGA	0.662													A|||	18	0.00359425	0.0	0.0101	5008	,	,		12632	0.0		0.007	False		,,,				2504	0.0041				p.K546Q		Atlas-SNP	.											.	CUX1	253	.	0			c.A1636C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	5,4401	8.1+/-20.4	0,5,2198	42.0	36.0	38.0		1588,1498,1519,1636,1630	4.6	1.0	7	dbSNP_133	38	88,8510	45.8+/-104.6	0,88,4211	yes	missense,missense,missense,missense,missense	CUX1	NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2	53,53,53,53,53	0,93,6409	CC,CA,AA		1.0235,0.1135,0.7152	,,,,	530/663,500/633,507/640,546/679,544/677	101921292	93,12911	2203	4299	6502	SO:0001583	missense	1523	exon18			AACATCAAGCTCT	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1630A>C	7.37:g.101921292A>C	ENSP00000414091:p.Lys544Gln	282.0	0.0	0		244.0	120.0	0.491803	NM_001913	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	A	21.6	4.169486	0.78452	0.001135	0.010235	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	4.55	4.55	0.56014	CASP, C-terminal (1);	.	.	.	.	T	0.45796	0.1360	M	0.66560	2.04	0.28388	N	0.919234	D;D;D;D;D	0.89917	1.0;0.999;0.972;1.0;0.998	D;D;P;D;D	0.85130	0.99;0.997;0.861;0.989;0.963	T	0.45220	-0.9276	9	0.52906	T	0.07	.	14.2558	0.66051	1.0:0.0:0.0:0.0	.	507;500;530;544;546	B4DZZ2;B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;.;CASP_HUMAN	Q	546;530;500;544	ENSP00000292538:K546Q;ENSP00000449371:K530Q;ENSP00000409745:K500Q;ENSP00000414091:K544Q	ENSP00000292538:K546Q	K	+	1	0	CUX1	101708012	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.671000	0.91174	1.849000	0.53698	0.374000	0.22700	AAG	A|0.993;C|0.007	0.007	strong		0.662	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913	
SLITRK1	114798	hgsc.bcm.edu	37	13	84455214	84455214	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:84455214T>C	ENST00000377084.2	-	1	1314	c.429A>G	c.(427-429)cgA>cgG	p.R143R		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	143					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGTCTATATCTCGTAATAAAT	0.458																																					p.R143R		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A429G						PASS	.						60.0	65.0	64.0					13																	84455214		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			TATATCTCGTAAT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.429A>G	13.37:g.84455214T>C		67.0	0.0	0		61.0	14.0	0.229508	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																			.	.	none		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559148	140559148	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559148C>T	ENST00000239444.2	+	1	1778	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	511	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACACAGACAACGGCCACCTGT	0.677																																					p.N511N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C1533T						PASS	.						94.0	148.0	130.0					5																	140559148		2203	4298	6501	SO:0001819	synonymous_variant	56128	exon1			AGACAACGGCCAC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1533C>T	5.37:g.140559148C>T		305.0	0.0	0		423.0	50.0	0.118203	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			.	.	none		0.677	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
CPN1	1369	hgsc.bcm.edu	37	10	101808540	101808540	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101808540G>A	ENST00000370418.3	-	8	1456	c.1205C>T	c.(1204-1206)aCc>aTc	p.T402I		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	402					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		AGGACCCACGGTCACAGTTAC	0.512																																					p.T402I		Atlas-SNP	.											.	CPN1	62	.	0			c.C1205T						PASS	.						181.0	142.0	156.0					10																	101808540		2203	4300	6503	SO:0001583	missense	1369	exon8			CCCACGGTCACAG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1205C>T	10.37:g.101808540G>A	ENSP00000359446:p.Thr402Ile	137.0	0.0	0		113.0	26.0	0.230089	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745365	0.30955	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.49139	0.79;0.79	5.5	4.6	0.57074	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.099528	0.64402	N	0.000002	T	0.45256	0.1333	M	0.66560	2.04	0.52099	D	0.999945	B	0.14438	0.01	B	0.19148	0.024	T	0.38824	-0.9643	10	0.38643	T	0.18	-16.477	10.2462	0.43343	0.1601:0.0:0.8399:0.0	.	402	P15169	CBPN_HUMAN	I	402;199	ENSP00000359446:T402I;ENSP00000410895:T199I	ENSP00000359446:T402I	T	-	2	0	CPN1	101798530	0.998000	0.40836	0.992000	0.48379	0.342000	0.28953	2.976000	0.49289	1.339000	0.45563	0.644000	0.83932	ACC	.	.	none		0.512	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
ZNF812	729648	hgsc.bcm.edu	37	19	9801257	9801257	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9801257T>C	ENST00000457674.2	-	5	1440	c.922A>G	c.(922-924)Aag>Gag	p.K308E	ZNF812_ENST00000536819.1_5'UTR	NM_001199814.1	NP_001186743.1	P0C7V5	ZN812_HUMAN	zinc finger protein 812	308					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1						CCACATTCCTTACATTCATAG	0.428																																					p.K308E		Atlas-SNP	.											.	ZNF812	27	.	0			c.A922G						PASS	.																																			SO:0001583	missense	729648	exon6			ATTCCTTACATTC		CCDS54215.1	19p13.2	2014-04-02			ENSG00000224689	ENSG00000224689		"""Zinc fingers, C2H2-type"", ""-"""	33242	protein-coding gene	gene with protein product							Standard	NM_001199814		Approved		uc021uop.1	P0C7V5	OTTHUMG00000167867	ENST00000457674.2:c.922A>G	19.37:g.9801257T>C	ENSP00000395629:p.Lys308Glu	116.0	0.0	0		87.0	24.0	0.275862	NM_001199814		Missense_Mutation	SNP	ENST00000457674.2	37	CCDS54215.1	.	.	.	.	.	.	.	.	.	.	t	14.71	2.617516	0.46736	.	.	ENSG00000224689	ENST00000457674	T	0.08370	3.1	1.42	0.35	0.16037	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09598	0.0236	N	0.16098	0.37	0.09310	N	1	D	0.64830	0.994	P	0.62298	0.9	T	0.30060	-0.9991	9	0.40728	T	0.16	.	4.7675	0.13139	0.0:0.1949:0.0:0.8051	.	308	P0C7V5	ZN812_HUMAN	E	308	ENSP00000395629:K308E	ENSP00000395629:K308E	K	-	1	0	ZNF812	9662257	0.000000	0.05858	0.147000	0.22382	0.506000	0.33950	-5.502000	0.00117	0.031000	0.15407	0.164000	0.16699	AAG	.	.	none		0.428	ZNF812-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396726.1		
PKHD1	5314	hgsc.bcm.edu	37	6	51890754	51890754	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51890754C>T	ENST00000371117.3	-	32	4129	c.3854G>A	c.(3853-3855)aGc>aAc	p.S1285N	PKHD1_ENST00000340994.4_Missense_Mutation_p.S1285N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1285	IPT/TIG 7.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CCCCACCAAGCTTGGTGAAGG	0.587																																					p.S1285N		Atlas-SNP	.											.	PKHD1	927	.	0			c.G3854A						PASS	.						88.0	78.0	82.0					6																	51890754		2203	4300	6503	SO:0001583	missense	5314	exon32			ACCAAGCTTGGTG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3854G>A	6.37:g.51890754C>T	ENSP00000360158:p.Ser1285Asn	114.0	0.0	0		103.0	27.0	0.262136	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	8.648	0.897477	0.17686	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87412	-2.05;-2.25	5.79	-0.718	0.11205	Cell surface receptor IPT/TIG (1);	1.934510	0.01638	N	0.023911	T	0.64962	0.2646	M	0.63428	1.95	0.09310	N	1	B;B	0.34015	0.435;0.011	B;B	0.25140	0.058;0.002	T	0.52873	-0.8517	10	0.12766	T	0.61	.	3.7658	0.08622	0.2648:0.4257:0.0:0.3094	.	1285;1285	P08F94-2;P08F94	.;PKHD1_HUMAN	N	1285	ENSP00000360158:S1285N;ENSP00000341097:S1285N	ENSP00000341097:S1285N	S	-	2	0	PKHD1	51998713	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.748000	0.04818	0.080000	0.16959	-0.169000	0.13324	AGC	.	.	none		0.587	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
GRIA2	2891	hgsc.bcm.edu	37	4	158242630	158242630	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158242630G>T	ENST00000264426.9	+	6	1040	c.761G>T	c.(760-762)gGt>gTt	p.G254V	GRIA2_ENST00000507898.1_Missense_Mutation_p.G207V|GRIA2_ENST00000449365.1_Missense_Mutation_p.G207V|GRIA2_ENST00000296526.7_Missense_Mutation_p.G254V|GRIA2_ENST00000393815.2_Missense_Mutation_p.G207V	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	254					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CAGTTTGGAGGTGCAAATGTC	0.348																																					p.G254V		Atlas-SNP	.											.	GRIA2	358	.	0			c.G761T						PASS	.						192.0	203.0	199.0					4																	158242630		2203	4300	6503	SO:0001583	missense	2891	exon6			TTGGAGGTGCAAA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.761G>T	4.37:g.158242630G>T	ENSP00000264426:p.Gly254Val	162.0	0.0	0		131.0	29.0	0.221374	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616977	0.87359	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.74	5.74	0.90152	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.99;0.94;1.0	D	0.89340	0.3653	10	0.87932	D	0	.	19.9317	0.97122	0.0:0.0:1.0:0.0	.	254;254;207	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	V	207;207;254;254;207	ENSP00000426845:G207V;ENSP00000377403:G207V;ENSP00000296526:G254V;ENSP00000264426:G254V;ENSP00000389837:G207V	ENSP00000264426:G254V	G	+	2	0	GRIA2	158462080	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	9.238000	0.95380	2.716000	0.92895	0.591000	0.81541	GGT	.	.	none		0.348	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
AATK	9625	hgsc.bcm.edu	37	17	79100340	79100340	+	Silent	SNP	C	C	T	rs139267162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79100340C>T	ENST00000326724.4	-	7	666	c.642G>A	c.(640-642)ctG>ctA	p.L214L	MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Silent_p.L111L|AATK_ENST00000572339.1_5'UTR|MIR338_ENST00000390137.2_RNA	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGCAGCTCCGCAGGTAGCCCT	0.692													C|||	28	0.00559105	0.0008	0.0144	5008	,	,		15493	0.0		0.0119	False		,,,				2504	0.0051				p.L214L		Atlas-SNP	.											.	AATK	102	.	0			c.G642A						PASS	.	C	,	6,3592		0,6,1793	5.0	7.0	6.0		642,333	2.0	1.0	17	dbSNP_134	6	87,7669		1,85,3792	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	1,91,5585	TT,TC,CC		1.1217,0.1668,0.8191	,	214/1375,111/1272	79100340	93,11261	1799	3878	5677	SO:0001819	synonymous_variant	9625	exon7			GCTCCGCAGGTAG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.642G>A	17.37:g.79100340C>T		60.0	0.0	0		59.0	31.0	0.525424	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	14	0.00641025641025641	0	0.0	6	0.016574585635359115	0	0.0	8	0.010554089709762533	C	10.62	1.402433	0.25291	0.001668	0.011217	ENSG00000181409	ENST00000417379	.	.	.	4.07	2.0	0.26442	.	.	.	.	.	T	0.26412	0.0645	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15925	-1.0420	4	.	.	.	.	1.1434	0.01770	0.162:0.3873:0.2417:0.2089	.	.	.	.	Y	167	.	.	C	-	2	0	AATK	76714935	0.991000	0.36638	0.999000	0.59377	0.919000	0.55068	0.370000	0.20433	0.330000	0.23485	0.467000	0.42956	TGC	C|0.994;T|0.006	0.006	strong		0.692	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
FGFR3	2261	hgsc.bcm.edu	37	4	1801511	1801511	+	Silent	SNP	C	C	T	rs3135867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1801511C>T	ENST00000260795.2	+	3	519	c.417C>T	c.(415-417)gaC>gaT	p.D139D	FGFR3_ENST00000352904.1_Silent_p.D139D|FGFR3_ENST00000481110.2_Silent_p.D139D|FGFR3_ENST00000340107.4_Silent_p.D139D|FGFR3_ENST00000440486.2_Silent_p.D139D|FGFR3_ENST00000412135.2_Silent_p.D139D			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	139					alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	ACGGGGAGGACGAGGCTGAGG	0.677		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				c|||	101	0.0201677	0.0015	0.0331	5008	,	,		17142	0.0		0.0487	False		,,,				2504	0.0276				p.D139D		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	0			c.C417T						PASS	.	C	,,	38,4360	42.3+/-75.8	1,36,2162	88.0	69.0	75.0		417,417,417	-1.1	1.0	4	dbSNP_103	75	447,8147	134.1+/-191.5	10,427,3860	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	11,463,6022	TT,TC,CC		5.2013,0.864,3.7331	,,	139/807,139/809,139/695	1801511	485,12507	2199	4297	6496	SO:0001819	synonymous_variant	2261	exon4	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGAGGACGAGGCT	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.417C>T	4.37:g.1801511C>T		196.0	0.0	0		156.0	78.0	0.5	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			C|0.965;T|0.035	0.035	strong		0.677	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
FAM188B	84182	hgsc.bcm.edu	37	7	30818142	30818142	+	Missense_Mutation	SNP	T	T	G	rs201946407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818142T>G	ENST00000265299.6	+	2	235	c.158T>G	c.(157-159)cTt>cGt	p.L53R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	53										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GTTTTGCATCTTGAATTTCTC	0.478													T|||	5	0.000998403	0.0	0.0014	5008	,	,		21672	0.0		0.004	False		,,,				2504	0.0				p.L53R		Atlas-SNP	.											.	FAM188B	62	.	0			c.T158G						PASS	.	T	ARG/LEU	5,3861		0,5,1928	125.0	120.0	122.0		158	4.4	0.9	7		122	62,8212		0,62,4075	yes	missense	FAM188B	NM_032222.2	102	0,67,6003	GG,GT,TT		0.7493,0.1293,0.5519	probably-damaging	53/758	30818142	67,12073	1933	4137	6070	SO:0001583	missense	84182	exon2			TGCATCTTGAATT	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.158T>G	7.37:g.30818142T>G	ENSP00000265299:p.Leu53Arg	226.0	0.0	0		209.0	47.0	0.22488	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	16.55	3.153666	0.57259	0.001293	0.007493	ENSG00000106125	ENST00000265299	T	0.24723	1.84	4.43	4.43	0.53597	.	0.070363	0.56097	D	0.000037	T	0.41236	0.1150	M	0.77103	2.36	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.49707	-0.8911	10	0.87932	D	0	1.9565	10.2353	0.43280	0.0:0.0:0.0:1.0	.	53	Q4G0A6	F188B_HUMAN	R	53	ENSP00000265299:L53R	ENSP00000265299:L53R	L	+	2	0	FAM188B	30784667	0.997000	0.39634	0.891000	0.34965	0.613000	0.37349	4.603000	0.61105	1.998000	0.58463	0.459000	0.35465	CTT	T|0.998;G|0.002	0.002	strong		0.478	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
KIAA1522	57648	hgsc.bcm.edu	37	1	33236824	33236824	+	Missense_Mutation	SNP	C	C	T	rs199566536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33236824C>T	ENST00000373480.1	+	6	1970	c.1867C>T	c.(1867-1869)Cca>Tca	p.P623S	KIAA1522_ENST00000373481.3_Missense_Mutation_p.P634S|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P682S	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	623	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GAGCCCTAACCCAGCTGCCCC	0.627													C|||	3	0.000599042	0.0008	0.0029	5008	,	,		7970	0.0		0.0	False		,,,				2504	0.0				p.P682S		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C2044T						PASS	.	C	,SER/PRO,SER/PRO	1,3823		0,1,1911	49.0	56.0	54.0		,2044,1867	3.8	0.8	1		54	17,8217		0,17,4100	yes	intron,missense,missense	KIAA1522	NM_001198973.1,NM_020888.2,NM_001198972.1	,74,74	0,18,6011	TT,TC,CC		0.2065,0.0262,0.1493	,benign,benign	,682/1095,623/1036	33236824	18,12040	1912	4117	6029	SO:0001583	missense	57648	exon6			CCTAACCCAGCTG	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.1867C>T	1.37:g.33236824C>T	ENSP00000362579:p.Pro623Ser	77.0	0.0	0		71.0	36.0	0.507042	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	2.344	-0.350520	0.05173	2.62E-4	0.002065	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.12569	2.67;2.69;2.7	3.78	3.78	0.43462	.	0.637153	0.12767	N	0.440802	T	0.05868	0.0153	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.004	T	0.32640	-0.9899	10	0.10111	T	0.7	-0.4029	10.0745	0.42351	0.2011:0.7989:0.0:0.0	.	634;623;682	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	S	682;634;623	ENSP00000383851:P682S;ENSP00000362580:P634S;ENSP00000362579:P623S	ENSP00000362579:P623S	P	+	1	0	KIAA1522	33009411	0.002000	0.14202	0.843000	0.33291	0.062000	0.15995	1.732000	0.38146	1.802000	0.52723	0.655000	0.94253	CCA	C|0.997;T|0.003	0.003	strong		0.627	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
PAPLN	89932	hgsc.bcm.edu	37	14	73720604	73720604	+	Missense_Mutation	SNP	C	C	A	rs146030488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:73720604C>A	ENST00000554301.1	+	11	1400	c.1237C>A	c.(1237-1239)Ccc>Acc	p.P413T	PAPLN_ENST00000340738.5_Missense_Mutation_p.P386T|PAPLN_ENST00000381166.3_Missense_Mutation_p.P413T|PAPLN_ENST00000427855.1_Missense_Mutation_p.P413T|PAPLN_ENST00000555445.1_Missense_Mutation_p.P413T			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	413	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCCTGGGAAGCCCCCTGCCAT	0.701													C|||	16	0.00319489	0.0015	0.0058	5008	,	,		17022	0.0		0.0089	False		,,,				2504	0.001				p.P386T		Atlas-SNP	.											.	PAPLN	180	.	0			c.C1156A						PASS	.	C	THR/PRO	4,4398		0,4,2197	27.0	29.0	28.0		1156	4.6	1.0	14	dbSNP_134	28	40,8558		0,40,4259	yes	missense	PAPLN	NM_173462.3	38	0,44,6456	AA,AC,CC		0.4652,0.0909,0.3385	probably-damaging	386/1252	73720604	44,12956	2201	4299	6500	SO:0001583	missense	89932	exon11			GGGAAGCCCCCTG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1237C>A	14.37:g.73720604C>A	ENSP00000451803:p.Pro413Thr	106.0	0.0	0		116.0	55.0	0.474138	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		14	0.00641025641025641	3	0.006097560975609756	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.78	3.890634	0.72524	9.09E-4	0.004652	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	4.57	4.57	0.56435	.	.	.	.	.	T	0.76506	0.3997	M	0.85945	2.785	0.49798	D	0.999828	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.83565	0.0109	9	0.87932	D	0	.	17.5437	0.87855	0.0:1.0:0.0:0.0	.	413;413;386	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	T	386;413;413;413;413	ENSP00000345395:P386T;ENSP00000403403:P413T;ENSP00000370558:P413T;ENSP00000451803:P413T;ENSP00000451729:P413T	ENSP00000216658:P413T	P	+	1	0	PAPLN	72790357	1.000000	0.71417	0.998000	0.56505	0.599000	0.36880	7.053000	0.76641	2.385000	0.81259	0.462000	0.41574	CCC	C|0.996;A|0.004	0.004	strong		0.701	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
VCX	26609	hgsc.bcm.edu	37	X	7811760	7811760	+	Silent	SNP	C	C	A	rs202230674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:7811760C>A	ENST00000381059.3	+	3	543	c.324C>A	c.(322-324)gcC>gcA	p.A108A	VCX_ENST00000341408.4_Silent_p.A108A	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	108	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.			A -> S (in Ref. 3; AAH98123). {ECO:0000305}.	chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GTCAGGAGGCCGAGCTGGAGG	0.662																																					p.A108A		Atlas-SNP	.											.	VCX	28	.	0			c.C324A						PASS	.						83.0	103.0	96.0					X																	7811760		2133	4081	6214	SO:0001819	synonymous_variant	26609	exon3			GGAGGCCGAGCTG	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"""variable charge, X chromosome"""			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.324C>A	X.37:g.7811760C>A		127.0	0.0	0		77.0	18.0	0.233766	NM_013452	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	37	CCDS14128.1																																																																																			.	.	alt		0.662	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452	
PAX5	5079	hgsc.bcm.edu	37	9	37033983	37033983	+	Splice_Site	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:37033983C>G	ENST00000358127.4	-	1	120	c.46G>C	c.(46-48)Gga>Cga	p.G16R	PAX5_ENST00000414447.1_Splice_Site_p.G16R|PAX5_ENST00000377847.2_Splice_Site_p.G16R|PAX5_ENST00000377853.2_Splice_Site_p.G16R|PAX5_ENST00000446742.1_Splice_Site_p.G16R|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000520154.1_Splice_Site_p.G16R|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000523241.1_Splice_Site_p.G16R|PAX5_ENST00000377852.2_Splice_Site_p.G16R|PAX5_ENST00000520281.1_Splice_Site_p.G16R	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	16	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)	p.?(10)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GCGGTCCTACCTGTCCTGCTG	0.552			"""T, Mis, D, F, S"""	"""IGH@, ETV6, PML, FOXP1, ZNF521, ELN"""	"""NHL, ALL, B-ALL"""																																p.G16R		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	10	Unknown(10)	haematopoietic_and_lymphoid_tissue(10)	c.G46C						PASS	.						70.0	65.0	66.0					9																	37033983		2203	4300	6503	SO:0001630	splice_region_variant	5079	exon1			TCCTACCTGTCCT		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"""Paired boxes"", ""Homeoboxes / PRD class"""	8619	protein-coding gene	gene with protein product	"""B-cell lineage specific activator"""	167414	"""paired box gene 5 (B-cell lineage specific activator protein)"", ""paired box gene 5 (B-cell lineage specific activator)"""			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.46+1G>C	9.37:g.37033983C>G		72.0	0.0	0		98.0	29.0	0.295918	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650847	0.87958	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.99474	-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97	6.08	6.08	0.98989	Paired box protein, N-terminal (3);	0.000000	0.64402	D	0.000001	D	0.99557	0.9841	M	0.82923	2.615	0.80722	D	1	D;B;P;D;P;P;D;D;D	0.89917	1.0;0.439;0.752;1.0;0.56;0.727;1.0;1.0;1.0	D;B;P;D;P;P;D;D;D	0.91635	0.999;0.196;0.627;0.999;0.533;0.664;0.999;0.999;0.999	D	0.99007	1.0813	9	.	.	.	.	20.2751	0.98485	0.0:1.0:0.0:0.0	.	16;16;16;16;16;16;16;16;16	C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;PAX5_HUMAN	R	16	ENSP00000350844:G16R;ENSP00000367084:G16R;ENSP00000367083:G16R;ENSP00000429637:G16R;ENSP00000429291:G16R;ENSP00000430773:G16R;ENSP00000404687:G16R;ENSP00000412188:G16R;ENSP00000367078:G16R	.	G	-	1	0	PAX5	37023983	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.083000	0.71326	2.890000	0.99128	0.655000	0.94253	GGA	.	.	none		0.552	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		Missense_Mutation
RTEL1	51750	hgsc.bcm.edu	37	20	62294236	62294236	+	Missense_Mutation	SNP	G	G	A	rs184051277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62294236G>A	ENST00000360203.5	+	6	857	c.532G>A	c.(532-534)Gta>Ata	p.V178I	RTEL1_ENST00000370018.3_Missense_Mutation_p.V178I|RTEL1_ENST00000318100.4_Missense_Mutation_p.V178I|RTEL1_ENST00000508582.2_Missense_Mutation_p.V202I|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.V178I					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			CTACAACAACGTAGAAGGTAC	0.577													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18896	0.001		0.0	False		,,,				2504	0.0				p.V202I		Atlas-SNP	.											.	RTEL1	114	.	0			c.G604A						PASS	.						85.0	74.0	78.0					20																	62294236		2203	4300	6503	SO:0001583	missense	51750	exon6			AACAACGTAGAAG	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.532G>A	20.37:g.62294236G>A	ENSP00000353332:p.Val178Ile	69.0	0.0	0		83.0	29.0	0.349398	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.04	2.119146	0.37436	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000356810	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	5.05	4.1	0.47936	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.137530	0.47455	D	0.000232	T	0.63534	0.2519	L	0.49571	1.57	0.42644	D	0.993425	B;B;B;B	0.33637	0.237;0.129;0.42;0.108	B;B;B;B	0.29942	0.105;0.059;0.109;0.015	T	0.64525	-0.6387	10	0.42905	T	0.14	-13.4976	14.0662	0.64831	0.0739:0.0:0.9261:0.0	.	202;202;178;178	Q9NZ71-7;D6RBA3;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	I	178;178;202;178;228	ENSP00000359035:V178I;ENSP00000322287:V178I;ENSP00000424307:V202I;ENSP00000353332:V178I;ENSP00000349265:V228I	ENSP00000349265:V228I	V	+	1	0	AL353715.1	61764680	1.000000	0.71417	0.746000	0.31095	0.277000	0.26821	4.731000	0.62022	1.266000	0.44231	0.511000	0.50034	GTA	G|1.000;A|0.000	0.000	strong		0.577	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
ATRNL1	26033	hgsc.bcm.edu	37	10	117075140	117075140	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:117075140A>C	ENST00000355044.3	+	18	3057	c.2931A>C	c.(2929-2931)tcA>tcC	p.S977S	ATRNL1_ENST00000423111.2_Silent_p.S74S|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	977	PSI 5.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AAGGTTCTTCACGGGGACCAA	0.458																																					p.S977S		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A2931C						PASS	.						151.0	134.0	140.0					10																	117075140		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon18			TTCTTCACGGGGA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2931A>C	10.37:g.117075140A>C		111.0	0.0	0		121.0	27.0	0.22314	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	A	9.126	1.010135	0.19277	.	.	ENSG00000107518	ENST00000526373	.	.	.	5.34	-3.83	0.04269	.	.	.	.	.	T	0.61974	0.2390	.	.	.	0.53688	D	0.999979	.	.	.	.	.	.	T	0.61806	-0.6987	4	.	.	.	-11.3344	12.8927	0.58080	0.2191:0.6573:0.1236:0.0	.	.	.	.	P	107	.	.	T	+	1	0	ATRNL1	117065130	0.000000	0.05858	0.587000	0.28692	0.980000	0.70556	-2.912000	0.00698	-0.532000	0.06332	0.374000	0.22700	ACG	.	.	none		0.458	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
FGFR2	2263	hgsc.bcm.edu	37	10	123279643	123279643	+	Silent	SNP	C	C	T	rs138315382		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123279643C>T	ENST00000358487.5	-	7	1061	c.789G>A	c.(787-789)ccG>ccA	p.P263P	FGFR2_ENST00000346997.2_Silent_p.P263P|FGFR2_ENST00000356226.4_Silent_p.P148P|FGFR2_ENST00000369056.1_Silent_p.P263P|FGFR2_ENST00000351936.6_Silent_p.P263P|FGFR2_ENST00000369059.1_Silent_p.P148P|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000478859.1_Silent_p.P35P|FGFR2_ENST00000369060.4_Silent_p.P263P|FGFR2_ENST00000457416.2_Silent_p.P263P|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000357555.5_Silent_p.P174P|FGFR2_ENST00000360144.3_Silent_p.P174P	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	263	Ig-like C2-type 3.		P -> L (in CS). {ECO:0000269|PubMed:11173845}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	AGGCATTTGCCGGCAGTCCGG	0.552		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				C|||	1	0.000199681	0.0	0.0014	5008	,	,		18486	0.0		0.0	False		,,,				2504	0.0				p.P263P		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G789A						PASS	.	C	,,,,,,,,	0,4406		0,0,2203	81.0	68.0	72.0		789,789,,522,444,789,444,522,789	-11.6	0.0	10	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,	263/822,263/770,,174/708,148/707,263/706,148/705,174/681,263/823	123279643	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	ATTTGCCGGCAGT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.789G>A	10.37:g.123279643C>T		78.0	0.0	0		63.0	18.0	0.285714	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|1.000;T|0.000	0.000	strong		0.552	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
RAVER2	55225	hgsc.bcm.edu	37	1	65243466	65243466	+	Silent	SNP	A	A	G	rs41285400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65243466A>G	ENST00000294428.3	+	3	555	c.477A>G	c.(475-477)gaA>gaG	p.E159E	RAVER2_ENST00000371072.4_Silent_p.E159E|RAVER2_ENST00000430964.2_5'Flank			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	159	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						AAGAGTTTGAAGAACTTGTTC	0.368													A|||	13	0.00259585	0.0015	0.0029	5008	,	,		18846	0.001		0.007	False		,,,				2504	0.001				p.E159E		Atlas-SNP	.											.	RAVER2	56	.	0			c.A477G						PASS	.	A		9,3707		0,9,1849	208.0	187.0	194.0		477	1.4	1.0	1	dbSNP_127	194	119,8097		0,119,3989	no	coding-synonymous	RAVER2	NM_018211.3		0,128,5838	GG,GA,AA		1.4484,0.2422,1.0727		159/679	65243466	128,11804	1858	4108	5966	SO:0001819	synonymous_variant	55225	exon3			GTTTGAAGAACTT	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.477A>G	1.37:g.65243466A>G		249.0	0.0	0		237.0	120.0	0.506329	NM_018211	Q6P141|Q9NPV7	Silent	SNP	ENST00000294428.3	37																																																																																				A|0.994;G|0.006	0.006	strong		0.368	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211	
ATP6V0A1	535	hgsc.bcm.edu	37	17	40665913	40665913	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40665913T>C	ENST00000343619.4	+	20	2288	c.2165T>C	c.(2164-2166)aTc>aCc	p.I722T	ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.I716T|RP11-400F19.18_ENST00000591237.1_RNA|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.I368T|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.I722T|MIR5010_ENST00000582846.1_RNA|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.I673T|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.I679T|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.I723T	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	722					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		CACCAGGCCATCCACACCATC	0.577																																					p.I723T		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.T2168C						PASS	.						207.0	182.0	191.0					17																	40665913		2203	4300	6503	SO:0001583	missense	535	exon19			AGGCCATCCACAC	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"""ATPases / V-type"""	865	protein-coding gene	gene with protein product		192130	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 1"", ""ATPase, H+ transporting, lysosomal V0 subunit A1"""	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.2165T>C	17.37:g.40665913T>C	ENSP00000342951:p.Ile722Thr	210.0	0.0	0		193.0	58.0	0.300518	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468889	0.84533	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83;-2.83	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97238	0.9097	H	0.98276	4.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.998;0.999;1.0	D	0.98713	1.0705	10	0.87932	D	0	-21.9263	14.7204	0.69302	0.0:0.0:0.0:1.0	.	673;679;723;722;716	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	T	722;722;716;723;673;368	ENSP00000342951:I722T;ENSP00000444676:I722T;ENSP00000377415:I716T;ENSP00000264649:I723T;ENSP00000443991:I673T;ENSP00000446377:I368T	ENSP00000264649:I723T	I	+	2	0	ATP6V0A1	37919439	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.868000	0.87116	2.067000	0.61834	0.459000	0.35465	ATC	.	.	none		0.577	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	
ZNF516	9658	hgsc.bcm.edu	37	18	74091766	74091766	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:74091766C>T	ENST00000443185.2	-	4	2621	c.2304G>A	c.(2302-2304)aaG>aaA	p.K768K	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	768					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGTAGTAGGTCTTGTGGCTGC	0.592																																					p.K768K		Atlas-SNP	.											.	ZNF516	102	.	0			c.G2304A						PASS	.						35.0	40.0	38.0					18																	74091766		2038	4187	6225	SO:0001819	synonymous_variant	9658	exon4			GTAGGTCTTGTGG	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2304G>A	18.37:g.74091766C>T		135.0	0.0	0		89.0	26.0	0.292135	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				.	.	none		0.592	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
PTPRU	10076	hgsc.bcm.edu	37	1	29606589	29606589	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:29606589G>C	ENST00000345512.3	+	11	1933	c.1804G>C	c.(1804-1806)Ggc>Cgc	p.G602R	PTPRU_ENST00000356870.3_Missense_Mutation_p.G602R|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000428026.2_Missense_Mutation_p.G602R|PTPRU_ENST00000460170.2_Missense_Mutation_p.G602R|PTPRU_ENST00000323874.8_Missense_Mutation_p.G602R|PTPRU_ENST00000373779.3_Missense_Mutation_p.G602R	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	602	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GTCACCCCTGGGCGAGTCTGA	0.652																																					p.G602R		Atlas-SNP	.											.	PTPRU	374	.	0			c.G1804C						PASS	.						65.0	66.0	65.0					1																	29606589		2203	4300	6503	SO:0001583	missense	10076	exon11			CCCCTGGGCGAGT	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.1804G>C	1.37:g.29606589G>C	ENSP00000334941:p.Gly602Arg	277.0	0.0	0		239.0	53.0	0.221757	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434280	0.62955	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.31510	1.53;1.55;1.55;1.55;1.49;1.55	5.25	5.25	0.73442	.	0.059602	0.64402	D	0.000002	T	0.24044	0.0582	N	0.25647	0.755	0.38689	D	0.952724	P;P;P;P;P	0.48089	0.905;0.905;0.905;0.846;0.846	B;B;B;B;B	0.43251	0.413;0.413;0.413;0.235;0.235	T	0.04454	-1.0950	9	.	.	.	.	13.2132	0.59836	0.0793:0.0:0.9207:0.0	.	602;602;602;602;602	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	R	602	ENSP00000334941:G602R;ENSP00000362884:G602R;ENSP00000349333:G602R;ENSP00000314987:G602R;ENSP00000392332:G602R;ENSP00000432906:G602R	.	G	+	1	0	PTPRU	29479176	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.471000	0.53107	2.432000	0.82394	0.544000	0.68410	GGC	.	.	none		0.652	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
MMP13	4322	hgsc.bcm.edu	37	11	102825227	102825227	+	Silent	SNP	G	G	A	rs368161332		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102825227G>A	ENST00000260302.3	-	3	499	c.471C>T	c.(469-471)caC>caT	p.H157H	MMP13_ENST00000340273.4_Silent_p.H157H	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	157					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CAATGCCATCGTGAAGTCTGG	0.343																																					p.H157H		Atlas-SNP	.											MMP13,NS,malignant_melanoma,-2,1	MMP13	75	1	0			c.C471T						PASS	.	G		0,4404		0,0,2202	64.0	64.0	64.0		471	-2.8	0.0	11		64	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MMP13	NM_002427.3		0,2,6499	AA,AG,GG		0.0233,0.0,0.0154		157/472	102825227	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	4322	exon3			GCCATCGTGAAGT	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.471C>T	11.37:g.102825227G>A		137.0	0.0	0		108.0	70.0	0.648148	NM_002427	A8K846|B2RCZ3|Q6NWN6	Silent	SNP	ENST00000260302.3	37	CCDS8324.1																																																																																			.	.	weak		0.343	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	
DOCK8	81704	hgsc.bcm.edu	37	9	340230	340230	+	Missense_Mutation	SNP	G	G	A	rs373187839		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:340230G>A	ENST00000453981.1	+	14	1700	c.1588G>A	c.(1588-1590)Gtg>Atg	p.V530M	DOCK8_ENST00000469391.1_Missense_Mutation_p.V462M|DOCK8_ENST00000432829.2_Missense_Mutation_p.V462M			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	530					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AATGCTGCCCGTGAAACCCTT	0.443																																					p.V530M		Atlas-SNP	.											DOCK8_ENST00000453981,NS,carcinoma,-2,2	DOCK8	401	2	0			c.G1588A						scavenged	.	G	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	85.0	87.0	86.0		1384,1384,1588	5.5	0.9	9		86	0,8600		0,0,4300	no	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	21,21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	462/2000,462/2032,530/2100	340230	1,13005	2203	4300	6503	SO:0001583	missense	81704	exon14			CTGCCCGTGAAAC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1588G>A	9.37:g.340230G>A	ENSP00000408464:p.Val530Met	81.0	1.0	0.0123457		91.0	37.0	0.406593	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988063	0.93106	2.27E-4	0.0	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.39229	1.09;1.09;1.09	5.49	5.49	0.81192	.	0.128635	0.52532	D	0.000073	T	0.63034	0.2477	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.67725	0.878;0.953	T	0.61964	-0.6954	10	0.52906	T	0.07	.	19.7314	0.96182	0.0:0.0:1.0:0.0	.	462;530	E9PH09;Q8NF50	.;DOCK8_HUMAN	M	530;530;462;462	ENSP00000408464:V530M;ENSP00000394888:V462M;ENSP00000419438:V462M	ENSP00000287364:V530M	V	+	1	0	DOCK8	330230	1.000000	0.71417	0.917000	0.36280	0.951000	0.60555	3.219000	0.51200	2.727000	0.93392	0.655000	0.94253	GTG	.	.	weak		0.443	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
VWA3A	146177	hgsc.bcm.edu	37	16	22144377	22144377	+	Silent	SNP	C	C	A	rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144377C>A	ENST00000389398.5	+	20	2125	c.2029C>A	c.(2029-2031)Cgg>Agg	p.R677R	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GGAGGTCACCCGGGCTGCAGG	0.577																																					p.R677R		Atlas-SNP	.											.	VWA3A	115	.	0			c.C2029A						PASS	.						38.0	42.0	40.0					16																	22144377		2054	4187	6241	SO:0001819	synonymous_variant	146177	exon20			GTCACCCGGGCTG	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2029C>A	16.37:g.22144377C>A		91.0	0.0	0		71.0	27.0	0.380282	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	alt		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
PCNX	22990	hgsc.bcm.edu	37	14	71443816	71443816	+	Silent	SNP	T	T	G	rs35702999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71443816T>G	ENST00000304743.2	+	6	1208	c.762T>G	c.(760-762)tcT>tcG	p.S254S	PCNX_ENST00000238570.5_Silent_p.S254S|PCNX_ENST00000439984.3_Silent_p.S254S	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	254						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTGATCAGTCTCTGTCCAGCG	0.498													T|||	35	0.00698882	0.0	0.0043	5008	,	,		18137	0.0069		0.0199	False		,,,				2504	0.0051				p.S254S		Atlas-SNP	.											.	PCNX	198	.	0			c.T762G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	141.0	119.0	126.0		762	0.8	1.0	14	dbSNP_126	126	86,8514	48.9+/-108.6	1,84,4215	no	coding-synonymous	PCNX	NM_014982.2		1,94,6408	GG,GT,TT		1.0,0.227,0.7381		254/2342	71443816	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			TCAGTCTCTGTCC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.762T>G	14.37:g.71443816T>G		227.0	0.0	0		218.0	94.0	0.431193	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1																																																																																			T|0.991;G|0.009	0.009	strong		0.498	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
TREX2	11219	hgsc.bcm.edu	37	X	152710185	152710185	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:152710185T>G	ENST00000334497.2	-	11	1974	c.833A>C	c.(832-834)gAg>gCg	p.E278A	TREX2_ENST00000330912.2_Missense_Mutation_p.E235A|TREX2_ENST00000338525.2_Missense_Mutation_p.E235A|TREX2_ENST00000370231.2_Missense_Mutation_p.E235A|TREX2_ENST00000414588.1_Missense_Mutation_p.E277A|TREX2_ENST00000402951.1_Missense_Mutation_p.E278A|TREX2_ENST00000393862.2_Missense_Mutation_p.E235A|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000370232.1_Missense_Mutation_p.E278A			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	278					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGCTCAGGCCTCCAGGCTGGG	0.692								Editing and processing nucleases																													p.E235A		Atlas-SNP	.											.	TREX2	36	.	0			c.A704C						PASS	.						13.0	10.0	11.0					X																	152710185		2176	4263	6439	SO:0001583	missense	11219	exon2			CAGGCCTCCAGGC	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.833A>C	X.37:g.152710185T>G	ENSP00000334993:p.Glu278Ala	139.0	0.0	0		50.0	18.0	0.36	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	T	14.14	2.445525	0.43429	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.53640	0.81;0.81;0.81;0.65;0.65;0.65;0.61;0.81	4.35	4.35	0.52113	.	0.576106	0.12955	U	0.425475	T	0.33818	0.0876	L	0.27053	0.805	0.09310	N	1	P;P	0.46987	0.888;0.608	B;B	0.38985	0.287;0.08	T	0.17018	-1.0383	10	0.87932	D	0	-15.0026	9.2945	0.37806	0.0:0.0:0.0:1.0	.	277;278	Q06S70;Q9BQ50	.;TREX2_HUMAN	A	235;235;235;278;278;278;277;235	ENSP00000377442:E235A;ENSP00000333441:E235A;ENSP00000345218:E235A;ENSP00000334993:E278A;ENSP00000359252:E278A;ENSP00000386078:E278A;ENSP00000401692:E277A;ENSP00000359251:E235A	ENSP00000333441:E235A	E	-	2	0	TREX2	152363379	0.010000	0.17322	0.007000	0.13788	0.003000	0.03518	1.834000	0.39171	1.523000	0.49018	0.381000	0.24937	GAG	.	.	none		0.692	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701	
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108.0	89.0	95.0		,1968	2.4	0.0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1881-781C>T	7.37:g.55238087C>T		152.0	0.0	0		145.0	66.0	0.455172	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
ADAM32	203102	hgsc.bcm.edu	37	8	39068684	39068684	+	Silent	SNP	T	T	A	rs61753544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39068684T>A	ENST00000379907.4	+	12	1201	c.1074T>A	c.(1072-1074)acT>acA	p.T358T	ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	358	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			GTGTGAAGACTTTTAGCAGTT	0.323													T|||	2	0.000399361	0.0	0.0014	5008	,	,		16759	0.0		0.001	False		,,,				2504	0.0				p.T358T		Atlas-SNP	.											.	ADAM32	70	.	0			c.T1074A						PASS	.	T		5,3635		0,5,1815	102.0	101.0	101.0		1074	-2.5	1.0	8	dbSNP_129	101	25,8143		0,25,4059	no	coding-synonymous	ADAM32	NM_145004.5		0,30,5874	AA,AT,TT		0.3061,0.1374,0.2541		358/788	39068684	30,11778	1820	4084	5904	SO:0001819	synonymous_variant	203102	exon12			GAAGACTTTTAGC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1074T>A	8.37:g.39068684T>A		89.0	0.0	0		71.0	56.0	0.788732	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.999;A|0.001	0.001	strong		0.323	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
FAM135A	57579	hgsc.bcm.edu	37	6	71195892	71195892	+	Intron	SNP	A	A	G	rs142935920		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:71195892A>G	ENST00000418814.2	+	10	1437				FAM135A_ENST00000505868.1_Intron|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000370479.3_Silent_p.L239L|FAM135A_ENST00000457062.2_Silent_p.L239L|FAM135A_ENST00000361499.3_Intron	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A											breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						TGCAGCTCCTATATGAGCGTC	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		16631	0.0		0.001	False		,,,				2504	0.0				p.L239L		Atlas-SNP	.											.	FAM135A	181	.	0			c.A717G						PASS	.	A	,,	0,4406		0,0,2203	88.0	79.0	82.0		,,717	-2.4	1.0	6	dbSNP_134	82	8,8592	6.4+/-24.3	0,8,4292	no	intron,intron,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	0,8,6495	GG,GA,AA		0.093,0.0,0.0615	,,	,,239/1303	71195892	8,12998	2203	4300	6503	SO:0001627	intron_variant	57579	exon9			GCTCCTATATGAG	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.823+4035A>G	6.37:g.71195892A>G		232.0	0.0	0		201.0	94.0	0.467662	NM_020819	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.999;G|0.001	0.001	strong		0.368	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.N550S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						scavenged	.						19.0	26.0	24.0					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	111.0	1.0	0.00900901		116.0	26.0	0.224138	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103116000	103116000	+	Silent	SNP	T	T	C	rs192003811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103116000T>C	ENST00000375735.2	+	65	10083	c.9939T>C	c.(9937-9939)gcT>gcC	p.A3313A	DYNC2H1_ENST00000398093.3_Silent_p.A3320A|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3313	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTATCACAGCTCTTGAATTAG	0.303													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		15868	0.0		0.004	False		,,,				2504	0.001				p.A3320A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T9960C						PASS	.	T	,	3,3549		0,3,1773	58.0	51.0	54.0		9960,9939	5.6	1.0	11		54	40,8010		0,40,3985	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	0,43,5758	CC,CT,TT		0.4969,0.0845,0.3706	,	3320/4315,3313/4308	103116000	43,11559	1776	4025	5801	SO:0001819	synonymous_variant	79659	exon66			CACAGCTCTTGAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.9939T>C	11.37:g.103116000T>C		62.0	0.0	0		51.0	8.0	0.156863	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.997;C|0.003	0.003	strong		0.303	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
DOCK4	9732	hgsc.bcm.edu	37	7	111375211	111375211	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111375211G>C	ENST00000437633.1	-	50	5547	c.5291C>G	c.(5290-5292)aCc>aGc	p.T1764S	DOCK4_ENST00000428084.1_Missense_Mutation_p.T1773S|DOCK4_ENST00000494651.2_Missense_Mutation_p.T647S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1764	Ser-rich.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GCTGCTAGGGGTGGGGTTCAC	0.507																																					p.T1764S		Atlas-SNP	.											.	DOCK4	365	.	0			c.C5291G						PASS	.						38.0	38.0	38.0					7																	111375211		1905	4125	6030	SO:0001583	missense	9732	exon50			CTAGGGGTGGGGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.5291C>G	7.37:g.111375211G>C	ENSP00000404179:p.Thr1764Ser	44.0	0.0	0		37.0	11.0	0.297297	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.24|17.24	3.338601|3.338601	0.60963|0.60963	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633	.|T;T;T	.|0.05717	.|4.13;3.4;4.14	6.04|6.04	5.16|5.16	0.70880|0.70880	.|.	.|0.093637	.|0.85682	.|D	.|0.000000	T|T	0.04182|0.04182	0.0116|0.0116	N|N	0.08118|0.08118	0|0	0.42876|0.42876	D|D	0.994156|0.994156	.|B;B;B;P	.|0.45902	.|0.206;0.146;0.146;0.868	.|B;B;B;B	.|0.41510	.|0.085;0.038;0.026;0.359	T|T	0.59348|0.59348	-0.7471|-0.7471	5|10	.|0.21540	.|T	.|0.41	.|.	14.7566|14.7566	0.69569|0.69569	0.0686:0.0:0.9314:0.0|0.0686:0.0:0.9314:0.0	.|.	.|647;1809;1764;77	.|F5GXW1;Q149N5;Q8N1I0;Q8N1I0-4	.|.;.;DOCK4_HUMAN;.	A|S	1797|1752;1773;647;1764	.|ENSP00000410746:T1773S;ENSP00000440944:T647S;ENSP00000404179:T1764S	.|ENSP00000262421:T1752S	P|T	-|-	1|2	0|0	DOCK4|DOCK4	111162447|111162447	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.062000|7.062000	0.76706|0.76706	2.876000|2.876000	0.98609|0.98609	0.650000|0.650000	0.86243|0.86243	CCC|ACC	.	.	none		0.507	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
TTN	7273	hgsc.bcm.edu	37	2	179393691	179393691	+	Missense_Mutation	SNP	G	G	A	rs55842557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179393691G>A	ENST00000591111.1	-	310	102088	c.101864C>T	c.(101863-101865)aCa>aTa	p.T33955I	TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T33028I|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T26531I|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T35596I|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T26656I|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T26723I|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33955			T -> I. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCCTGTGATGTTTTAGTGAT	0.398													G|||	19	0.00379393	0.0	0.0043	5008	,	,		22209	0.0		0.0159	False		,,,				2504	0.0				p.T35596I		Atlas-SNP	.											.	TTN	18412	.	0			c.C106787T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,3779		0,3,1888	147.0	135.0	139.0		80168,79967,99083,79592	4.7	1.0	2	dbSNP_129	139	56,8158		1,54,4052	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	1,57,5940	AA,AG,GG		0.6818,0.0793,0.4918	benign,benign,benign,benign	26723/27119,26656/27052,33028/33424,26531/26927	179393691	59,11937	1891	4107	5998	SO:0001583	missense	7273	exon360			TGTGATGTTTTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.101864C>T	2.37:g.179393691G>A	ENSP00000465570:p.Thr33955Ile	229.0	0.0	0		202.0	80.0	0.39604	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	G	14.74	2.624609	0.46840	7.93E-4	0.006818	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62941	-0.01;0.25;0.23;0.22	5.69	4.74	0.60224	Ribonuclease H-like (1);	.	.	.	.	T	0.32763	0.0840	N	0.24115	0.695	0.25561	N	0.986992	B;B;B;B;B	0.29805	0.026;0.026;0.026;0.026;0.257	B;B;B;B;B	0.26310	0.029;0.029;0.029;0.029;0.068	T	0.42565	-0.9444	9	0.87932	D	0	.	13.2479	0.60033	0.0:0.0:0.7689:0.2311	rs55842557	26531;26656;26723;33955;33028	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	I	33028;26531;26723;26656;26528	ENSP00000343764:T33028I;ENSP00000434586:T26531I;ENSP00000340554:T26723I;ENSP00000352154:T26656I	ENSP00000340554:T26723I	T	-	2	0	TTN	179101937	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.452000	0.52971	2.677000	0.91161	0.655000	0.94253	ACA	G|0.993;A|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TUBB4A	10382	hgsc.bcm.edu	37	19	6495199	6495199	+	Silent	SNP	C	C	T	rs369467354		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6495199C>T	ENST00000264071.2	-	4	1682	c.1311G>A	c.(1309-1311)gaG>gaA	p.E437E	CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000540257.1_Silent_p.E437E|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	437					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										CCTCCGCCTCCTCCTCGAACT	0.622																																					p.E437E		Atlas-SNP	.											.	.	.	.	0			c.G1311A						PASS	.	C		0,4406		0,0,2203	70.0	64.0	66.0		1311	2.9	1.0	19		66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TUBB4	NM_006087.2		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		437/445	6495199	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	10382	exon4			CGCCTCCTCCTCG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1311G>A	19.37:g.6495199C>T		54.0	0.0	0		49.0	18.0	0.367347	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	37	CCDS12168.1																																																																																			.	.	weak		0.622	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087	
FAT4	79633	hgsc.bcm.edu	37	4	126336348	126336348	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336348C>G	ENST00000394329.3	+	5	6243	c.6230C>G	c.(6229-6231)cCa>cGa	p.P2077R	FAT4_ENST00000335110.5_Missense_Mutation_p.P375R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P2077>?(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCAACTGACCCAGATAGTGGC	0.418																																					p.P2077R		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6230G						PASS	.						137.0	140.0	139.0					4																	126336348		2203	4300	6503	SO:0001583	missense	79633	exon5			CTGACCCAGATAG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6230C>G	4.37:g.126336348C>G	ENSP00000377862:p.Pro2077Arg	126.0	0.0	0		107.0	7.0	0.0654206	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	2.239	-0.374320	0.05034	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51574	0.7;0.7	5.0	4.11	0.48088	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.32763	0.0840	N	0.17379	0.485	0.42532	D	0.99304	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.004	T	0.10109	-1.0644	10	0.20519	T	0.43	.	16.9703	0.86297	0.0:0.8614:0.1386:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	R	2077;375	ENSP00000377862:P2077R;ENSP00000335169:P375R	ENSP00000335169:P375R	P	+	2	0	FAT4	126555798	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.908000	0.69916	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
SMO	6608	hgsc.bcm.edu	37	7	128843277	128843277	+	Silent	SNP	C	C	T	rs45571737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128843277C>T	ENST00000249373.3	+	2	664	c.384C>T	c.(382-384)gcC>gcT	p.A128A		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	128	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	TGCTGTGTGCCGTATACATGC	0.667			Mis		skin basal cell								C|||	20	0.00399361	0.0	0.0058	5008	,	,		17322	0.0		0.0119	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C384T						PASS	.	C		5,4381		0,5,2188	26.0	22.0	23.0		384	-8.7	0.7	7	dbSNP_127	23	110,8456		0,110,4173	no	coding-synonymous	SMO	NM_005631.4		0,115,6361	TT,TC,CC		1.2841,0.114,0.8879		128/788	128843277	115,12837	2193	4283	6476	SO:0001819	synonymous_variant	6608	exon2			GTGTGCCGTATAC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.384C>T	7.37:g.128843277C>T		99.0	0.0	0		103.0	40.0	0.38835	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			C|0.993;T|0.007	0.007	strong		0.667	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
CCDC158	339965	hgsc.bcm.edu	37	4	77272155	77272155	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77272155C>A	ENST00000388914.3	-	17	2810	c.2658G>T	c.(2656-2658)ctG>ctT	p.L886L		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	886										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TTACATGAGACAGGAAGCTGG	0.368																																					p.L886L		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2658T						PASS	.						150.0	147.0	148.0					4																	77272155		1960	4149	6109	SO:0001819	synonymous_variant	339965	exon17			ATGAGACAGGAAG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2658G>T	4.37:g.77272155C>A		81.0	0.0	0		89.0	18.0	0.202247	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			.	.	none		0.368	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
HS6ST3	266722	hgsc.bcm.edu	37	13	96743584	96743584	+	Silent	SNP	G	G	T	rs144263527	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:96743584G>T	ENST00000376705.2	+	1	492	c.468G>T	c.(466-468)acG>acT	p.T156T		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	156	5'-phosphosulfate-binding. {ECO:0000255}.				heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)	p.T156T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TCCAGAAGACGGGGGGCACCA	0.602													c|||	6	0.00119808	0.0015	0.0	5008	,	,		11700	0.0		0.002	False		,,,				2504	0.002				p.T156T		Atlas-SNP	.											HS6ST3,NS,carcinoma,0,1	HS6ST3	54	1	1	Substitution - coding silent(1)	pancreas(1)	c.G468T						PASS	.	G		4,4402		0,4,2199	34.0	36.0	36.0		468	-0.6	1.0	13	dbSNP_134	36	18,8582		0,18,4282	no	coding-synonymous	HS6ST3	NM_153456.2		0,22,6481	TT,TG,GG		0.2093,0.0908,0.1692		156/472	96743584	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	266722	exon1			GAAGACGGGGGGC	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"""Sulfotransferases, membrane-bound"""	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.468G>T	13.37:g.96743584G>T		50.0	0.0	0		41.0	18.0	0.439024	NM_153456	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	37	CCDS9481.1																																																																																			G|0.998;T|0.002	0.002	strong		0.602	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456	
KCND1	3750	hgsc.bcm.edu	37	X	48826490	48826490	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:48826490G>A	ENST00000218176.3	-	1	1486	c.189C>T	c.(187-189)gaC>gaT	p.D63D	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	63					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	CCAGCAAGGTGTCTGGGTAGC	0.567																																					p.D63D		Atlas-SNP	.											.	KCND1	63	.	0			c.C189T						PASS	.						46.0	31.0	36.0					X																	48826490		2203	4300	6503	SO:0001819	synonymous_variant	3750	exon1			CAAGGTGTCTGGG	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.189C>T	X.37:g.48826490G>A		254.0	0.0	0		166.0	53.0	0.319277	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	37	CCDS14314.1																																																																																			.	.	none		0.567	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979	
ZBBX	79740	hgsc.bcm.edu	37	3	167045779	167045779	+	Silent	SNP	G	G	A	rs375095384		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167045779G>A	ENST00000392766.2	-	11	1153	c.813C>T	c.(811-813)acC>acT	p.T271T	ZBBX_ENST00000392767.2_Silent_p.T271T|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000455345.2_Silent_p.T271T|ZBBX_ENST00000392764.1_Silent_p.T242T|ZBBX_ENST00000307529.5_Silent_p.T271T	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	271						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T271T(2)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CATGATTTCCGGTTCTCCATT	0.378													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15273	0.0		0.0	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - coding silent(2)	endometrium(2)	c.C813T						PASS	.	G	,,	1,3745		0,1,1872	218.0	199.0	205.0		813,726,813	-3.4	0.0	3		205	0,8220		0,0,4110	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	0,1,5982	AA,AG,GG		0.0,0.0267,0.0084	,,	271/840,242/772,271/801	167045779	1,11965	1873	4110	5983	SO:0001819	synonymous_variant	79740	exon11			ATTTCCGGTTCTC	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.813C>T	3.37:g.167045779G>A		170.0	0.0	0		123.0	26.0	0.211382	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.	.	weak		0.378	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
MS4A14	84689	hgsc.bcm.edu	37	11	60183483	60183483	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60183483T>C	ENST00000300187.6	+	5	1319	c.1042T>C	c.(1042-1044)Tct>Cct	p.S348P	MS4A14_ENST00000531787.1_Missense_Mutation_p.S236P|MS4A14_ENST00000395005.2_Missense_Mutation_p.S331P|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531783.1_Missense_Mutation_p.S381P	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	348						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CAAACAGTCTTCTAATCTGAC	0.443																																					p.S381P		Atlas-SNP	.											.	MS4A14	120	.	0			c.T1141C						PASS	.						133.0	108.0	116.0					11																	60183483		2203	4300	6503	SO:0001583	missense	84689	exon6			CAGTCTTCTAATC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1042T>C	11.37:g.60183483T>C	ENSP00000300187:p.Ser348Pro	230.0	0.0	0		214.0	162.0	0.757009	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	7.724	0.697733	0.15106	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.32023	1.47;2.69;1.47;3.05	3.68	-1.06	0.10002	.	18.346600	0.00424	N	0.000065	T	0.15609	0.0376	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12811	-1.0533	10	0.30078	T	0.28	-0.6079	3.9787	0.09486	0.2178:0.542:0.0:0.2402	.	331;348	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	P	236;348;331;381	ENSP00000437222:S236P;ENSP00000300187:S348P;ENSP00000378453:S331P;ENSP00000433761:S381P	ENSP00000300187:S348P	S	+	1	0	MS4A14	59940059	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.134000	0.15932	-0.196000	0.10366	0.528000	0.53228	TCT	.	.	none		0.443	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
APOL6	80830	hgsc.bcm.edu	37	22	36055130	36055130	+	Missense_Mutation	SNP	T	T	A	rs5999923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36055130T>A	ENST00000409652.4	+	3	795	c.519T>A	c.(517-519)aaT>aaA	p.N173K		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	173			N -> K (in dbSNP:rs5999923). {ECO:0000269|PubMed:17974005}.		lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TTATCTATAATCTTAGAAACA	0.493													T|||	120	0.0239617	0.0537	0.0086	5008	,	,		20620	0.002		0.0169	False		,,,				2504	0.0245				p.N173K		Atlas-SNP	.											.	APOL6	26	.	0			c.T519A						PASS	.	T	LYS/ASN	205,4201	124.1+/-161.4	7,191,2005	61.0	63.0	62.0		519	-8.1	0.0	22	dbSNP_114	62	168,8432	78.1+/-140.7	5,158,4137	yes	missense	APOL6	NM_030641.3	94	12,349,6142	AA,AT,TT		1.9535,4.6527,2.8679	benign	173/344	36055130	373,12633	2203	4300	6503	SO:0001583	missense	80830	exon3			CTATAATCTTAGA	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.519T>A	22.37:g.36055130T>A	ENSP00000386280:p.Asn173Lys	61.0	0.0	0		54.0	23.0	0.425926	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	37	CCDS13919.1	42	0.019230769230769232	26	0.052845528455284556	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.015	-1.542021	0.00934	0.046527	0.019535	ENSG00000221963	ENST00000409652	T	0.03358	3.96	4.05	-8.09	0.01090	.	1.657170	0.04414	N	0.366552	T	0.00440	0.0014	L	0.41632	1.29	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.43523	-0.9386	10	0.14252	T	0.57	-4.2671	1.0684	0.01616	0.2834:0.3061:0.2313:0.1793	rs5999923;rs52798245;rs5999923	173	Q9BWW8	APOL6_HUMAN	K	173	ENSP00000386280:N173K	ENSP00000386280:N173K	N	+	3	2	APOL6	34385076	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.755000	0.00375	-3.583000	0.00137	-1.567000	0.00876	AAT	T|0.973;A|0.027	0.027	strong		0.493	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
CACTIN	58509	hgsc.bcm.edu	37	19	3612035	3612035	+	Silent	SNP	G	G	A	rs61738769		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:3612035G>A	ENST00000429344.2	-	10	2215	c.2163C>T	c.(2161-2163)ttC>ttT	p.F721F	CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000248420.5_Silent_p.F721F|CACTIN_ENST00000221899.3_Silent_p.F653F	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	721					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										TGACGATCTTGAAAGCGATGT	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17582	0.0		0.001	False		,,,				2504	0.0				p.F721F		Atlas-SNP	.											C19orf29_ENST00000429344,NS,neuroblastoma,0,2	.	.	2	0			c.C2163T						PASS	.	G	,	0,4120		0,0,2060	110.0	126.0	121.0		2163,2163	3.3	1.0	19	dbSNP_129	121	3,8363		0,3,4180	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	0,3,6240	AA,AG,GG		0.0359,0.0,0.024	,	721/759,721/759	3612035	3,12483	2060	4183	6243	SO:0001819	synonymous_variant	58509	exon10			GATCTTGAAAGCG	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.2163C>T	19.37:g.3612035G>A		148.0	0.0	0		156.0	74.0	0.474359	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.54	2.863785	0.51482	0.0	3.59E-4	ENSG00000226800	ENST00000447295	.	.	.	4.31	3.27	0.37495	.	.	.	.	.	T	0.54711	0.1875	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48603	-0.9021	5	0.30078	T	0.28	.	7.8484	0.29440	0.1936:0.0:0.8064:0.0	.	.	.	.	K	103	.	ENSP00000412459:E103K	E	+	1	0	C19orf29OS	3563035	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.449000	0.44935	1.171000	0.42768	0.643000	0.83706	GAA	G|0.999;A|0.001	0.001	strong		0.617	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
KRT84	3890	hgsc.bcm.edu	37	12	52779159	52779159	+	Missense_Mutation	SNP	G	G	A	rs145217788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52779159G>A	ENST00000257951.3	-	1	277	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	71	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TGGATGGGCCGAGAGCCTACA	0.597													G|||	6	0.00119808	0.0	0.0	5008	,	,		18426	0.0		0.005	False		,,,				2504	0.001				p.R71W		Atlas-SNP	.											.	KRT84	61	.	0			c.C211T						PASS	.	G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	99.0	95.0	96.0		211	3.3	0.7	12	dbSNP_134	96	21,8579	15.3+/-51.7	0,21,4279	yes	missense	KRT84	NM_033045.3	101	0,24,6479	AA,AG,GG		0.2442,0.0681,0.1845	probably-damaging	71/601	52779159	24,12982	2203	4300	6503	SO:0001583	missense	3890	exon1			TGGGCCGAGAGCC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.211C>T	12.37:g.52779159G>A	ENSP00000257951:p.Arg71Trp	165.0	0.0	0		118.0	52.0	0.440678	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	9.259	1.042600	0.19748	6.81E-4	0.002442	ENSG00000161849	ENST00000257951	D	0.82344	-1.6	5.15	3.33	0.38152	.	0.736856	0.12245	N	0.486182	T	0.79341	0.4429	M	0.69358	2.11	0.09310	N	1	D	0.59357	0.985	B	0.37508	0.252	T	0.72243	-0.4350	10	0.62326	D	0.03	.	12.4648	0.55751	0.1438:0.0:0.8562:0.0	.	71	Q9NSB2	KRT84_HUMAN	W	71	ENSP00000257951:R71W	ENSP00000257951:R71W	R	-	1	2	KRT84	51065426	0.048000	0.20356	0.713000	0.30519	0.014000	0.08584	0.355000	0.20163	1.553000	0.49476	-0.192000	0.12808	CGG	G|0.998;A|0.002	0.002	strong		0.597	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
COG1	9382	hgsc.bcm.edu	37	17	71193525	71193525	+	Missense_Mutation	SNP	G	G	C	rs117208167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:71193525G>C	ENST00000299886.4	+	4	983	c.903G>C	c.(901-903)caG>caC	p.Q301H	RP11-143K11.5_ENST00000580671.1_RNA	NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	301					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			TCACAGGCCAGCATCCTGCCG	0.522													G|||	15	0.00299521	0.0008	0.0	5008	,	,		18880	0.001		0.0099	False		,,,				2504	0.0031				p.Q301H		Atlas-SNP	.											.	COG1	46	.	0			c.G903C						PASS	.	G	HIS/GLN	6,4400	11.4+/-27.6	0,6,2197	64.0	62.0	63.0		903	3.3	0.9	17	dbSNP_132	63	71,8529	43.1+/-100.9	0,71,4229	yes	missense	COG1	NM_018714.2	24	0,77,6426	CC,CG,GG		0.8256,0.1362,0.592	probably-damaging	301/981	71193525	77,12929	2203	4300	6503	SO:0001583	missense	9382	exon4			AGGCCAGCATCCT		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.903G>C	17.37:g.71193525G>C	ENSP00000299886:p.Gln301His	75.0	0.0	0		49.0	24.0	0.489796	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	8.408	0.843455	0.16963	0.001362	0.008256	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.24908	1.83;1.84	5.31	3.26	0.37387	.	0.492896	0.23176	N	0.051061	T	0.27798	0.0684	M	0.72479	2.2	0.40675	D	0.982259	D;D;D	0.57571	0.98;0.964;0.98	P;P;P	0.52267	0.694;0.679;0.694	T	0.06661	-1.0814	10	0.44086	T	0.13	-3.2025	7.9278	0.29885	0.1457:0.1339:0.7204:0.0	.	301;301;301	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	H	301	ENSP00000400111:Q301H;ENSP00000299886:Q301H	ENSP00000299886:Q301H	Q	+	3	2	COG1	68705120	0.612000	0.27000	0.889000	0.34880	0.675000	0.39556	1.226000	0.32563	0.686000	0.31488	0.655000	0.94253	CAG	G|0.994;C|0.006	0.006	strong		0.522	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
RIN2	54453	hgsc.bcm.edu	37	20	19955713	19955713	+	Silent	SNP	G	G	C	rs149398614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:19955713G>C	ENST00000255006.6	+	8	1340	c.1191G>C	c.(1189-1191)ctG>ctC	p.L397L	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	348					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						ACGTAGCTCTGCCTGGAACGA	0.562													G|||	37	0.00738818	0.0015	0.0058	5008	,	,		333	0.0		0.0298	False		,,,				2504	0.001				p.L397L		Atlas-SNP	.											.	RIN2	126	.	0			c.G1191C						PASS	.	G	,	20,4018		0,20,1999	107.0	116.0	113.0		1191,1044	3.5	0.1	20	dbSNP_134	113	236,8124		5,226,3949	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	5,246,5948	CC,CG,GG		2.823,0.4953,2.0648	,	397/945,348/896	19955713	256,12142	2019	4180	6199	SO:0001819	synonymous_variant	54453	exon8			AGCTCTGCCTGGA	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1191G>C	20.37:g.19955713G>C		36.0	0.0	0		34.0	19.0	0.558824	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			G|0.983;C|0.017	0.017	strong		0.562	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13716797	13716797	+	Silent	SNP	A	A	G	rs61744054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716797A>G	ENST00000265104.4	-	74	12812	c.12708T>C	c.(12706-12708)ggT>ggC	p.G4236G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4236					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCAGGAGACACCCTGGGAAA	0.403									Kartagener syndrome				A|||	174	0.0347444	0.1097	0.0216	5008	,	,		16997	0.001		0.005	False		,,,				2504	0.0082				p.G4236G		Atlas-SNP	.											DNAH5,NS,carcinoma,-1,1	DNAH5	868	1	0			c.T12708C						scavenged	.	A		355,4051	180.5+/-208.7	16,323,1864	57.0	52.0	54.0		12708	-11.1	0.0	5	dbSNP_129	54	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DNAH5	NM_001369.2		16,340,6147	GG,GA,AA		0.1977,8.0572,2.8602		4236/4625	13716797	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAGACACCCTGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12708T>C	5.37:g.13716797A>G		88.0	1.0	0.0113636		101.0	42.0	0.415842	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.971;G|0.029	0.029	strong		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
U2SURP	23350	hgsc.bcm.edu	37	3	142747227	142747227	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142747227G>A	ENST00000473835.2	+	15	1515	c.1425G>A	c.(1423-1425)tgG>tgA	p.W475*	U2SURP_ENST00000493598.2_Nonsense_Mutation_p.W474*|U2SURP_ENST00000397933.2_Nonsense_Mutation_p.W66*	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	475					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ACTATAGGTGGAAGCTTTATT	0.313																																					p.W475X		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1425A						PASS	.						75.0	70.0	72.0					3																	142747227		1796	4067	5863	SO:0001587	stop_gained	23350	exon15			TAGGTGGAAGCTT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"""RNA binding motif (RRM) containing"""	30855	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein a"", ""Ser/Arg-rich domain protein, 140 kDa"", ""U2 associated SR140 protein"""					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1425G>A	3.37:g.142747227G>A	ENSP00000418563:p.Trp475*	210.0	0.0	0		182.0	43.0	0.236264	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Nonsense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	39	7.674541	0.98425	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598;ENST00000480029	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0436	20.2187	0.98312	0.0:0.0:1.0:0.0	.	.	.	.	X	475;475;66;474;42	.	ENSP00000322376:W475X	W	+	3	0	U2SURP	144229917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.444000	0.97578	2.780000	0.95670	0.655000	0.94253	TGG	.	.	none		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415	
POLR3F	10621	hgsc.bcm.edu	37	20	18449662	18449662	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18449662A>C	ENST00000377603.4	+	2	517	c.137A>C	c.(136-138)gAa>gCa	p.E46A	DZANK1_ENST00000329494.5_5'Flank|MIR3192_ENST00000584920.1_RNA|DZANK1_ENST00000262547.5_5'Flank|POLR3F_ENST00000462997.1_3'UTR|DZANK1_ENST00000357236.4_5'Flank	NM_006466.2	NP_006457.2	Q9H1D9	RPC6_HUMAN	polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa	46				HIEAQQRAVA -> QYRSPAAGSS (in Ref. 1; AAB63677). {ECO:0000305}.	defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)	2						CCTCATATAGAAGCCCAGCAG	0.368																																					p.E46A	GBM(69;898 1468 19907 52011)	Atlas-SNP	.											.	POLR3F	14	.	0			c.A137C						PASS	.						100.0	100.0	100.0					20																	18449662		2203	4300	6503	SO:0001583	missense	10621	exon2			ATATAGAAGCCCA	U93869	CCDS13135.1	20p11.23	2013-01-21	2002-08-29		ENSG00000132664	ENSG00000132664		"""RNA polymerase subunits"""	15763	protein-coding gene	gene with protein product	"""RNA polymerase III C39 subunit"""		"""polymerase (RNA) III (DNA directed) polypeptide F (39 kDa)"""			9171375	Standard	NM_006466		Approved	RPC39, RPC6	uc002wqv.3	Q9H1D9	OTTHUMG00000031971	ENST00000377603.4:c.137A>C	20.37:g.18449662A>C	ENSP00000366828:p.Glu46Ala	238.0	0.0	0		267.0	67.0	0.250936	NM_006466	A8K4C7|O15319	Missense_Mutation	SNP	ENST00000377603.4	37	CCDS13135.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534697	0.45073	.	.	ENSG00000132664	ENST00000377603	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	L	0.51422	1.61	0.80722	D	1	B	0.25563	0.129	B	0.30251	0.113	T	0.55147	-0.8186	9	0.30078	T	0.28	.	16.3126	0.82898	1.0:0.0:0.0:0.0	.	46	Q9H1D9	RPC6_HUMAN	A	46	.	ENSP00000366828:E46A	E	+	2	0	POLR3F	18397662	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.904000	0.92590	2.333000	0.79357	0.482000	0.46254	GAA	.	.	none		0.368	POLR3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078170.2	NM_006466	
VWA3A	146177	hgsc.bcm.edu	37	16	22144378	22144378	+	Missense_Mutation	SNP	G	G	A	rs200086497		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144378G>A	ENST00000389398.5	+	20	2126	c.2030G>A	c.(2029-2031)cGg>cAg	p.R677Q	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GAGGTCACCCGGGCTGCAGGT	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		17694	0.001		0.0	False		,,,				2504	0.0				p.R677Q		Atlas-SNP	.											.	VWA3A	115	.	0			c.G2030A						PASS	.						38.0	42.0	41.0					16																	22144378		2055	4184	6239	SO:0001583	missense	146177	exon20			TCACCCGGGCTGC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2030G>A	16.37:g.22144378G>A	ENSP00000374049:p.Arg677Gln	91.0	0.0	0		72.0	27.0	0.375	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.23	1.294063	0.23564	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.10668	2.85	5.49	-3.57	0.04612	.	0.842998	0.10736	N	0.640019	T	0.04003	0.0112	N	0.04880	-0.145	0.80722	D	1	B;B	0.22080	0.04;0.064	B;B	0.12156	0.003;0.007	T	0.50136	-0.8863	10	0.02654	T	1	.	12.9659	0.58483	0.7034:0.0:0.2966:0.0	.	677;301	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	Q	677;300	ENSP00000374049:R677Q	ENSP00000299840:R300Q	R	+	2	0	VWA3A	22051879	0.545000	0.26449	0.959000	0.39883	0.756000	0.42949	-0.213000	0.09305	-0.507000	0.06549	-0.157000	0.13467	CGG	G|1.000;A|0.000	0.000	strong		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
SSC5D	284297	hgsc.bcm.edu	37	19	56029489	56029489	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56029489C>T	ENST00000389623.6	+	14	3869	c.3846C>T	c.(3844-3846)caC>caT	p.H1282H		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1282	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						cgacccctcaccccaccacga	0.627																																					p.H1282H		Atlas-SNP	.											SSC5D,NS,carcinoma,+2,1	SSC5D	65	1	0			c.C3846T						scavenged	.						469.0	431.0	443.0					19																	56029489		692	1591	2283	SO:0001819	synonymous_variant	284297	exon14			CCCTCACCCCACC		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3846C>T	19.37:g.56029489C>T		146.0	0.0	0		128.0	12.0	0.09375	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			.	.	none		0.627	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
OR4C13	283092	hgsc.bcm.edu	37	11	49974626	49974626	+	Missense_Mutation	SNP	G	G	A	rs150606357		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:49974626G>A	ENST00000555099.1	+	1	684	c.652G>A	c.(652-654)Gtc>Atc	p.V218I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						CTCCTGCGTGGTCATACTGTA	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		17462	0.0		0.001	False		,,,				2504	0.0				p.V218I		Atlas-SNP	.											.	OR4C13	96	.	0			c.G652A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	189.0	153.0	165.0		652	0.8	1.0	11	dbSNP_134	165	10,8582		0,10,4286	yes	missense	OR4C13	NM_001001955.2	29	0,10,6487	AA,AG,GG		0.1164,0.0,0.077	benign	218/310	49974626	10,12984	2201	4296	6497	SO:0001583	missense	283092	exon1			TGCGTGGTCATAC	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"""GPCR / Class A : Olfactory receptors"""	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.652G>A	11.37:g.49974626G>A	ENSP00000452277:p.Val218Ile	219.0	0.0	0		157.0	111.0	0.707006	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	3.409	-0.120655	0.06838	0.0	0.001164	ENSG00000258817	ENST00000555099	T	0.00091	8.74	2.7	0.748	0.18376	GPCR, rhodopsin-like superfamily (1);	0.168066	0.28125	N	0.016511	T	0.00144	0.0004	L	0.60957	1.885	0.09310	N	0.999999	B	0.02656	0.0	B	0.17722	0.019	T	0.38714	-0.9648	9	.	.	.	.	2.838	0.05521	0.3033:0.2481:0.4486:0.0	.	218	Q8NGP0	OR4CD_HUMAN	I	218	ENSP00000452277:V218I	.	V	+	1	0	OR4C13	49931202	0.000000	0.05858	0.988000	0.46212	0.089000	0.18198	-2.155000	0.01284	0.474000	0.27392	0.186000	0.17326	GTC	G|0.999;A|0.001	0.001	strong		0.488	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955	
ECD	11319	hgsc.bcm.edu	37	10	74899209	74899209	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:74899209G>A	ENST00000372979.4	-	11	1485	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ECD_ENST00000430082.2_Silent_p.L460L|ECD_ENST00000454759.2_Silent_p.L384L	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	427					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GCTTCCTGCAGCAGCTGGTCC	0.438																																					p.L460L		Atlas-SNP	.											.	ECD	50	.	0			c.C1378T						PASS	.						89.0	92.0	91.0					10																	74899209		2203	4300	6503	SO:0001819	synonymous_variant	11319	exon12			CCTGCAGCAGCTG	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1279C>T	10.37:g.74899209G>A		101.0	0.0	0		77.0	18.0	0.233766	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			.	.	none		0.438	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
BAZ2B	29994	hgsc.bcm.edu	37	2	160241785	160241785	+	Silent	SNP	T	T	C	rs372315034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160241785T>C	ENST00000392783.2	-	23	4062	c.3567A>G	c.(3565-3567)ggA>ggG	p.G1189G	BAZ2B_ENST00000392782.1_Silent_p.G1153G|AC008277.1_ENST00000420020.1_RNA|BAZ2B_ENST00000355831.2_Silent_p.G1155G|BAZ2B_ENST00000343439.5_Silent_p.G1089G	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GCTCAGTTTGTCCACAGTGGG	0.428													T|||	1	0.000199681	0.0	0.0	5008	,	,		15755	0.0		0.001	False		,,,				2504	0.0				p.G1189G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A3567G						PASS	.	T		2,3722		0,2,1860	120.0	117.0	118.0		3567	2.0	1.0	2		118	12,8192		0,12,4090	no	coding-synonymous	BAZ2B	NM_013450.2		0,14,5950	CC,CT,TT		0.1463,0.0537,0.1174		1189/2169	160241785	14,11914	1862	4102	5964	SO:0001819	synonymous_variant	29994	exon23			AGTTTGTCCACAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.3567A>G	2.37:g.160241785T>C		96.0	0.0	0		135.0	60.0	0.444444	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	37	CCDS2209.2																																																																																			.	.	weak		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
FASTKD2	22868	hgsc.bcm.edu	37	2	207631446	207631446	+	Missense_Mutation	SNP	G	G	C	rs147727753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:207631446G>C	ENST00000236980.6	+	2	377	c.29G>C	c.(28-30)aGt>aCt	p.S10T	MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S10T|MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000454776.2_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.S10T|MDH1B_ENST00000449792.1_5'Flank	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	10					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		CCATTTGGAAGTGTTTCAGTG	0.398													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17193	0.0		0.0089	False		,,,				2504	0.0031				p.S10T		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G29C						PASS	.	G	THR/SER,THR/SER,THR/SER	15,4391	22.3+/-47.3	0,15,2188	63.0	69.0	67.0		29,29,29	3.3	0.4	2	dbSNP_134	67	60,8540	35.9+/-90.5	1,58,4241	yes	missense,missense,missense	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	58,58,58	1,73,6429	CC,CG,GG		0.6977,0.3404,0.5767	possibly-damaging,possibly-damaging,possibly-damaging	10/711,10/711,10/711	207631446	75,12931	2203	4300	6503	SO:0001583	missense	22868	exon2			TTGGAAGTGTTTC	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.29G>C	2.37:g.207631446G>C	ENSP00000236980:p.Ser10Thr	174.0	0.0	0		148.0	79.0	0.533784	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	16.23	3.065708	0.55539	0.003404	0.006977	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.50548	2.41;0.74;2.41;2.41	4.14	3.26	0.37387	.	1.872060	0.02814	N	0.124770	T	0.37812	0.1017	L	0.40543	1.245	0.09310	N	1	P;P	0.46512	0.879;0.808	P;B	0.46076	0.503;0.242	T	0.42327	-0.9458	10	0.87932	D	0	-2.845	4.6425	0.12556	0.1112:0.0:0.6698:0.219	.	10;10	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	T	10	ENSP00000236980:S10T;ENSP00000409927:S10T;ENSP00000385990:S10T;ENSP00000384929:S10T	ENSP00000236980:S10T	S	+	2	0	FASTKD2	207339691	0.019000	0.18553	0.385000	0.26158	0.482000	0.33219	1.205000	0.32308	2.316000	0.78162	0.491000	0.48974	AGT	G|0.996;C|0.004	0.004	strong		0.398	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
USH2A	7399	hgsc.bcm.edu	37	1	215848914	215848914	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215848914C>A	ENST00000307340.3	-	63	12725	c.12339G>T	c.(12337-12339)ttG>ttT	p.L4113F	USH2A_ENST00000366943.2_Missense_Mutation_p.L4113F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4113	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTGACGATTCAAACCAGAGT	0.507										HNSCC(13;0.011)																											p.L4113F		Atlas-SNP	.											.	USH2A	1168	.	0			c.G12339T						PASS	.						69.0	65.0	67.0					1																	215848914		2203	4300	6503	SO:0001583	missense	7399	exon63			ACGATTCAAACCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12339G>T	1.37:g.215848914C>A	ENSP00000305941:p.Leu4113Phe	128.0	0.0	0		138.0	29.0	0.210145	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	1.035	-0.680618	0.03353	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54279	0.58;0.58	5.25	1.15	0.20763	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.220262	0.22515	N	0.059043	T	0.41351	0.1155	M	0.72894	2.215	0.09310	N	1	B	0.23735	0.09	B	0.20384	0.029	T	0.21861	-1.0233	10	0.18710	T	0.47	.	2.3656	0.04318	0.1182:0.4436:0.2314:0.2067	.	4113	O75445	USH2A_HUMAN	F	4113	ENSP00000305941:L4113F;ENSP00000355910:L4113F	ENSP00000305941:L4113F	L	-	3	2	USH2A	213915537	0.001000	0.12720	0.000000	0.03702	0.084000	0.17831	0.243000	0.18106	0.205000	0.20568	-0.143000	0.13931	TTG	.	.	none		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604621	140604621	+	Missense_Mutation	SNP	C	C	T	rs144421802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140604621C>T	ENST00000239449.4	+	1	1544	c.1544C>T	c.(1543-1545)gCc>gTc	p.A515V	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A362V	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	515	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACCTGTTTGCCCTCAGGTCG	0.677													c|||	17	0.00339457	0.0	0.0014	5008	,	,		16912	0.0		0.007	False		,,,				2504	0.0092				p.A515V	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C1544T						PASS	.	C	VAL/ALA	8,4398		0,8,2195	96.0	100.0	99.0		1544	4.2	1.0	5	dbSNP_134	99	98,8502		0,98,4202	no	missense	PCDHB14	NM_018934.2	64	0,106,6397	TT,TC,CC		1.1395,0.1816,0.815	benign	515/799	140604621	106,12900	2203	4300	6503	SO:0001583	missense	56122	exon1			TGTTTGCCCTCAG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1544C>T	5.37:g.140604621C>T	ENSP00000239449:p.Ala515Val	159.0	0.0	0		169.0	92.0	0.544379	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	14.32	2.499118	0.44455	0.001816	0.011395	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.01647	4.71;4.71	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.02083	0.0065	L	0.41124	1.26	0.35681	D	0.814049	P	0.45957	0.869	B	0.43838	0.433	T	0.55835	-0.8078	9	0.62326	D	0.03	.	16.4819	0.84160	0.0:1.0:0.0:0.0	.	515	Q9Y5E9	PCDBE_HUMAN	V	362;515	ENSP00000444518:A362V;ENSP00000239449:A515V	ENSP00000239449:A515V	A	+	2	0	PCDHB14	140584805	0.027000	0.19231	0.956000	0.39512	0.165000	0.22458	1.595000	0.36708	2.048000	0.60808	0.556000	0.70494	GCC	C|0.994;T|0.006	0.006	strong		0.677	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
KIF21A	55605	hgsc.bcm.edu	37	12	39716675	39716675	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:39716675T>A	ENST00000361418.5	-	27	3481	c.3466A>T	c.(3466-3468)Aga>Tga	p.R1156*	KIF21A_ENST00000395670.3_Nonsense_Mutation_p.R1156*|KIF21A_ENST00000544797.2_Nonsense_Mutation_p.R1136*|KIF21A_ENST00000541463.2_Nonsense_Mutation_p.R1120*|KIF21A_ENST00000361961.3_Nonsense_Mutation_p.R1143*|KIF21A_ENST00000547745.1_5'Flank			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1156					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GTGGTGGTTCTCCTTCGGGCC	0.453																																					p.R1156X		Atlas-SNP	.											.	KIF21A	238	.	0			c.A3466T						PASS	.						136.0	129.0	131.0					12																	39716675		2203	4300	6503	SO:0001587	stop_gained	55605	exon27			TGGTTCTCCTTCG	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3466A>T	12.37:g.39716675T>A	ENSP00000354878:p.Arg1156*	107.0	0.0	0		117.0	28.0	0.239316	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Nonsense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	T	37	5.997374	0.97184	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.	.	.	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3659	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	X	1143;1156;1156;203;197;1136;1156;1120	.	ENSP00000344501:R1156X	R	-	1	2	KIF21A	38002942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.732000	0.62029	2.020000	0.59435	0.528000	0.53228	AGA	.	.	none		0.453	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
CCSER1	401145	hgsc.bcm.edu	37	4	92519814	92519814	+	Missense_Mutation	SNP	C	C	T	rs370719096		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:92519814C>T	ENST00000509176.1	+	11	2597	c.2309C>T	c.(2308-2310)tCg>tTg	p.S770L	CCSER1_ENST00000333691.8_Missense_Mutation_p.S770L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	770																	TTTAGGTATTCGGCAGCGGAC	0.443																																					p.S770L		Atlas-SNP	.											.	.	.	.	0			c.C2309T						PASS	.						58.0	51.0	53.0					4																	92519814		692	1591	2283	SO:0001583	missense	401145	exon11			GGTATTCGGCAGC		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2309C>T	4.37:g.92519814C>T	ENSP00000425040:p.Ser770Leu	107.0	0.0	0		74.0	21.0	0.283784	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429555	0.43122	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	T;T	0.35973	1.28;1.28	5.77	4.93	0.64822	.	.	.	.	.	T	0.25494	0.0620	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22417	-1.0217	9	0.72032	D	0.01	-2.0E-4	13.2923	0.60278	0.0:0.9256:0.0:0.0744	.	770	Q9C0I3	F190A_HUMAN	L	770	ENSP00000425040:S770L;ENSP00000329482:S770L	ENSP00000329482:S770L	S	+	2	0	FAM190A	92738837	0.154000	0.22792	0.003000	0.11579	0.009000	0.06853	5.253000	0.65452	1.584000	0.49913	-0.157000	0.13467	TCG	.	.	weak		0.443	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	3'UTR	SNP	A	A	G	rs1137282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:25362777A>G	ENST00000256078.4	-	0	706				KRAS_ENST00000557334.1_Silent_p.D60D|KRAS_ENST00000311936.3_Silent_p.D173D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			TCTTTTTACCATCTTTGCTCA	0.279		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			A|||	879	0.175519	0.18	0.1931	5008	,	,		18305	0.0923		0.2187	False		,,,				2504	0.1984				p.D173D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	.	KRAS	30930	.	0			c.T519C						PASS	.	A	,	753,3647	305.5+/-289.0	61,631,1508	68.0	64.0	65.0		519,	3.4	1.0	12	dbSNP_86	65	1853,6727	328.5+/-318.3	168,1517,2605	no	coding-synonymous,utr-3	KRAS	NM_004985.3,NM_033360.2	,	229,2148,4113	GG,GA,AA		21.5967,17.1136,20.077	,	173/189,	25362777	2606,10374	2200	4290	6490	SO:0001624	3_prime_UTR_variant	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TTTACCATCTTTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.*73T>C	12.37:g.25362777A>G		166.0	0.0	0		127.0	126.0	0.992126	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																			T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong		0.279	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
DLGAP1	9229	hgsc.bcm.edu	37	18	3534224	3534224	+	Missense_Mutation	SNP	C	C	T	rs35822832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3534224C>T	ENST00000315677.3	-	10	3042	c.2447G>A	c.(2446-2448)cGg>cAg	p.R816Q	DLGAP1_ENST00000400149.3_Missense_Mutation_p.R506Q|DLGAP1_ENST00000539435.1_Missense_Mutation_p.R524Q|DLGAP1_ENST00000400147.2_Missense_Mutation_p.R514Q|DLGAP1_ENST00000400145.2_Missense_Mutation_p.R514Q|DLGAP1_ENST00000400155.1_Missense_Mutation_p.R522Q|DLGAP1_ENST00000534970.1_Missense_Mutation_p.R500Q|DLGAP1_ENST00000400150.3_Missense_Mutation_p.R532Q|DLGAP1_ENST00000515196.2_Missense_Mutation_p.R816Q|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000581699.1_Missense_Mutation_p.R522Q	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	816			R -> Q (in dbSNP:rs35822832).		synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				CCGTTCTTCCCGCTCCATCTG	0.602													C|||	30	0.00599042	0.003	0.0101	5008	,	,		19947	0.0		0.0179	False		,,,				2504	0.001				p.R816Q		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G2447A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	15,4391	22.3+/-47.3	0,15,2188	109.0	99.0	103.0		1541,2447,1499,1613,1565,1541,1571,2447	5.9	1.0	18	dbSNP_126	103	219,8381	92.1+/-154.2	2,215,4083	yes	missense,missense,missense,missense,missense,missense,missense,missense	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	43,43,43,43,43,43,43,43	2,230,6271	TT,TC,CC		2.5465,0.3404,1.7992	benign,benign,benign,benign,benign,benign,benign,benign	514/676,816/930,500/662,538/700,522/684,514/628,524/686,816/978	3534224	234,12772	2203	4300	6503	SO:0001583	missense	9229	exon10			TCTTCCCGCTCCA	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.2447G>A	18.37:g.3534224C>T	ENSP00000316377:p.Arg816Gln	160.0	0.0	0		160.0	70.0	0.4375	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	37	CCDS11836.1	20	0.009157509157509158	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	12	0.0158311345646438	C	17.14	3.314540	0.60524	0.003404	0.025465	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	T;T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.93	5.93	0.95920	.	0.106561	0.64402	D	0.000004	T	0.03915	0.0110	N	0.11724	0.165	0.45490	D	0.998455	B;B;B;B;B;B;B;B	0.21309	0.054;0.054;0.017;0.054;0.017;0.043;0.017;0.014	B;B;B;B;B;B;B;B	0.14578	0.006;0.011;0.01;0.006;0.01;0.002;0.004;0.006	T	0.24476	-1.0159	10	0.23891	T	0.37	-19.2872	20.3312	0.98718	0.0:1.0:0.0:0.0	rs35822832	816;500;512;522;524;514;816;514	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490-3;O14490;O14490-2	.;.;.;.;.;.;DLGP1_HUMAN;.	Q	816;514;532;506;522;500;524;514;816	ENSP00000316377:R816Q;ENSP00000383011:R514Q;ENSP00000383014:R532Q;ENSP00000383013:R506Q;ENSP00000383019:R522Q;ENSP00000437817:R500Q;ENSP00000446312:R524Q;ENSP00000383010:R514Q;ENSP00000445973:R816Q	ENSP00000316377:R816Q	R	-	2	0	DLGAP1	3524224	1.000000	0.71417	0.988000	0.46212	0.986000	0.74619	4.810000	0.62598	2.797000	0.96272	0.655000	0.94253	CGG	C|0.984;T|0.016	0.016	strong		0.602	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234735	26234735	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26234735C>T	ENST00000244534.5	-	1	481	c.427G>A	c.(427-429)Gct>Act	p.A143T		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	143					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GCGGCGCCAGCCACCTTCTTG	0.572																																					p.A143T		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.G427A						PASS	.						65.0	71.0	69.0					6																	26234735		2203	4300	6503	SO:0001583	missense	3007	exon1			CGCCAGCCACCTT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.427G>A	6.37:g.26234735C>T	ENSP00000244534:p.Ala143Thr	125.0	0.0	0		99.0	27.0	0.272727	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	0.960	-0.703518	0.03255	.	.	ENSG00000124575	ENST00000244534	T	0.14022	2.54	4.7	-4.82	0.03171	.	0.725492	0.13325	N	0.396354	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45396	-0.9264	10	0.06891	T	0.86	-17.2311	5.5857	0.17274	0.2338:0.4156:0.0:0.3506	.	143	P16402	H13_HUMAN	T	143	ENSP00000244534:A143T	ENSP00000244534:A143T	A	-	1	0	HIST1H1D	26342714	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.356000	0.07661	-0.537000	0.06290	-0.295000	0.09555	GCT	.	.	none		0.572	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
TMEM72	643236	hgsc.bcm.edu	37	10	45430257	45430257	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45430257C>T	ENST00000544540.1	+	4	633	c.149C>T	c.(148-150)aCc>aTc	p.T50I	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	168						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						ACAGAGCAAACCTACACTTTC	0.607																																					p.T168I		Atlas-SNP	.											.	TMEM72	25	.	0			c.C503T						PASS	.						122.0	130.0	127.0					10																	45430257		1568	3582	5150	SO:0001583	missense	643236	exon5			AGCAAACCTACAC	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.149C>T	10.37:g.45430257C>T	ENSP00000439911:p.Thr50Ile	83.0	0.0	0		86.0	37.0	0.430233	NM_001123376	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	37		.	.	.	.	.	.	.	.	.	.	C	14.56	2.570678	0.45798	.	.	ENSG00000187783	ENST00000389583;ENST00000544540	.	.	.	5.28	3.41	0.39046	.	0.000000	0.64402	D	0.000006	T	0.58736	0.2143	M	0.69823	2.125	0.39365	D	0.965998	B	0.15930	0.015	B	0.16722	0.016	T	0.61903	-0.6967	9	0.56958	D	0.05	-28.2717	9.2035	0.37275	0.0:0.8229:0.0:0.1771	.	168	A0PK05	TMM72_HUMAN	I	168;50	.	ENSP00000374234:T168I	T	+	2	0	TMEM72	44750263	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	3.002000	0.49496	1.372000	0.46190	0.563000	0.77884	ACC	.	.	none		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	
FAM13B	51306	hgsc.bcm.edu	37	5	137275968	137275968	+	Missense_Mutation	SNP	C	C	G	rs201094212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:137275968C>G	ENST00000033079.3	-	23	3145	c.2694G>C	c.(2692-2694)aaG>aaC	p.K898N	FAM13B_ENST00000425075.2_Missense_Mutation_p.K774N|PKD2L2_ENST00000290431.5_3'UTR|FAM13B_ENST00000420893.2_Missense_Mutation_p.K870N|PKD2L2_ENST00000508638.1_3'UTR|PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000502810.1_3'UTR	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	898					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						GAAGCCTAAGCTTGGCTTTAA	0.348													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18964	0.0		0.001	False		,,,				2504	0.0				p.K898N		Atlas-SNP	.											FAM13B,NS,carcinoma,0,2	FAM13B	46	2	0			c.G2694C						PASS	.						112.0	110.0	111.0					5																	137275968		2203	4300	6503	SO:0001583	missense	51306	exon23			CCTAAGCTTGGCT	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2694G>C	5.37:g.137275968C>G	ENSP00000033079:p.Lys898Asn	197.0	0.0	0		163.0	83.0	0.509202	NM_016603	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.29	3.591185	0.66219	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.37411	2.24;1.2;2.12	5.37	1.84	0.25277	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.72894	2.215	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.51028	-0.8757	10	0.87932	D	0	-13.3199	7.0159	0.24887	0.0:0.4207:0.0:0.5793	.	774;870;898	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	N	898;774;870	ENSP00000033079:K898N;ENSP00000394669:K774N;ENSP00000388521:K870N	ENSP00000033079:K898N	K	-	3	2	FAM13B	137303867	0.468000	0.25839	1.000000	0.80357	0.997000	0.91878	-0.247000	0.08866	0.446000	0.26666	0.591000	0.81541	AAG	C|0.999;G|0.001	0.001	strong		0.348	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
ASPM	259266	hgsc.bcm.edu	37	1	197069640	197069640	+	Missense_Mutation	SNP	A	A	G	rs200856894		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:197069640A>G	ENST00000367409.4	-	18	8997	c.8741T>C	c.(8740-8742)aTc>aCc	p.I2914T	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2914	IQ 33. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGAATAATGATAACACTGCT	0.299																																					p.I2914T		Atlas-SNP	.											ASPM,NS,carcinoma,+1,1	ASPM	444	1	0			c.T8741C						PASS	.	A	,THR/ILE	0,4406		0,0,2203	59.0	62.0	61.0		,8741	2.7	0.0	1		61	2,8590	2.2+/-6.3	0,2,4294	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,89	0,2,6497	GG,GA,AA		0.0233,0.0,0.0154	,benign	,2914/3478	197069640	2,12996	2203	4296	6499	SO:0001583	missense	259266	exon18			ATAATGATAACAC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8741T>C	1.37:g.197069640A>G	ENSP00000356379:p.Ile2914Thr	88.0	0.0	0		48.0	17.0	0.354167	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822080	0.32237	0.0	2.33E-4	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.73897	-0.79	5.09	2.7	0.31948	.	0.360702	0.26708	N	0.022904	T	0.80778	0.4688	M	0.68317	2.08	0.09310	N	0.999996	B;D	0.71674	0.024;0.998	B;D	0.65987	0.012;0.94	T	0.70029	-0.4984	10	0.52906	T	0.07	.	7.9874	0.30220	0.7908:0.1371:0.0721:0.0	.	900;2914	E7EQ84;Q8IZT6	.;ASPM_HUMAN	T	2914;900	ENSP00000356379:I2914T	ENSP00000356376:I900T	I	-	2	0	ASPM	195336263	0.020000	0.18652	0.001000	0.08648	0.465000	0.32709	2.427000	0.44740	0.341000	0.23771	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	weak		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
NFKBIZ	64332	hgsc.bcm.edu	37	3	101571753	101571753	+	Missense_Mutation	SNP	A	A	G	rs61730026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:101571753A>G	ENST00000326172.5	+	4	599	c.484A>G	c.(484-486)Agt>Ggt	p.S162G	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.S62G|NFKBIZ_ENST00000326151.5_Missense_Mutation_p.S162G	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	162					inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						AGTATCATACAGTGGGAAAAG	0.383													A|||	2	0.000399361	0.0	0.0014	5008	,	,		17347	0.0		0.001	False		,,,				2504	0.0				p.S162G		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.A484G						PASS	.	A	GLY/SER,GLY/SER	4,4402	8.1+/-20.4	0,4,2199	135.0	135.0	135.0		184,484	2.0	0.2	3	dbSNP_129	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	NFKBIZ	NM_001005474.2,NM_031419.3	56,56	0,21,6482	GG,GA,AA		0.1977,0.0908,0.1615	benign,benign	62/619,162/719	101571753	21,12985	2203	4300	6503	SO:0001583	missense	64332	exon4			TCATACAGTGGGA	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.484A>G	3.37:g.101571753A>G	ENSP00000325663:p.Ser162Gly	180.0	0.0	0		155.0	78.0	0.503226	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.840705	0.00573	9.08E-4	0.001977	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172;ENST00000491281	T;T;T;T	0.55760	0.57;0.53;0.5;0.56	5.62	1.98	0.26296	.	0.734859	0.13799	N	0.361934	T	0.29355	0.0731	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18178	-1.0345	10	0.18276	T	0.48	-12.5889	10.5998	0.45360	0.7332:0.0:0.2668:0.0	rs61730026	162;162	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	G	62;62;162;162;62	ENSP00000419800:S62G;ENSP00000377618:S62G;ENSP00000325593:S162G;ENSP00000325663:S162G	ENSP00000325593:S162G	S	+	1	0	NFKBIZ	103054443	0.619000	0.27059	0.159000	0.22649	0.020000	0.10135	1.190000	0.32126	0.081000	0.16988	-2.096000	0.00365	AGT	A|0.998;G|0.002	0.002	strong		0.383	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
FAM83B	222584	hgsc.bcm.edu	37	6	54735301	54735301	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:54735301C>G	ENST00000306858.7	+	2	373	c.257C>G	c.(256-258)aCc>aGc	p.T86S		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	86										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TGTGATGATACCTTATCTTCA	0.443																																					p.T86S		Atlas-SNP	.											.	FAM83B	186	.	0			c.C257G						PASS	.						130.0	131.0	131.0					6																	54735301		2203	4300	6503	SO:0001583	missense	222584	exon2			ATGATACCTTATC	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.257C>G	6.37:g.54735301C>G	ENSP00000304078:p.Thr86Ser	131.0	0.0	0		128.0	27.0	0.210938	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474403	0.26423	.	.	ENSG00000168143	ENST00000306858	T	0.10960	2.82	5.49	3.63	0.41609	.	0.784700	0.12264	N	0.484499	T	0.01765	0.0056	N	0.10782	0.045	0.09310	N	0.99999	B	0.24317	0.101	B	0.25506	0.061	T	0.48151	-0.9060	10	0.18710	T	0.47	-1.312	10.1089	0.42550	0.2692:0.5927:0.1381:0.0	.	86	Q5T0W9	FA83B_HUMAN	S	86	ENSP00000304078:T86S	ENSP00000304078:T86S	T	+	2	0	FAM83B	54843260	0.216000	0.23585	0.731000	0.30826	0.811000	0.45836	2.409000	0.44583	0.732000	0.32470	0.460000	0.39030	ACC	.	.	none		0.443	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
CFAP74	85452	hgsc.bcm.edu	37	1	1900225	1900225	+	IGR	SNP	C	C	T	rs72636304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1900225C>T								TMEM52 (49513 upstream) : C1orf222 (19337 downstream)																							TTTCAGAATCCGACTGATGAT	0.572													c|||	9	0.00179712	0.0	0.0029	5008	,	,		17712	0.0		0.007	False		,,,				2504	0.0				p.R365Q		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1094A						PASS	.	C	GLN/ARG	5,4041		0,5,2018	141.0	150.0	147.0		1094	1.7	0.0	1	dbSNP_130	147	78,8256		0,78,4089	no	missense	KIAA1751	NM_001080484.1	43	0,83,6107	TT,TC,CC		0.9359,0.1236,0.6704	possibly-damaging	365/763	1900225	83,12297	2023	4167	6190	SO:0001628	intergenic_variant	85452	exon11			AGAATCCGACTGA																													1.37:g.1900225C>T		118.0	0.0	0		59.0	17.0	0.288136	NM_001080484		Missense_Mutation	SNP		37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	15.07	2.725287	0.48833	0.001236	0.009359	ENSG00000142609	ENST00000270720	.	.	.	3.67	1.74	0.24563	.	0.241675	0.27019	N	0.021330	T	0.19005	0.0456	L	0.41824	1.3	0.18873	N	0.999982	D;D	0.57571	0.973;0.98	B;B	0.41988	0.314;0.372	T	0.09729	-1.0661	9	0.39692	T	0.17	-15.2726	8.0725	0.30697	0.0:0.7846:0.0:0.2154	.	365;365	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	Q	365	.	ENSP00000270720:R365Q	R	-	2	0	C1orf222	1890085	0.231000	0.23751	0.001000	0.08648	0.004000	0.04260	1.053000	0.30442	0.309000	0.22966	0.556000	0.70494	CGG	C|0.994;T|0.006	0.006	strong	0	0.572								
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	T	rs186450029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495725C>T	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000367857.5_Missense_Mutation_p.A16T|SGK1_ENST00000367858.5_Splice_Site|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000489458.2_5'Flank	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCATGAAAGCTGTGGATGAA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.77-1G>A						PASS	.						73.0	73.0	73.0					6																	134495725		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon3			TGAAAGCTGTGGA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.77-1G>A	6.37:g.134495725C>T		84.0	0.0	0	1611	36.0	11.0	0.305556	NM_005627	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	37	CCDS5170.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	29.2|29.2	4.985656|4.985656	0.93044|0.93044	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000528577;ENST00000475719;ENST00000461976|ENST00000367857	.|T	.|0.30182	.|1.54	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|.	.|.	.|.	.|.	.|T	.|0.14399	.|0.0348	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B	.|0.27971	.|0.196	.|B	.|0.25759	.|0.063	.|T	.|0.05419	.|-1.0886	.|7	.|.	.|.	.|.	.|.	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|16	.|O00141-4	.|.	.|T	-1|16	.|ENSP00000356831:A16T	.|.	.|A	-|-	.|1	.|0	SGK1|SGK1	134537418|134537418	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	7.818000|7.818000	0.86416|0.86416	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	.|GCT	C|1.000;T|0.000	0.000	strong		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Intron
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39880818C>T	ENST00000260356.5	+	10	1728	c.1563C>T	c.(1561-1563)aaC>aaT	p.N521N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	521	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCTGCAACAACCCCACACCCC	0.537													C|||	64	0.0127796	0.003	0.0274	5008	,	,		20155	0.0		0.0318	False		,,,				2504	0.0092				p.N521N		Atlas-SNP	.											.	THBS1	106	.	0			c.C1563T						PASS	.	C		34,4366	39.2+/-71.8	0,34,2166	94.0	89.0	91.0		1563	4.8	1.0	15	dbSNP_127	91	301,8293	109.6+/-170.1	4,293,4000	no	coding-synonymous	THBS1	NM_003246.2		4,327,6166	TT,TC,CC		3.5024,0.7727,2.5781		521/1171	39880818	335,12659	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CAACAACCCCACA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1563C>T	15.37:g.39880818C>T		76.0	0.0	0		70.0	34.0	0.485714	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.975;T|0.025	0.025	strong		0.537	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
PPP1R32	220004	hgsc.bcm.edu	37	11	61254455	61254455	+	Silent	SNP	T	T	C	rs77676987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61254455T>C	ENST00000338608.2	+	10	995	c.870T>C	c.(868-870)agT>agC	p.S290S	PPP1R32_ENST00000432063.2_Silent_p.S270S|PPP1R32_ENST00000366212.4_5'Flank|PPP1R32_ENST00000538185.1_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	290							phosphatase binding (GO:0019902)										GCAGCGTGAGTCACCAGCAGT	0.607													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19523	0.001		0.008	False		,,,				2504	0.0092				p.S290S		Atlas-SNP	.											.	.	.	.	0			c.T870C						PASS	.	C	,	514,3890	778.9+/-414.3	37,440,1725	213.0	213.0	213.0		810,870	2.9	0.1	11	dbSNP_131	213	62,8536	816.5+/-406.9	0,62,4237	no	coding-synonymous,coding-synonymous	C11orf66	NM_001170753.1,NM_145017.2	,	37,502,5962	CC,CT,TT		0.7211,11.6712,4.4301	,	270/406,290/426	61254455	576,12426	2202	4299	6501	SO:0001819	synonymous_variant	220004	exon10			CGTGAGTCACCAG	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.870T>C	11.37:g.61254455T>C		200.0	1.0	0.005		148.0	120.0	0.810811	NM_145017	Q4G0P4|Q96M77	Silent	SNP	ENST00000338608.2	37	CCDS8008.1																																																																																			T|0.960;C|0.040	0.040	strong		0.607	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381936	39381936	+	Silent	SNP	G	G	A	rs138362043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39381936G>A	ENST00000333467.3	+	3	339	c.294G>A	c.(292-294)ccG>ccA	p.P98P	APOBEC3B_ENST00000407298.3_Silent_p.P98P|APOBEC3B_ENST00000402182.3_Silent_p.P98P	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	98	CMP/dCMP deaminase zinc-binding 1.		P -> L (in dbSNP:rs2076110).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					CCCCCTGCCCGGACTGTGTGG	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		15975	0.0		0.0	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											APOBEC3B,colon,carcinoma,+1,1	APOBEC3B	32	1	0			c.G294A						PASS	.	G		1,4403		0,1,2201	139.0	133.0	135.0		294	-4.2	0.0	22	dbSNP_134	135	5,8591		0,5,4293	no	coding-synonymous	APOBEC3B	NM_004900.3		0,6,6494	AA,AG,GG		0.0582,0.0227,0.0462		98/383	39381936	6,12994	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			CTGCCCGGACTGT	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"""Apolipoprotein B mRNA editing enzymes"""	17352	protein-coding gene	gene with protein product	"""phorbolin 3"""	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.294G>A	22.37:g.39381936G>A		244.0	0.0	0		168.0	117.0	0.696429	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			G|1.000;A|0.000	0.000	weak		0.557	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
NOL8	55035	hgsc.bcm.edu	37	9	95069242	95069242	+	Silent	SNP	A	A	G	rs375530094		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95069242A>G	ENST00000535387.1	-	9	2636	c.2637T>C	c.(2635-2637)aaT>aaC	p.N879N	NOL8_ENST00000542053.1_Silent_p.N849N|NOL8_ENST00000545558.1_Silent_p.N917N|NOL8_ENST00000358855.4_Silent_p.N849N|NOL8_ENST00000442668.2_Silent_p.N917N					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTGTACAACATTCAGGGCTT	0.343																																					p.N917N		Atlas-SNP	.											.	NOL8	118	.	0			c.T2751C						PASS	.	A		0,3634		0,0,1817	141.0	137.0	139.0		2751	3.4	0.5	9		139	1,8159		0,1,4079	no	coding-synonymous	NOL8	NM_017948.5		0,1,5896	GG,GA,AA		0.0123,0.0,0.0085		917/1168	95069242	1,11793	1817	4080	5897	SO:0001819	synonymous_variant	55035	exon11			TACAACATTCAGG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2637T>C	9.37:g.95069242A>G		170.0	0.0	0		141.0	56.0	0.397163	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	weak		0.343	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
CLCN7	1186	hgsc.bcm.edu	37	16	1500567	1500567	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1500567C>T	ENST00000382745.4	-	17	2153	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P	LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Silent_p.P492P|CLCN7_ENST00000262318.8_Silent_p.P492P	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	516					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				TGAGCAGGGACGGGATGAAGA	0.687																																					p.P516P		Atlas-SNP	.											.	CLCN7	53	.	0			c.G1548A						PASS	.						38.0	42.0	41.0					16																	1500567		2181	4298	6479	SO:0001819	synonymous_variant	1186	exon17			CAGGGACGGGATG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1548G>A	16.37:g.1500567C>T		90.0	0.0	0		136.0	106.0	0.779412	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			.	.	none		0.687	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
OR51A4	401666	hgsc.bcm.edu	37	11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	rs201205025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4967834C>G	ENST00000380373.2	-	1	522	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCAAGTTTCTTAAAGTGAA	0.413													.|||	12	0.00239617	0.003	0.0029	5008	,	,		24981	0.0		0.003	False		,,,				2504	0.0031				p.R166T		Atlas-SNP	.											OR51A4,colon,carcinoma,-1,1	OR51A4	73	1	0			c.G497C						scavenged	.						212.0	198.0	203.0					11																	4967834		2177	4245	6422	SO:0001583	missense	401666	exon1			AAGTTTCTTAAAG	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.497G>C	11.37:g.4967834C>G	ENSP00000369731:p.Arg166Thr	980.0	0.0	0		155.0	11.0	0.0709677	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080491	0.20309	.	.	ENSG00000205497	ENST00000380373	T	0.71817	-0.6	3.44	-3.66	0.04489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59046	0.2165	L	0.41027	1.25	0.09310	N	1	B	0.23249	0.082	B	0.27608	0.081	T	0.52041	-0.8628	9	0.66056	D	0.02	.	9.2359	0.37466	0.0:0.303:0.0:0.697	.	166	Q8NGJ6	O51A4_HUMAN	T	166	ENSP00000369731:R166T	ENSP00000369731:R166T	R	-	2	0	OR51A4	4924410	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.905000	0.04075	-1.059000	0.03193	0.479000	0.44913	AGA	.	.	weak		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
CD3G	917	hgsc.bcm.edu	37	11	118219742	118219742	+	Splice_Site	SNP	G	G	A	rs146393315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118219742G>A	ENST00000532917.1	+	2	124	c.56G>A	c.(55-57)gGt>gAt	p.G19D	CD3G_ENST00000392883.2_5'UTR|CD3G_ENST00000532903.1_3'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	19					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	GTCTTTACAGGTACTTTGGCC	0.413													G|||	2	0.000399361	0.0	0.0014	5008	,	,		21792	0.0		0.001	False		,,,				2504	0.0				p.G19D		Atlas-SNP	.											.	CD3G	31	.	0			c.G56A						PASS	.	G	ASP/GLY	0,4400		0,0,2200	183.0	172.0	176.0		56	4.5	0.7	11	dbSNP_134	176	11,8581	8.4+/-32.0	0,11,4285	yes	missense-near-splice	CD3G	NM_000073.2	94	0,11,6485	AA,AG,GG		0.128,0.0,0.0847	probably-damaging	19/183	118219742	11,12981	2200	4296	6496	SO:0001630	splice_region_variant	917	exon2			TTACAGGTACTTT	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.56-1G>A	11.37:g.118219742G>A		186.0	0.0	0		192.0	43.0	0.223958	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	37	CCDS8395.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	18.08	3.543791	0.65198	0.0	0.00128	ENSG00000160654	ENST00000532917	T	0.59083	0.29	5.43	4.49	0.54785	.	0.356469	0.27327	N	0.019871	T	0.73644	0.3613	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.75077	-0.3445	9	.	.	.	.	9.1867	0.37174	0.1016:0.0:0.8984:0.0	.	19	P09693	CD3G_HUMAN	D	19	ENSP00000431445:G19D	.	G	+	2	0	CD3G	117724952	0.989000	0.36119	0.731000	0.30826	0.039000	0.13416	2.669000	0.46825	1.461000	0.47929	0.655000	0.94253	GGT	G|0.999;A|0.001	0.001	strong		0.413	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	Missense_Mutation
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436289	8436289	+	Missense_Mutation	SNP	G	G	A	rs139998264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8436289G>A	ENST00000301455.2	+	6	1093	c.922G>A	c.(922-924)Gtg>Atg	p.V308M	RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.V270M|ANGPTL4_ENST00000541807.1_Missense_Mutation_p.V141M	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	308	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		V -> M (in dbSNP:rs139998264). {ECO:0000269|PubMed:17322881}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						CACTGCACCCGTGGCCGGCCA	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		16262	0.001		0.001	False		,,,				2504	0.0				p.V308M		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.G922A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	43.0	38.0	40.0		808,922	1.6	0.4	19	dbSNP_134	40	7,8591	5.7+/-21.5	0,7,4292	no	missense,missense	ANGPTL4	NM_001039667.1,NM_139314.1	21,21	0,8,6494	AA,AG,GG		0.0814,0.0227,0.0615	benign,benign	270/369,308/407	8436289	8,12996	2203	4299	6502	SO:0001583	missense	51129	exon6			GCACCCGTGGCCG	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.922G>A	19.37:g.8436289G>A	ENSP00000301455:p.Val308Met	92.0	0.0	0		81.0	40.0	0.493827	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.392	0.257560	0.10239	2.27E-4	8.14E-4	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.76709	-1.04;-1.04;-1.04	5.09	1.65	0.23941	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	2.318390	0.01258	N	0.009095	T	0.73938	0.3651	L	0.45422	1.42	0.09310	N	1	B;B	0.29646	0.253;0.253	B;B	0.34301	0.179;0.126	T	0.56836	-0.7913	10	0.49607	T	0.09	.	6.3492	0.21367	0.168:0.2821:0.5498:0.0	.	270;308	A8MY84;Q9BY76	.;ANGL4_HUMAN	M	308;270;141	ENSP00000301455:V308M;ENSP00000377534:V270M;ENSP00000439833:V141M	ENSP00000301455:V308M	V	+	1	0	ANGPTL4	8342289	0.038000	0.19896	0.434000	0.26772	0.003000	0.03518	1.289000	0.33307	0.130000	0.18549	-0.263000	0.10527	GTG	G|0.999;A|0.001	0.001	strong		0.672	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
ADAM28	10863	hgsc.bcm.edu	37	8	24177788	24177788	+	Missense_Mutation	SNP	A	A	G	rs200839167		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:24177788A>G	ENST00000265769.4	+	7	726	c.616A>G	c.(616-618)Ata>Gta	p.I206V	ADAM28_ENST00000437154.2_Missense_Mutation_p.I206V|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_5'UTR	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	206	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGAGAAATACATAGAATATTA	0.303																																					p.I206V	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A616G						PASS	.	A	VAL/ILE,VAL/ILE	0,4406		0,0,2203	88.0	96.0	93.0		616,616	1.7	0.8	8		93	4,8578	3.7+/-12.6	0,4,4287	no	missense,missense	ADAM28	NM_014265.4,NM_021777.3	29,29	0,4,6490	GG,GA,AA		0.0466,0.0,0.0308	benign,benign	206/776,206/541	24177788	4,12984	2203	4291	6494	SO:0001583	missense	10863	exon7			AAATACATAGAAT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.616A>G	8.37:g.24177788A>G	ENSP00000265769:p.Ile206Val	96.0	0.0	0		91.0	19.0	0.208791	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	8.894	0.954625	0.18431	0.0	4.66E-4	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.63580	-0.05;-0.05	5.34	1.71	0.24356	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.34454	0.0898	N	0.05351	-0.065	0.58432	D	0.999999	B;B	0.18013	0.02;0.025	B;B	0.29862	0.068;0.108	T	0.21621	-1.0240	9	0.02654	T	1	.	6.5373	0.22361	0.7202:0.0:0.2798:0.0	.	206;206	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	V	206	ENSP00000265769:I206V;ENSP00000393699:I206V	ENSP00000265769:I206V	I	+	1	0	ADAM28	24233733	0.039000	0.19947	0.825000	0.32803	0.758000	0.43043	0.086000	0.14935	0.429000	0.26202	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	weak		0.303	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
H2AFV	94239	hgsc.bcm.edu	37	7	44875203	44875203	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44875203G>C	ENST00000308153.4	-	4	341	c.250C>G	c.(250-252)Ccg>Gcg	p.P84A	H2AFV_ENST00000350771.3_Missense_Mutation_p.P58A|H2AFV_ENST00000349299.3_Missense_Mutation_p.P46A|H2AFV_ENST00000437072.1_Missense_Mutation_p.P46A|H2AFV_ENST00000222690.6_Missense_Mutation_p.P84A|H2AFV_ENST00000446531.1_Missense_Mutation_p.P84A|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000521529.1_Intron	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	84						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						AAGTGACGCGGAGTGATACGC	0.453																																					p.P84A		Atlas-SNP	.											.	H2AFV	14	.	0			c.C250G						PASS	.						123.0	99.0	107.0					7																	44875203		2203	4300	6503	SO:0001583	missense	94239	exon4			GACGCGGAGTGAT	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.250C>G	7.37:g.44875203G>C	ENSP00000308405:p.Pro84Ala	87.0	0.0	0		56.0	15.0	0.267857	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850542	0.71719	.	.	ENSG00000105968	ENST00000222690;ENST00000437072;ENST00000349299;ENST00000308153;ENST00000350771;ENST00000446531	T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.68	5.68	0.88126	Histone-fold (2);Histone core (1);Histone H2A (2);	.	.	.	.	D	0.84415	0.5467	H	0.94698	3.57	0.80722	D	1	B;P;B;B	0.47302	0.118;0.893;0.083;0.235	B;P;B;B	0.49387	0.247;0.609;0.014;0.122	D	0.88628	0.3167	9	0.87932	D	0	-12.7012	17.2793	0.87124	0.0:0.0:1.0:0.0	.	58;46;84;84	A6NKY0;A6NFA8;Q71UI9;A6NN01	.;.;H2AV_HUMAN;.	A	84;46;46;84;58;84	ENSP00000222690:P84A;ENSP00000397115:P46A;ENSP00000342714:P46A;ENSP00000308405:P84A;ENSP00000340708:P58A;ENSP00000406901:P84A	ENSP00000222690:P84A	P	-	1	0	H2AFV	44841728	1.000000	0.71417	0.671000	0.29857	0.989000	0.77384	9.179000	0.94861	2.698000	0.92095	0.585000	0.79938	CCG	.	.	none		0.453	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
GOLGB1	2804	hgsc.bcm.edu	37	3	121410844	121410844	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121410844T>G	ENST00000340645.5	-	14	7477	c.7352A>C	c.(7351-7353)gAa>gCa	p.E2451A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2456A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2451					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CTGAATGTTTTCCTTTTTGAT	0.398																																					p.E2456A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A7367C						PASS	.						172.0	171.0	171.0					3																	121410844		2203	4300	6503	SO:0001583	missense	2804	exon14			ATGTTTTCCTTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7352A>C	3.37:g.121410844T>G	ENSP00000341848:p.Glu2451Ala	491.0	0.0	0		483.0	236.0	0.488613	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952731	0.34471	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.28255	1.62;1.62	5.79	5.79	0.91817	.	0.090631	0.47852	D	0.000201	T	0.44052	0.1275	L	0.56769	1.78	0.43588	D	0.995931	D;P;D	0.61697	0.972;0.925;0.99	P;P;P	0.55391	0.616;0.691;0.775	T	0.21552	-1.0242	10	0.30854	T	0.27	.	14.0831	0.64937	0.0:0.0:0.0:1.0	.	2456;2456;2451	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	A	2451;2456	ENSP00000341848:E2451A;ENSP00000377275:E2456A	ENSP00000341848:E2451A	E	-	2	0	GOLGB1	122893534	1.000000	0.71417	0.908000	0.35775	0.972000	0.66771	5.884000	0.69729	2.208000	0.71279	0.460000	0.39030	GAA	.	.	none		0.398	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
CEP164	22897	hgsc.bcm.edu	37	11	117214881	117214881	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117214881G>A	ENST00000278935.3	+	4	229		c.e4-1			NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa						cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		TCTCCTTGCAGAAATTCTTGA	0.453																																					.		Atlas-SNP	.											CEP164,colon,carcinoma,-2,1	CEP164	121	1	0			c.83-1G>A						PASS	.						33.0	30.0	31.0					11																	117214881		2201	4296	6497	SO:0001630	splice_region_variant	22897	exon3			CTTGCAGAAATTC	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.83-1G>A	11.37:g.117214881G>A		183.0	0.0	0		157.0	28.0	0.178344	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Splice_Site	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874286	0.51695	.	.	ENSG00000110274	ENST00000525734;ENST00000278935;ENST00000527609;ENST00000533570;ENST00000529538	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4489	0.87586	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP164	116720091	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	9.156000	0.94705	2.274000	0.75844	0.563000	0.77884	.	.	.	none		0.453	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	Intron
ZFYVE16	9765	hgsc.bcm.edu	37	5	79735832	79735832	+	Silent	SNP	C	C	T	rs114761271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79735832C>T	ENST00000338008.5	+	4	2580	c.2400C>T	c.(2398-2400)tgC>tgT	p.C800C	ZFYVE16_ENST00000505560.1_Silent_p.C800C|ZFYVE16_ENST00000510158.1_Silent_p.C800C	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	800					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GTGTAGTCTGCTATGAAACTA	0.274													C|||	20	0.00399361	0.0	0.0043	5008	,	,		18426	0.0		0.0159	False		,,,				2504	0.001				p.C800C	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C2400T						PASS	.	C	,	15,4391	23.3+/-48.9	0,15,2188	149.0	167.0	161.0		2400,2400	5.5	1.0	5	dbSNP_132	161	160,8440	75.7+/-138.4	1,158,4141	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	1,173,6329	TT,TC,CC		1.8605,0.3404,1.3455	,	800/1540,800/1540	79735832	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon5			AGTCTGCTATGAA	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.2400C>T	5.37:g.79735832C>T		79.0	0.0	0		67.0	23.0	0.343284	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			C|0.986;T|0.014	0.014	strong		0.274	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
KIAA1107	23285	hgsc.bcm.edu	37	1	92649498	92649498	+	Missense_Mutation	SNP	T	T	A	rs75212872		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:92649498T>A	ENST00000370378.4	+	9	3774	c.3676T>A	c.(3676-3678)Tat>Aat	p.Y1226N	KIAA1107_ENST00000409154.4_Missense_Mutation_p.Y1281N	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	1281										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						GTCTCCAATATATGAGATGGA	0.373													T|||	1	0.000199681	0.0	0.0	5008	,	,		19930	0.0		0.001	False		,,,				2504	0.0				p.Y1226N		Atlas-SNP	.											.	KIAA1107	60	.	0			c.T3676A						PASS	.						96.0	79.0	84.0					1																	92649498		692	1591	2283	SO:0001583	missense	23285	exon9			CCAATATATGAGA	AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.3676T>A	1.37:g.92649498T>A	ENSP00000359404:p.Tyr1226Asn	251.0	0.0	0		206.0	84.0	0.407767	NM_015237	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	15.18	2.757464	0.49468	.	.	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.15952	2.38;2.38	5.44	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.26919	0.0659	M	0.71581	2.175	0.54753	D	0.999983	D	0.76494	0.999	D	0.69479	0.964	T	0.04781	-1.0927	10	0.87932	D	0	.	11.4864	0.50356	0.0:0.0717:0.0:0.9283	.	1226	E9PEZ5	.	N	1281;1226	ENSP00000386957:Y1281N;ENSP00000359404:Y1226N	ENSP00000359404:Y1226N	Y	+	1	0	KIAA1107	92422086	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.797000	0.55514	0.853000	0.35312	0.460000	0.39030	TAT	T|0.999;A|0.001	0.001	strong		0.373	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
ITGA4	3676	hgsc.bcm.edu	37	2	182392096	182392096	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:182392096A>G	ENST00000397033.2	+	22	2842	c.2412A>G	c.(2410-2412)aaA>aaG	p.K804K		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	804					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TGGTGGAGAAAATGAACTTAA	0.333																																					p.K804K		Atlas-SNP	.											.	ITGA4	142	.	0			c.A2412G						PASS	.						91.0	87.0	88.0					2																	182392096		1891	4125	6016	SO:0001819	synonymous_variant	3676	exon22			GGAGAAAATGAAC		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2412A>G	2.37:g.182392096A>G		84.0	0.0	0		58.0	32.0	0.551724	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			.	.	none		0.333	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
TECPR1	25851	hgsc.bcm.edu	37	7	97861156	97861156	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:97861156C>A	ENST00000447648.2	-	13	2233	c.1934G>T	c.(1933-1935)aGc>aTc	p.S645I	TECPR1_ENST00000542604.1_Missense_Mutation_p.S575I|TECPR1_ENST00000379795.3_Missense_Mutation_p.S646I			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	645	PH.				autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GAAGAGGATGCTGTCCCGGAC	0.657																																					p.S645I		Atlas-SNP	.											.	TECPR1	77	.	0			c.G1934T						PASS	.						88.0	98.0	94.0					7																	97861156		2088	4208	6296	SO:0001583	missense	25851	exon13			AGGATGCTGTCCC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.1934G>T	7.37:g.97861156C>A	ENSP00000404923:p.Ser645Ile	57.0	0.0	0		61.0	14.0	0.229508	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	37	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500612	0.85176	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.38722	1.14;1.12;1.15	5.25	5.25	0.73442	Pleckstrin homology domain (1);	0.043912	0.85682	D	0.000000	T	0.62146	0.2404	L	0.60455	1.87	0.46749	D	0.999184	D;D	0.89917	1.0;0.999	D;D	0.72338	0.977;0.949	T	0.64976	-0.6280	10	0.87932	D	0	-32.2674	17.8224	0.88654	0.0:1.0:0.0:0.0	.	575;645	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	I	645;646;575	ENSP00000404923:S645I;ENSP00000369121:S646I;ENSP00000441121:S575I	ENSP00000369121:S646I	S	-	2	0	TECPR1	97699092	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.805000	0.62561	2.459000	0.83118	0.655000	0.94253	AGC	.	.	none		0.657	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
PLCG1	5335	hgsc.bcm.edu	37	20	39802374	39802374	+	Silent	SNP	C	C	T	rs150104210		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:39802374C>T	ENST00000373271.1	+	29	3882	c.3477C>T	c.(3475-3477)ttC>ttT	p.F1159F	PLCG1_ENST00000244007.3_Silent_p.F1159F|PLCG1_ENST00000373272.2_Silent_p.F1159F|PLCG1_ENST00000608689.1_3'UTR	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1159	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TTCTGCGCTTCGTGGTGTATG	0.507											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1159F		Atlas-SNP	.											.	PLCG1	111	.	0			c.C3477T						PASS	.	C	,	0,4406		0,0,2203	137.0	116.0	123.0		3477,3477	-1.6	1.0	20	dbSNP_134	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	PLCG1	NM_002660.2,NM_182811.1	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	1159/1292,1159/1291	39802374	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5335	exon29			GCGCTTCGTGGTG	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.3477C>T	20.37:g.39802374C>T		239.0	0.0	0	888	226.0	135.0	0.597345	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																			C|1.000;T|0.000	0.000	weak		0.507	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
FAM19A4	151647	hgsc.bcm.edu	37	3	68782299	68782299	+	Silent	SNP	C	C	T	rs146641270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:68782299C>T	ENST00000295569.7	-	6	909	c.417G>A	c.(415-417)acG>acA	p.T139T		NM_001005527.2|NM_182522.4	NP_001005527.1|NP_872328.1	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A4	139						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(5)|skin(2)	10		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		TTCGCTACCGCGTTACCTAAA	0.483													C|||	5	0.000998403	0.0	0.0	5008	,	,		18682	0.0		0.001	False		,,,				2504	0.0041				p.T139T		Atlas-SNP	.											.	FAM19A4	23	.	0			c.G417A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	128.0	119.0	122.0		417,417	-6.3	1.0	3	dbSNP_134	122	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous	FAM19A4	NM_001005527.1,NM_182522.3	,	0,17,6486	TT,TC,CC		0.186,0.0227,0.1307	,	139/141,139/141	68782299	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	151647	exon6			CTACCGCGTTACC	AY325117	CCDS2907.1	3p14.1	2014-08-14			ENSG00000163377	ENSG00000163377			21591	protein-coding gene	gene with protein product						15028294, 25109685	Standard	NM_182522		Approved	TAFA-4	uc021xah.1	Q96LR4	OTTHUMG00000158744	ENST00000295569.7:c.417G>A	3.37:g.68782299C>T		81.0	0.0	0		62.0	29.0	0.467742	NM_182522	A8MVT2	Silent	SNP	ENST00000295569.7	37	CCDS2907.1																																																																																			C|0.999;T|0.001	0.001	strong		0.483	FAM19A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352002.1	NM_182522	
ATOH7	220202	hgsc.bcm.edu	37	10	69991266	69991266	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69991266T>C	ENST00000373673.3	-	1	605	c.169A>G	c.(169-171)Aac>Gac	p.N57D	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	57	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AAGGCAGTGTTGAGCCCCTGC	0.701																																					p.N57D		Atlas-SNP	.											.	ATOH7	4	.	0			c.A169G						PASS	.						38.0	37.0	38.0					10																	69991266		2203	4299	6502	SO:0001583	missense	220202	exon1			CAGTGTTGAGCCC	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"""Basic helix-loop-helix proteins"""	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.169A>G	10.37:g.69991266T>C	ENSP00000362777:p.Asn57Asp	42.0	0.0	0		55.0	32.0	0.581818	NM_145178		Missense_Mutation	SNP	ENST00000373673.3	37	CCDS7276.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.800203	0.70567	.	.	ENSG00000179774	ENST00000373673	D	0.99394	-5.82	5.01	2.52	0.30459	Helix-loop-helix DNA-binding (5);	0.043911	0.85682	D	0.000000	D	0.99612	0.9859	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98476	1.0603	9	.	.	.	-34.2974	11.5762	0.50862	0.0:0.0:0.2838:0.7162	.	57	Q8N100	ATOH7_HUMAN	D	57	ENSP00000362777:N57D	.	N	-	1	0	ATOH7	69661272	1.000000	0.71417	0.992000	0.48379	0.079000	0.17450	6.216000	0.72212	0.207000	0.20607	0.459000	0.35465	AAC	.	.	none		0.701	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1		
VPS37A	137492	hgsc.bcm.edu	37	8	17123477	17123477	+	Missense_Mutation	SNP	A	A	G	rs372276569		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17123477A>G	ENST00000324849.4	+	2	861	c.187A>G	c.(187-189)Att>Gtt	p.I63V	VPS37A_ENST00000324815.3_Missense_Mutation_p.I63V|VPS37A_ENST00000521829.1_Intron	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	63					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		CAACCTGACAATTAACATTAA	0.284																																					p.I63V		Atlas-SNP	.											.	VPS37A	22	.	0			c.A187G						PASS	.	A	,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	94.0	96.0	96.0		,187	4.8	1.0	8		96	0,8588		0,0,4294	no	intron,missense	VPS37A	NM_001145152.1,NM_152415.2	,29	0,1,6496	GG,GA,AA		0.0,0.0227,0.0077	,possibly-damaging	,63/398	17123477	1,12993	2203	4294	6497	SO:0001583	missense	137492	exon2			CTGACAATTAACA		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"""hepatocellular carcinoma related protein 1"""	609927	"""vacuolar protein sorting 37A (yeast)"", ""polyglutamine binding protein 2"""	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.187A>G	8.37:g.17123477A>G	ENSP00000318629:p.Ile63Val	230.0	0.0	0		183.0	42.0	0.229508	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	37	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348643	0.41599	2.27E-4	0.0	ENSG00000155975	ENST00000324849;ENST00000324815	T	0.56776	0.44	4.77	4.77	0.60923	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.52141	0.1716	M	0.64997	1.995	0.53005	D	0.999963	B	0.33212	0.402	B	0.36186	0.219	T	0.51284	-0.8725	10	0.27785	T	0.31	-20.1891	14.9938	0.71415	1.0:0.0:0.0:0.0	.	63	Q8NEZ2	VP37A_HUMAN	V	63	ENSP00000318629:I63V	ENSP00000318173:I63V	I	+	1	0	VPS37A	17167848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.108000	0.89559	2.084000	0.62774	0.528000	0.53228	ATT	.	.	weak		0.284	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415	
OR10V1	390201	hgsc.bcm.edu	37	11	59481214	59481214	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:59481214A>G	ENST00000307552.2	-	1	123	c.105T>C	c.(103-105)taT>taC	p.Y35Y	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						GGCTGGTCAGATACATCATCA	0.438																																					p.Y35Y		Atlas-SNP	.											.	OR10V1	40	.	0			c.T105C						PASS	.						70.0	66.0	67.0					11																	59481214		2201	4295	6496	SO:0001819	synonymous_variant	390201	exon1			GGTCAGATACATC	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.105T>C	11.37:g.59481214A>G		90.0	0.0	0		76.0	24.0	0.315789	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	37	CCDS31565.1																																																																																			.	.	none		0.438	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85459100	85459100	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:85459100A>C	ENST00000393217.2	+	9	2513	c.2452A>C	c.(2452-2454)Aca>Cca	p.T818P		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	818										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GGCAGAGTGTACAAATCTTCA	0.398																																					p.T818P		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A2452C						PASS	.						146.0	138.0	141.0					12																	85459100		2203	4300	6503	SO:0001583	missense	84125	exon9			GAGTGTACAAATC	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.2452A>C	12.37:g.85459100A>C	ENSP00000376910:p.Thr818Pro	105.0	0.0	0		82.0	16.0	0.195122	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	8.766	0.924819	0.18056	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.09817	2.94	5.6	-8.78	0.00824	.	1.013500	0.07926	N	0.976669	T	0.04272	0.0118	N	0.16833	0.445	0.09310	N	0.999996	B;B	0.12630	0.003;0.006	B;B	0.14578	0.002;0.011	T	0.39165	-0.9627	10	0.38643	T	0.18	.	1.7967	0.03062	0.1469:0.2665:0.1369:0.4496	.	818;793	Q96JM4;C9JI57	LRIQ1_HUMAN;.	P	818;793;818	ENSP00000376910:T818P	ENSP00000256007:T818P	T	+	1	0	LRRIQ1	83983231	0.002000	0.14202	0.150000	0.22450	0.780000	0.44128	-1.292000	0.02772	-1.451000	0.01933	0.477000	0.44152	ACA	.	.	none		0.398	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
PRDM9	56979	hgsc.bcm.edu	37	5	23527273	23527273	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527273T>C	ENST00000296682.3	+	11	2258	c.2076T>C	c.(2074-2076)taT>taC	p.Y692Y		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	692					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AGAAGCCCTATGTCTGCAGGG	0.607										HNSCC(3;0.000094)																											p.Y692Y		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	0			c.T2076C						PASS	.						11.0	8.0	9.0					5																	23527273		1606	3274	4880	SO:0001819	synonymous_variant	56979	exon11			GCCCTATGTCTGC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2076T>C	5.37:g.23527273T>C		74.0	0.0	0		98.0	26.0	0.265306	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			.	.	none		0.607	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
VIT	5212	hgsc.bcm.edu	37	2	36970364	36970364	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:36970364A>G	ENST00000389975.3	+	4	542	c.240A>G	c.(238-240)gcA>gcG	p.A80A	VIT_ENST00000379241.3_Silent_p.A80A|VIT_ENST00000379242.3_Silent_p.A80A|VIT_ENST00000457137.2_Silent_p.A80A|VIT_ENST00000404084.1_Silent_p.A58A|VIT_ENST00000401530.1_Silent_p.A80A|VIT_ENST00000497382.1_5'UTR	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	80	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.			A -> T (in Ref. 1; AAL18263). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				ACGTGTATGCATCCTACTCCA	0.493																																					p.A80A		Atlas-SNP	.											.	VIT	138	.	0			c.A240G						PASS	.						142.0	117.0	125.0					2																	36970364		2203	4300	6503	SO:0001819	synonymous_variant	5212	exon4			GTATGCATCCTAC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.240A>G	2.37:g.36970364A>G		129.0	0.0	0		98.0	45.0	0.459184	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			.	.	none		0.493	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A|TH_ENST00000352909.3_Silent_p.A70A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32.0	34.0	34.0		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.303T>C	11.37:g.2190982A>G		110.0	0.0	0		143.0	116.0	0.811189	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
CANX	821	hgsc.bcm.edu	37	5	179135309	179135309	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179135309G>A	ENST00000247461.4	+	5	574	c.374G>A	c.(373-375)cGg>cAg	p.R125Q	CANX_ENST00000504734.1_Missense_Mutation_p.R125Q|CANX_ENST00000415618.2_Missense_Mutation_p.R160Q|CANX_ENST00000512607.2_Missense_Mutation_p.R17Q|CANX_ENST00000452673.2_Missense_Mutation_p.R125Q|CANX_ENST00000503126.1_3'UTR	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	125					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)	p.R125L(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	TTGATGTCTCGGGCCAAGCAT	0.443																																					p.R125Q		Atlas-SNP	.											.	CANX	47	.	1	Substitution - Missense(1)	lung(1)	c.G374A						PASS	.						227.0	212.0	217.0					5																	179135309		2203	4300	6503	SO:0001583	missense	821	exon5			TGTCTCGGGCCAA	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"""major histocompatibility complex class I antigen-binding protein p88"""	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.374G>A	5.37:g.179135309G>A	ENSP00000247461:p.Arg125Gln	202.0	0.0	0		246.0	78.0	0.317073	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Missense_Mutation	SNP	ENST00000247461.4	37	CCDS4447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.66|19.66	3.869769|3.869769	0.72065|0.72065	.|.	.|.	ENSG00000127022|ENSG00000127022	ENST00000510810;ENST00000508787|ENST00000514383;ENST00000502296;ENST00000504734;ENST00000415618;ENST00000452673;ENST00000247461;ENST00000502498;ENST00000502673;ENST00000506654;ENST00000512607;ENST00000354394;ENST00000376953	.|T;T;T;T;T;T;T;T;T;T	.|0.52295	.|0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.|0.060915	.|0.64402	.|D	.|0.000003	T|T	0.39358|0.39358	0.1075|0.1075	L|L	0.35542|0.35542	1.07|1.07	0.52099|0.52099	D|D	0.999942|0.999942	.|B;B;B	.|0.32245	.|0.361;0.292;0.247	.|B;B;B	.|0.21151	.|0.033;0.018;0.03	T|T	0.19712|0.19712	-1.0297|-1.0297	5|10	.|0.46703	.|T	.|0.11	-17.6381|-17.6381	20.071|20.071	0.97724|0.97724	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|160;61;125	.|B4DGP8;Q6ZP56;P27824	.|.;.;CALX_HUMAN	R|Q	94;8|125;125;125;160;125;125;125;61;17;17;117;61	.|ENSP00000424341:R125Q;ENSP00000424745:R125Q;ENSP00000424063:R125Q;ENSP00000394817:R160Q;ENSP00000391646:R125Q;ENSP00000247461:R125Q;ENSP00000425246:R125Q;ENSP00000421107:R61Q;ENSP00000426555:R17Q;ENSP00000423588:R17Q	.|ENSP00000247461:R125Q	G|R	+|+	1|2	0|0	CANX|CANX	179067915|179067915	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.727000|6.727000	0.74764|0.74764	2.754000|2.754000	0.94517|0.94517	0.561000|0.561000	0.74099|0.74099	GGG|CGG	.	.	none		0.443	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649	
RNF26	79102	hgsc.bcm.edu	37	11	119206427	119206427	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119206427G>A	ENST00000311413.4	+	1	1191	c.595G>A	c.(595-597)Gcc>Acc	p.A199T	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	199						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		TGTGGCCATGGCCATCCTCCT	0.622																																					p.A199T		Atlas-SNP	.											RNF26,NS,carcinoma,-1,1	RNF26	23	1	0			c.G595A						PASS	.						122.0	102.0	109.0					11																	119206427		2199	4295	6494	SO:0001583	missense	79102	exon1			GCCATGGCCATCC	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"""RING-type (C3HC4) zinc fingers"""	14646	protein-coding gene	gene with protein product	"""ring finger protein with leucine zipper"""	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.595G>A	11.37:g.119206427G>A	ENSP00000312439:p.Ala199Thr	197.0	0.0	0		179.0	46.0	0.256983	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996878	0.54147	.	.	ENSG00000173456	ENST00000311413	T	0.78816	-1.21	5.12	3.22	0.36961	.	0.171581	0.38663	N	0.001619	T	0.67618	0.2912	L	0.43152	1.355	0.37508	D	0.917046	B	0.10296	0.003	B	0.08055	0.003	T	0.64584	-0.6373	10	0.72032	D	0.01	-5.96	7.4994	0.27509	0.0812:0.0:0.593:0.3257	.	199	Q9BY78	RNF26_HUMAN	T	199	ENSP00000312439:A199T	ENSP00000312439:A199T	A	+	1	0	RNF26	118711637	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.146000	0.42216	0.543000	0.28864	0.561000	0.74099	GCC	.	.	none		0.622	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015	
CEP290	80184	hgsc.bcm.edu	37	12	88520192	88520192	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:88520192A>T	ENST00000552810.1	-	12	1309	c.966T>A	c.(964-966)gaT>gaA	p.D322E	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Missense_Mutation_p.D322E	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	322					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CAATAATTTCATCATCTTTAG	0.294																																					p.D322E		Atlas-SNP	.											.	CEP290	195	.	0			c.T966A						PASS	.						68.0	62.0	64.0					12																	88520192		1794	4063	5857	SO:0001583	missense	80184	exon12			AATTTCATCATCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.966T>A	12.37:g.88520192A>T	ENSP00000448012:p.Asp322Glu	234.0	0.0	0		197.0	56.0	0.284264	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	3.324	-0.138216	0.06669	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.50813	0.73;0.73	5.26	4.12	0.48240	.	0.239053	0.38897	N	0.001528	T	0.23289	0.0563	N	0.19112	0.55	0.80722	D	1	B;B	0.14805	0.004;0.011	B;B	0.18561	0.009;0.022	T	0.15723	-1.0427	10	0.02654	T	1	.	3.2543	0.06826	0.5547:0.0:0.1648:0.2805	.	322;322	Q05BJ6;O15078	.;CE290_HUMAN	E	322;322;322;224	ENSP00000448012:D322E;ENSP00000308021:D322E	ENSP00000308021:D322E	D	-	3	2	CEP290	87044323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.545000	0.36169	0.838000	0.34948	0.455000	0.32223	GAT	.	.	none		0.294	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
SACS	26278	hgsc.bcm.edu	37	13	23910850	23910850	+	Missense_Mutation	SNP	C	C	T	rs142869943		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23910850C>T	ENST00000382292.3	-	9	7438	c.7165G>A	c.(7165-7167)Gtg>Atg	p.V2389M	SACS_ENST00000382298.3_Missense_Mutation_p.V2389M|SACS_ENST00000402364.1_Missense_Mutation_p.V1639M			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2389					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CTCACACCCACGGTTTCAAAA	0.353													C|||	1	0.000199681	0.0	0.0	5008	,	,		18298	0.0		0.001	False		,,,				2504	0.0				p.V2389M		Atlas-SNP	.											.	SACS	871	.	0			c.G7165A						PASS	.	C	MET/VAL	0,4406		0,0,2203	35.0	36.0	35.0		7165	4.9	1.0	13	dbSNP_134	35	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SACS	NM_014363.4	21	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign	2389/4580	23910850	2,13002	2203	4299	6502	SO:0001583	missense	26278	exon10			CACCCACGGTTTC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7165G>A	13.37:g.23910850C>T	ENSP00000371729:p.Val2389Met	85.0	0.0	0		81.0	44.0	0.54321	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.390	0.440092	0.12104	0.0	2.33E-4	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.94000	-3.33;-3.33;-3.33	5.84	4.88	0.63580	.	0.248470	0.41500	D	0.000871	D	0.87541	0.6203	L	0.27053	0.805	0.34084	D	0.659888	B	0.23185	0.081	B	0.18871	0.023	D	0.86770	0.1972	10	0.33940	T	0.23	.	12.7477	0.57289	0.0:0.8603:0.0:0.1397	.	2389	Q9NZJ4	SACS_HUMAN	M	2389;1639;2389	ENSP00000371729:V2389M;ENSP00000385844:V1639M;ENSP00000371735:V2389M	ENSP00000371729:V2389M	V	-	1	0	SACS	22808850	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	3.105000	0.50314	2.779000	0.95612	0.655000	0.94253	GTG	C|1.000;T|0.000	0.000	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
ZNF592	9640	hgsc.bcm.edu	37	15	85326939	85326939	+	Missense_Mutation	SNP	C	C	A	rs138966830		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85326939C>A	ENST00000560079.2	+	4	1321	c.1033C>A	c.(1033-1035)Cca>Aca	p.P345T	ZNF592_ENST00000299927.3_Missense_Mutation_p.P345T	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	345					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P345S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AAGTATCAAGCCATCGGACAG	0.547																																					p.P345T		Atlas-SNP	.											ZNF592,arm,malignant_melanoma,0,1	ZNF592	95	1	1	Substitution - Missense(1)	skin(1)	c.C1033A						PASS	.						72.0	82.0	78.0					15																	85326939		2203	4299	6502	SO:0001583	missense	9640	exon4			ATCAAGCCATCGG	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1033C>A	15.37:g.85326939C>A	ENSP00000452877:p.Pro345Thr	117.0	0.0	0		121.0	42.0	0.347107	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171393	0.57584	.	.	ENSG00000166716	ENST00000299927	T	0.00620	6.17	5.59	5.59	0.84812	.	0.158983	0.56097	D	0.000026	T	0.02494	0.0076	M	0.61703	1.905	0.43771	D	0.996292	D	0.67145	0.996	P	0.59948	0.866	T	0.65467	-0.6161	10	0.40728	T	0.16	-5.8358	17.0815	0.86600	0.0:1.0:0.0:0.0	.	345	Q92610	ZN592_HUMAN	T	345	ENSP00000299927:P345T	ENSP00000299927:P345T	P	+	1	0	ZNF592	83127943	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.786000	0.69006	2.628000	0.89032	0.655000	0.94253	CCA	A|0.001;C|0.999	0.001	weak		0.547	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
GPR98	84059	hgsc.bcm.edu	37	5	90086955	90086955	+	Missense_Mutation	SNP	G	G	A	rs41304892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:90086955G>A	ENST00000405460.2	+	70	14405	c.14309G>A	c.(14308-14310)cGc>cAc	p.R4770H	GPR98_ENST00000425867.2_Missense_Mutation_p.R431H	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4770					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TATTCGGATCGCCAGTCAATA	0.453													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19442	0.0		0.005	False		,,,				2504	0.0				p.R4770H		Atlas-SNP	.											.	GPR98	605	.	0			c.G14309A						PASS	.	G	HIS/ARG	1,3827		0,1,1913	105.0	95.0	98.0		14309	-7.1	0.0	5	dbSNP_127	98	50,8186		0,50,4068	yes	missense	GPR98	NM_032119.3	29	0,51,5981	AA,AG,GG		0.6071,0.0261,0.4227	benign	4770/6307	90086955	51,12013	1914	4118	6032	SO:0001583	missense	84059	exon70			CGGATCGCCAGTC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.14309G>A	5.37:g.90086955G>A	ENSP00000384582:p.Arg4770His	255.0	1.0	0.00392157		269.0	115.0	0.427509	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	6.244	0.413073	0.11812	2.61E-4	0.006071	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.35236	1.32;1.32	5.77	-7.1	0.01547	.	1.043920	0.07336	N	0.879923	T	0.10423	0.0255	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.01281	0.0;0.0;0.0	T	0.36890	-0.9729	10	0.19147	T	0.46	.	16.6102	0.84881	0.6714:0.0:0.3286:0.0	rs41304892;rs61999354	431;4770;431	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	H	4770;4770;431	ENSP00000384582:R4770H;ENSP00000392618:R431H	ENSP00000296619:R4770H	R	+	2	0	GPR98	90122711	0.000000	0.05858	0.000000	0.03702	0.846000	0.48090	-0.098000	0.11024	-1.543000	0.01723	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.453	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
BAGE2	85319	hgsc.bcm.edu	37	21	11058316	11058316	+	RNA	SNP	G	G	T	rs3877860		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:11058316G>T	ENST00000470054.1	-	0	331							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTTACAAAATGCACATCGCTG	0.388																																					p.H42N		Atlas-SNP	.											.	.	.	.	0			c.C124A						PASS	.																																					85318	exon3			CAAAATGCACATC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058316G>T		198.0	0.0	0		238.0	13.0	0.0546218	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				.	.	weak		0.388	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
